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  1. ORAL ISSUE OF THE JOURNAL "USPEKHI FIZICHESKIKH NAUK": Special session of the Uspekhi Fizicheskikh Nauk Editorial Board celebrating the 90th anniversary of the journal(19 November 2008)

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    Ginzburg, Vitalii L.; Dremin, Igor M.; Shirkov, Dmitrii V.; Smirnov, Boris M.; Aleksandrov, Evgenii B.; Vershovskii, Anton K.; Maksimov, Evgenii G.; Fortov, Vladimir E.

    2009-06-01

    A special session of the Uspekhi Fizicheskikh Nauk (UFN) Editorial Board (UFN's oral issue) celebrating the 90th anniversary of the journal and the 50th anniversary of its English version (first under the title Soviet Physics-Uspekhi and then under the current title Physics-Uspekhi) took place on November 19, 2008 in the conference hall of the P N Lebedev Physical Institute (FIAN) of the Russian Academy of Sciences. The following reports were presented at the session: (1) Ginzburg V L (P N Lebedev Physical Institute, RAS, Moscow), Aksent'eva M S (Uspekhi Fizicheskikh Nauk, RAS, Moscow) "On the history of UFN (introductory talk)"; (2) Dremin I M (P N Lebedev Physical Institute, RAS, Moscow) "The physics of the Large Hadron Collider"; (3) Shirkov D V (Joint Institute for Nuclear Research, Dubna, Moscow region) "Pair correlations and spontaneous symmetry breaking"; (4) Smirnov B M (Institute for High Temperatures, RAS, Moscow) "Modeling of gas-discharge plasma"; (5) Sadovskii M V (Institute of Electrophysics, RAS Ural Branch, Ekaterinburg) "High-temperature superconductivity in iron-based layered compounds"; (6) Aleksandrov E B (All-Russian Research Center, S I Vavilov State Optical Institute, St. Petersburg) Physical limits in the metrology of a magnetic field by atomic spectroscopy techniques"; (7) Maksimov E G (P N Lebedev Physical Institute, RAS, Moscow) "Microscopic studies of the nature of the ferroelectric transition"; (8) Fortov V E (Institute for High Energy Density, RAS, Moscow) "Extreme states of matter". Articles based on reports 1-4 and 6-8 are published below in this special issue of the Uspekhi Fizicheskikh Nauk journal devoted to the jubilees of the Russian and English versions of the journal.

  2. A simple ssr analysis for genetic diversity estimation of maize landraces

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    Ignjatovic-Micic Dragana

    2015-01-01

    Full Text Available collection of 2217 landraces from western Balkan (former Yugoslavia is maintained at Maize Research Institute Zemun Polje gene bank. Nine flint and nine dent accessions from six agro-ecological groups (races, chosen on the basis of diverse pedigrees, were analyzed for genetic relatedness using phenotypic and simple sequence repeat (SSR markers. One of the aims was to establish a reliable set of SSR markers for a rapid diversity analysis using polyacrilamide gels and ethidium bromide staining. In the principal component analysis (PCA the first three principal components accounted for 80.86% of total variation and separated most of the flint from dent landraces. Ten SSR primers revealed a total of 56 and 63 alleles in flint and dent landraces, respectively, with low stuttering and good allele resolution on the gels. High average PIC value (0.822 also supports informativeness and utility of the markers used in this study. Higher genetic variation was observed among flint genotypes, as genetic distances between flint landraces covered a larger range of values (0.11- 0.38 than between dent (0.22 - 0.33 genotypes. Both phenotypic and SSR analyses distinguished flint and dent landraces, but neither of them could abstract agro-ecological groups. The SSR method used gave clear, easy to read band patterns that could be used for reliable allele frequency determination. Genetic diversity revealed for both markers indicated that the landraces were highly adapted to specific environmental conditions and purposes and could be valuable sources of genetic variability. [Projekat Ministarstva nauke Republike Srbije, br. TR31028: Exploitation of maize diversity to improve grain quality and drought tolerance

  3. Review of the Methods for Developing SSR Molecular Markers

    Institute of Scientific and Technical Information of China (English)

    ZHAO Xue; CHANG Wei; HAN Yingpeng; LI Wenbin

    2008-01-01

    Microsatellite marker (or Simple Sequence Repeate,SSR) is a marker technology based on DNA molecular length polymorphism.It is also one of the most commonly used molecular markers.Traditional SSR marker development methods are relatively time-consuming and mostly relying on the known genome sequence information while recently developed methods of SSR marker based on RAPD,ISSR-PCR SSR,the use of hybrid options, sequence tag SSR library access and screening EST-SSR have been widely used.This paper gave an overview of the methods mentioned above for the development of SSR markers.

  4. Development of simple sequence repeats (SSR) markers of ramie and comparison of SSR and inter-SSR marker systems

    Institute of Scientific and Technical Information of China (English)

    ZHOU Jianlin; JIE Yucheng; JIANG Yanbo; ZHONG Yingli; LIU Yunhai; ZHANG Jian

    2005-01-01

    Ramie (Boehmeria nivea L. ) is an important bast fiber crop. To study genetic background of this species, we isolated and characterized microsatellite markers of ramie. A genomic library containing inserts of rapid amplification of polymorphic DNA (RAPD)fragments was constructed, and screened by PCR amplification using anchored simple sequence repeats as primers. A total of 26 clones were identified as positives, and 13 microsatellite loci were found after sequencing. The polymorphism of these 13 microsatellite loci was examined and the utility of simple sequence repeats (SSR) and inter-SSR (ISSR) marker systems for genetic characterization compared using 19 selected ramie cultivars. Both approaches successfully discriminated the 19 cultivars which differed in the amount of polymorphism detected. The level of polymorphism detected by SSR was 95.0 %, higher than that by ISSR (72.3 % ), but the average polymorphism information content (PIC) of ISSR (0. 651) was higher than that of SSR (0. 441). The higher PIC value of ISSR suggests that ISSR is more efficient for fingerprinting ramie cultivars than SSR markers. However, because the SSR loci are codominant, they are more suitable for determining the homozygosity levels of ramie, constructing linkage map, quantitative trait loci study of complex traits and marker-as-sisted selection.

  5. ORAL ISSUE OF THE JOURNAL "USPEKHI FIZICHESKIKH NAUK": Special scientific session of the Editorial Board of the journal "Uspekhi Fizicheskikh Nauk" honoring Vitalii Lazarevich Ginzburg on his 90th birthday (3 October 2006)

    Science.gov (United States)

    2007-04-01

    A Special scientific session of the Editorial Board of the journal Uspekhi Fizicheskikh Nauk (an oral issue of the journal UFN) was held in the Conference Hall of the P N Lebedev Physical Institute, Russian Academy of Sciences (Moscow), on 3 October 2006. Several topical physical problems from the list given by Vitalii Lazarevich Ginzburg in his Nobel Lecture (Ginzburg's list) were discussed [in the order of the problems appeared on Ginzburg's list (see p. 332)].

  6. Reimagining SSR in Contexts of Security Pluralism

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    Megan Price

    2017-07-01

    Full Text Available Within the repertoire of international stabilization interventions, security sector reform (SSR and other conventional efforts to strengthen security and governance institutions remain central. There is increasing recognition that the policies and practices operating under the rubric of SSR are blind to the empirical reality of 'security pluralism' in most stabilization contexts. In these contexts, both security providers directly authorized by the state (police, army and a multitude of other coercive actors engage in producing and reproducing order, and enjoy varying degrees of public authority and legitimacy. Recognizing this, research was undertaken in three cities (Beirut, Nairobi, and Tunis to discern the conditions enabling various security providers to forge constructive relations with local populations and governance actors. Drawing on insights generated by these case studies, this article problematizes conventional state-centric approaches and argues for a bold reimagining of SSR. It makes the case for an SSR approach that prioritizes promoting the accountability and responsiveness of all security providers, integrating efforts to strengthen the social determinants of security, and enabling a phased transition from relational to rules-based systems of security provision and governance.

  7. SSR and EST-SSR-based genetic linkage map of cassava (Manihot esculenta Crantz).

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    Sraphet, Supajit; Boonchanawiwat, Athipong; Thanyasiriwat, Thanwanit; Boonseng, Opas; Tabata, Satoshi; Sasamoto, Shigemi; Shirasawa, Kenta; Isobe, Sachiko; Lightfoot, David A; Tangphatsornruang, Sithichoke; Triwitayakorn, Kanokporn

    2011-04-01

    Simple sequence repeat (SSR) markers provide a powerful tool for genetic linkage map construction that can be applied for identification of quantitative trait loci (QTL). In this study, a total of 640 new SSR markers were developed from an enriched genomic DNA library of the cassava variety 'Huay Bong 60' and 1,500 novel expressed sequence tag-simple sequence repeat (EST-SSR) loci were developed from the Genbank database. To construct a genetic linkage map of cassava, a 100 F(1) line mapping population was developed from the cross Huay Bong 60 by 'Hanatee'. Polymorphism screening between the parental lines revealed that 199 SSRs and 168 EST-SSRs were identified as novel polymorphic markers. Combining with previously developed SSRs, we report a linkage map consisted of 510 markers encompassing 1,420.3 cM, distributed on 23 linkage groups with a mean distance between markers of 4.54 cM. Comparison analysis of the SSR order on the cassava linkage map and the cassava genome sequences allowed us to locate 284 scaffolds on the genetic map. Although the number of linkage groups reported here revealed that this F(1) genetic linkage map is not yet a saturated map, it encompassed around 88% of the cassava genome indicating that the map was almost complete. Therefore, sufficient markers now exist to encompass most of the genomes and efficiently map traits in cassava.

  8. An online conserved SSR discovery through cross-species comparison

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    Tun-Wen Pai

    2009-02-01

    Full Text Available Tun-Wen Pai1, Chien-Ming Chen1, Meng-Chang Hsiao1, Ronshan Cheng2, Wen-Shyong Tzou3, Chin-Hua Hu31Department of Computer Science and Engineering; 2Department of Aquaculture, 3Institute of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan, Republic of ChinaAbstract: Simple sequence repeats (SSRs play important roles in gene regulation and genome evolution. Although there exist several online resources for SSR mining, most of them only extract general SSR patterns without providing functional information. Here, an online search tool, CG-SSR (Comparative Genomics SSR discovery, has been developed for discovering potential functional SSRs from vertebrate genomes through cross-species comparison. In addition to revealing SSR candidates in conserved regions among various species, it also combines accurate coordinate and functional genomics information. CG-SSR is the first comprehensive and efficient online tool for conserved SSR discovery.Keywords: microsatellites, genome, comparative genomics, functional SSR, gene ontology, conserved region

  9. SSR markers: a tool for species identification in Psidium (Myrtaceae).

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    Tuler, A C; Carrijo, T T; Nóia, L R; Ferreira, A; Peixoto, A L; da Silva Ferreira, M F

    2015-11-01

    Molecular DNA markers are used for detection of polymorphisms in individuals. As they are independent of developmental stage of the plant and environmental influences, they can be useful tools in taxonomy. The alleles of simple sequence repeat (SSR) markers (or microsatellites) are traditionally used to identify taxonomic units. This application demands the laborious and costly delimitation of exclusive alleles in order to avoid homoplasy. Here, we propose a method for identification of species based on the amplification profile of groups of SSR markers obtained by a transferability study. The approach considers that the SSR are conserved among related species. In this context, using Psidium as a model, 141 SSR markers developed for Psidium guajava were transferred to 13 indigenous species of Psidium from the Atlantic Rainforest. Transferability of the markers was high and 28 SSR were conserved in all species. Four SSR groups were defined and they can help in the identification of all 13 Psidium species studied. A group of 31 SSR was genotyped, with one to six alleles each. The H0 varied from 0.0 to 0.46, and PIC from 0.0 to 0.74. Cluster analysis revealed shared alleles among species. The high percentage of SSR transferability found in Psidium evidences the narrow phylogenetic relationship existing among these species since transferability occurs by the preservation of the microsatellites and anchoring regions. The proposed method was useful for distinguishing the species of Psidium, being useful in taxonomic studies.

  10. Factors Affecting SSR in Holstein Dairy Cows

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    Alireza Heravi Mosavi

    2016-08-01

    Full Text Available Introduction Secondary sex ratio (SSR is the proportion of males to females at birth. It has been shown in many different mammalian species, many factors are associated with SSR. Changes in secondary sex ratio in dairy cows is considered economically important and the ability to change it could affect the revenues and profitability of a dairy farm. Thus, sperm or embryo sexing techniques in recent years has attracted more attention. Most breed of dairy cattle are more likely to have female calf is born to use them as replacement heifers and in order to maintain their productive herd number. On the contrary, when the goal is the production of meat, bull calves due to higher growth rates and production efficiency, are more convenient and more economically efficient. The aim of present study was to investigate some key factors affecting SSR in Iranian Holstein cows. According to Fisher, the sex ratio in the population under the control of natural selection is not always the same. There is overwhelming evidence to support the theory that shows Fisher Primary and secondary sex ratio sex ratio can deviate from this balance and natural selection caused a change in this ratio can be in certain circumstances. For example, the secondary sex ratio of 52:48 has been reported in dairy cows. Studies on mammalian species suggest that several factors, including latitude of the location, the dominant regional climate model, time and frequency of mating to ovulation, diet, age of parents, physical score, breed and produced eggs from ovarian left or right can have a significant effect on the secondary sex ratio. Weather conditions may modify the internal environment and the effect on physiological mechanisms or through the impact on the frequency and type of foods available to parents, the secondary sex ratio is impressive. The impact on the quantity and quality of parent's access to food sources in many species of mammals, the sex ratio has been fixed. Previous

  11. Analysis of SSR Fingerprints in Introduced Silkworm Germplasm Resources

    Institute of Scientific and Technical Information of China (English)

    HOU Cheng-xiang; HUANG Yong-ping; LI Mu-wang; ZHANG Yue-hua; QIAN He-ying; SUN Ping-jiang; XU An-ying; MIAO Xue-xia; GUO Qiu-hong; XIANG Hui

    2007-01-01

    Thirty-five SSR markers were used to construct 96 silkworm races fingerprint. All the SSR markers were polymorphic and unambiguously separated silkworm strains from each other. A total of 467 alleles were detected with a mean value of 13.34 alleles/locus (range 3-28). The mean polymorphism index content (PIC) was 0.71 (range 0.299-0.919). UPGMA cluster analysis of Nei's genetic distance grouped silkworm strains on the basis of their origin. The results indicated that SSR markers are efficient tools for fingerprinting cultivars and conducting genetic diversity studies in the silkworm.

  12. Comparison of gSSR and EST-SSR markers for analyzing genetic variability among tomato cultivars (Solanum lycopersicum L.).

    Science.gov (United States)

    Zhou, R; Wu, Z; Jiang, F L; Liang, M

    2015-10-27

    In order to study genetic variability and develop better strategies for the utilization of 48 tomato cultivars from America, China, the Netherlands, and Portugal, genomic simple sequence repeat (gSSR) and EST-derived SSR (EST-SSR) markers were applied. In all, 15 of 82 gSSR and 18 of 115 EST-SSR markers showed polymorphic loci. There were 995 and 2072 clear fragments amplified by polymorphic gSSR and EST-SSR markers, respectively. The total and average number of alleles detected by EST-SSRs (75, 4.2) was more than gSSRs (54, 3.6) as a result of some multi-locus EST-SSRs. A lower polymorphism information content value was found in gSSRs (0.529) compared to EST-SSRs (0.620). Similarity coefficient matrixes of the 48 tomato cultivars were established based on the gSSRs and EST-SSRs, and UPGMA dendrograms were constructed from the gSSRs and EST-SSRs similarity coefficient matrixes. A high similarity was observed between the gSSRs and EST-SSRs dendrograms. Genetic variability of four tomato populations from different countries showed that the observed number of alleles and Nei's genetic diversity were highest in the American population, and the effective number of alleles was highest in the Dutch population. The estimated genetic structure showed some tomato cultivars from different countries shared a common genetic background, which might be related to gene flow. It was inferred that both gSSR and EST-SSR markers were effective to assess genetic variability of tomato cultivars, and the combination of both markers could be more effective for genetic diversity analysis in tomato.

  13. Genetic characterization of an elite coffee germplasm assessed by gSSR and EST-SSR markers.

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    Missio, R F; Caixeta, E T; Zambolim, E M; Pena, G F; Zambolim, L; Dias, L A S; Sakiyama, N S

    2011-10-06

    Coffee is one of the main agrifood commodities traded worldwide. In 2009, coffee accounted for 6.1% of the value of Brazilian agricultural production, generating a revenue of US$6 billion. Despite the importance of coffee production in Brazil, it is supported by a narrow genetic base, with few accessions. Molecular differentiation and diversity of a coffee breeding program were assessed with gSSR and EST-SSR markers. The study comprised 24 coffee accessions according to their genetic origin: arabica accessions (six traditional genotypes of C. arabica), resistant arabica (six leaf rust-resistant C. arabica genotypes with introgression of Híbrido de Timor), robusta (five C. canephora genotypes), Híbrido de Timor (three C. arabica x C. canephora), triploids (three C. arabica x C. racemosa), and racemosa (one C. racemosa). Allele and polymorphism analysis, AMOVA, the Student t-test, Jaccard's dissimilarity coefficient, cluster analysis, correlation of genetic distances, and discriminant analysis, were performed. EST-SSR markers gave 25 exclusive alleles per genetic group, while gSSR showed 47, which will be useful for differentiating accessions and for fingerprinting varieties. The gSSR markers detected a higher percentage of polymorphism among (35% higher on average) and within (42.9% higher on average) the genetic groups, compared to EST-SSR markers. The highest percentage of polymorphism within the genetic groups was found with gSSR markers for robusta (89.2%) and for resistant arabica (39.5%). It was possible to differentiate all genotypes including the arabica-related accessions. Nevertheless, combined use of gSSR and EST-SSR markers is recommended for coffee molecular characterization, because EST-SSRs can provide complementary information.

  14. Highly Informative Simple Sequence Repeat (SSR) Markers for Fingerprinting Hazelnut

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    Simple sequence repeat (SSR) or microsatellite markers have many applications in breeding and genetic studies of plants, including fingerprinting of cultivars and investigations of genetic diversity, and therefore provide information for better management of germplasm collections. They are repeatab...

  15. simple sequence repeat (SSR) markers in genetic analysis of

    African Journals Online (AJOL)

    Yomi

    2012-08-28

    Aug 28, 2012 ... In the present study, 78 mapped simple sequence repeat (SSR) markers representing 11 ... mean (UPGMA) with each cluster representing a particular Vigna species. ..... were reported to be more frequent than the compound.

  16. FullSSR: Microsatellite Finder and Primer Designer

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    Sebastián Metz

    2016-01-01

    Full Text Available Microsatellites are genomic sequences comprised of tandem repeats of short nucleotide motifs widely used as molecular markers in population genetics. FullSSR is a new bioinformatic tool for microsatellite (SSR loci detection and primer design using genomic data from NGS assay. The software was tested with 2000 sequences of Oryza sativa shotgun sequencing project from the National Center of Biotechnology Information Trace Archive and with partial genome sequencing with ROCHE 454® from Caiman latirostris, Salvator merianae, Aegla platensis, and Zilchiopsis collastinensis. FullSSR performance was compared against other similar SSR search programs. The results of the use of this kind of approach depend on the parameters set by the user. In addition, results can be affected by the analyzed sequences because of differences among the genomes. FullSSR simplifies the detection of SSRs and primer design on a big data set. The command line interface of FullSSR was intended to be used as part of genomic analysis tools pipeline; however, it can be used as a stand-alone program because the results are easily interpreted for a nonexpert user.

  17. FullSSR: Microsatellite Finder and Primer Designer

    Science.gov (United States)

    Metz, Sebastián; Cabrera, Juan Manuel; Rueda, Eva; Giri, Federico; Amavet, Patricia

    2016-01-01

    Microsatellites are genomic sequences comprised of tandem repeats of short nucleotide motifs widely used as molecular markers in population genetics. FullSSR is a new bioinformatic tool for microsatellite (SSR) loci detection and primer design using genomic data from NGS assay. The software was tested with 2000 sequences of Oryza sativa shotgun sequencing project from the National Center of Biotechnology Information Trace Archive and with partial genome sequencing with ROCHE 454® from Caiman latirostris, Salvator merianae, Aegla platensis, and Zilchiopsis collastinensis. FullSSR performance was compared against other similar SSR search programs. The results of the use of this kind of approach depend on the parameters set by the user. In addition, results can be affected by the analyzed sequences because of differences among the genomes. FullSSR simplifies the detection of SSRs and primer design on a big data set. The command line interface of FullSSR was intended to be used as part of genomic analysis tools pipeline; however, it can be used as a stand-alone program because the results are easily interpreted for a nonexpert user. PMID:27366148

  18. XML Genetic Structure of SSR1 & SSR2 loci from Iranian Mycobacterium Avium Subspecies Paratuberculosis Isolates by a Short Sequence Repeat Analysis Approach

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    Aida Chalesh (MSc

    2016-01-01

    Full Text Available Background and Objective: Paratuberculosis has been repeatedly reported from Iranian ruminant herds. The extrem fastidious nature of Mycobacterium avium subspecies paratuberculsos hinders genomic diversity studies of the pathogen. Short Sequence Repeat analysis is one of the genome-based approches recently developed to overcome this difficulty. In this study we describe the application of SSR genotyping on three Iranian MAP type strains plus the III & V vaccinal strain. Methods: All the bacteria were examined by PCR-F57 and PCR-IS900 experiments in order to authenticate their identity as MAP. SSR genotyping using SSR1 & SSR2 loci was conducted according to the Amonsin method. PCR amplicons were sequenced to guarantee the accuracy of findings. Results: At SSR1 locus two allels were identified, a larger allel of 770 bp and a smaller allel of 763 bp long. At SSR2 only a single allele, 800 bp long, was detected. Two Iranian bovine and ovine MAP isolates along with the vaccinal III & V strain shared a single SSR1/SSR2 pattern while a different SSR1/SSR2 was represented by the third (caprine Iranian MAP isolate. Conclusion: While finding a shared SSR type between the two Iranian MAP isolates and the III & V strain might represent a mutual ancestral background but this has to be assessed through further studies. Detection of two SSR genotypes between three Iranian type strains is likely a reflection of more MAP clones in Iran.

  19. Genetic diversity revealed by genomic-SSR and EST-SSR markers among common wheat, spelt and compactum

    Institute of Scientific and Technical Information of China (English)

    YANG Xinquan; LIU Peng; HAN Zongfu; NI Zhongfu; SUN Qixin

    2005-01-01

    In this study, two SSR molecular markers, named genomic-SSR and EST-SSR, are used to measure the genetic diversity among three hexaploid wheat populations, which include 28 common wheat ( Triticum aestivum L. ), 13 spelt ( Triticum spelta L. ),and 11 compactum ( Triticum compactum Host. ). The results show that common wheat has the highest genetic polymorphism, followed by spelt and then compactum. The mean genetic distance between the populations is higher than that within a population, and similar tendency is detected for individual genomes A, B and D. Therefore, spelt and compactum can be used as potential germplasms for wheat breeding, especially for enriching the genetic variation in genome D. As compared with spelt, the genetic diversity between common wheat and compactum is much smaller, indicating a closer consanguine relationship between these two species. Although the polymorphism revealed by EST-SSR is lower than that by genomic-SSR, it can effectively differentiate diverse genotypes as well. Together with our present results, it is concluded that EST-SSR marker is an ideal marker for assessing the genetic diversity in wheat. Meanwhile, the origin and evolution of hexaploid wheat is also analyzed and discussed.

  20. Identification of the regulatory logic controlling Salmonella pathoadaptation by the SsrA-SsrB two-component system.

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    Ana M Tomljenovic-Berube

    2010-03-01

    Full Text Available Sequence data from the past decade has laid bare the significance of horizontal gene transfer in creating genetic diversity in the bacterial world. Regulatory evolution, in which non-coding DNA is mutated to create new regulatory nodes, also contributes to this diversity to allow niche adaptation and the evolution of pathogenesis. To survive in the host environment, Salmonella enterica uses a type III secretion system and effector proteins, which are activated by the SsrA-SsrB two-component system in response to the host environment. To better understand the phenomenon of regulatory evolution in S. enterica, we defined the SsrB regulon and asked how this transcription factor interacts with the cis-regulatory region of target genes. Using ChIP-on-chip, cDNA hybridization, and comparative genomics analyses, we describe the SsrB-dependent regulon of ancestral and horizontally acquired genes. Further, we used a genetic screen and computational analyses integrating experimental data from S. enterica and sequence data from an orthologous regulatory system in the insect endosymbiont, Sodalis glossinidius, to identify the conserved yet flexible palindrome sequence that defines DNA recognition by SsrB. Mutational analysis of a representative promoter validated this palindrome as the minimal architecture needed for regulatory input by SsrB. These data provide a high-resolution map of a regulatory network and the underlying logic enabling pathogen adaptation to a host.

  1. Ice core from Akademii Nauk ice cap, Severnaya Zemlya (Russian Arctic), dated with a Nye model modified for a growing glacier

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    Fritzsche, Diedrich; Opel, Thomas; Meyer, Hanno

    2010-05-01

    From 1999 to 2001 a 724 m deep ice core has been drilled from surface to bedrock close to summit of the Akademii Nauk ice cap, Severnaya Zemlya (Russian Arctic), within a joint German-Russian project. The analysis of stable water isotopes and major ion concentration in high resolution were used for reconstruction of past climate and environmental changes. The upper 304 m of the core were dated by counting annual stable isotope cycles considering radioactive (1986, 1963) and volcanic events (1956, 1912, 1783, 1259) as reference horizons. The resulting depth-age relationship and the corresponding annual-layer thickness imply that the ice cap was not in dynamic steady state but had been growing until recent times. That does not comply with requirements of a standard Nye or Dansgaard-Johnson flow model approach. To take into account the peculiarities of Akademii Nauk ice cap a Nye model was modified by adding a growing term according to the found relationship between annual layer thickness and depth. Using the volcanoes identified an average increase of altitude of about 0.08 m w.e. per year was calculated since AD 1259. The model enables us to reconstruct the altitude changes of the ice cap with time and to consider an altitude effect to correct the stable isotope values and to explain decreasing sea-salt ion data. Using the suggested model annual layer thickness can be decompressed to accumulation rates at the altitude where the precipitation was originally deposited. The model can also be used for dating deeper parts of ice core where volcanoes are not identified up to now. Applying this model, the ice core has an age of about 2 500 years, much less than claimed for an older core from Akademii Nauk ice cap. Consequently, the ice cap is much younger and only of Late Holocene age, as also assumed for most Arctic ice caps and glaciers outside Greenland. However, the lowest part of Akademii Nauk ice cap is probably a remnant of an older ice cap stage.

  2. SSR Analysis of Genetic Diversity Among 192 Diploid Potato Cultivars

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    Xiaoyan Song

    2016-05-01

    Full Text Available In potato breeding, it is difficult to improve the traits of interest at the tetraploid level due to the tetrasomic inheritance. A promising alternative is diploid breeding. Thus it is necessary to assess the genetic diversity of diploid potato germplasm for efficient exploration and deployment of desirable traits. In this study, we used SSR markers to evaluate the genetic diversity of diploid potato cultivars. To screen polymorphic SSR markers, 55 pairs of SSR primers were employed to amplify 39 cultivars with relatively distant genetic relationships. Among them, 12 SSR markers with high polymorphism located at 12 chromosomes were chosen to evaluate the genetic diversity of 192 diploid potato cultivars. The primers produced 6 to 18 bands with an average of 8.2 bands per primer. In total, 98 bands were amplified from 192 cultivars, and 97 of them were polymorphic. Cluster analysis using UPGMA showed the genetic relationships of all accessions tested: 186 of the 192 accessions could be distinguished by only 12 pairs of SSR primers, and the 192 diploid cultivars were divided into 11 groups, and 83.3% constituted the first group. Clustering results showed relatively low genetic diversity among 192 diploid cultivars, with closer relationship at the molecular level. The results can provide molecular basis for diploid potato breeding.

  3. First genetic linkage map of Taraxacum koksaghyz Rodin based on AFLP, SSR, COS and EST-SSR markers

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    Arias, Marina; Hernandez, Monica; Remondegui, Naroa; Huvenaars, Koen; van Dijk, Peter; Ritter, Enrique

    2016-01-01

    Taraxacum koksaghyz Rodin (TKS) has been studied in many occasions as a possible alternative source for natural rubber production of good quality and for inulin production. Some tire companies are already testing TKS tire prototypes. There are also many investigations on the production of bio-fuels from inulin and inulin applications for health improvement and in the food industry. A limited amount of genomic resources exist for TKS and particularly no genetic linkage map is available in this species. We have constructed the first TKS genetic linkage map based on AFLP, COS, SSR and EST-SSR markers. The integrated linkage map with eight linkage groups (LG), representing the eight chromosomes of Russian dandelion, has 185 individual AFLP markers from parent 1, 188 individual AFLP markers from parent 2, 75 common AFLP markers and 6 COS, 1 SSR and 63 EST-SSR loci. Blasting the EST-SSR sequences against known sequences from lettuce allowed a partial alignment of our TKS map with a lettuce map. Blast searches against plant gene databases revealed some homologies with useful genes for downstream applications in the future. PMID:27488242

  4. First genetic linkage map of Taraxacum koksaghyz Rodin based on AFLP, SSR, COS and EST-SSR markers.

    Science.gov (United States)

    Arias, Marina; Hernandez, Monica; Remondegui, Naroa; Huvenaars, Koen; van Dijk, Peter; Ritter, Enrique

    2016-08-04

    Taraxacum koksaghyz Rodin (TKS) has been studied in many occasions as a possible alternative source for natural rubber production of good quality and for inulin production. Some tire companies are already testing TKS tire prototypes. There are also many investigations on the production of bio-fuels from inulin and inulin applications for health improvement and in the food industry. A limited amount of genomic resources exist for TKS and particularly no genetic linkage map is available in this species. We have constructed the first TKS genetic linkage map based on AFLP, COS, SSR and EST-SSR markers. The integrated linkage map with eight linkage groups (LG), representing the eight chromosomes of Russian dandelion, has 185 individual AFLP markers from parent 1, 188 individual AFLP markers from parent 2, 75 common AFLP markers and 6 COS, 1 SSR and 63 EST-SSR loci. Blasting the EST-SSR sequences against known sequences from lettuce allowed a partial alignment of our TKS map with a lettuce map. Blast searches against plant gene databases revealed some homologies with useful genes for downstream applications in the future.

  5. Development and validation of SSR markers for Coffea arabica L.

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    Robson Fernando Missio

    2009-01-01

    Full Text Available With the objective of developing new SSR markers for Coffea arabica, two enriched genomic libraries withprobes (GT15 and (AGG10 were constructed. A total of 835 clones were sequenced and 756 presented good quality sequences.Redundant sequences were observed for 113 clones (14.94%. SSRs were found in 287 clones (38%. An estimated size of417.5Kb of the C. arabica genome was sampled, with an average of one SSR per 1.46Kb. Dinucleotide repeats were morefrequent than trinucleotides. Four repeat sequences, (AG/CTn, (AC/GTn, (AAG/CTTn, and (AGG/CCTn represented 61.1%of the total observed. A total of 96 SSR primers were designed and tested by PCR for two C. arabica genotypes. Ninety new SSRmarkers were validated for further genetic studies of C. arabica.

  6. Analysis of Genetic Polymorphic SSR Markers in Germplasm Resources of the Natural Colored Cotton

    Institute of Scientific and Technical Information of China (English)

    WANG Ju-qin; LI Fu-zhen; QIU Xin-mian; BAO Li-sheng; LU Yan-ting

    2008-01-01

    @@ Short sequence repeats (microsatellite,SSR) and expressed sequence tags-SSR (EST-SSR) markers were employed to analyze the genetic diversity of natural colored cotton varieties.About 490 pairs of SSR markers spanning the 26 chromosomes were selected from the cotton microsatellite database,they were composed of the NAU,BNL,MUSS,and CIR markers,and there was one marker every 5 cM on average.

  7. Cross-species amplification of 105 Lolium perenne SSR loci in 23 species within the Poaceae

    DEFF Research Database (Denmark)

    Jensen, Louise Bach; Holm, Preben Bach; Lübberstedt, Thomas

    2007-01-01

    Amplification of 105 Lolium perenne SSR markers was studied in 23 grass species representing seven tribes from three subfamilies of Poaceae. Twelve of the SSR markers are published for the first time. Between 2% and 96% of the SSR markers could be amplified within a given species. A subset of eight...

  8. Sociological Research on the Byelorussian S.S.R.

    Science.gov (United States)

    Davidyuk, Georgy P.

    1978-01-01

    Characterizes trends in the development of applied sociology in the Byelorussian S.S.R., which reflects general developments in the USSR as a whole. Applied sociology studies the specific laws of development and functioning of social structures, processes, systems, organizations, and their component parts. It researches specific social groups,…

  9. SSR-Patchwork: An Optimized Protocol to Obtain a Rapid and Inexpensive SSR Library Using First-Generation Sequencing Technology

    Directory of Open Access Journals (Sweden)

    Antonietta Di Maio

    2013-01-01

    Full Text Available Premise of the study: We have optimized a version of a microsatellite loci isolation protocol for first-generation sequencing (FGS technologies. The protocol is optimized to reduce the cost and number of steps, and it combines some procedures from previous simple sequence repeat (SSR protocols with several key improvements that significantly affect the final yield of the SSR library. This protocol may be accessible for laboratories with a moderate budget or for which next-generation sequencing (NGS is not readily available. Methods and Results: We drew from classic protocols for library enrichment by digestion, ligation, amplification, hybridization, cloning, and sequencing. Three different systems were chosen: two with very different genome sizes (Galdieria sulphuraria, 10 Mbp; Pancratium maritimum, 30000 Mbp, and a third with an undetermined genome size (Kochia saxicola. Moreover, we also report the optimization of the sequencing reagents. A good frequency of the obtained microsatellite loci was achieved. Conclusions: The method presented here is very detailed; comparative tests with other SSR protocols are also reported. This optimized protocol is a promising tool for low-cost genetic studies and the rapid, simple construction of homemade SSR libraries for small and large genomes.

  10. SSR-patchwork: An optimized protocol to obtain a rapid and inexpensive SSR library using first-generation sequencing technology.

    Science.gov (United States)

    Di Maio, Antonietta; De Castro, Olga

    2013-01-01

    We have optimized a version of a microsatellite loci isolation protocol for first-generation sequencing (FGS) technologies. The protocol is optimized to reduce the cost and number of steps, and it combines some procedures from previous simple sequence repeat (SSR) protocols with several key improvements that significantly affect the final yield of the SSR library. This protocol may be accessible for laboratories with a moderate budget or for which next-generation sequencing (NGS) is not readily available. • We drew from classic protocols for library enrichment by digestion, ligation, amplification, hybridization, cloning, and sequencing. Three different systems were chosen: two with very different genome sizes (Galdieria sulphuraria, 10 Mbp; Pancratium maritimum, 30 000 Mbp), and a third with an undetermined genome size (Kochia saxicola). Moreover, we also report the optimization of the sequencing reagents. A good frequency of the obtained microsatellite loci was achieved. • The method presented here is very detailed; comparative tests with other SSR protocols are also reported. This optimized protocol is a promising tool for low-cost genetic studies and the rapid, simple construction of homemade SSR libraries for small and large genomes.

  11. Allelic divergence and cultivar-specific SSR alleles revealed by capillary electrophoresis using fluorescence-labeled SSR markers in sugarcane

    Science.gov (United States)

    Though sugarcane cultivars (Saccharum spp. hybrids) are complex aneu-polyploid hybrids, genetic evaluation and tracking of clone- or cultivar-specific alleles become possible due to capillary electrophoregrams (CE) using fluorescence-labeled SSR primer pairs. Twenty-four sugarcane cultivars, 12 each...

  12. EST and EST-SSR marker resources for Iris

    Directory of Open Access Journals (Sweden)

    Taylor Christopher A

    2009-06-01

    Full Text Available Abstract Background Limited DNA sequence and DNA marker resources have been developed for Iris (Iridaceae, a monocot genus of 200–300 species in the Asparagales, several of which are horticulturally important. We mined an I. brevicaulis-I. fulva EST database for simple sequence repeats (SSRs and developed ortholog-specific EST-SSR markers for genetic mapping and other genotyping applications in Iris. Here, we describe the abundance and other characteristics of SSRs identified in the transcript assembly (EST database and the cross-species utility and polymorphisms of I. brevicaulis-I. fulva EST-SSR markers among wild collected ecotypes and horticulturally important cultivars. Results Collectively, 6,530 ESTs were produced from normalized leaf and root cDNA libraries of I. brevicaulis (IB72 and I. fulva (IF174, and assembled into 4,917 unigenes (1,066 contigs and 3,851 singletons. We identified 1,447 SSRs in 1,162 unigenes and developed 526 EST-SSR markers, each tracing a different unigene. Three-fourths of the EST-SSR markers (399/526 amplified alleles from IB72 and IF174 and 84% (335/399 were polymorphic between IB25 and IF174, the parents of I. brevicaulis × I. fulva mapping populations. Forty EST-SSR markers were screened for polymorphisms among 39 ecotypes or cultivars of seven species – 100% amplified alleles from wild collected ecotypes of Louisiana Iris (I.brevicaulis, I.fulva, I. nelsonii, and I. hexagona, whereas 42–52% amplified alleles from cultivars of three horticulturally important species (I. pseudacorus, I. germanica, and I. sibirica. Ecotypes and cultivars were genetically diverse – the number of alleles/locus ranged from two to 18 and mean heterozygosity was 0.76. Conclusion Nearly 400 ortholog-specific EST-SSR markers were developed for comparative genetic mapping and other genotyping applications in Iris, were highly polymorphic among ecotypes and cultivars, and have broad utility for genotyping applications within

  13. Analysis of SSR in Citrus Sequences from EMBL Database

    Institute of Scientific and Technical Information of China (English)

    MENG Hai-jun; CAO Qing-qin; HU Zhi-yong; LIU Gao-ping; CHENG Yun-jiang; DENG Xiu-xin

    2005-01-01

    Abundance of simple sequence repeat (SSR) in Citrus sequences from EMBL database was investigated by using computer program MISA (MIcroSAtellite), which aimed to provide useful information for the development of SSR markers.Among 32 896 sequences of Citrus, 4987 SSRs were found in 4167 sequences and the average distance between SSRs was approximately 3.5 kb. Mononucleotide repeats (50.6%) were the most abundant repeats. And di-, tri-, tetra-, penta- and hexa-nucleotide repeats were 22.8, 25.2, 1, 0.08, and 0.36%, respectively. The most abundant motif was A/T followed in descending order by AG/CT, AC/GT, AT/TA. AAT/ATT, AAG/CTT, AGC/CGT, ACG/CTG and C/G. They comprised about90% of all microsatellites. Ten primer pairs were designed, and three of them produced clear visible bands among Citrus and its related genera.

  14. SSR markers for Quercus suber tree identification and embryo analysis.

    Science.gov (United States)

    Gómez, A; Pintos, B; Aguiriano, E; Manzanera, J A; Bueno, M A

    2001-01-01

    Three Quercus simple sequence repeat (SSR) markers were amplified by polymerase chain reaction (PCR) from nuclear DNA extracts of trees and in vitro-induced haploid embryos from anther cultures of Quercus suber L. These markers were sufficiently polymorphic to identify 10 of 12 trees located in two Spanish natural areas. The same loci have been analyzed in anther-derived haploid embryos showing the parental tree allele segregation. All the alleles were present in the haploid progeny. The presence of diverse alleles in embryos derived from the same anther demonstrated that they were induced on multiple microspores or pollen grains and they were not clonally propagated. Also, diploid cultures and mixtures of haploid-diploid tissues were obtained. The origin of such cultures, either somatic or gametic, was elucidated by SSR markers. All the embryos showed only one allele, corroborating a haploid origin. Allelic composition of the haploid progeny permitted parental identification among all analyzed trees.

  15. Genetic Relationships Among Chinese Maize OPVs Based on SSR Markers

    Institute of Scientific and Technical Information of China (English)

    SONG Li-ya; LIU Xue; CHEN Wei-guo; HAO Zhuan-fang; BAI Li; ZHANG De-gui

    2013-01-01

    Bulk-SSR method was used to analyze the genetic diversity of 44 open-pollinated varieties collected from Henan, Shandong, Shanxi, and Jilin provinces and Guangxi Zhuang Autonomous Region, China using 70 pairs of SSR primers. The purposes of this study were to (1) compare the genetic diversity among 44 Chinese maize open-pollinated varieties;(2) estimate the minimum number of alleles for construction of a stable dendrogram;and (3) trace the genetic relationships among local germplasm from different regions of China. In total, these 70 SSR primers yielded 292 alleles in 176 samples (4×44) analyzed. The number of alleles per locus was 4.17 on average and ranged from 2 to 8. The highest number of alleles per open-pollinated variety (55.25) was detected in Shanxi germplasm, which indicated that open-pollinated varieties from Shanxi possessed the largest genetic diversity among those from the five locations. The correlation coefficients between different genetic similarity matrices suggested that 200 alleles were sufficient for analysis of the genetic diversity of these 44 open-pollinated varieties. The cluster analysis showed that 44 open-pollinated varieties collected from three growing regions in China were accurately classified into three groups that were highly consistent with their geographic origins, and there is no correlation between GS and geographic distance in this study.

  16. Uniform color processing of scanned topographic maps based on SSR

    Science.gov (United States)

    Fu, Zhongliang; Tong, Chunya; Liu, Lu; Huang, Yan

    2009-10-01

    Nowadays, large amount of paper-based topographic maps are still existed in many government department. The scanned maps of them are very useful for research on city history migration, city planning and so on. However, the brightness of these maps is not uniform, and creases are existed, so uniform color process is always needed. If the classical Retinex algorithm is used, the map would have a low brightness and contrast ratio. Therefore, a normal intercepting SSR algorithm of linear extending is presented in this paper. This algorithm first uses the classical SSR algorithm to process the data, and then the average value of image and variance are introduced to do normal intercepting linear extending on the map. Experiment results show that, the improved SSR can not only efficiently eliminate creases and uniform the map brightness, but also increase the global brightness and contrast ratio. Moreover, this algorithm can also be used in the pretreatment of grid image registration, thus to enhance the precision, velocity and accuracy of registration.

  17. Development of SSR markers and construction of a linkage map in jute

    Indian Academy of Sciences (India)

    Maumita Das; Sumana Banerjee; Raman Dhariwal; Shailendra Vyas; Reyazul R. Mir; Niladri Topdar; Avijit Kundu; Jitendra P. Khurana; Akhilesh K. Tyagi; Debabrata Sarkar; Mohit K. Sinha; Harindra S. Balyan; Pushpendra K. Gupta

    2011-04-01

    Jute is an important natural fibre crop, which is only second to cotton in its importance at the global level. It is mostly grown in Indian subcontinent and has been recently used for the development of genomics resources.We recently initiated a programme to develop simple sequence repeat markers and reported a set of 2469 SSR that were developed using four SSR-enriched libraries (Mir et al. 2009). In this communication, we report an additional set of 607 novel SSR in 393 SSR containing sequences. However, primers could be designed for only 417 potentially useful SSR. Polymorphism survey was carried out for 374 primer pairs using two parental genotypes (JRO 524 and PPO4) of a mapping population developed for fibre fineness; only 66 SSR were polymorphic. Owing to a low level of polymorphism between the parental genotypes and a high degree of segregation distortion in recombinant inbred lines, genotypic data of only 53 polymorphic SSR on the mapping population consisting of 120 RIL could be used for the construction of a linkage map; 36 SSR loci were mapped on six linkage groups that covered a total genetic distance of 784.3 cM. Hopefully, this map will be enriched with more SSR loci in future and will prove useful for identification of quantitative trait loci/genes for molecular breeding involving improvement of fibre fineness and other related traits in jute.

  18. Development of SSR markers and construction of a linkage map in jute.

    Science.gov (United States)

    Das, Moumita; Banerjee, Sumana; Dhariwal, Raman; Vyas, Shailendra; Mir, Reyazul R; Topdar, Niladri; Kundu, Avijit; Khurana, Jitendra P; Tyagi, Akhilesh K; Sarkar, Debabrata; Sinha, Mohit K; Balyan, Harindra S; Gupta, Pushpendra K

    2012-01-01

    Jute is an important natural fibre crop, which is only second to cotton in its importance at the global level. It is mostly grown in Indian subcontinent and has been recently used for the development of genomics resources.We recently initiated a programme to develop simple sequence repeat markers and reported a set of 2469 SSR that were developed using four SSR-enriched libraries (Mir et al. 2009). In this communication, we report an additional set of 607 novel SSR in 393 SSR containing sequences. However, primers could be designed for only 417 potentially useful SSR. Polymorphism survey was carried out for 374 primer pairs using two parental genotypes (JRO 524 and PPO4) of a mapping population developed for fibre fineness; only 66 SSR were polymorphic. Owing to a low level of polymorphism between the parental genotypes and a high degree of segregation distortion in recombinant inbred lines, genotypic data of only 53 polymorphic SSR on the mapping population consisting of 120 RIL could be used for the construction of a linkage map; 36 SSR loci were mapped on six linkage groups that covered a total genetic distance of 784.3 cM. Hopefully, this map will be enriched with more SSR loci in future and will prove useful for identification of quantitative trait loci/genes for molecular breeding involving improvement of fibre fineness and other related traits in jute.

  19. Analysis of vanillic acid in polar ice cores as a biomass burning proxy - preliminary results from the Akademii Nauk Ice Cap in Siberia

    Science.gov (United States)

    Grieman, M. M.; Jimenez, R.; McConnell, J. R.; Fritzsche, D.; Saltzman, E. S.

    2013-12-01

    Biomass burning influences global climate change and the composition of the atmosphere. The drivers, effects, and climate feedbacks related to fire are poorly understood. Many different proxies have been used to reconstruct past fire frequency from lake sediments and polar ice cores. Reconstruction of historical trends in biomass burning is challenging because of regional variability and the qualitative nature of various proxies. Vanillic acid (4-hydroxy-3-methoxybenzoic acid) is a product of the combustion of conifer lignin that is known to occur in biomass burning aerosols. Biomass burning is likely the only significant source of vanillic acid in polar ice. In this study we describe an analytical method for quantifying vanillic acid in polar ice using HPLC with electrospray ionization and tandem mass spectrometric detection. The method has a detection limit of 100 pM and a precision of × 10% at the 100 pM level for analysis of 100 μl of ice melt water. The method was used to analyze more than 1000 discrete samples from the Akademii Nauk ice cap on Severnaya Zemlya in the high Russia Arctic (79°30'N, 97°45'E) (Fritzsche et al., 2002; Fritzsche et al., 2005; Weiler et al., 2005). The samples range in age over the past 2,000 years. The results show a mean vanillic acid concentration of 440 × 710 pM (1σ), with elevated levels during the periods from 300-600 and 1450-1550 C.E.

  20. High Gradient Tests of the Fermilab SSR1 Cavity

    CERN Document Server

    Khabiboulline, T; Gonin, I; Madrak, R; Melnychuk, O; Ozelis, J; Pischalnikov, Y; Ristori, L; Rowe, A; Sergatskov, D A; Sukhanov, A; Terechkine, I; Wagner, R; Webber, R; Yakovlev, V

    2013-01-01

    In Fermilab we are build and tested several superconducting Single Spoke Resonators (SSR1, \\beta=0.22) which can be used for acceleration of low beta ions. Fist two cavities performed very well during cold test in Vertical Test Station at FNAL. One dressed cavity was also tested successfully in Horizontal Test Station. Currently we are building 8 cavity cryomodule for PIXIE project. Additional 10 cavities were manufactured in the industry and on-going cold test results will be presented in this poster.

  1. High-throughput development of genome-wide locus-specific informative SSR markers in wheat

    Science.gov (United States)

    Although simple sequence repeat (SSR) markers are not new, they are still useful and often used markers in molecular mapping and marker-assisted breeding, particularly in developing countries. However, locus-specific SSR markers could be more useful and informative in wheat breeding and genetic stud...

  2. SAT, a flexible and optimized Web application for SSR marker development

    Directory of Open Access Journals (Sweden)

    Rami Jean-François

    2007-11-01

    Full Text Available Abstract Background Simple Sequence Repeats (SSRs, or microsatellites, are among the most powerful genetic markers known. A common method for the development of SSR markers is the construction of genomic DNA libraries enriched for SSR sequences, followed by DNA sequencing. However, designing optimal SSR markers from bulk sequence data is a laborious and time-consuming process. Results SAT (SSR Analysis Tool is a user-friendly Web application developed to minimize tedious manual operations and reduce errors. This tool facilitates the integration, analysis and display of sequence data from SSR-enriched libraries. SAT is designed to successively perform base calling and quality evaluation of chromatograms, eliminate cloning vector, adaptors and low quality sequences, detect chimera or partially digested sequences, search for SSR motifs, cluster and assemble the redundant sequences, and design SSR primer pairs. An additional virtual PCR step establishes primer specificity. Users may modify the different parameters of each step of the SAT analysis. Although certain steps are compulsory, such as SSR motifs search and sequence assembly, users do not have to run the entire pipeline, and they can choose selectively which steps to perform. A database allows users to store and query results, and to redo individual steps of the workflow. Conclusion The SAT Web application is available at http://sat.cirad.fr/sat, and a standalone command-line version is also freely downloadable. Users must send an email to the SAT administrator tropgene@cirad.fr to request a login and password.

  3. Construction of Genetic Linkage Map Based on SSR Markers in Peanut(Arachis hypogaea L.)

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Molecular genetic maps of crop species can be used in a variety of ways in breeding and genomic research such as identification and mapping of genes and quantitative trait loci (QTLs) for morphological, physiological and economic traits of crop species. However, a comprehensive genetic linkage map for cultivated peanut has not yet been developed due to the extremely low frequency of DNA polymorphism in cultivated peanut. In this study, 142 recombinant inbred lines (RILs) derived from a cross between Yueyou 13 and Zhenzhuhei were used as mapping population in peanut (Arachis hypogaea L.). A total 652 pairs of genomic-SSR primer and 392 pairs of EST-SSR primer were used to detect the polymorphisms between the two parents. 141 SSR primer pairs, 127 genomic-SSR and 14 EST-SSR ones, which can be used to detect polymorphisms between the two parents, were selected to analyze the RILs population. Thus, a linkage genetic map which consists of 131 SSR loci in 20 linkage groups, with a coverage of 679 cM and an average of 6.12 cM of inter-maker distance was constructed. The putative functions of 12 EST-SSR markers located on the map were analyzed. Eleven showed homology to gene sequences deposited in GenBank. This is the first report of construction of a comprehensive genetic map with SSR markers in peanut (Arachis hypogaea L.). The map presented here will provide a genetic framework for mapping the qualitative and quantitative trait in peanut.

  4. Development and mapping of a public reference set of SSR markers in Lolium perenne L.

    NARCIS (Netherlands)

    Bach, J.L.; Muylle, H.; Arens, P.F.P.; Andersen, C.H.; Bach Holm, P.; Ghesquiere, M.; Julier, B.; Lubberstedt, T.; Nielsen, K.K.; Riek, de J.; Roldán-Ruiz, I.; Roulund, N.; Taylor, C.; Vosman, B.J.; Barre, P.

    2005-01-01

    We report on the characterization and mapping of 76 simple sequence repeat (SSR) markers for Lolium perenne. These markers are publicly available or obtained either from genomic libraries enriched for SSR motifs or L. perenne expressed sequence tag (EST) clones. Four L. perenne mapping populations w

  5. Development and validation of new SSR markers from expressed regions in the garlic genome

    Science.gov (United States)

    Limited number of simple sequence repeat (SSR) markers is available for the genome of garlic (Allium sativum L.) although SSR markers have become one of the most preferred marker systems because they are typically co-dominant, reproducible, cross species transferable and highly polymorphic. In this ...

  6. ESAP plus: a web-based server for EST-SSR marker development.

    Science.gov (United States)

    Ponyared, Piyarat; Ponsawat, Jiradej; Tongsima, Sissades; Seresangtakul, Pusadee; Akkasaeng, Chutipong; Tantisuwichwong, Nathpapat

    2016-12-22

    Simple sequence repeats (SSRs) have become widely used as molecular markers in plant genetic studies due to their abundance, high allelic variation at each locus and simplicity to analyze using conventional PCR amplification. To study plants with unknown genome sequence, SSR markers from Expressed Sequence Tags (ESTs), which can be obtained from the plant mRNA (converted to cDNA), must be utilized. With the advent of high-throughput sequencing technology, huge EST sequence data have been generated and are now accessible from many public databases. However, SSR marker identification from a large in-house or public EST collection requires a computational pipeline that makes use of several standard bioinformatic tools to design high quality EST-SSR primers. Some of these computational tools are not users friendly and must be tightly integrated with reference genomic databases. A web-based bioinformatic pipeline, called EST Analysis Pipeline Plus (ESAP Plus), was constructed for assisting researchers to develop SSR markers from a large EST collection. ESAP Plus incorporates several bioinformatic scripts and some useful standard software tools necessary for the four main procedures of EST-SSR marker development, namely 1) pre-processing, 2) clustering and assembly, 3) SSR mining and 4) SSR primer design. The proposed pipeline also provides two alternative steps for reducing EST redundancy and identifying SSR loci. Using public sugarcane ESTs, ESAP Plus automatically executed the aforementioned computational pipeline via a simple web user interface, which was implemented using standard PHP, HTML, CSS and Java scripts. With ESAP Plus, users can upload raw EST data and choose various filtering options and parameters to analyze each of the four main procedures through this web interface. All input EST data and their predicted SSR results will be stored in the ESAP Plus MySQL database. Users will be notified via e-mail when the automatic process is completed and they can

  7. Multiplex PCR System Optimization with Potato SSR Markers

    Institute of Scientific and Technical Information of China (English)

    Wang Shao-peng; Liu Shang-wu; Li Yong; Liu Wei-ting; Lv Dian-qiu

    2012-01-01

    Potato variety Kexin18 was used as testing materials in this research to study the influence on main components in multiplex PCR system, different primer ratios and annealing temperatures in SSR marker amplification. Concentration and gradient experiments for four components (enzyme, MgCl2, DNA template and dNTPs) in PCR system were used in the research with the concentration of the other component remained the same; the orthogonal design L9 (34) was applied in the optimization of four sets of primers (STM0014, Pat, SSI, and UGP) in the reaction system at three levels; the temperature gradient selection was used to find out the optimum annealing temperature for the primer. The optimized multiplex PCR system of potato SSR marker with a total volume of 20 μL : 2.5 μL 25 mmol.L-1 MgCl2, 0.6 μL 10 mmol·L-1 dNTPs, 0.8 U Taq, 80 ng DNA template was ultimately established through the comparison and analysis of test results; the ratio of four pairs of 4 mmol. L1 primers was 2 : 1 : 2 : 3, and the annealing temperature was 54.7℃. The optimized reaction system could be repeated stably; and the stable and reliable amplification results were able to clearly distinguish different potato varieties. This research built the solid foundation for the further study of genetic diversity of potato germplasms and construction of DNA fingerprinting..

  8. GENETIC DIVERSITY OF WHEAT CULTIVARS ESTIMATED BY SSR MARKERS

    Directory of Open Access Journals (Sweden)

    K. Dvojković

    2008-09-01

    Full Text Available Presence and utilization of the genetic variability in the breeding programmes is prerequisite for their successfulness. Important factor for crop improvement is knowledge about the genetic diversity which providing a basis for the precise selection of parental combinations. Since beginning of 20th century, generation of wheat breeders and scientists in Croatia developed numerous advanced and successful wheat cultivars. Previous researches aimed to genetic diversity evaluation in Croatia were conducted by means of morphological traits, pedigree data (coefficients of parentage, proteins (glutenins and gliadins and RAPD DNA markers. DNA markers detect directly variation of DNA sequence for particular loci and they are not under influence of environment, epistatic and pleiotropic effects. Microsatellite markers (Simple Sequence Repeats; SSRs, as highly polymorphic, informative and codominant DNA marker system, have been extensively used for genetic diversity studies on wheat world wide. A set of 98 wheat cultivars released in Croatia during the period 1905-2007, and 24 foreign cultivar (included because of their ancestral significance or as standards, were screened by 45 microsatellite markers, covering all three wheat genomes. The objectives of this study were to evaluate the microsatellites-based genetic diversity with emphasize on cultivars created at the Agricultural Institute Osijek, as well as to investigate SSR application for selection of genetically the most distant parental pairs. Preliminary data obtained by means of SSR markers showed a satisfactory level of genetic diversity and usefulness of microsatellites for parental selection.

  9. SSR Cluster and Fertility Loci Analysis of GC13

    Institute of Scientific and Technical Information of China (English)

    NONG Bao-xuan; XIA Xiu-zhong; LIANG Yao-mao; LU Gang; ZHANG Zong-qiong; LI Dan-ting

    2011-01-01

    [Objective] The research aimed to clarify the genetic mechanism of special wide compatibility of GC13.[Method] The clustering analyses of GC13,five indica,five japonica and five wide compatibility varieties were carried out by using 70 SSR primers.[Result] GC13 was clustered into japonica group and had far genetic relationship with indica and wide compatibility variety.Two fertility loci were detected in GC13,in which one closely linked to RM225 on chromosome 6.According to the position on the chromosome,it speculated that this locus was allelic to S5.GC13 carried the allelic gene S5-n at this locus.The other locus closely linked to RM408 on chromosome 8 and was provisionally designated as Sg(t).At this locus,GC13 carried Sg(t)-i allelic gene,which was consistent with IR36.The effect of S5 locus was stronger than that of Sg(t).[Conclusion] The research laid the good foundation for using the wide compatibility line GC13 to breed the hybrid between subspecies.%[Objective] The research aimed to clarify the genetic mechanism of special wide compatibility of GC13.[Method] The clustering analyses of GC13,five indica,five japonica and five wide compatibility varieties were carried out by using 70 SSR primers.[Result

  10. In silico comparative analysis of SSR markers in plants

    Directory of Open Access Journals (Sweden)

    da Maia Luciano C

    2011-01-01

    Full Text Available Abstract Background The adverse environmental conditions impose extreme limitation to growth and plant development, restricting the genetic potential and reflecting on plant yield losses. The progress obtained by classic plant breeding methods aiming at increasing abiotic stress tolerances have not been enough to cope with increasing food demands. New target genes need to be identified to reach this goal, which requires extensive studies of the related biological mechanisms. Comparative analyses in ancestral plant groups can help to elucidate yet unclear biological processes. Results In this study, we surveyed the occurrence patterns of expressed sequence tag-derived microsatellite markers for model plants. A total of 13,133 SSR markers were discovered using the SSRLocator software in non-redundant EST databases made for all eleven species chosen for this study. The dimer motifs are more frequent in lower plant species, such as green algae and mosses, and the trimer motifs are more frequent for the majority of higher plant groups, such as monocots and dicots. With this in silico study we confirm several microsatellite plant survey results made with available bioinformatics tools. Conclusions The comparative studies of EST-SSR markers among all plant lineages is well suited for plant evolution studies as well as for future studies of transferability of molecular markers.

  11. An efficient identification strategy of clonal tea cultivars using long-core motif SSR markers.

    Science.gov (United States)

    Wang, Rang Jian; Gao, Xiang Feng; Kong, Xiang Rui; Yang, Jun

    2016-01-01

    Microsatellites, or simple sequence repeats (SSRs), especially those with long-core motifs (tri-, tetra-, penta-, and hexa-nucleotide) represent an excellent tool for DNA fingerprinting. SSRs with long-core motifs are preferred since neighbor alleles are more easily separated and identified from each other, which render the interpretation of electropherograms and the true alleles more reliable. In the present work, with the purpose of characterizing a set of core SSR markers with long-core motifs for well fingerprinting clonal cultivars of tea (Camellia sinensis), we analyzed 66 elite clonal tea cultivars in China with 33 initially-chosen long-core motif SSR markers covering all the 15 linkage groups of tea plant genome. A set of 6 SSR markers were conclusively selected as core SSR markers after further selection. The polymorphic information content (PIC) of the core SSR markers was >0.5, with ≤5 alleles in each marker containing 10 or fewer genotypes. Phylogenetic analysis revealed that the core SSR markers were not strongly correlated with the trait 'cultivar processing-property'. The combined probability of identity (PID) between two random cultivars for the whole set of 6 SSR markers was estimated to be 2.22 × 10(-5), which was quite low, confirmed the usefulness of the proposed SSR markers for fingerprinting analyses in Camellia sinensis. Moreover, for the sake of quickly discriminating the clonal tea cultivars, a cultivar identification diagram (CID) was subsequently established using these core markers, which fully reflected the identification process and provided the immediate information about which SSR markers were needed to identify a cultivar chosen among the tested ones. The results suggested that long-core motif SSR markers used in the investigation contributed to the accurate and efficient identification of the clonal tea cultivars and enabled the protection of intellectual property.

  12. Genetic variability assessment in the genus Passiflora by SSR markers

    Directory of Open Access Journals (Sweden)

    Claudia Lougon Paiva

    2014-09-01

    Full Text Available The genus Passiflora encompasses many species that are endemic to the Brazilian territory, including some with economic value. Studies on genetic diversity in this genus are fundamental because they allow understanding genetic variability and distance. The present study aimed to determine the genetic variability and distances among 10 species of the genus Passiflora by using microsatellite markers (Simple Sequence Repeat, SSR. Twenty-eight heterologous microsatellite markers were tested, but only 12 were used in the diversity analysis because they amplified in at least 80% of the species. A clear separation was observed among the subgenuses studied, as well as wide variation among the accessions of Passiflora. This knowledge enables breeders to explore diversity and transfer favorable alleles found in wild species.

  13. Assessment of wheat variety distinctness using SSR markers

    Institute of Scientific and Technical Information of China (English)

    WANG Li-xin; QIU Jun; CHANG Li-fang; LIU Li-hua; LI Hong-bo; PANG Bin-shuang; ZHAO Chang-ping

    2015-01-01

    Assessment of variety distinctness is important for both the registration and the protection of particular variety. However, the current testing system, which assesses a range of morphological characters of each pair of varieties grown side-by-side, is time-consuming and is not suitable for the assessment of hundreds of samples. The objective of this study was to develop a procedure for the assessment of wheat variety distinctness using simple sequence repeat (SSR) markers. A comparison between the molecular and morphological proifle of 797 varieties was made. On the basis of the comparison, pairs of va-rieties with a genetic similarity value (GSV) ≤90% were deemed to be distinct, accounting for ~85% of varieties assessed in wheat regional trials. For the remaining ~15% of varieties, GSVs between different varieties were >90%, among which ~35% were not distinct and the other ~65% were distinct. Therefore, if given a GSV>90%, the pairs of varieties should be morphologicaly assessed in the ifeld. To avoid any errors in the assessments, we proposed the elimination of contaminant plants from the sample before comparing the varietal genotypes, scoring of the genotype at each locus with a pair of alele numbers when constructing a molecular proifle, and faithfuly recording two aleles at a non-homozygous locus. To reduce the workload and cost, a three-grade markers comparison among varieties is suggested. In addition, 80 SSR markers and a technical procedure for assessment of wheat variety distinctness have been proposed. Based on the procedure, the distinctness assessment of ~85% of al wheat varieties is completed in our laboratory annualy. Consequently, total ifeld assessment has been reduced considerably.

  14. Genetic diversity of wild and cultivated Rubus species in Colombia using AFLP and SSR markers

    Directory of Open Access Journals (Sweden)

    Sandra Bibiana Aguilar

    2007-01-01

    Full Text Available The Andean blackberry belongs to the genus Rubus, the largest of the Rosaceae family and one of the mostdiverse of the plant kingdom. In Colombia Rubus glaucus Benth, known as the Andean raspberry or blackberry, is one of thenine edible of the genus out of forty-four reported species. In this study wild and cultivated genotypes, collected in the CentralAndes of Colombia were analyzed by AFLP and SSR markers. Sexual reproduction seems to play an important role inmaintaining the genetic variability in R. glaucus, and the viability of using the SSR of Rubus alceifolius to characterizeColombian Rubus species was clearly demonstrated. All species evaluated produced very specific banding patterns,differentiating them from the others. Both AFLP and SSR produced bands exclusive to each of the following species: R.robustus, R. urticifolius, R. glaucus, and R. rosifolius. The SSR markers differentiated diploid and tetraploid genotypes of R.glaucus.

  15. DNA Profiles of MTG (Moderat Tahan Gano) Oil Palm Variety Based on SSR Marker

    Science.gov (United States)

    Putri, L. A. P.; Setiado, H.; Hardianti, R.

    2017-03-01

    The oil palm, an economically important tree in Indonesia, has been one of the world’s major sources of edible oil and a significant precursor of biodiesel fuel. The objectives of this study were to know DNA profile of commercial MTG (Moderat Tahan Gano) oil palm variety collections. A total of 10 trees MTG oil palm variety were used for analysis. In this experiment, the DNA profile diversity was assessed using mEgCIR0174 and SSR-1 loci of oil palm’s specific SSR markers. The results of the experiment indicated out of 3 alleles of pcr product of mEgCIR0174 (198, 203 and 208 bp) and SSR-1 (201, 217 and 232 bp). These preliminary results demonstrated SSR marker can be used to evaluate genetic relatedness among trees of MTG (Moderat Tahan Gano) oil palm variety derived from different crossing or difference to desease resistance trait or misslabeled.

  16. Assessment of the Genetic Diversity of Pummelo Germplasms Using AFLP and SSR Markers

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    The genetic diversities of 110 pummelo germplasms and 12 of their relatives were analyzed by SSR and AFLP methods. Approximately 99.1% of the 335 SSR loci were polymorphic, and 9.85 alleles per SSR locus were identified. The gene diversity values changed from 0.1939 to 0.9073, and 46 SSR polymorphic bands were scored. 72% of the 343 AFLP loci were polymorphic, and 82 polymorphic loci per AFLP were identified. Heterozygosity changed from 0.21863 to 0.28445,and 44 AFLP polymorphic bands were scored. The UPGMA result showed that 122 pummelo genotypes and their relatives could be divided into eight groups, and the pummelo genotypes composed mainly of Shatian pummelo varieties group,Wendan pummelo vareties group and a huge hybrid pummelo varieties group. The classification result was expected to widen the genetic background of pummelos using various target varieties.

  17. Supplementary Controller Design for SSR Damping in a Series-Compensated DFIG-Based Wind Farm

    Directory of Open Access Journals (Sweden)

    Minqiang Hu

    2012-11-01

    Full Text Available The increasing presence of wind power in power systems will likely drive the integration of large wind farms with electrical networks that are series-compensated to sustain large power flows. This may potentially lead to subsynchronous resonance (SSR issues. In this paper, a supplementary controller on the grid-side converter (GSC control loop is designed to mitigate SSR for wind power systems based on doubly fed induction generators (DFIGs with back-to-back converters. Different supplementary controller feedback signals and modulated-voltage injecting points are proposed and compared based on modal analysis and verified through root locus analysis to identify the optimal feedback signal and the most effective control location for SSR damping. The validity and effectiveness of the proposed supplemental control are demonstrated on the IEEE first benchmark model for computer simulations of SSR by means of time domain simulation analysis using Matlab/Simulink.

  18. SSR genetic linkage map construction of pea(Pisum sativum L.) based on Chinese native varieties

    Institute of Scientific and Technical Information of China (English)

    Xuelian; Sun; Tao; Yang; Junjie; Hao; Xiaoyan; Zhang; Rebecca; Ford; Junye; Jiang; Fang; Wang; Jianping; Guan; Xuxiao; Zong

    2014-01-01

    Simple sequence repeat(SSR)markers have previously been applied to linkage mapping of the pea(Pisum sativum L.)genome.However,the transferability of existing loci to the molecularly distinct Chinese winter pea gene pool was limited.A novel set of pea SSR markers was accordingly developed.Together with existing SSR sequences,the genome of the G0003973(winter hardy)×G0005527(cold sensitive)cross was mapped using 190 F2individuals.In total,157 SSR markers were placed in 11 linkage groups with an average interval of 9.7 cM and total coverage of 1518 cM.The novel markers and genetic linkage map will be useful for marker-assisted pea breeding.

  19. Development of genomic SSR markers for fingerprinting lettuce (Lactuca sativa L.) cultivars and mapping genes.

    Science.gov (United States)

    Rauscher, Gilda; Simko, Ivan

    2013-01-22

    Lettuce (Lactuca sativa L.) is the major crop from the group of leafy vegetables. Several types of molecular markers were developed that are effectively used in lettuce breeding and genetic studies. However only a very limited number of microsattelite-based markers are publicly available. We have employed the method of enriched microsatellite libraries to develop 97 genomic SSR markers. Testing of newly developed markers on a set of 36 Lactuca accession (33 L. sativa, and one of each L. serriola L., L. saligna L., and L. virosa L.) revealed that both the genetic heterozygosity (UHe = 0.56) and the number of loci per SSR (Na = 5.50) are significantly higher for genomic SSR markers than for previously developed EST-based SSR markers (UHe = 0.32, Na = 3.56). Fifty-four genomic SSR markers were placed on the molecular linkage map of lettuce. Distribution of markers in the genome appeared to be random, with the exception of possible cluster on linkage group 6. Any combination of 32 genomic SSRs was able to distinguish genotypes of all 36 accessions. Fourteen of newly developed SSR markers originate from fragments with high sequence similarity to resistance gene candidates (RGCs) and RGC pseudogenes. Analysis of molecular variance (AMOVA) of L. sativa accessions showed that approximately 3% of genetic diversity was within accessions, 79% among accessions, and 18% among horticultural types. The newly developed genomic SSR markers were added to the pool of previously developed EST-SSRs markers. These two types of SSR-based markers provide useful tools for lettuce cultivar fingerprinting, development of integrated molecular linkage maps, and mapping of genes.

  20. Genetic structure of wild emmer wheat populations as reflected by transcribed versus anonymous SSR markers.

    Science.gov (United States)

    Peleg, Zvi; Fahima, Tzion; Abbo, Shahal; Krugman, Tamar; Saranga, Yehoshua

    2008-03-01

    Simple sequence repeat (SSR) markers have become a major tool in population genetic analyses. The anonymous genomic SSRs (gSSRs) have been recently supplemented with expressed sequence tag (EST) derived SSRs (eSSRs), which represent the transcribed regions of the genome. In the present study, we used 8 populations of wild emmer wheat (Triticum turgidum subsp. dicoccoides) to compare the usefulness of the two types of SSR markers in assessing allelic diversity and population structure. gSSRs revealed significantly higher diversity than eSSRs in terms of average number of alleles (14.92 vs. 7.4, respectively), polymorphic information content (0.87 vs. 0.68, respectively), and gene diversity (He; 0.55 vs. 0.38, respectively). Despite the overall differences in the level of diversity, Mantel tests for correlations between eSSR and gSSR pairwise genetic distances were found to be significant for each population as well as for all accessions jointly (RM=0.54, p=0.01). Various genetic structure analyses (AMOVA, PCoA, STRUCTURE, unrooted UPGMA tree) revealed a better capacity of eSSRs to distinguish between populations, while gSSRs showed a higher proportion of intrapopulation (among accessions) diversity. We conclude that eSSR and gSSR markers should be employed in conjunction to obtain a high inter- and intra-specific (or inter- and intra-varietal) distinctness.

  1. Cultivar identification and genetic relationship of pineapple (Ananas comosus) cultivars using SSR markers.

    Science.gov (United States)

    Lin, Y S; Kuan, C S; Weng, I S; Tsai, C C

    2015-11-25

    The genetic relationships among 27 pineapple [Ananas comosus (L.) Merr.] cultivars and lines were examined using 16 simple sequence repeat (SSR) markers. The number of alleles per locus of the SSR markers ranged from 2 to 6 (average 3.19), for a total of 51 alleles. Similarity coefficients were calculated on the basis of 51 amplified bands. A dendrogram was created according to the 16 SSR markers by the unweighted pair-group method. The banding patterns obtained from the SSR primers allowed most of the cultivars and lines to be distinguished, with the exception of vegetative clones. According to the dendrogram, the 27 pineapple cultivars and lines were clustered into three main clusters and four individual clusters. As expected, the dendrogram showed that derived cultivars and lines are closely related to their parental cultivars; the genetic relationships between pineapple cultivars agree with the genealogy of their breeding history. In addition, the analysis showed that there is no obvious correlation between SSR markers and morphological characters. In conclusion, SSR analysis is an efficient method for pineapple cultivar identification and can offer valuable informative characters to identify pineapple cultivars in Taiwan.

  2. Development of advanced BWR fuel bundle with spectral shift rod - BWR core characteristics with SSR

    Energy Technology Data Exchange (ETDEWEB)

    Hino, T.; Kondo, T.; Chaki, M.; Ohga, Y. [Hitachi-GE Nuclear Energy, Ltd., 1-1, Saiwai-cho, 3-chome, Hitachi-shi, Ibaraki-ken, 317-0073 (Japan); Makigami, T. [Tokyo Electric Power Company Inc., 1-1-3, Uchisaiwai-cho, Chiyoda-ku, Tokyo, 100-0011 (Japan)

    2012-07-01

    The neutron energy spectrum can be varied during an operation cycle to generate and utilize more plutonium from the non-fissile {sup 238}U by changing the void fraction in the core through control of the core coolant flow rate. This operation method, which is called a spectral shift operation, is practiced in BWRs to save natural uranium. A new component called a spectral shift rod (SSR), which is utilized instead of a conventional water rod, has been introduced to amplify the void fraction change and increase the spectral shift effect. In this study, fuel bundle design with the SSR and core design were carried out for the ABWR and the next generation BWR, HP-ABWR (High-Performance ABWR).The core characteristics with the SSR were evaluated and compared with those when using the conventional water rod. Influences of uncertainty of the water level in the SSR on the safety limit minimum critical power ratio (SLMCPR) were considered for evaluation of the uranium saving effect attained by the SSR. As a result, it was found that the amount of natural uranium needed for an operation cycle could be reduced more than 3% with 20% core coolant flow change and more than 5% with 30% core coolant flow change, in the form of increased discharge exposure by using the SSR compared with the conventional water rod use. (authors)

  3. Grey correlational and SSR analyses of cotton hybrids

    Institute of Scientific and Technical Information of China (English)

    Ma Xiongfeng; Zhang Wensheng; Yang Daigang; Zhou Xiaojian; Zhang Xianliang; Guo Ruilin; Wang Haifeng; Meng Qingqin; Pei Xiaoyu; Zhou Kehai

    2013-01-01

    Ten upland cotton strains exhibiting 3 fiber quality traits and 8 yield traits,were grown for two years in an investigation of the correlation between grey relational analysis (GRA) and genetic identity in heterosis of cot-ton hybrid. The aim was to establish the optimal approach for heterosis prediction and parent selection. Plant traits data were collected and analyzed for GRA. In addition,72 simple sequence repeat (SSR) markers were examined and 148 polymorphisms were detected. Correlation analysis of GRA,genetic identity,F1 fiber quality and yield heterosis was conducted. Significant differences were observed between the two analytic methods,whereas compa-rable predictions were given for yield heterosis. GRA for yield exhibited slightly higher correlation than genetic identity analysis,with a correlation coefficient of 0.49. GRA and genetic analysis exhibited overlapping yet dis-tinct advantages in heterosis prediction. Therefore,these analytical methods should be integrated to achieve the op-timal heterosis prediction and parent selection.

  4. STUDY OF GENETIC VARIABILITY OF TRITICALE VARIETIES BY SSR MARKERS

    Directory of Open Access Journals (Sweden)

    Jana Ondroušková

    2013-04-01

    Full Text Available For the detection of genetic variability ten genotypes of winter triticale (×Triticosecale Wittmack, 2n = 6x = 42; BBAARR were selected: nine varieties and one breeding line with good bread-making quality KM 4-09 with the chromosome translocation 1R.1D 5+10-2. 25 microsatellites markers located in the genome A, B, D and R were chosen for analysis. Eighty-four alleles were detected with an average of 3.36 alleles per locus were detected. For each microsatellite statistical values were calculated diversity index (DI, probabilities of identity (PI and polymorphic information content (PIC were calculated and averages statistical values are: DI 0.55, PI 0.27 and 0.5 PIC. Overall dendrogram based on the UPGMA method (Jaccards similarity coefficient significantly distinguished two groups of genotypes and these groups were divided into sub-clusters. A set of 5 SSR markers (Xwms0752, Xbarc128, Xrems1237, Xwms0861 and Xbrac170 which have the calculated PIC value higher than 0.68 that are sufficient for the identification of the analyzed genotypes was described.

  5. SSR-patchwork: An optimized protocol to obtain a rapid and inexpensive SSR library using first-generation sequencing technology1

    Science.gov (United States)

    Di Maio, Antonietta; De Castro, Olga

    2013-01-01

    • Premise of the study: We have optimized a version of a microsatellite loci isolation protocol for first-generation sequencing (FGS) technologies. The protocol is optimized to reduce the cost and number of steps, and it combines some procedures from previous simple sequence repeat (SSR) protocols with several key improvements that significantly affect the final yield of the SSR library. This protocol may be accessible for laboratories with a moderate budget or for which next-generation sequencing (NGS) is not readily available. • Methods and Results: We drew from classic protocols for library enrichment by digestion, ligation, amplification, hybridization, cloning, and sequencing. Three different systems were chosen: two with very different genome sizes (Galdieria sulphuraria, 10 Mbp; Pancratium maritimum, 30 000 Mbp), and a third with an undetermined genome size (Kochia saxicola). Moreover, we also report the optimization of the sequencing reagents. A good frequency of the obtained microsatellite loci was achieved. • Conclusions: The method presented here is very detailed; comparative tests with other SSR protocols are also reported. This optimized protocol is a promising tool for low-cost genetic studies and the rapid, simple construction of homemade SSR libraries for small and large genomes. PMID:25202476

  6. Antithrombotic properties of SSR182289A, a new, orally active thrombin inhibitor.

    Science.gov (United States)

    Lorrain, J; Millet, L; Lechaire, I; Lochot, S; Ferrari, P; Visconte, C; Sainte-Marie, M; Lunven, C; Berry, C N; Schaeffer, P; Herbert, J-M; O'Connor, S E

    2003-02-01

    N-[3-[[[(1S)-4-(5-Amino-2-pyridinyl)-1-[[4-difluoromethylene)-1-piperidinyl]carbonyl]butyl]amino]sulfonyl][1,1'-biphenyl]-2-yl]acetamide hydrochloride (SSR182289A) is a novel, potent, and selective thrombin inhibitor. We have examined the antithrombotic properties of SSR182289A administered by i.v. and p.o. routes in several different animal thrombosis models in comparison with reference antithrombotic agents. Oral administration of SSR182289A produced dose-related antithrombotic effects in the following models; rat venous thrombosis (ED(50) 0.9 mg/kg p.o.), rat silk thread arterio-venous (AV) shunt (ED(50) 3.8 mg/kg p.o.), rat thromboplastin-induced AV shunt (ED(50) 3.1 mg/kg p.o.), rat carotid artery thrombosis (ED(200) 5.9 mg/kg p.o.), and rabbit venous thrombosis (ED(50) 7.5 mg/kg p.o.). Administered as an i.v. bolus, SSR182289A showed antithrombotic activity in the above models with ED(50)/ED(200) values in the range of 0.2 to 1.9 mg/kg i.v. SSR182289A increased rat tail transection bleeding time at doses > or =10 mg/kg p.o. In the rat thromboplastin-induced AV shunt model, SSR182289A 10 mg/kg p.o. produced marked antithrombotic effects at 30, 60, 120, and 240 min after administration. Hence, SSR182289A demonstrates potent oral antithrombotic properties in animal venous, AV-shunt, and arterial thrombosis models.

  7. Characterization and development of EST-derived SSR markers in cultivated sweetpotato (Ipomoea batatas

    Directory of Open Access Journals (Sweden)

    Li Yujun

    2011-10-01

    Full Text Available Abstract Background Currently there exists a limited availability of genetic marker resources in sweetpotato (Ipomoea batatas, which is hindering genetic research in this species. It is necessary to develop more molecular markers for potential use in sweetpotato genetic research. With the newly developed next generation sequencing technology, large amount of transcribed sequences of sweetpotato have been generated and are available for identifying SSR markers by data mining. Results In this study, we investigated 181,615 ESTs for the identification and development of SSR markers. In total, 8,294 SSRs were identified from 7,163 SSR-containing unique ESTs. On an average, one SSR was found per 7.1 kb of EST sequence with tri-nucleotide motifs (42.9% being the most abundant followed by di- (41.2%, tetra- (9.2%, penta- (3.7% and hexa-nucleotide (3.1% repeat types. The top five motifs included AG/CT (26.9%, AAG/CTT (13.5%, AT/TA (10.6%, CCG/CGG (5.8% and AAT/ATT (4.5%. After removing possible duplicate of published EST-SSRs of sweetpotato, a total of non-repeat 7,958 SSR motifs were identified. Based on these SSR-containing sequences, 1,060 pairs of high-quality SSR primers were designed and used for validation of the amplification and assessment of the polymorphism between two parents of one mapping population (E Shu 3 Hao and Guang 2k-30 and eight accessions of cultivated sweetpotatoes. The results showed that 816 primer pairs could yield reproducible and strong amplification products, of which 195 (23.9% and 342 (41.9% primer pairs exhibited polymorphism between E Shu 3 Hao and Guang 2k-30 and among the 8 cultivated sweetpotatoes, respectively. Conclusion This study gives an insight into the frequency, type and distribution of sweetpotato EST-SSRs and demonstrates successful development of EST-SSR markers in cultivated sweetpotato. These EST-SSR markers could enrich the current resource of molecular markers for the sweetpotato community and would

  8. Genetic diversity and DNA fingerprinting in jute (Corchorus spp. based on SSR markers

    Directory of Open Access Journals (Sweden)

    Liwu Zhang

    2015-10-01

    Full Text Available Genetic diversity analysis and DNA finger printing are very useful in breeding programs, seed conservation and management. Jute (Corchorus spp. is the second most important natural fiber crop after cotton. DNA fingerprinting studies in jute using SSR markers are limited. In this study, 58 jute accessions, including two control varieties (Huangma 179 and Kuanyechangguo from the official variety registry in China were evaluated with 28 pairs of SSR primers. A total of 184 polymorphic loci were identified. Each primer detected 3 to 15 polymorphic loci, with an average of 6.6. The 58 jute accessions were DNA-fingerprinted with 67 SSR markers from the 28 primer pairs. These markers differentiated the 58 jute accessions from one another, with CoSSR305-120 and CoSSR174-195 differentiating Huangma 179 and Kuanyechangguo, respectively. NTSYS-pc2.10 software was used to analyze the genetic diversity in the 58 jute accessions. Their genetic similarity coefficients ranged from 0.520 to 0.910 with an average of 0.749, indicating relatively great genetic diversity among them. The 58 jute accessions were divided into four groups with the coefficient 0.710 used as a value for classification, consistent with their species and pedigrees. All these results may be useful both for protection of intellectual property rights of jute accessions and for jute improvement.

  9. Assessment of inter- and intra-cultivar variations in olive using SSR markers

    Directory of Open Access Journals (Sweden)

    Ahmet Ipek

    2012-10-01

    Full Text Available Olive (Olea europaea L. production in the world has been made by using many cultivars, and the genetic uniformity of commercial cultivars is important for standard olive oil and table olive production. The genetic variation among and within commonly cultivated olive cultivars in Turkey was analyzed using SSR markers. A total of 135 leaf samples were collected from 11 commonly cultivated olive cultivars from 11 provinces in four geographical regions of Turkey. Seven SSR primer pairs generated 46 SSR markers, and the number of SSR markers per primer pair ranged from 4 (UDO-14 to 9 (GAPU-89 with an average of 6.57. This high level of SSR polymorphism suggests that olive production in Turkey has been made using genetically diverse olive cultivars and this high level of genetic variation is probably due to the location of Turkey in the center of the origin of olive. The UPGMA dendrogram, developed to visualize the estimated genetic relationships among the 135 samples, demonstrated that the clustering of olive cultivars was not based on geographical regions of cultivation. Presence of genetic variation was detected within a nationwide grown Turkish olive cultivar, called 'Gemlik'. Olive growers successfully discriminated olive cultivars with distinct morphological and pomological characters. However, there was some confusion about the identification of cultivars with similar phenotypic traits. To prevent misidentification of olive cultivars and to minimize intra-cultivar variation, certified propagation materials which were characterized using DNA based molecular markers should be used during the establishment of new olive orchards.

  10. SSR-based genetic linkage map of Cucurbita moschata and its synteny with Cucurbita pepo.

    Science.gov (United States)

    Gong, L; Pachner, M; Kalai, K; Lelley, T

    2008-11-01

    The first SSR-based genetic linkage map of Cucurbita moschata was created by integrating the maps of two F2 populations with one common parent developed from the crosses Waltham Butternut (WB) x Nigerian Local (NL) and ZHOU (a hull-less type) x WB. The integrated C. moschata map comprises 205 SSR markers and two morphological traits (Gr and n). The map is composed of 27 linkage groups with a marker density of 7 cM. Comparing the C. moschata map with the published Cucurbita pepo map, we found a high level of macrosynteny. Seventy-two of 76 common SSR markers between C. moschata and C. pepo were located in homologous linkage groups. These markers in general have conserved orders and similar genetic distances; they represent orthologous loci. A reference map based on these SSRs was obtained. No major chromosomal rearrangement between the two species could be detected at present, although four SSR markers were mapped in nonhomologous linkage groups. The comparative alignment of SSR markers did not provide any indication of a possible ancient polyploid origin of the species. The comparative mapping of C. moschata and C. pepo reported here will be useful for further studies on Cucurbit evolution, gene isolation, and breeding work.

  11. Association of AFLP and SSR markers with agronomic and fibre quality traits in Gossypium hirsutum L.

    Indian Academy of Sciences (India)

    Arunita Rakshit; S. Rakshit; J. Singh; S. K. Chopra; H. S. Balyan; P. K. Gupta; Shripad R. Bhat

    2010-08-01

    Molecular markers linked to QTL contributing to agronomic and fibre quality traits would be useful for cotton improvement. We have attempted to tag yield and fibre quality traits with AFLP and SSR markers using F2 and F3 populations of a cross between two Gossypium hirsutum varieties, PS56-4 and RS2013. Out of 50 AFLP primer combinations and 177 SSR primer pairs tested, 32 AFLP and four SSR primers were chosen for genotyping F2 individuals.Marker-trait associations were studied for eight agronomic and five fibre quality traits through simple and multiple regression analysis (MRA) using a set of 92 AFLP polymorphic loci and four SSR markers. Simple linear regression analysis (SLRA) identified 23 markers for eight different traits whereas multiple regression analysis identified 30 markers for at least one of the 13 traits. SSR marker BNL 3502 was consistently identified to be associated with fibre strength. While all the markers identified in SLRA were also detected in MRA, as many as 16 of the 30 markers were identified to be associated with respective traits in both F2 and F3 generations. The markers explained up to 41 per cent of phenotypic variation for individual traits. A number of markers were found to be associated with multiple traits suggesting clustering of QTLs for fibre quality traits in cotton.

  12. Comparison of Cheng's Index-and SSR Marker-based Classification of Asian Cultivated Rice

    Institute of Scientific and Technical Information of China (English)

    WANG Cai-hong; XU Qun; YU Ping; YUAN Xiao-ping; YU Han-yong; WANG Yi-ping; TANG Sheng-xiang

    2013-01-01

    A total of 100 cultivated rice accessions,with a clear isozyme-based classification,were analyzed based on Cheng's index and simple sequence repeat (SSR) marker.The results showed that the isozyme-based classification was in high accordance with that based on Cheng's index and SSR markers.Mantel-test revealed that the Euclidean distance of Cheng's index was significantly correlated with Nei's unbiased genetic distance of SSR markers (r =0.466,P ≤ 0.01).According to the model-based group and cluster analysis,the Cheng's index-and SSR-based classification coincided with each other,with the goodness of fit of 82.1% and 84.7% in indica,97.4% and 95.1% in japonica,respectively,showing higher accordance than that within subspecies.Therefore,Cheng's index could be used to classify subspecies,while SSR marker could be more efficient to analyze the subgroups within subspecies.

  13. Molecular evaluations of thirty one clones of poplar based on RAPD and SSR molecular markers

    Directory of Open Access Journals (Sweden)

    Singh M.K.

    2014-01-01

    Full Text Available Poplar is an important tree species valued all over the world for its wood importance. Despite limited knowledge of the levels of genetic diversity and relatedness, their cultivation as a source of plywood is widespread. In order to facilitate reasoned scientific decisions on its management and conservation and prepare for selective breeding programme, genetic analysis of 31 genotypes was performed using RAPD and SSR molecular markers. Twenty six RAPD primers and 14 SSR primers amplified a total of 236 and 85 scoreable bands of which 86.44% and 86.02% were polymorphic. The mean coefficient of gene differentiation (Gst was 0.388 and 0.341 indicating that 61.2% and 65.9% of the genetic variation resided within the populations. Analysis of molecular variance (AMOVA indicated that majority of genetic variation (94.6% using RAPD and 89% using SSR occurred among genotypes, while the variation between the three groups (categorized as tall, medium and small plants height was 5.4% (using RAPD and 11% (using SSR. The dendrogram obtained from NJ and STRUCTURE analysis revealed splitting of genotypes into four clusters with clear distinction between short, medium and tall height genotypes, indicated that genetic differentiations measure with respect to RAPD and SSR. However, both the markers were equally useful in providing some understanding about the genetic relationship of different genotypes of poplar that are important in the conservation and exploitation of poplar genetic resources.

  14. GENETIC DIVERSITY OF S3 MAIZE GENOTYPES RESISTANT TO DOWNY MILDEW BASED ON SSR MARKERS

    Directory of Open Access Journals (Sweden)

    Amran Muis

    2016-02-01

    Full Text Available The compulsory requirement for releasing new high yielding maize varieties is resistance to downy mildew. The study aimed to determine the level of homozygosity, genetic diversity, and  genetic distance of 30 S3 genotypes of maize. Number of primers to be used were 30 polymorphic SSR loci which are distributed over the entire maize genomes. The S3 genotypes used were resistant to downy mildew with homozygosity level of >80%, genetic distance between the test and tester strains >0.7, and anthesis silking interval (ASI between inbred lines and tester lines was maximum 3 days. The results showed that 30 SSR primers used were spread evenly across the maize genomes which were manifested in the representation of SSR loci on each chromosome of a total of 10 chromosomes. The levels of polymorphism ranged from 0.13 to 0.78, an average of 0.51, and the number of alleles ranged from 2 to 8 alleles per SSR locus, an average of 4 alleles per SSR locus. The size of nucleotides in each locus also varied from 70 to 553 bp. Cophenetic correlation value (r at 0.67 indicated that the Unweighted Pair-Group Method Using Arithmetic Averages (UPGMA was less reliable for differentiating genotypes in five groups. Of the total of 30 genotypes analyzed, 17 genotypes had homozygosity level of >80% so it can be included in the hybrid assembly program.

  15. Genetic diversity and DNA fingerprinting in jute(Corchorus spp.) based on SSR markers

    Institute of Scientific and Technical Information of China (English)

    Liwu; Zhang; Rongrong; Cai; Minhang; Yuan; Aifen; Tao; Jiantang; Xu; Lihui; Lin; Pingping; Fang; Jianmin; Qi

    2015-01-01

    Genetic diversity analysis and DNA finger printing are very useful in breeding programs,seed conservation and management. Jute(Corchorus spp.) is the second most important natural fiber crop after cotton. DNA fingerprinting studies in jute using SSR markers are limited. In this study, 58 jute accessions, including two control varieties(Huangma 179 and Kuanyechangguo) from the official variety registry in China were evaluated with 28 pairs of SSR primers. A total of 184 polymorphic loci were identified. Each primer detected 3 to 15 polymorphic loci, with an average of 6.6. The 58 jute accessions were DNA-fingerprinted with 67 SSR markers from the 28 primer pairs. These markers differentiated the 58 jute accessions from one another, with Co SSR305-120 and Co SSR174-195 differentiating Huangma 179 and Kuanyechangguo, respectively. NTSYS-pc2.10 software was used to analyze the genetic diversity in the 58 jute accessions. Their genetic similarity coefficients ranged from 0.520 to 0.910 with an average of 0.749, indicating relatively great genetic diversity among them. The 58 jute accessions were divided into four groups with the coefficient 0.710 used as a value for classification, consistent with their species and pedigrees. All these results may be useful both for protection of intellectual property rights of jute accessions and for jute improvement.

  16. Development and Characterization of 37 Novel EST-SSR Markers in Pisum sativum (Fabaceae

    Directory of Open Access Journals (Sweden)

    Xiaofeng Zhuang

    2013-01-01

    Full Text Available Premise of the study: Simple sequence repeat markers were developed based on expressed sequence tags (EST-SSR and screened for polymorphism among 23 Pisum sativum individuals to assist development and refinement of pea linkage maps. In particular, the SSR markers were developed to assist in mapping of white mold disease resistance quantitative trait loci. Methods and Results: Primer pairs were designed for 46 SSRs identified in EST contiguous sequences assembled from a 454 pyrosequenced transcriptome of the pea cultivar, ‘LIFTER’. Thirty-seven SSR markers amplified PCR products, of which 11 (30% SSR markers produced polymorphism in 23 individuals, including parents of recombinant inbred lines, with two to four alleles. The observed and expected heterozygosities ranged from 0 to 0.43 and from 0.31 to 0.83, respectively. Conclusions: These EST-SSR markers for pea will be useful for refinement of pea linkage maps, and will likely be useful for comparative mapping of pea and as tools for marker-based pea breeding.

  17. Genetic Variation of Inbred Lines of Maize Detected by SSR Markers

    Institute of Scientific and Technical Information of China (English)

    LI Xin-hai; FU Jun-hua; ZHANG Shi-huang; YUAN Li-xing; LI Ming-shun

    2001-01-01

    Simple sequence repeats (SSRs) were used to detect genetic variation among 21 maize(Zea mays L. ) inbred lines. Forty-three SSR primers selected from 69 primers gave stable amplification profiles, which could be clearly resolved on 3% Metaphor agarose gel, and produced 127 polymorphic amplified fragments.The average number of alleles per SSR locus was 2.95 with a range from 2 to 7. The polymorphism information content (PIC) for the SSR loci varied from 0.172 to 0.753 with an average of 0.511. Genetic similarities among the 21 lines ranged from 0.480 between the combination of Zhongzi451 vs. K12 up to 0.768 between CA156 vs. Ye478. The cluster analysis showed that 21 inbred lines could be classified into two distinct clusters with several subclusters, which corresponded to the heterotic groups determined by their pedigree information.Eight SSR primers, which had high level of polymorphism, could allow a rapid and efficient identification of 21 inbreds. Consequently, SSR markers could be used for measuring genetic variation of maize inbred lines and assigning them to heterotic groups.

  18. Development of unigene-derived SSR markers in cowpea (Vigna unguiculata) and their transferability to other Vigna species.

    Science.gov (United States)

    Gupta, S K; Gopalakrishna, T

    2010-07-01

    Unigene sequences available in public databases provide a cost-effective and valuable source for the development of molecular markers. In this study, the identification and development of unigene-based SSR markers in cowpea (Vigna unguiculata (L.) Walp.) is presented. A total of 1071 SSRs were identified in 15 740 cowpea unigene sequences downloaded from the National Center for Biotechnology Information. The most frequent SSR motifs present in the unigenes were trinucleotides (59.7%), followed by dinucleotides (34.8%), pentanucleotides (4%), and tetranucleotides (1.5%). The copy number varied from 6 to 33 for dinucleotide, 5 to 29 for trinucleotide, 5 to 7 for tetranucleotide, and 4 to 6 for pentanucleotide repeats. Primer pairs were successfully designed for 803 SSR motifs and 102 SSR markers were finally characterized and validated. Putative function was assigned to 64.7% of the unigene SSR markers based on significant homology to reported proteins. About 31.7% of the SSRs were present in coding sequences and 68.3% in untranslated regions of the genes. About 87% of the SSRs located in the coding sequences were trinucleotide repeats. Allelic variation at 32 SSR loci produced 98 alleles in 20 cowpea genotypes. The polymorphic information content for the SSR markers varied from 0.10 to 0.83 with an average of 0.53. These unigene SSR markers showed a high rate of transferability (88%) across other Vigna species, thereby expanding their utility. Alignment of unigene sequences with soybean genomic sequences revealed the presence of introns in amplified products of some of the SSR markers. This study presents the distribution of SSRs in the expressed portion of the cowpea genome and is the first report of the development of functional unigene-based SSR markers in cowpea. These SSR markers would play an important role in molecular mapping, comparative genomics, and marker-assisted selection strategies in cowpea and other Vigna species.

  19. Evaluation of Germplasm Using SSR Markers of Functional Genes in Rice

    Institute of Scientific and Technical Information of China (English)

    ZHAO Yong; YANG Kai; Akbar Ali Cheema; WENG Yue-jin

    2002-01-01

    16 SSR (Simple sequence repeats) primers of functional genes in rice were used to detect genetic diversity among 23 accessions of rice germplasm from 5 countries in the world. The average number of alleles per SSR locus was 5.2 with a range from 2 to 10. Genetic similarities among the 23 rice accessions ranged from 0.13 to 0.64. UPGMA cluster analysis showed that the 23 rice accessions could be classified into two distinct classes at similarities with a coefficient of 0.13. The Japonicas from Brazil, Japan and China were classified into Class I, along with upland rice from Brazil. The Indicas from Pakistan and Korea were classified into Class Ⅱ. Consequently, the function of genes SSR markers could be used as a useful tool for measuring genetic diversity, assigning rice to geographical distribution, ecotype, and pedigree relationship.

  20. Molecular analysis of East Anatolian traditional plum and cherry accessions using SSR markers.

    Science.gov (United States)

    Öz, M H; Vurgun, H; Bakir, M; Büyük, İ; Yüksel, C; Ünlü, H M; Çukadar, K; Karadoğan, B; Köse, Ö; Ergül, A

    2013-01-01

    We conducted SSR analyses of 59 accessions, including 29 traditional plum (Prunus domestica), 24 sweet cherry (Prunus avium), and 1 sour cherry (Prunus cerasus) selected from East Anatolian gene sources and 3 plum and 2 cherry reference accessions for molecular characterization and investigation of genetic relationships. Eight SSR loci [1 developed from the apricot (UDAp-404), 4 from the peach (UDP96-010, UDP96-001, UDP96-019, Pchgms1) and 3 from the cherry (UCD-CH13, UCD-CH17, UCD-CH31) genome] for plum accessions and 9 SSR loci [5 developed from the cherry (PS12A02, UCD-CH13, UCD-CH17, UCD-CH31, UCD-CH21), 3 from the peach (Pchgms1, UDP96-001, UDP96-005) and 1 from the plum (CPSCT010) genome] for cherry accessions were used for genetic identification. A total of 66 and 65 alleles were obtained in the genetic analyses of 31 plum and 28 cherry accessions, respectively. The number of alleles revealed by SSR analysis ranged from 4 to 14 alleles per locus, with a mean value of 8.25 in plum accessions, and from 5 to 10 alleles per locus with a mean value of 7.2 in cherry accessions. Only one case of synonym was identified among the cherry accessions, while no case of synonym was observed among the plum accessions. Genomic SSR markers used in discrimination of plum and cherry accessions showed high cross-species transferability in the Prunus genus. Because of their appreciable polymorphism and cross species transferability, the SSR markers that we evaluated in this study will be useful for studies involving fingerprinting of cherry and plum cultivars.

  1. GMATA: an integrated software package for genome-scale SSR mining, marker development and viewing

    Directory of Open Access Journals (Sweden)

    Xuewen Wang

    2016-09-01

    Full Text Available Simple sequence repeats (SSRs, also referred to as microsatellites, are highly variable tandem DNAs that are widely used as genetic markers. The increasing availability of whole-genome and transcript sequences provides information resources for SSR marker development. However, efficient software is required to efficiently identify and display SSR information along with other gene features at a genome scale. We developed novel software package Genome-wide Microsatellite Analyzing Tool Package (GMATA integrating SSR mining, statistical analysis and plotting, marker design, polymorphism screening and marker transferability, and enabled simultaneously display SSR markers with other genome features. GMATA applies novel strategies for SSR analysis and primer design in large genomes, which allows GMATA to perform faster calculation and provides more accurate results than existing tools. Our package is also capable of processing DNA sequences of any size on a standard computer. GMATA is user friendly, only requires mouse clicks or types inputs on the command line, and is executable in multiple computing platforms. We demonstrated the application of GMATA in plants genomes and reveal a novel distribution pattern of SSRs in 15 grass genomes. The most abundant motifs are dimer GA/TC, the A/T monomer and the GCG/CGC trimer, rather than the rich G/C content in DNA sequence. We also revealed that SSR count is a linear to the chromosome length in fully assembled grass genomes. GMATA represents a powerful application tool that facilitates genomic sequence analyses. GAMTA is freely available at http://sourceforge.net/projects/gmata/?source=navbar.

  2. GMATA: An Integrated Software Package for Genome-Scale SSR Mining, Marker Development and Viewing

    Science.gov (United States)

    Wang, Xuewen; Wang, Le

    2016-01-01

    Simple sequence repeats (SSRs), also referred to as microsatellites, are highly variable tandem DNAs that are widely used as genetic markers. The increasing availability of whole-genome and transcript sequences provides information resources for SSR marker development. However, efficient software is required to efficiently identify and display SSR information along with other gene features at a genome scale. We developed novel software package Genome-wide Microsatellite Analyzing Tool Package (GMATA) integrating SSR mining, statistical analysis and plotting, marker design, polymorphism screening and marker transferability, and enabled simultaneously display SSR markers with other genome features. GMATA applies novel strategies for SSR analysis and primer design in large genomes, which allows GMATA to perform faster calculation and provides more accurate results than existing tools. Our package is also capable of processing DNA sequences of any size on a standard computer. GMATA is user friendly, only requires mouse clicks or types inputs on the command line, and is executable in multiple computing platforms. We demonstrated the application of GMATA in plants genomes and reveal a novel distribution pattern of SSRs in 15 grass genomes. The most abundant motifs are dimer GA/TC, the A/T monomer and the GCG/CGC trimer, rather than the rich G/C content in DNA sequence. We also revealed that SSR count is a linear to the chromosome length in fully assembled grass genomes. GMATA represents a powerful application tool that facilitates genomic sequence analyses. GAMTA is freely available at http://sourceforge.net/projects/gmata/?source=navbar. PMID:27679641

  3. Comparative analysis of genetic diversity in sacred lotus (Nelumbo nucifera Gaertn.) using AFLP and SSR markers.

    Science.gov (United States)

    Hu, Jihong; Pan, Lei; Liu, Honggao; Wang, Shuzhen; Wu, Zhihua; Ke, Weidong; Ding, Yi

    2012-04-01

    The sacred lotus (Nelumbo nucifera Gaertn.) is an aquatic plant of economic and ornamental importance in China. In this study, we developed twenty novel sacred lotus SSR markers, and used AFLP and SSR markers to investigate the genetic diversity and genetic relationships among 58 accessions of N. nucifera including 15 seed lotus, 12 rhizome lotus, 24 flower lotus and 7 wild lotus. Our results showed that sacred lotus exhibited a low level of genetic diversity, which may attribute to asexual reproduction and long-term artificial selection. A dendrogram based on both AFLP and SSR clustering data showed that: (1) the seed lotus accessions and rhizome lotus accessions were distinctly clustered into different groups, which indicated the significant genetic differentiation between them. This may be attributed to the two modes of reproduction and lack of genetic exchange; (2) the accessions of Thailand wild lotus were separated from other wild lotus accessions. This implied that the Thailand lotus might be genetically differentiated from other wild lotuses. In addition, Mantel test conducted gave highly significant correlation between AFLP-SSR data and each of the AFLP and SSR ones, with the values of r = 0.941 and r = 0.879, respectively, indicating the higher efficiency of the combination of these techniques (AFLP and SSR) in estimation and validation of the genetic diversity among the accession of sacred lotus. This knowledge of the genetic diversity and genetic relatedness of N. nucifera is potentially useful to improve the current strategies in breeding and germplasm conservation to enhance the ornamental and economic value of sacred lotus.

  4. The response regulator SsrB activates transcription and binds to a region overlapping OmpR binding sites at Salmonella pathogenicity island 2.

    Science.gov (United States)

    Feng, Xiuhong; Walthers, Don; Oropeza, Ricardo; Kenney, Linda J

    2004-11-01

    OmpR activates expression of the two-component regulatory system located on Salmonella pathogenicity island 2 (SPI-2) that controls the expression of a type III secretion system, as well as many other genes required for systemic infection in mice. Measurements of SsrA and SsrB protein levels under different growth conditions indicate that expression of these two components is uncoupled, i.e. SsrB is produced in the absence of ssrA and vice versa. This result was suggested from our previous studies, in which two promoters at ssrA/B were identified. The isolated C-terminus of SsrB binds to DNA and protects regions upstream of ssrA, ssrB and srfH from DNase I digestion. Furthermore, the C-terminus of SsrB alone is capable of activating transcription in the absence of the N-terminus. Results from beta-galactosidase assays indicate that the N-terminal phosphorylation domain inhibits the C-terminal effector domain. A previous study from our laboratory reported that ssrA-lacZ and ssrB-lacZ transcriptional fusions were substantially reduced in an ssrB null strain. Results from DNase I protection assays provide direct evidence that SsrB binds at ssrA and ssrB, although the binding sites lie within the transcribed regions. Additional regulators clearly affect gene expression at this important locus, and here we provide evidence that SlyA, a transcription factor that contributes to Salmonella virulence, also affects ssrA/B gene expression.

  5. Transferability of SSR markers from related Uredinales species to the coffee rust Hemileia vastatrix.

    Science.gov (United States)

    Cristancho, M; Escobar, C

    2008-10-28

    The aim of the present research was to test the transferability of simple sequence repeat (SSR) markers developed in two Uredinales species to Hemileia vastatrix, coffee rust. The development of efficient techniques for the identification of H. vastatrix isolates is imperative, given the continuous development of new races. The transferability of 25 SSR markers developed in the related Uredinales species Puccinia coronata f. sp lolli and Melampsora linii to H. vastatrix was tested. A low level of transferability of SSRs was detected, and only 4 potential markers that can be used to fingerprint the coffee rust races were identified.

  6. A new image of plantain diversity assessed by SSR, AFLP and MSAP markers.

    Science.gov (United States)

    Noyer, J L; Causse, S; Tomekpe, K; Bouet, A; Baurens, F C

    2005-05-01

    Using both SSR and AFLP markers, the genetic diversity of 30 plantains constituting a representative sample of the phenotypic diversity was assessed. The results confirmed a very narrow genetic base of this cultivar group. SSR and AFLP data support the hypothesis that these cultivars may have arisen from vegetative multiplication of a single seed. MSAP were used to survey cytosine methylation status at CCGG sites in order to obtain an alternative source of diversity data. A higher degree of polymorphism was revealed allowing the classification of the samples into three clusters. No correlation was observed between the phenotypic classification and methylation diversity. Implications for breeding programs are discussed.

  7. Development and validation of genic-SSR markers in sesame by RNA-seq.

    Science.gov (United States)

    Zhang, Haiyang; Wei, Libin; Miao, Hongmei; Zhang, Tide; Wang, Cuiying

    2012-07-16

    Sesame (Sesamum indicum L.) is one of the most important oil crops; however, a lack of useful molecular markers hinders current genetic research. We performed transcriptome sequencing of samples from different sesame growth and developmental stages, and mining of genic-SSR markers to identify valuable markers for sesame molecular genetics research. In this study, 75 bp and 100 bp paired-end RNA-seq was used to sequence 24 cDNA libraries, and 42,566 uni-transcripts were assembled from more than 260 million filtered reads. The total length of uni-transcript sequences was 47.99 Mb, and 7,324 SSRs (SSRs ≥15 bp) and 4,440 SSRs (SSRs ≥18 bp) were identified. On average, there was one genic-SSR per 6.55 kb (SSRs ≥15 bp) or 10.81 kb (SSRs ≥18 bp). Among perfect SSRs (≥18 bp), di-nucleotide motifs (48.01%) were the most abundant, followed by tri- (20.96%), hexa- (25.37%), penta- (2.97%), tetra- (2.12%), and mono-nucleotides (0.57%). The top four motif repeats were (AG/CT)n [1,268 (34.51%)], (CA/TG)n [281 (7.65%)], (AT/AT)n [215 (5.85%)], and (GAA/TTC)n [131 (3.57%)]. A total of 2,164 SSR primer pairs were identified in the 4,440 SSR-containing sequences (≥18 bp), and 300 SSR primer pairs were randomly chosen for validation. These SSR markers were amplified and validated in 25 sesame accessions (24 cultivated accessions, one wild species). 276 (92.0%) primer pairs yielded PCR amplification products in 24 cultivars. Thirty two primer pairs (11.59%) exhibited polymorphisms. Moreover, 203 primer pairs (67.67%) yielded PCR amplicons in the wild accession and 167 (60.51%) were polymorphic between species. A UPGMA dendrogram based on genetic similarity coefficients showed that the correlation between genotype and geographical source was low and that the genetic basis of sesame in China is narrow, as previously reported. The 32 polymorphic primer pairs were validated using an F2 mapping population; 18 primer pairs exhibited polymorphisms between the parents, and 14

  8. APPLICATION OF RYE SSR MARKERS FOR DETECTION OF GENETIC DIVERSITY IN TRITICALE

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    Želmíra Balážová

    2016-06-01

    Full Text Available Present study aims to testify usefulness of particular rye SSR markers for the detection of genetic diversity degree in the set of 20 triticale cultivars coming from different European countries. For this purpose, a set of six rye SSR markers were used. The set of six polymorphic markers provided 22 alleles with an average frequency of 3.67 alleles per locus. The number of alleles ranged between 2 (SCM43 and 5 (SCM28, SCM86. Resulting from the number and frequency of alleles diversity index (DI, polymorphic information content (PIC and probability of identity (PI were calculated. An average value of PIC for 6 SSR markers was 0.505, the highest value was calculated for rye SSR marker SCM86 (0.706. Based on UPGMA algorithm, a dendrogram was constructed. In dendrogram cultivars were divided into two main clusters. The first cluster contained two cultivars, Russian cultivar Greneder and Slovak cultivar Largus, and second included 18 cultivars. Genetically the closest were two Greek cultivars (Niobi and Thisbi and were close to other Greek cultivar Vrodi. It was possible to separate triticale cultivars of spring and winter form in dendrogram. Results showed the utility of rye microsatellite markers for estimation of genetic diversity of European triticale genotypes leading to genotype identification.

  9. SNP and SSR marker analysis and mapping of a maize population

    Directory of Open Access Journals (Sweden)

    Šimić Domagoj

    2009-01-01

    Full Text Available Although highly polymorphic SSRs are currently the marker of choice worldwide in maize breeding, single nucleotide polymorphisms (SNPs as a newer marker system are recently used more extensively. The objective of this study was investigate the utility of SSR and SNP markers for mapping of a maize population adapted to conditions of Southeast Europe. Total of 294 F2:3 lines derived from a biparental mapping population were genotyped using 121 polymorphic SNP and SSR markers. The SNP markers were analyzed using the SNPlex technology. 56 of the 142 tested SNPs (39% were polymorphic between the parents of the mapping population and were successfully mapped. The remaining markers were either not functional (5 = 3.5% or not polymorphic (81 = 57%. No mapped SNP marker showed more than 10% missing data. On average, the level of missing data for SNPs (1.5% was considerably lower than that for SSRs (3.4%. For the mapping procedure, the SNP data were combined SSR data. A comparison of the mapping data with the publicly available mapping data on SSR markers and the proprietary mapping data indicates that the map is of good quality and that the map position of almost all markers agrees with their published map position. Thus, information obtained from both marker systems is utilizable for further QTL analysis.

  10. Identification and Purity Test of Super Hybrid Rice with SSR Molecular Markers

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    Five super hybrid rice combinations, i.e. HYS-1/R105, Pei'ai 64S/E32, Liangyoupeijiu (Pei'ai 64S/9311 ), 88S/0293, and J23A/Q611, and their parental lines were tested by means of SSR analysis. A total of 144 SSR primer pairs distributed on 12 rice chromosomes were used, out of which 47 detected polymorphism among the tested rice lines. Among all these primers, RM337 and RM154 produced polymorphic patterns in four or more of the tested experimental materials respectively, and they could distinguish among most rice genotypes tested. Twenty-four primer pairs, two on each rice chromosome, were selected to make a reference SSR marker-based fingerprinting for the rice lines. For most of the primer pairs, F1 hybrids mainly showed complementary pattern of both parents, which could be very useful to distinguish the F1 from its parental lines. In addition, 5 primer pairs were selected as special primer pairs for five hybrid rice combinations respectively. By combining the rapid, simple method on DNA extraction, it is suggested that SSR technique has wide prospective in variety authentication and purity identification.

  11. Construction of a SNP and SSR linkage map in autotetraploid blueberry using genotyping by sequencing

    Science.gov (United States)

    A mapping population developed from a cross between two key highbush blueberry cultivars, Draper × Jewel (Vaccinium corymbosum), segregating for a number of important phenotypic traits, has been utilized to produce a genetic linkage map. Data on 233 single sequence repeat (SSR) markers and 1794 sing...

  12. Construction of an integrated map of rose with AFLP, SSR, PK, RGA, SCAR and morphological markers

    NARCIS (Netherlands)

    Yan Zifu, Z.; Denneboom, C.; Hattendorf, A.; Dolstra, O.; Debener, T.; Stam, P.; Visser, P.B.

    2005-01-01

    A high-density genetic map with a number of anchor markers has been created to be used as a tool to dissect genetic variation in rose. Linkage maps for the diploid 94/1 population consisting of 88 individuals were constructed using a total of 520 molecular markers including AFLP, SSR, PK, RGA, RFLP,

  13. Characterization of variable EST SSR markers for Norway spruce (Picea abies L.

    Directory of Open Access Journals (Sweden)

    Spiess Nadine

    2011-10-01

    Full Text Available Abstract Background Norway spruce is widely distributed across Europe and the predominant tree of the Alpine region. Fast growth and the fact that timber can be harvested cost-effectively in relatively young populations define its status as one of the economically most important tree species of Northern Europe. In this study, EST derived simple sequence repeat (SSR markers were developed for the assessment of putative functional diversity in Austrian Norway spruce stands. Results SSR sequences were identified by analyzing 14,022 publicly available EST sequences. Tri-nucleotide repeat motifs were most abundant in the data set followed by penta- and hexa-nucleotide repeats. Specific primer pairs were designed for sixty loci. Among these, 27 displayed polymorphism in a testing population of 16 P. abies individuals sampled across Austria and in an additional screening population of 96 P. abies individuals from two geographically distinct Austrian populations. Allele numbers per locus ranged from two to 17 with observed heterozygosity ranging from 0.075 to 0.99. Conclusions We have characterized variable EST SSR markers for Norway spruce detected in expressed genes. Due to their moderate to high degree of variability in the two tested screening populations, these newly developed SSR markers are well suited for the analysis of stress related functional variation present in Norway spruce populations.

  14. Development of genic and genomic SSR markers of robusta coffee (Coffea canephora Pierre Ex A. Froehner.

    Directory of Open Access Journals (Sweden)

    Prasad S Hendre

    Full Text Available Coffee breeding and improvement efforts can be greatly facilitated by availability of a large repository of simple sequence repeats (SSRs based microsatellite markers, which provides efficiency and high-resolution in genetic analyses. This study was aimed to improve SSR availability in coffee by developing new genic-/genomic-SSR markers using in-silico bioinformatics and streptavidin-biotin based enrichment approach, respectively. The expressed sequence tag (EST based genic microsatellite markers (EST-SSRs were developed using the publicly available dataset of 13,175 unigene ESTs, which showed a distribution of 1 SSR/3.4 kb of coffee transcriptome. Genomic SSRs, on the other hand, were developed from an SSR-enriched small-insert partial genomic library of robusta coffee. In total, 69 new SSRs (44 EST-SSRs and 25 genomic SSRs were developed and validated as suitable genetic markers. Diversity analysis of selected coffee genotypes revealed these to be highly informative in terms of allelic diversity and PIC values, and eighteen of these markers (∼ 27% could be mapped on a robusta linkage map. Notably, the markers described here also revealed a very high cross-species transferability. In addition to the validated markers, we have also designed primer pairs for 270 putative EST-SSRs, which are expected to provide another ca. 200 useful genetic markers considering the high success rate (88% of marker conversion of similar pairs tested/validated in this study.

  15. Development of genic and genomic SSR markers of robusta coffee (Coffea canephora Pierre Ex A. Froehner).

    Science.gov (United States)

    Hendre, Prasad S; Aggarwal, Ramesh K

    2014-01-01

    Coffee breeding and improvement efforts can be greatly facilitated by availability of a large repository of simple sequence repeats (SSRs) based microsatellite markers, which provides efficiency and high-resolution in genetic analyses. This study was aimed to improve SSR availability in coffee by developing new genic-/genomic-SSR markers using in-silico bioinformatics and streptavidin-biotin based enrichment approach, respectively. The expressed sequence tag (EST) based genic microsatellite markers (EST-SSRs) were developed using the publicly available dataset of 13,175 unigene ESTs, which showed a distribution of 1 SSR/3.4 kb of coffee transcriptome. Genomic SSRs, on the other hand, were developed from an SSR-enriched small-insert partial genomic library of robusta coffee. In total, 69 new SSRs (44 EST-SSRs and 25 genomic SSRs) were developed and validated as suitable genetic markers. Diversity analysis of selected coffee genotypes revealed these to be highly informative in terms of allelic diversity and PIC values, and eighteen of these markers (∼ 27%) could be mapped on a robusta linkage map. Notably, the markers described here also revealed a very high cross-species transferability. In addition to the validated markers, we have also designed primer pairs for 270 putative EST-SSRs, which are expected to provide another ca. 200 useful genetic markers considering the high success rate (88%) of marker conversion of similar pairs tested/validated in this study.

  16. Sequence alignment status and amplicon size difference affecting EST-SSR primer performance and polymorphism

    Science.gov (United States)

    Little attention has been given to failed, poorly-performing, and non-polymorphic expressed sequence tag (EST) simple sequence repeat (SSR) primers. This is due in part to a lack of interest and value in reporting them but also because of the difficulty in addressing the causes of failure on a prime...

  17. Sequence Analysis of SSR-Flanking Regions Identifies Genome Affinities between Pasture Grass Fungal Endophyte Taxa

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    Eline van Zijll de Jong

    2011-01-01

    Full Text Available Fungal species of the Neotyphodium and Epichloë genera are endophytes of pasture grasses showing complex differences of life-cycle and genetic architecture. Simple sequence repeat (SSR markers have been developed from endophyte-derived expressed sequence tag (EST collections. Although SSR array size polymorphisms are appropriate for phenetic analysis to distinguish between taxa, the capacity to resolve phylogenetic relationships is limited by both homoplasy and heteroploidy effects. In contrast, nonrepetitive sequence regions that flank SSRs have been effectively implemented in this study to demonstrate a common evolutionary origin of grass fungal endophytes. Consistent patterns of relationships between specific taxa were apparent across multiple target loci, confirming previous studies of genome evolution based on variation of individual genes. Evidence was obtained for the definition of endophyte taxa not only through genomic affinities but also by relative gene content. Results were compatible with the current view that some asexual Neotyphodium species arose following interspecific hybridisation between sexual Epichloë ancestors. Phylogenetic analysis of SSR-flanking regions, in combination with the results of previous studies with other EST-derived SSR markers, further permitted characterisation of Neotyphodium isolates that could not be assigned to known taxa on the basis of morphological characteristics.

  18. Ssr analysis for genetic structure and diversity determination of maize local populations from former Yugoslavia territories.

    Science.gov (United States)

    Ignjatović-Micić, D; Drinić, S Mladenović; Nikolić, A; Lazić-Jancić, V

    2008-11-01

    A collection of 2178 local populations from ex-Yugoslavia territories is maintained in Maize Research Institute (MRI) gene bank. These populations were characterized mainly by morphological markers. In this work 21 local populations belonging to seven different agro-ecological groups have been subjected to SSR analysis using a DNA-pooling strategy. The objective of this work was to develop genetic fingerprints for characterization, identification and classification of the populations, as well as for estimation of their genetic diversity. Also, a DNA-pooling strategy was employed with the aim to certify if it could be applied for population analysis with SSR markers. Statistical analysis of 25 informative SSR primers revealing 224 alleles (bands) showed that the average within-population mean number of alleles was 2.55, the average values for total and within-population diversity were 0.784 and 0.502, respectively and G(ST) value was 0.360. Genetic distance values calculated using Modified Rogers' Distance were in the range from 0.35 to 0.60. The silver staining method of DNA used for bulked samples showed some weakness that could be overcome with a more sensitive staining method. Nevertheless, the results in this work indicate that the SSR analysis of bulks could be used for characterizing a large number of populations in gene banks.

  19. High density SNP and SSR-based genetic maps of two independent oil palm hybrids

    NARCIS (Netherlands)

    Ting, N.C.; Jansen, J.; Mayes, S.; Massawe, F.; Sambanthamurthi, R.; Cheng-Li Ooi, L.; Chin, C.W.; Arulandoo, X.; Seng, T.Y.; Alwee, S.S.R.S.; Ithnin, M.; Singh, R.

    2014-01-01

    BACKGROUND: Oil palm is an important perennial oil crop with an extremely long selection cycle of 10 to 12 years. As such, any tool that speeds up its genetic improvement process, such as marker-assisted breeding is invaluable. Previously, genetic linkage maps based on AFLP, RFLP and SSR markers

  20. A genetic linkage map for hazelnut (Corylus avellana L.) based on RAPD and SSR markers.

    Science.gov (United States)

    Mehlenbacher, Shawn A; Brown, Rebecca N; Nouhra, Eduardo R; Gökirmak, Tufan; Bassil, Nahla V; Kubisiak, Thomas L

    2006-02-01

    A linkage map for European hazelnut (Corylus avellana L.) was constructed using random amplified polymorphic DNA (RAPD) and simple sequence repeat (SSR) markers and the 2-way pseudotestcross approach. A full-sib population of 144 seedlings from the cross OSU 252.146 x OSU 414.062 was used. RAPD markers in testcross configuration, segregating 1:1, were used to construct separate maps for each parent. Fifty additional RAPD loci were assigned to linkage groups as accessory markers whose exact location could not be determined. Markers in intercross configuration, segregating 3:1, were used to pair groups in one parent with their homologues in the other. Eleven groups were identified for each parent, corresponding to the haploid chromosome number of hazelnut (n = x = 11). Thirty of the 31 SSR loci were able to be assigned to a linkage group. The maternal map included 249 RAPD and 20 SSR markers and spanned a distance of 661 cM. The paternal map included 271 RAPD and 28 SSR markers and spanned a distance of 812 cM. The maps are quite dense, with an average of 2.6 cM between adjacent markers. The S-locus, which controls pollen-stigma incompatibility, was placed on chromosome 5S where 6 markers linked within a distance of 10 cM were identified. A locus for resistance to eastern filbert blight, caused by Anisogramma anomala, was placed on chromosome 6R for which two additional markers tightly linked to the dominant allele were identified and sequenced. These maps will serve as a starting point for future studies of the hazelnut genome, including map-based cloning of important genes. The inclusion of SSR loci on the map will make it useful in other populations.

  1. Characterization and compilation of polymorphic simple sequence repeat (SSR markers of peanut from public database

    Directory of Open Access Journals (Sweden)

    Zhao Yongli

    2012-07-01

    Full Text Available Abstract Background There are several reports describing thousands of SSR markers in the peanut (Arachis hypogaea L. genome. There is a need to integrate various research reports of peanut DNA polymorphism into a single platform. Further, because of lack of uniformity in the labeling of these markers across the publications, there is some confusion on the identities of many markers. We describe below an effort to develop a central comprehensive database of polymorphic SSR markers in peanut. Findings We compiled 1,343 SSR markers as detecting polymorphism (14.5% within a total of 9,274 markers. Amongst all polymorphic SSRs examined, we found that AG motif (36.5% was the most abundant followed by AAG (12.1%, AAT (10.9%, and AT (10.3%.The mean length of SSR repeats in dinucleotide SSRs was significantly longer than that in trinucleotide SSRs. Dinucleotide SSRs showed higher polymorphism frequency for genomic SSRs when compared to trinucleotide SSRs, while for EST-SSRs, the frequency of polymorphic SSRs was higher in trinucleotide SSRs than in dinucleotide SSRs. The correlation of the length of SSR and the frequency of polymorphism revealed that the frequency of polymorphism was decreased as motif repeat number increased. Conclusions The assembled polymorphic SSRs would enhance the density of the existing genetic maps of peanut, which could also be a useful source of DNA markers suitable for high-throughput QTL mapping and marker-assisted selection in peanut improvement and thus would be of value to breeders.

  2. RAPD and SSR Polymorphisms in Mutant Lines of Transgenic Wheat Mediated by Low Energy Ion Beam

    Institute of Scientific and Technical Information of China (English)

    WANG Tiegu; HUANG Qunce; FENG Weisen

    2007-01-01

    Two types of markers-random amplified polymorphic DNA (RAPD) and simple sequence repeat DNA (SSR)-have been used to characterize the genetic diversity among nine mutant lines of transgenic wheat intermediated by low energy ion beam and their four receptor cultivars. The objectives of this study were to analyze RAPD-based and SSR-based genetic variance among transgenic wheat lines and with their receptors, and to find specific genetic markers of special traits of transgenic wheat lines. 170 RAPD primers were amplified to 733 fragments in all the experimental materials. There were 121 polymorphic fragments out of the 733 fragments with a ratio of polymorphic fragments of 16.5%. 29 SSR primer pairs were amplified to 83 fragments in all the experiment materials. There were 57 polymorphic fragments out of the 83 fragments with a ratio of polymorphic fragments of 68.7%. The dendrograms were prepared based on a genetic distance matrix using the UPGMA (Unweighted Pair-group Method with Arithmetic averaging) algorithm, which corresponded well to the results of the wheat pedigree analysis and separated the 13 genotypes into four groups. Association analysis between RAPD and SSR markers with the special traits of transgenic wheat mutant lines discovered that three RAPD markers, si, opt-16, and fl4, were significantly associated with the muticate trait, while three SSR markers, Rht8 (Xgwm261), Rht-Blb, and Rht-Dlb, highly associated with the dwarf trait. These markers will be useful for marker-assistant breeding and can be used as candidate markers for further gene mapping and cloning.

  3. SSR Markers for Fusarium Head Blight Resistance QTLs in Three Wheat Populations

    Institute of Scientific and Technical Information of China (English)

    REN Li-juan; SHEN Xiao-rong; ZHOU Miao-ping; ZHANG Xu; MA Hong-xiang; LU Wei-zhong; Paul Nichoson

    2003-01-01

    The objective of this research is to identify DNA markers linked to QTLs controlling FHB resistance in wheat, and to compare if the QTLs in three resistant germplasm are common. Three wheat recombinant inbred populations derived from the crosses between Alondra (susceptible) and three resistant lines, Wangshuibai, Sumai3, and 894037, respectively, were evaluated for reaction to Fusarium graminearum in greenhouse and in field conditions over years. Simple sequence repeat (SSR) markers were screened in the populations and regression analysis was used to identify markers associated with FHB resistance. For the population of Sumai3 (resistant)/Alondra (susceptible), which contained 161 recombinant inbred lines, two SSR markers located on chromosome 3B were found to be associated with resistant QTLs. These markers accounted for 2.6-6.7% phenotypic variation. The 894037 (resistant)/Alondra (susceptible) population was consisted of 147 recombinant inbred lines. A total of 59 SSR primers were screened in this population and seven of them were linked to resistant QTLs. The QTLs on chromosome 3B accounted for 47.4% phenotypic variation. Minor QTLs were also located on 2D, 7A, 6B, and 4B chromosomes, and the resistant QTLs on 2D and 4B chromosomes were from Alondra. The last population of 80 recombinant inbred lines was from the cross Wangshuibai (resistant)/Alondra (susceptible). A total of 120 SSR primers were screened in this population, eight of which were linked to resistant QTLs. These markers were located on 3B, 4B, 2D, 4D, and 6D (uncertain) chromosomes respectively. The QTLs on chromosome 3B accounted for 8.9-27.0% phenotypic variation. The resistant QTLs on chromosomes 4B and 6D (uncertain) were from Alondra. The other QTLs were from Wangshuibai. SSR markers linked to resistant QTLs on chromosome 3B were found in all three populations, and account for higher phenotypic variation. So these markers should be useful in marker-assisted selection.

  4. SSR504734 enhances basal expression of prepulse inhibition but exacerbates the disruption of prepulse inhibition by apomorphine

    Science.gov (United States)

    Singer, Philipp; Zhang, Weining; Yee, Benjamin K.

    2013-01-01

    Rationale Inhibition of glycine transporter 1 (GlyT1) elevates extracellular glycine and can thus increase N-methyl-D-aspartate receptor (NMDAR) excitability in the brain. The potent GlyT1 inhibitor, SSR504734, has also been shown to potentiate the behavioural effects of direct and indirect dopamine agonists. Thus, an acute systemic dose of SSR504734 was sufficient to exacerbate the motor-stimulant effect of the dopamine releaser amphetamine in C57BL/6 mice, even though SSR504734 alone exerted no significant effect on motor activity. Objectives Here, we explore if SSR504734 might modulate dopamine-dependent sensory gating in the paradigm of prepulse inhibition (PPI) of the acoustic startle reflex. Methods Experiment 1 characterized the effect of SSR504734 (10 and 30 mg/kg i.p.) on PPI expression when administered alone. Experiments 2 and 3 investigated the impact of SSR504734 when administered in conjunction with the dopamine receptor agonist, apomorphine (1 and 2 mg/kg s.c.), which is known to reliably disrupt PPI. Results When administered alone, acute SSR504734 enhanced PPI only at 30 mg/kg – a dose that has been shown to improve cognitive functions including working memory, which has been linked to enhanced NMDAR function resulting from the elevation of extracellular glycine. However, this effect did not allow SSR504734 to antagonise the PPI-disruptive effect of apomorphine. At the lower dose of 10 mg/kg – that was insufficient to enhance PPI when administered alone - SSR504734 even exacerbated the deleterious effect of apomorphine on PPI. Conclusions The therapeutic potential of GlyT1 inhibition against distinct behavioural/cognitive deficiency might require different magnitudes of GlyT1 inhibition. [246 words] PMID:23736281

  5. Regulation of ssrB on gene expression of Salmonella enterica serovar Typhi at early stage of oxidative stress%SsrB对伤寒沙门菌氧应激早期基因表达的调节

    Institute of Scientific and Technical Information of China (English)

    王敏; 罗哲; 杜鸿; 孟彦辰; 王菲; 倪斌; 徐顺高; 黄新祥

    2011-01-01

    Objective : To investigate the regulation of ssrB on gene expression of Salmonella enterica serovar Typhi (S. Typhi) at early-stage of oxidative stress. Methods: The ssrB deleted mutant of S. Typhi was generated through homologous recombination mecliated by suicide plasmid ; the gene expression profiles of the wild-type strain and the ssrB deleted mutant at early -stage of oxidative stress was investigated by genormc microarray assay; qRT-PCR was performed to further validate the results of microarray assay . The HeLa cells were invacled by S. Typhi to explore the influence of ssrB on invasion of epithelial cells. Results: The ssrB deleted mutant of S. Typhi was preparecl successfully ; analysis of genomic assay showed that , compared to the wild -type strain , 68 genes were up -regulated and 20 genes were down -regulated in the ssrB deleted mutant at early stage of oxidative stress . The results of qRT-PCR assay were consistent with the results of microarray assay. The ability of the ssrB deleted mutant to invade the epithelial cells was only 34. 6% of the wilcl-type strain. Conclusion: SsrB of S. Typhi played an important role in regulating gene expression at early stage of oxidative stress and enhanced the ability of S. Typhi to invade epithelial cells.%目的:研究伤寒沙门菌ssrB基因在氧应激早期对其他基因表达的调节.方法:通过同源重组的方法利用自杀质粒制备伤寒沙门菌ssrB基因缺陷变异株;采用伤寒沙门菌全基因组芯片比较野生株和ssrB基因缺陷变异株在氧应激早期的基因表达差异,并对其中部分表达差异基因进行实时定量PCR验证;利用HeLa细胞进行细菌侵袭实验,研究ssrB基因对伤寒沙门菌侵袭能力的影响.结果:成功制备伤寒沙门菌ssrB基因缺陷变异株;基因芯片结果分析显示,在氧应激早期,与野生株相比,伤寒沙门菌ssrB基因缺陷变异株有68个基因表达下调,有20个基因表达上调,其中与侵袭相关的基

  6. 松阿扁叶蜂SSR-PCR反应体系的优化%Optimization of SSR-PCR System for Acantholyda posticalis

    Institute of Scientific and Technical Information of China (English)

    金娜; 南小宁; 贺虹

    2012-01-01

    以SDS-蛋白酶K法提取的松阿扁叶蜂(Acantholyda posticalis Matsumura)基因组DNA为模板,利用L16(45)正交设计对影响松阿扁叶蜂SSR-PCR反应的主要参数DNA模板、Taq DNA聚合酶、Mg2+、引物和dNTPs进行优化.结果表明,松阿扁叶蜂SSR-PCR最优的反应体系为25 μL体系中含1.00U Taq DNA 聚合酶、3.00 mmol/L Mg2+、3.75 mmol/L dNTPs、25.00 ng/μL DNA模板和10.00 μmol/L引物.%In order to establish the SSR-PCR amplification system using genomic DNA of Acantholyda posticalis which was extracted by SDS-proteinase K method as template, orthogonal design was used to optimize main PCR factors such as template DNA, Taq DNA polymerase, Mg2+, primer and dNTPs. The results showed that the optimized PCR system included 1.00 U Taq DNA polymerase, 3.00 mmol/L Mg2+, 3.75 mmol/L dNTPs, 25.00 ng/μL DNA template and 20.00 μmol/L each primer in the total volume 25 μL.

  7. Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea [Cajanus cajan (L. Millspaugh

    Directory of Open Access Journals (Sweden)

    Bashasab Fakrudin

    2011-01-01

    Full Text Available Abstract Background Pigeonpea [Cajanus cajan (L. Millspaugh], one of the most important food legumes of semi-arid tropical and subtropical regions, has limited genomic resources, particularly expressed sequence based (genic markers. We report a comprehensive set of validated genic simple sequence repeat (SSR markers using deep transcriptome sequencing, and its application in genetic diversity analysis and mapping. Results In this study, 43,324 transcriptome shotgun assembly unigene contigs were assembled from 1.696 million 454 GS-FLX sequence reads of separate pooled cDNA libraries prepared from leaf, root, stem and immature seed of two pigeonpea varieties, Asha and UPAS 120. A total of 3,771 genic-SSR loci, excluding homopolymeric and compound repeats, were identified; of which 2,877 PCR primer pairs were designed for marker development. Dinucleotide was the most common repeat motif with a frequency of 60.41%, followed by tri- (34.52%, hexa- (2.62%, tetra- (1.67% and pentanucleotide (0.76% repeat motifs. Primers were synthesized and tested for 772 of these loci with repeat lengths of ≥18 bp. Of these, 550 markers were validated for consistent amplification in eight diverse pigeonpea varieties; 71 were found to be polymorphic on agarose gel electrophoresis. Genetic diversity analysis was done on 22 pigeonpea varieties and eight wild species using 20 highly polymorphic genic-SSR markers. The number of alleles at these loci ranged from 4-10 and the polymorphism information content values ranged from 0.46 to 0.72. Neighbor-joining dendrogram showed distinct separation of the different groups of pigeonpea cultivars and wild species. Deep transcriptome sequencing of the two parental lines helped in silico identification of polymorphic genic-SSR loci to facilitate the rapid development of an intra-species reference genetic map, a subset of which was validated for expected allelic segregation in the reference mapping population. Conclusion We

  8. Genetic diversity ofUstilago hordei in Tibetan areas as revealed by RAPD and SSR

    Institute of Scientific and Technical Information of China (English)

    ZHOU Yu; CHAO Gui-mei; LIU Jia-jia; ZHU Ming-qi; WANG Yang; FENG Bai-li

    2016-01-01

    Covered smut, which is caused byUstilago hordei(Pers.) Lagerh., is one of the most damaging diseases of highland barley (Hordeum vulgare Linn. var. nudum Hook. f) in Tibetan areas of China. To understand the molecular diversity ofU. hordei, a total of 27 isolates, which were colected from highland barley plants from Tibet, Sichuan, Qinghai, and Gansu provinces/autonomous region, were analyzed using random ampliifed polymorphic DNA (RAPD) and simple sequence repeat (SSR) markers. Among the 100 RAPD primers used, 24 primers exhibited polymorphism. A total of 111 fragments were ampliifed, of which 103 were polymorphic with a polymorphic rate of 92.79%. The average observed number of aleles (Na), effective number of aleles (Ne), Nei’s genetic diversity (H), Shannon’s information index (I) and polymorphism information content (PIC) value in the RAPD markers were 1.9279, 1.5016, 0.2974, 0.4503 and 0.6428, respectively. For the SSR markers, 40 of the 111 primer pairs exhibited polymorphism and provided a total of 119 bands, of which 109 were polymorphic and accounted for 91.60% of the total bands. TheNa,Ne,H,I andPIC values of the SSR markers were 1.9160, 1.4639, 0.2757, 0.4211 and 0.4340, respectively. The similarity coefifcients ranged from 0.4957 to 0.9261 with an average of 0.7028 among al the 27 isolates used. The dendrogram, which was developed based on the RAPD and SSR combined marker dataset showed that the 27U. hordei isolates were divided into 3 clusters at similarity coefifcient of 0.7314. We determined that RAPD and SSR markers can be successfuly used to assess the genetic variation amongU. hordei isolates. The RAPD markers revealed higher levels of genetic polymorphism than did the SSR markers in this study. There existed a moderate genetic difference among isolates. The molecular variation and differentiation was somewhat associated with geographical origin but not for al of the isolates.

  9. 78 FR 22361 - Social Security Ruling, SSR 13-1p; Titles II and XVI: Agency Processes for Addressing Allegations...

    Science.gov (United States)

    2013-04-15

    ... From the Federal Register Online via the Government Publishing Office SOCIAL SECURITY ADMINISTRATION Social Security Ruling, SSR 13-1p; Titles II and XVI: Agency Processes for Addressing Allegations of Unfairness, Prejudice, Partiality, Bias, Misconduct, or Discrimination by Administrative...

  10. 78 FR 8217 - Social Security Ruling, SSR 13-1p; Titles II and XVI: Agency Processes for Addressing Allegations...

    Science.gov (United States)

    2013-02-05

    ... From the Federal Register Online via the Government Publishing Office SOCIAL SECURITY ADMINISTRATION Social Security Ruling, SSR 13-1p; Titles II and XVI: Agency Processes for Addressing Allegations of Unfairness, Prejudice, Partiality, Bias, Misconduct, or Discrimination by Administrative...

  11. 78 FR 9987 - Social Security Ruling, SSR 13-1p; Titles II and XVI: Agency Processes for Addressing Allegations...

    Science.gov (United States)

    2013-02-12

    ... From the Federal Register Online via the Government Publishing Office SOCIAL SECURITY ADMINISTRATION Social Security Ruling, SSR 13-1p; Titles II and XVI: Agency Processes for Addressing Allegations of Unfairness, Prejudice, Partiality, Bias, Misconduct, or Discrimination by Administrative...

  12. Genetic variation assessment of acid lime accessions collected from south of Iran using SSR and ISSR molecular markers.

    Science.gov (United States)

    Sharafi, Ata Allah; Abkenar, Asad Asadi; Sharafi, Ali; Masaeli, Mohammad

    2016-01-01

    Iran has a long history of acid lime cultivation and propagation. In this study, genetic variation in 28 acid lime accessions from five regions of south of Iran, and their relatedness with other 19 citrus cultivars were analyzed using Simple Sequence Repeat (SSR) and Inter-Simple Sequence Repeat (ISSR) molecular markers. Nine primers for SSR and nine ISSR primers were used for allele scoring. In total, 49 SSR and 131 ISSR polymorphic alleles were detected. Cluster analysis of SSR and ISSR data showed that most of the acid lime accessions (19 genotypes) have hybrid origin and genetically distance with nucellar of Mexican lime (9 genotypes). As nucellar of Mexican lime are susceptible to phytoplasma, these acid lime genotypes can be used to evaluate their tolerance against biotic constricts like lime "witches' broom disease".

  13. Construction of an SSR and RAD-Marker Based Molecular Linkage Map of Vigna vexillata (L.) A. Rich.

    Science.gov (United States)

    Marubodee, Rusama; Ogiso-Tanaka, Eri; Isemura, Takehisa; Chankaew, Sompong; Kaga, Akito; Naito, Ken; Ehara, Hiroshi; Tomooka, Norihiko

    2015-01-01

    Vigna vexillata (L.) A. Rich. (tuber cowpea) is an underutilized crop for consuming its tuber and mature seeds. Wild form of V. vexillata is a pan-tropical perennial herbaceous plant which has been used by local people as a food. Wild V. vexillata has also been considered as useful gene(s) source for V. unguiculata (cowpea), since it was reported to have various resistance gene(s) for insects and diseases of cowpea. To exploit the potential of V. vexillata, an SSR-based linkage map of V. vexillata was developed. A total of 874 SSR markers successfully amplified single DNA fragment in V. vexillata among 1,336 SSR markers developed from Vigna angularis (azuki bean), V. unguiculata and Phaseolus vulgaris (common bean). An F2 population of 300 plants derived from a cross between salt resistant (V1) and susceptible (V5) accessions was used for mapping. A genetic linkage map was constructed using 82 polymorphic SSR markers loci, which could be assigned to 11 linkage groups spanning 511.5 cM in length with a mean distance of 7.2 cM between adjacent markers. To develop higher density molecular linkage map and to confirm SSR markers position in a linkage map, RAD markers were developed and a combined SSR and RAD markers linkage map of V. vexillata was constructed. A total of 559 (84 SSR and 475 RAD) markers loci could be assigned to 11 linkage groups spanning 973.9 cM in length with a mean distance of 1.8 cM between adjacent markers. Linkage and genetic position of all SSR markers in an SSR linkage map were confirmed. When an SSR genetic linkage map of V. vexillata was compared with those of V. radiata and V. unguiculata, it was suggested that the structure of V. vexillata chromosome was considerably differentiated. This map is the first SSR and RAD marker-based V. vexillata linkage map which can be used for the mapping of useful traits.

  14. Construction of an SSR and RAD-Marker Based Molecular Linkage Map of Vigna vexillata (L. A. Rich.

    Directory of Open Access Journals (Sweden)

    Rusama Marubodee

    Full Text Available Vigna vexillata (L. A. Rich. (tuber cowpea is an underutilized crop for consuming its tuber and mature seeds. Wild form of V. vexillata is a pan-tropical perennial herbaceous plant which has been used by local people as a food. Wild V. vexillata has also been considered as useful gene(s source for V. unguiculata (cowpea, since it was reported to have various resistance gene(s for insects and diseases of cowpea. To exploit the potential of V. vexillata, an SSR-based linkage map of V. vexillata was developed. A total of 874 SSR markers successfully amplified single DNA fragment in V. vexillata among 1,336 SSR markers developed from Vigna angularis (azuki bean, V. unguiculata and Phaseolus vulgaris (common bean. An F2 population of 300 plants derived from a cross between salt resistant (V1 and susceptible (V5 accessions was used for mapping. A genetic linkage map was constructed using 82 polymorphic SSR markers loci, which could be assigned to 11 linkage groups spanning 511.5 cM in length with a mean distance of 7.2 cM between adjacent markers. To develop higher density molecular linkage map and to confirm SSR markers position in a linkage map, RAD markers were developed and a combined SSR and RAD markers linkage map of V. vexillata was constructed. A total of 559 (84 SSR and 475 RAD markers loci could be assigned to 11 linkage groups spanning 973.9 cM in length with a mean distance of 1.8 cM between adjacent markers. Linkage and genetic position of all SSR markers in an SSR linkage map were confirmed. When an SSR genetic linkage map of V. vexillata was compared with those of V. radiata and V. unguiculata, it was suggested that the structure of V. vexillata chromosome was considerably differentiated. This map is the first SSR and RAD marker-based V. vexillata linkage map which can be used for the mapping of useful traits.

  15. Exploiting BAC-end sequences for the mining, characterization and utility of new short sequences repeat (SSR) markers in Citrus.

    Science.gov (United States)

    Biswas, Manosh Kumar; Chai, Lijun; Mayer, Christoph; Xu, Qiang; Guo, Wenwu; Deng, Xiuxin

    2012-05-01

    The aim of this study was to develop a large set of microsatellite markers based on publicly available BAC-end sequences (BESs), and to evaluate their transferability, discriminating capacity of genotypes and mapping ability in Citrus. A set of 1,281 simple sequence repeat (SSR) markers were developed from the 46,339 Citrus clementina BAC-end sequences (BES), of them 20.67% contained SSR longer than 20 bp, corresponding to roughly one perfect SSR per 2.04 kb. The most abundant motifs were di-nucleotide (16.82%) repeats. Among all repeat motifs (TA/AT)n is the most abundant (8.38%), followed by (AG/CT)n (4.51%). Most of the BES-SSR are located in the non-coding region, but 1.3% of BES-SSRs were found to be associated with transposable element (TE). A total of 400 novel SSR primer pairs were synthesized and their transferability and polymorphism tested on a set of 16 Citrus and Citrus relative's species. Among these 333 (83.25%) were successfully amplified and 260 (65.00%) showed cross-species transferability with Poncirus trifoliata and Fortunella sp. These cross-species transferable markers could be useful for cultivar identification, for genomic study of Citrus, Poncirus and Fortunella sp. Utility of the developed SSR marker was demonstrated by identifying a set of 118 markers each for construction of linkage map of Citrus reticulata and Poncirus trifoliata. Genetic diversity and phylogenetic relationship among 40 Citrus and its related species were conducted with the aid of 25 randomly selected SSR primer pairs and results revealed that citrus genomic SSRs are superior to genic SSR for genetic diversity and germplasm characterization of Citrus spp.

  16. [Development of new SSR markers from EST of SSH cDNA libraries on rose fragrance].

    Science.gov (United States)

    Yan, Hui-Jun; Zhang, Hao; Xie, Ji-Rong; Li, Shu-Fa; Jian, Hong-Ying; Qiu, Xian-Qin; Wang, Qi-Gang; Wang, Ji-Hua; Tang, Kai-Xue

    2009-09-01

    The new SSR markers of rose related fragrance were developed based on the SSH cDNA libraries of rose floral scent mutant. In this study, 10 EST-SSRs (2.6%) from 391 ESTs in the libraries were identified. Six EST-SSRs primers were designed to sequence flanking SSRs. The primer pairs designed were screened on the wild-type Jinyindao, which has flowers full of pleasant scent, and the mutant-type Wangriqinghuai without perceivable floral scent. Five primer pairs were amplified effectively in Jinyindao and Wangriqinghuai, and 3 were polymorphic between Jinyindao and Wangriqinghuai. Eighteen rose cultivars including fragrant roses and nonfragrant roses were identified by the five prime pairs. These results proved that EST-SSR markers are effective markers to identify the polymorphism of the rose.

  17. Development of Molecular Marker Linked to Cf-10 Gene Using SSR and AFLP Method in Tomato

    Institute of Scientific and Technical Information of China (English)

    Li Ning; Jiang Jing-bin; Li Jing-fu; Xu Xiang-yang

    2012-01-01

    The leaf mould resistance gene Cf-10 on tomato confered resistant or immune to all prevalent physiological races of Cladosporium fulvum presented in three northeastern provinces of China in inoculation test. In order to better utilize Cf-10 gene in a marker-assisted selection program and to permit the pyramiding of one or several resistance genes in a cultivar, tightly linked SSR and AFLP markers were obtained by the bulked segregant analysis method. One SSR marker and three AFLP markers were identified linked to Cf-10 gene, with the distance of 9.73, 5.8, 8.5, and 10.6 cM, respectively. These markers will facilitate the selection of resistant tomato germplasm containing Cf-10 gene.

  18. Genome-wide functional analysis of SSR for an edible mushroom Pleurotus ostreatus.

    Science.gov (United States)

    Qu, Jibin; Huang, Chenyang; Zhang, Jinxia

    2016-01-10

    Simple sequence repeats (SSRs) play specific roles in many biological activities. In this paper, we focused on SSRs in the genome of Pleurotus ostreatus, which is a widely cultivated edible mushroom. The distribution curves of SSRs and exons are opposite throughout the genome, which means that SSRs are mostly located in non-coding regions. A comparative analysis of nine fungi suggests that Agaricomycotina fungi have similar SSR distributions. Functional enrichment analysis on the SSR-containing gene set uncovers enriched functions about environmental interactions and important cellular functions for life. Trinucleotide SSRs account for an extremely high fraction of all SSRs, and in exonic regions, they are equivalent to inserting repeating amino acids (RAAs) into the protein sequences. The RAA indel could partly explain some enriched functions of the genes they modify. Agaricomycotina fungi have similar distributions of RAAs, indicating that this may be a potential common mechanism for some specific functions.

  19. Development and Characterization of 25 EST-SSR markers in Pinus sylvestris var. mongolica (Pinaceae

    Directory of Open Access Journals (Sweden)

    Pan Fang

    2014-01-01

    Full Text Available Premise of the study: A set of novel expressed sequence tag (EST microsatellite markers was developed in Pinus sylvestris var. mongolica to promote further genetic studies in this species. Methods and Results: One hundred seventy-five EST–simple sequence repeat (SSR primers were designed and synthesized for 31,653 isotigs based on P. tabuliformis EST sequences. The primer pairs were used to identify 25 polymorphic loci in 48 individuals. The number of alleles ranged from two to eight with observed and expected heterozygosity values of 0.0435 to 0.8125 and 0.0430 to 0.7820, respectively. Conclusions: These new polymorphic EST-SSR markers will be useful for assessing genetic diversity, molecular breeding and genetic improvement, and conservation of P. sylvestris var. mongolica.

  20. NOTE-Polymorphic information content of SSR markers for Coffea spp.

    Directory of Open Access Journals (Sweden)

    Robson Fernando Missio

    2010-01-01

    Full Text Available Thirty-three coffee SSR primers from enriched genomic library with (GT15 and (AGG10 repeats were analyzedin 24 coffee tree accessions. Twenty-two primers were polymorphic among accessions; the number of alleles ranged from 2 to13, with the mean number of 5.1 alleles per primer. PIC values ranged from 0.08 to 0.79. The highest mean PIC values werefound for C. canephora (0.46, and the lowest values for C. arabica (0.22 and triploids (0.22 accessions. The polymorphicSSR markers used in this study were useful for genetic fingerprinting in the coffee tree, especially in the C. canephora and theleaf rust resistant arabica cultivars.

  1. Genetic diversity in wild sweet cherries (Prunus avium) in Turkey revealed by SSR markers.

    Science.gov (United States)

    Ercisli, S; Agar, G; Yildirim, N; Duralija, B; Vokurka, A; Karlidag, H

    2011-06-21

    Wild sweet cherry (Prunus avium) trees are abundant in the northern part of Turkey, including the Coruh Valley. We analyzed 18 wild sweet cherry genotypes collected from diverse environments in the upper Coruh Valley in Turkey to determine genetic variation, using 10 SSR primers. These SSR primers generated 46 alleles; the number of alleles per primer ranged from 3 to 7, with a mean of 4.6. The primer PS12A02 gave the highest number of polymorphic bands (N = 7), while CPSCT010, UDAp-401 and UDAp-404 gave the lowest number (N = 3). Seven groups were separated in the dendrogram, although most of the genotypes did not cluster according to phenological and morphological traits. This level of genetic diversity in these wild sweet cherry genotypes is very high and therefore these trees would be useful as breeders for crosses between cultivated sweet cherry and wild genotypes.

  2. Genetic diversity of Phytophthora sojae isolates in Heilongjiang Province in China assessed by RAPD and EST-SSR

    Science.gov (United States)

    Wu, J. J.; Xu, P. F.; Liu, L. J.; Wang, J. S.; Lin, W. G.; Zhang, S. Z.; Wei, L.

    Random-amplified polymorphic DNA (RAPD) and EST-SSR markers were used to estimate the genetic relationship among thirty-nine P.sojae isolates from three locations in Heilongjiang Province, and nine isolates from Ohio in America were made as reference strains. 10 of 50 RAPD primers and 5 of 33 EST-SSR were polymorphic across 48 P.sojae isolates. Similarity values among P.sojae isolates were from 49% to 82% based on the RAPD data. The similarities based on EST-SSR markers ranged from 47% to 85%. The genetic diversity revealed by EST-SSR marker analysis was higher than that obtained from RAPD. The similarity matrices for the SSR data and the RAPD data were moderately correlated (r = 0.47). Genetic similarity coefficients were also relatively lower, which demonstrated complicated genetic background within each location. The high similarity values range revealed the ability of RAPD/EST-SSR markers to distinguish even among morphological similar phytophthora.

  3. Use of genome sequence data in the design and testing of SSR markers for Phytophthora species

    Directory of Open Access Journals (Sweden)

    Cardle Linda

    2008-12-01

    Full Text Available Abstract Background Microsatellites or single sequence repeats (SSRs are a powerful choice of marker in the study of Phytophthora population biology, epidemiology, ecology, genetics and evolution. A strategy was tested in which the publicly available unigene datasets extracted from genome sequences of P. infestans, P. sojae and P. ramorum were mined for candidate SSR markers that could be applied to a wide range of Phytophthora species. Results A first approach, aimed at the identification of polymorphic SSR loci common to many Phytophthora species, yielded 171 reliable sequences containing 211 SSRs. Microsatellites were identified from 16 target species representing the breadth of diversity across the genus. Repeat number ranged from 3 to 16 with most having seven repeats or less and four being the most commonly found. Trinucleotide repeats such as (AAGn, (AGGn and (AGCn were the most common followed by pentanucleotide, tetranucleotide and dinucleotide repeats. A second approach was aimed at the identification of useful loci common to a restricted number of species more closely related to P. sojae (P. alni, P. cambivora, P. europaea and P. fragariae. This analysis yielded 10 trinucleotide and 2 tetranucleotide SSRs which were repeated 4, 5 or 6 times. Conclusion Key studies on inter- and intra-specific variation of selected microsatellites remain. Despite the screening of conserved gene coding regions, the sequence diversity between species was high and the identification of useful SSR loci applicable to anything other than the most closely related pairs of Phytophthora species was challenging. That said, many novel SSR loci for species other than the three 'source species' (P. infestans, P. sojae and P. ramorum are reported, offering great potential for the investigation of Phytophthora populations. In addition to the presence of microsatellites, many of the amplified regions may represent useful molecular marker regions for other studies as

  4. Development and characterization of EST-SSR markers in the eastern oyster Crassostrea virginica.

    Science.gov (United States)

    Wang, Yongping; Guo, Ximing

    2007-01-01

    Simple sequence repeat (SSR) markers were developed from expressed sequence tags (ESTs) in the eastern oyster (Crassostrea virginica). ESTs of the eastern oyster were downloaded from GenBank and screened for SSRs with at least eight units of dinucleotide or five units of tri-, tetra-, penta-, and hexa-nucleotide repeats. The screening of 9101 ESTs identified 127 (1.4%) SSR-containing sequences. Primers were designed for 88 SSR-containing ESTs with good and sufficient flanking sequences. Polymerase chain reaction (PCR) amplification was successful for 71 primer pairs, including 19 (27%) pairs that amplified fragments longer than expected sizes, probably due to introns. Sixty-six pairs that produced fragments shorter than 800 bp were screened for polymorphism in five oysters from three populations via polyacrylamide gels, and 53 of them (80%) were polymorphic. Fifty-three polymorphic SSRs were labeled and genotyped in 30 oysters from three populations via an automated sequencer. Five of the SSRs amplified more than two fragments per oyster, suggesting locus duplication. The remaining 48 SSRs had 2 alleles per individual, including 11 with null alleles. In the 30 oysters analyzed, the SSRs had an average of 9.3 alleles per locus, ranging from 2 to 24. Forty-three loci segregated in a family with 100 progeny, with nine showing significant deviation from Mendelian ratios (three after Bonferroni correction). Seventy percent of the loci were successfully amplified in C. rhizophorae and 34% in C. gigas. This study demonstrates that ESTs are valuable resources for the development of SSR markers in the eastern oyster, and EST-derived SSRs are more transferable across species than genomic SSRs.

  5. Genetic diversity in watermelon (Citrullus lanatus) landraces from Zimbabwe revealed by RAPD and SSR markers.

    Science.gov (United States)

    Mujaju, C; Sehic, J; Werlemark, G; Garkava-Gustavsson, L; Fatih, M; Nybom, H

    2010-08-01

    Low polymorphism in cultivated watermelon has been reported in previous studies, based mainly on US Plant Introductions and watermelon cultivars, most of which were linked to breeding programmes associated with disease resistance. Since germplasm sampled in a putative centre of origin in southern Africa may harbour considerably higher variability, DNA marker-based diversity was estimated among 81 seedlings from eight accessions of watermelon collected in Zimbabwe; five accessions of cow-melons (Citrullus lanatus var. citroides) and three of sweet watermelons (C. lanatus var. lanatus). Two molecular marker methods were used, random amplified polymorphic DNA (RAPD) and simple sequence repeats (SSR) also known as microsatellite DNA. Ten RAPD primers produced 138 markers of which 122 were polymorphic. Nine SSR primer pairs detected a total of 43 alleles with an average of 4.8 alleles per locus. The polymorphic information content (PIC) ranged from 0.47 to 0.77 for the RAPD primers and from 0.39 to 0.97 for the SSR loci. Similarity matrices obtained with SSR and RAPD, respectively, were highly correlated but only RAPD was able to provide each sample with an individual-specific DNA profile. Dendrograms and multidimensional scaling (MDS) produced two major clusters; one with the five cow-melon accessions and the other with the three sweet watermelon accessions. One of the most variable cow-melon accessions took an intermediate position in the MDS analysis, indicating the occurrence of gene flow between the two subspecies. Analysis of molecular variation (AMOVA) attributed most of the variability to within-accessions, and contrary to previous reports, sweet watermelon accessions apparently contain diversity of the same magnitude as the cow-melons.

  6. Development and mapping of SSR markers linked to resistance-gene homologue clusters in common bean

    Institute of Scientific and Technical Information of China (English)

    Luz; Nayibe; Garzon; Matthew; Wohlgemuth; Blair

    2014-01-01

    Common bean is an important but often a disease-susceptible legume crop of temperate,subtropical and tropical regions worldwide. The crop is affected by bacterial, fungal and viral pathogens. The strategy of resistance-gene homologue(RGH) cloning has proven to be an efficient tool for identifying markers and R(resistance) genes associated with resistances to diseases. Microsatellite or SSR markers can be identified by physical association with RGH clones on large-insert DNA clones such as bacterial artificial chromosomes(BACs). Our objectives in this work were to identify RGH-SSR in a BAC library from the Andean genotype G19833 and to test and map any polymorphic markers to identify associations with known positions of disease resistance genes. We developed a set of specific probes designed for clades of common bean RGH genes and then identified positive BAC clones and developed microsatellites from BACs having SSR loci in their end sequences. A total of 629 new RGH-SSRs were identified and named BMr(bean microsatellite RGH-associated markers). A subset of these markers was screened for detecting polymorphism in the genetic mapping population DOR364 × G19833. A genetic map was constructed with a total of 264 markers,among which were 80 RGH loci anchored to single-copy RFLP and SSR markers. Clusters of RGH-SSRs were observed on most of the linkage groups of common bean and in positions associated with R-genes and QTL. The use of these new markers to select for disease resistance is discussed.

  7. Eighteen SSR-primers for tetraploid Adansonia digitata and its relatives

    OpenAIRE

    Larsen, Anders Søndergaard; Vaillant, Alexandre; Verhaegen, Daniel; Kjær, Erik Dahl

    2009-01-01

    International audience; Co-dominant markers suitable for molecular ecological studies in the genus Adansonia are highly desirable in order to be able to address a number of interesting research questions related to the special life history traits, gene flow, and distribution dynamics of the Adansonia species. This note presents a set of 18 SSR- primers developed for Adansonia digitata, and tested for cross-amplification on all members of the Adansonia genus. All reported primers were found to a...

  8. An EST-SSR linkage map of Raphanus sativus and comparative genomics of the Brassicaceae.

    Science.gov (United States)

    Shirasawa, Kenta; Oyama, Maki; Hirakawa, Hideki; Sato, Shusei; Tabata, Satoshi; Fujioka, Takashi; Kimizuka-Takagi, Chiaki; Sasamoto, Shigemi; Watanabe, Akiko; Kato, Midori; Kishida, Yoshie; Kohara, Mitsuyo; Takahashi, Chika; Tsuruoka, Hisano; Wada, Tsuyuko; Sakai, Takako; Isobe, Sachiko

    2011-08-01

    Raphanus sativus (2n = 2x = 18) is a widely cultivated member of the family Brassicaceae, for which genomic resources are available only to a limited extent in comparison to many other members of the family. To promote more genetic and genomic studies and to enhance breeding programmes of R. sativus, we have prepared genetic resources such as complementary DNA libraries, expressed sequences tags (ESTs), simple sequence repeat (SSR) markers and a genetic linkage map. A total of 26 606 ESTs have been collected from seedlings, roots, leaves, and flowers, and clustered into 10 381 unigenes. Similarities were observed between the expression patterns of transcripts from R. sativus and those from representative members of the genera Arabidopsis and Brassica, indicating their functional relatedness. The EST sequence data were used to design 3800 SSR markers and consequently 630 polymorphic SSR loci and 213 reported marker loci have been mapped onto nine linkage groups, covering 1129.2 cM with an average distance of 1.3 cM between loci. Comparison of the mapped EST-SSR marker positions in R. sativus with the genome sequence of A. thaliana indicated that the Brassicaceae members have evolved from a common ancestor. It appears that genomic fragments corresponding to those of A. thaliana have been doubled and tripled in R. sativus. The genetic map developed here is expected to provide a standard map for the genetics, genomics, and molecular breeding of R. sativus as well as of related species. The resources are available at http://marker.kazusa.or.jp/Daikon.

  9. Generation and Characterization of a Sugarbeet Transcriptome and Transcript-Based SSR Markers

    Directory of Open Access Journals (Sweden)

    Karen Klotz Fugate

    2014-07-01

    Full Text Available Sugarbeet is a major source of refined sucrose and increasingly grown for biofuel production. Demand for higher productivity for this crop requires greater knowledge of sugarbeet physiology, pathology, and genetics, which can be advanced by the development of new genomic resources. Towards this end, a sugarbeet transcriptome of expressed genes from leaf and root tissues at varying stages of development and production, and after elicitation with jasmonic acid (JA or salicylic acid (SA, was constructed and used to generate simple sequence repeat (SSR markers. The transcriptome was generated via paired-end RNA sequencing and contains 82,404 unigenes. A total of 37,207 unigenes were annotated, of which 9480 were functionally classified using clusters of orthologous groups (COG annotations, 17,191 were classified into biological process, molecular function, or cellular component using gene ontology (GO terms, and 17,409 were assigned to 126 metabolic pathways using Kyoto Encyclopedia of Genes and Genomes (KEGG identifiers. A SSR search of the transcriptome identified 7680 SSRs, including 6577 perfect SSRs, of which 3834 were located in unigenes with ungapped sequence. Primer-pairs were designed for 288 SSR loci, and 72 of these primer-pairs were tested for their ability to detect polymorphisms. Forty-three primer-pairs detected single polymorphic loci and effectively distinguished diversity among eight genotypes. The transcriptome and SSR markers provide additional, public domain genomic resources for an important crop plant and can be used to increase understanding of the functional elements of the sugarbeet genome, aid in discovery of novel genes, facilitate RNA-sequencing based expression research, and provide new tools for sugarbeet genetic research and selective breeding.

  10. 木薯基因组SSR和EST-SSR在麻疯树和橡胶树中的通用性分析%Transferability Analysis of Cassava EST-SSR and Genomic-SSR Markers in Jatropha and Rubber Tree

    Institute of Scientific and Technical Information of China (English)

    文明富; 陈新; 王海燕; 卢诚; 王文泉

    2011-01-01

    利用木薯的419对EST-SSR引物和182对基因组SSR引物在5个麻疯树品系和2个橡胶树品系中进行通用性分析.结果显示,木薯EST-SSR在麻疯树和橡胶树中的通用性比例分别为55.85%和38.90%,而木薯基因组SSR在麻疯树和橡胶树中的通用性比例分别为37.36%和26.37%.由此推测,EST-SSR的通用性高于基因组SSR.此外,木薯EST-SSR和基因组SSR的通用件在麻疯树中高于在橡胶树中.本研究发掘的通用性SSR引物可以用于木薯、麻疯树和橡胶树间的比较作网、基因发掘和QTL定位研究.%Euphorbiaceae family includes abundant economic species, such as rubber tree, cassava, castor bean, and Jatropha.Cassava (Manihot esculenta Crantz) ranks in the sixth food crop in the world.In China, cassava is also an important tropical economic crop.The genomic-SSRs derived from cassava genome, and EST-SSRs derived from expressed sequence tags (ESTs).In this study, the transferability of 419 pairs of EST-SSR primer and 182 pairs of genomic-SSR primer from cassava was tested in five Jatropha lines and two rubber tree lines.The results showed that the transferability rate of cassava EST-SSR in Jatropha and rubber tree was 55.85% and 38.90%, and the transferability rate of cassava genomic-SSR in Jatropha and rubber tree was 37.36% and 26.37%, respectively.The transferability EST-SSR was higher for cssava than that of genomic-SSR.Besides, the transferability of cassava EST-SSR and genomic-SSR was higher in Jatropha than in rubber tree.These results suggested that the cassava SSR can be used for comparative mapping, gene tagging and QTL mapping among cassava, Jatropha, and rubber tree.

  11. Genetic diversity among melon accessions (Cucumis melo) from Turkey based on SSR markers.

    Science.gov (United States)

    Kaçar, Y A; Simsek, O; Solmaz, I; Sari, N; Mendi, Y Y

    2012-12-19

    Melon (Cucumis melo) is an important vegetable crop in Turkey, where it is grown in many regions; the most widely planted lines are local winter types belonging to the var. inodorous. We examined 81 melon genotypes collected from different provinces of Turkey, compared with 15 reference melon genotypes obtained from INRA/France, to determine genetic diversity among Turkish melons. Twenty polymorphic primers were used to generate the SSR markers. PCR amplification was performed and electrophoresis was conducted. SSR data were used to generate a binary matrix. For cluster analysis, UPGMA was employed to construct a clustering dendrogram based on the genetic distance matrix. The cophenetic correlation was compared with the similarity matrix using the Mantel matrix correspondence test to evaluate the representativeness of the dendrogram. A total of 123 alleles were amplified using the 20 SSR primer sets. The number of alleles detected by a single primer set ranged from 2 to 12, with an average of 6.15. The similarity ranged from 0.22 to 1.00 in the dendrogram developed from microsatellite analysis. Based on this molecular data, we concluded that genetic diversity among these Turkish accessions is relatively high.

  12. Newly developed SSR markers reveal genetic diversity and geographical clustering in spinach (Spinacia oleracea).

    Science.gov (United States)

    Göl, Şurhan; Göktay, Mehmet; Allmer, Jens; Doğanlar, Sami; Frary, Anne

    2017-08-01

    Spinach is a popular leafy green vegetable due to its nutritional composition. It contains high concentrations of vitamins A, E, C, and K, and folic acid. Development of genetic markers for spinach is important for diversity and breeding studies. In this work, Next Generation Sequencing (NGS) technology was used to develop genomic simple sequence repeat (SSR) markers. After cleaning and contig assembly, the sequence encompassed 2.5% of the 980 Mb spinach genome. The contigs were mined for SSRs. A total of 3852 SSRs were detected. Of these, 100 primer pairs were tested and 85% were found to yield clear, reproducible amplicons. These 85 markers were then applied to 48 spinach accessions from worldwide origins, resulting in 389 alleles with 89% polymorphism. The average gene diversity (GD) value of the markers (based on a GD calculation that ranges from 0 to 0.5) was 0.25. Our results demonstrated that the newly developed SSR markers are suitable for assessing genetic diversity and population structure of spinach germplasm. The markers also revealed clustering of the accessions based on geographical origin with clear separation of Far Eastern accessions which had the overall highest genetic diversity when compared with accessions from Persia, Turkey, Europe, and the USA. Thus, the SSR markers have good potential to provide valuable information for spinach breeding and germplasm management. Also they will be helpful for genome mapping and core collection establishment.

  13. Molecular diversity of brinjal (Solanum melongena L. and S. aethiopicum L. genotypes revealed by SSR markers

    Directory of Open Access Journals (Sweden)

    Abdul Majid Ansari, and Y. V. Singh

    2014-12-01

    Full Text Available In the present study, simple sequence repeat (SSR markers were used to study the genetic diversity among 14 genotypes of brinjal. A total of 14 polymorphic SSR primer pairs were used. Amplification of genomic DNA of 14 genotypes yielded 50 fragments, of which 43 were polymorphic. A clear cut differentiation was exhibited among the genotypes. The range of similarity coefficient varied from 17.8% [between S. aethiopicum L. (2n=2x=24 and Pant Rituraj (S. melongena L., 2n=2x=24] to 94.1% [between PB-71 and NDB-1] followed by 88.9% [between SMB-115 and KS-331] and 88.6% [between BARI and PB-67]. SAHN cluster analysis using UPGMA method separated the genotypes into six cluster groups. Solanum aethiopicum and PB-67 were positioned as single genotype in separate groups i.e., cluster-I & II, SMB-115 and KS-331 in cluster-III, BARI, PB-66 and Pant Rituraj in cluster-IV, WB-1, PB-4, PB-70 and LC-7 in cluster-V and PB-71, Pant Samrat and NDB-1 in cluster-VI. Morphological characters viz., shape, size and peel colour of brinjal fruits and plant type showed a positive relationship with the DNA based molecular analysis through SSR markers.

  14. Evaluation of Genetic Diversity of Sichuan Common Wheat Landraces in China by SSR Markers

    Institute of Scientific and Technical Information of China (English)

    LI Wei; BIAN Chun-mei; WEI Yu-ming; LIU An-jun; CHEN Guo-yue; PU Zhi-en; LIU Ya-xi; ZHENG You-liang

    2013-01-01

    Genetic diversity of 62 Sichuan wheat landraces accessions of China was investigated by agronomic traits and SSR markers. The landrace population showed the characters of higher tiller capability and more kernels/spike, especially tiller no./plant of six accessions was over 40 and kernels/spike of three accessions was more than 70. A total of 547 alleles in 124 polymorphic loci were detected with an average of 4.76 alleles per locus by 114 SSR markers. Parameters analysis indicated that the genetic diversity ranked as genome A>genome B>genome D, and the homoeologous groups ranked as 5>4>3>1>2>7>6 based on genetic richness (Ri). Furthermore, chromosomes 2A, 1B and 3D had more diversity than that of chromosomes 4A, 7A and 6B. The variation of SSR loci on chromosomes 1B, 2A, 2D, 3B, and 4B implied that, in the past, different selective pressures might have acted on different chromosome regions of these landraces. Our results suggested that Sichuan common wheat landraces is a useful genetic resource for genetic research and wheat improvement.

  15. SSR-based detection of genetic variability in the charcoal root rot pathogen Macrophomina phaseolina.

    Science.gov (United States)

    Jana, Tarakanta; Sharma, Tilak R; Singh, Nagendra K

    2005-01-01

    Macrophomina phaseolina, the causal agent of charcoal root or collar rot, is an important plant pathogen especially in soybean and cotton. Single primers of simple sequence repeats (SSR) or microsatellite markers have been used for the characterization of genetic variability of different populations of M. phaseolina obtained from soybean and cotton grown in India and the USA. Genetic similarity between isolates was calculated, and cluster analysis was used to generate a dendrogram showing relationships between isolates collected from the two hosts. Forty isolates could be clustered into three major groups corresponding to their hosts and geographical region. The wide distribution of microsatellites in M. phaseolina genome was assessed by agarose gel electrophoresis of the PCR products generated by direct amplification of inter SSR regions DNA. This is the first report of the use of microsatellite markers to characterize the charcoal root rot pathogen. The SSR fingerprints (0.25-3.5 kb) generated using DNA from different populations of M. phaseolina of two hosts indicated that these repeats are interspersed within the genome of this pathogen. The variability found within closely related isolates of M. phaseolina indicated that such microsatellites are useful in population studies and represents a step towards identification of potential isolate diagnostic markers specific to soybean and cotton.

  16. Nuclear SSR markers for Miscanthus, Saccharum, and related grasses (Saccharinae, Poaceae)1

    Science.gov (United States)

    Hodkinson, Trevor R.; de Cesare, Mariateresa; Barth, Susanne

    2013-01-01

    • Premise of the study: We developed nuclear simple sequence repeat (SSR) markers for the characterization of the biomass crop Miscanthus, especially M. sacchariflorus, M. sinensis, and M. ×giganteus, and tested for cross-species amplification. • Methods and Results: Twenty-nine SSR markers (di- and tetranucleotide repeats) were developed from DNA sequences obtained from 192 clones from an enriched genomic library of M. sinensis. All markers were successfully amplified in M. sacchariflorus, M. sinensis, and M. ×giganteus, and 19 amplified across a broad range of Miscanthus species. Polymorphism information content and expected heterozygosity values (19 locus sample) were 0.88 and 0.89, respectively, for M. sinensis, 0.48 and 0.54 for M. sacchariflorus, and were the lowest in M. ×giganteus (0.33, 0.41). Thirteen out of 19 primer pairs showed cross-species amplification in non-Miscanthus sensu stricto taxa. • Conclusions: The new set of 29 SSR markers will be of high value for characterizing Miscanthus germplasm collections, for prebreeding, and for assessing variation in natural populations. PMID:25202497

  17. Identification of SSR loci in Betula luminifera using birch EST data

    Institute of Scientific and Technical Information of China (English)

    LU Yong-quan; LI Hai-ying; JIA Qing; HUANG Hua-hong; TONG Zai-kang

    2011-01-01

    Expressed sequence tags (ESTs) are generated from single-pass sequencing of randomly picked cDNA clones and can be used for development of simple sequence repeat (SSR) markers or microsatellites.However,EST databases have been developed for only a small number of species.This paper provides a case study of the utility of freely available birch EST reources for the development of markers necessary for the genetic analysis of Betula luminifera.Based on birch EST data,primers for 80 EST-SSR candidate loci were developed and tested in birch.Of these,59 EST-SSR loci yielded single,stable and clear PCR products.We then tested the utility of those 59 markers in B.luminifera.The results showed 28 (47.6%) yielded stable and clear PCR products for at least one B.luminifera genotype.In addition,this study describes a rapid and inexpensive alternative for the development of SSRs in species with scarce available sequence data.

  18. Alleviation SSR and Low Frequency Power Oscillations in Series Compensated Transmission Line using SVC Supplementary Controllers

    Science.gov (United States)

    Kumar, Sanjiv; Kumar, Narendra

    2016-07-01

    In this work, supplementary sub-synchronous damping controllers (SSDC) are proposed for damping sub-synchronous oscillations in power systems with series compensated transmission lines. Series compensation have extensively been used as effective means of increasing the power transfer capability of a transmission lines and improving transient stability limits of power systems. Series compensation with transmission lines may cause sub-synchronous resonance (SSR). The eigenvalue investigation tool is used to ascertain the existence of SSR. It is shown that the addition of supplementary controller is able to stabilize all unstable modes for T-network model. Eigenvalue investigation and time domain transient simulation of detailed nonlinear system are considered to investigate the performance of the controllers. The efficacies of the suggested supplementary controllers are compared on the IEEE first benchmark model for computer simulations of SSR by means of time domain simulation in Matlab/Simulink environment. Supplementary SSDC are considered in order to compare effectiveness of SSDC during higher loading in alleviating the small signal stability problem.

  19. A genetic linkage map of quinoa ( Chenopodium quinoa) based on AFLP, RAPD, and SSR markers.

    Science.gov (United States)

    Maughan, P J; Bonifacio, A; Jellen, E N; Stevens, M R; Coleman, C E; Ricks, M; Mason, S L; Jarvis, D E; Gardunia, B W; Fairbanks, D J

    2004-10-01

    Quinoa ( Chenopodium quinoa Willd.) is an important seed crop for human consumption in the Andean region of South America. It is the primary staple in areas too arid or saline for the major cereal crops. The objective of this project was to build the first genetic linkage map of quinoa. Selection of the mapping population was based on a preliminary genetic similarity analysis of four potential mapping parents. Breeding lines 'Ku-2' and '0654', a Chilean lowland type and a Peruvian Altiplano type, respectively, showed a low similarity coefficient of 0.31 and were selected to form an F(2) mapping population. The genetic map is based on 80 F(2) individuals from this population and consists of 230 amplified length polymorphism (AFLP), 19 simple-sequence repeat (SSR), and six randomly amplified polymorphic DNA markers. The map spans 1,020 cM and contains 35 linkage groups with an average marker density of 4.0 cM per marker. Clustering of AFLP markers was not observed. Additionally, we report the primer sequences and map locations for 19 SSR markers that will be valuable tools for future quinoa genome analysis. This map provides a key starting point for genetic dissection of agronomically important characteristics of quinoa, including seed saponin content, grain yield, maturity, and resistance to disease, frost, and drought. Current efforts are geared towards the generation of more than 200 mapped SSR markers and the development of several recombinant-inbred mapping populations.

  20. Alleviation SSR and Low Frequency Power Oscillations in Series Compensated Transmission Line using SVC Supplementary Controllers

    Science.gov (United States)

    Kumar, Sanjiv; Kumar, Narendra

    2017-06-01

    In this work, supplementary sub-synchronous damping controllers (SSDC) are proposed for damping sub-synchronous oscillations in power systems with series compensated transmission lines. Series compensation have extensively been used as effective means of increasing the power transfer capability of a transmission lines and improving transient stability limits of power systems. Series compensation with transmission lines may cause sub-synchronous resonance (SSR). The eigenvalue investigation tool is used to ascertain the existence of SSR. It is shown that the addition of supplementary controller is able to stabilize all unstable modes for T-network model. Eigenvalue investigation and time domain transient simulation of detailed nonlinear system are considered to investigate the performance of the controllers. The efficacies of the suggested supplementary controllers are compared on the IEEE first benchmark model for computer simulations of SSR by means of time domain simulation in Matlab/Simulink environment. Supplementary SSDC are considered in order to compare effectiveness of SSDC during higher loading in alleviating the small signal stability problem.

  1. Global dimming and urbanization: did stronger negative SSR trends collocate with regions of population growth?

    Directory of Open Access Journals (Sweden)

    A. Imamovic

    2015-11-01

    Full Text Available Global dimming refers to the decrease in surface solar radiation (SSR observed from the 1960s to the 1980s at different measurement sites all around the world. It is under debate whether anthropogenic aerosols emitted from urban areas close to the measurement sites are mainly responsible for the dimming. In order to assess this urbanization impact on SSR, we use spatially explicit population density data of 0.08° resolution to construct population indices (PI at 157 high data quality sites. Our study extends previous population-based studies by incorporating distance-weighting as a simple aerosol diffusion model. We measured urbanization in the surrounding of a site as the PI change form 1960 to 1990 and found no negative correlation with the corresponding SSR trends from 1964 to 1989 for the 92 sites in Europe and Japan. For the 39 sites in China the correlation coefficients are significant at the 5 % level and reach around −0.35, while for the 26 remaining Asian, mostly Russian sites the correlation coefficients reach around −0.55 at the 1 % significance level. Results are similar, when the absolute levels of PIs are taken as an indicator for urbanization. Our findings call into question the existence of an urbanization effect for the sites in Europe and Japan, while such an effect cannot be ruled out for the sites in Asia, especially in Russia.

  2. Global dimming and urbanization: did stronger negative SSR trends collocate with regions of population growth?

    Science.gov (United States)

    Imamovic, Adel; Tanaka, Katsumasa; Folini, Doris; Wild, Martin

    2016-04-01

    Global dimming refers to the decrease in surface solar radiation (SSR) observed from the 1960s to the 1980s at different measurement sites all around the world. It is under debate whether anthropogenic aerosols emitted from urban areas close to the measurement sites are mainly responsible for the dimming. In order to assess this urbanization impact on SSR, we use spatially explicit population density data of 0.08° resolution to construct population indices (PI) at 157 high data quality sites. Our study extends previous population-based studies by incorporating distance-weighting as a simple aerosol diffusion model. We measured urbanization in the surrounding of a site as the PI change form 1960 to 1990 and found no negative correlation with the corresponding SSR trends from 1964 to 1989 for the 92 sites in Europe and Japan. For the 39 sites in China the correlation coefficients are significant at the 5 % level and reach around -0.35, while for the 26 remaining Asian, mostly Russian sites the correlation coefficients reach around -0.55 at the 1 % significance level. Results are similar, when the absolute levels of PIs are taken as an indicator for urbanization. Our findings call into question the existence of an urbanization effect for the sites in Europe and Japan, while such an effect cannot be ruled out for the sites in Asia, especially in Russia.

  3. Development of SSR markers from ESTs of gramineous species and their chromosome location on wheat

    Institute of Scientific and Technical Information of China (English)

    Linzhi Li; Sishen Li; Junjun Wang; Ying Guo; Fangshan Jiang; Yunfeng Xu; Yingying Wang; Haitao Pan; Guanzhu Han; Ruijun Li

    2008-01-01

    A total of 407,663 expressed sequence tags (ESTs) of wheat,barley,maize,rice,and sorghum,obtained from GenBank/dbEST,were used to search for simple sequence repeats (SSRs).A total of 10,253 EST-SSRs,which accounted for 2.52% of all the ESTs,were iden-tiffed.Using Primer Premier 5.0,1367 EST-SSR primer pairs were designed,of which 715 with high quality were synthesized.The 715 primer pairs were tested on wheat,rice,maize,cotton,and soybean under the same PCR conditions,and the effective primer pairs in the five crops were 500 (69.93%),383 (53.57%),452 (63.22%),357 (49.93%),and 388 (56.27%),respectively.This indicated a high transfer-ability of EST-SSR markers between far-ranging species.In addition,139 EST-SSR primer pairs with 240 loci were localized on all the 21 wheat chromosomes by using Chinese Spring nulli-tetrasomic lines of wheat.

  4. Optimizing SSR-PCR system of Panax ginseng by orthogonal design

    Institute of Scientific and Technical Information of China (English)

    YANG Tian-tian; MU Li-qiang; WANG Jun

    2007-01-01

    An orthogonal design was used to optimize SSR-PCR amplification system using Panax ginseng genomic DNA as template. Four levels of five factors (DNA template, Taq DNA polymerase, Mg2+, primer, and dNTP) and annealing temperature have been tested separately in this system. The results demonstrated the reaction efficiency was affected by these factors. Based on the results, a stable, productive and reproducible PCR system and cycling program for amplifying a ginseng SSR locus were obtained: 20 μL system containing 1.0 U Taq DNA polymerase, 2.0 mmol·L-1 Mg2+, 0.2 mmol· L-1 dNTPs, 0.3 μmol· L-1 SSR primer, 60 ng·μL-1 DNA template, performed with a program of 94℃ for 5 min, 94℃ for 30 s, annealing at 56.3℃ for 30 s, 72℃ for 1 min, 37 cycles, finishing at 72℃ for 7 min, and storing at 4℃.

  5. Confirmation of root-knot nematode resistant gene Rmi1 using SSR markers

    Directory of Open Access Journals (Sweden)

    Musarrat Ramzan

    2017-02-01

    Full Text Available Background: The Root Knot Nematode (RKN is a serious economic threat to various cultivated crops worldwide. It is a devastating pest of soybean and responsible to cause severe yield loss in Pakistan. The cultivation of resistant soybean varieties against this pest is the sustainable strategy to manage the heavy loss and increase yield. There is an utmost need to identify RKN resistant varieties of soybean against cultivated in Pakistan. The presented study is an attempt to identify and confirm the presence of resistant gene Rmi1 in soybean. Method: Molecular studies have been done using Simple Sequence Repeat (SSR marker system to identify resistant soybean varieties against Root Knot Nematode (RKN using fifteen (15 indigenous cultivars and four (4 US cultivars. DNA was isolated, purified, quantified and then used to employ various SSR markers. The amplified product is observed using gel documentation system after electrophoresis. Results: Diagnostic SSR markers Satt-358 and Satt-492 have shown the presence of Rmi1 gene in all resistance carrying genotypes. Satt-358 amplified the fragment of 200 bp and Satt-492 generated 232 bp bands in all resistant genotypes. This study confirmed the Rmi gene locus (G248A-1 in all internationally confirmed resistant including six (6 native varieties. Conclusion: These investigations have identified six (6 resistant cultivars revealing the effective and informative sources that can be utilized in breeding programs for the selection of RKN resistance soybean genotypes in Pakistan.

  6. Phylogenetic analysis of Mexican Babesia bovis isolates using msa and ssrRNA gene sequences.

    Science.gov (United States)

    Genis, Alma D; Mosqueda, Juan J; Borgonio, Verónica M; Falcón, Alfonso; Alvarez, Antonio; Camacho, Minerva; de Lourdes Muñoz, Maria; Figueroa, Julio V

    2008-12-01

    Variable merozoite surface antigens of Babesia bovis are exposed glycoproteins having a role in erythrocyte invasion. Members of this gene family include msa-1 and msa-2 (msa-2c, msa-2a(1), msa-2a(2), and msa-2b). Small subunit ribosomal (ssr)RNA gene is subject to evolutive pressure and has been used in phylogenetic studies. To determine the phylogenetic relationship among B. bovis Mexican isolates using different genetic markers, PCR amplicons, corresponding to msa-1, msa-2c, msa-2b, and ssrRNA genes, were cloned and plasmids carrying the corresponding inserts were sequenced. Comparative analysis of nucleotide and deduced amino acid sequences revealed distinct degrees of variability and identity among the coding gene sequences obtained from 12 geographically different B. bovis isolates and a reference strain. Overall sequence identities of 47.7%, 72.3%, 87.7%, and 94% were determined for msa-1, msa-2b, msa-2c, and ssrRNA, respectively. A robust phylogenetic tree was obtained with msa-2b sequences. The phylogenetic analysis suggests that Mexican B. bovis isolates group in clades not concordant with the Mexican geography. However, the Mexican isolates group together in an American clade separated from the Australian clade. Sequence heterogeneity in msa-1, msa-2b, and msa-2c coding regions of Mexican B. bovis isolates present in different geographical regions can be a result of either differential evolutive pressure or cattle movement from commercial trade.

  7. AN AZERBAIDZHAN SSR. INSTITUTE OF ADDITIVE CHEMISTRY ADDITIVES TO LUBRICATING OILS. PROBLEMS OF SYNTHESIS, INVESTIGATION AND USE OF OIL ADDITIVES; FUELS AND POLYMER MATERIALS (SELECTED ARTICLES),

    Science.gov (United States)

    An Azerbaidzhan SSR. Institute of additive chemistry additives to lubricating oils . Problems of synthesis, investigation and use of oil additives; fuels and polymer materials (Selected articles)--Translation.

  8. Russian Kandidat Nauk Dissertation Reviewing Mode and Its Referable Experience%俄罗斯副博士学位论文评阅模式及其合理借鉴

    Institute of Scientific and Technical Information of China (English)

    黄思记; 李申申

    2016-01-01

    博士学位论文的评阅与审核是保障研究生教育质量的重要环节。俄罗斯副博士学位论文评阅模式颇具特色,其突出特点表现为正式评阅与非正式评阅相结合、评阅人与评阅单位相结合、非匿名的全参照评阅等。受其启发,我们宜从建立多主体参与的评阅机制、加强评阅人与申请者之间的互动、尝试采用非匿名全参照评价方式等方面改进我国博士学位论文评阅制度,提高博士生教育质量。%The process of reviewing and approval of doctoral dissertation is a key link to ensure the quality of postgraduate education .The reviewing mode of Russian Kandidat Nauk doctoral dissertation is quite distinctive . It features a non-anonymous ,all-reference reviewing process characterized by collaborative formal and informal readings with the participation of reviewers and reviewing units . Inspired thereby , the authors of this paper suggest that a reviewing mechanism with a participation of more parties be established to strength interaction between the reviewer and degree applicants ,and that the non-anonymous ,all-reference reviewing method be adopted to improve the doctoral dissertation reviewing system and enhance Ph . D .student education quality in China .

  9. Expressed Sequence Tag-Simple Sequence Repeat (EST-SSR Marker Resources for Diversity Analysis of Mango (Mangifera indica L.

    Directory of Open Access Journals (Sweden)

    Natalie L. Dillon

    2014-01-01

    Full Text Available In this study, a collection of 24,840 expressed sequence tags (ESTs generated from five mango (Mangifera indica L. cDNA libraries was mined for EST-based simple sequence repeat (SSR markers. Over 1,000 ESTs with SSR motifs were detected from more than 24,000 EST sequences with di- and tri-nucleotide repeat motifs the most abundant. Of these, 25 EST-SSRs in genes involved in plant development, stress response, and fruit color and flavor development pathways were selected, developed into PCR markers and characterized in a population of 32 mango selections including M. indica varieties, and related Mangifera species. Twenty-four of the 25 EST-SSR markers exhibited polymorphisms, identifying a total of 86 alleles with an average of 5.38 alleles per locus, and distinguished between all Mangifera selections. Private alleles were identified for Mangifera species. These newly developed EST-SSR markers enhance the current 11 SSR mango genetic identity panel utilized by the Australian Mango Breeding Program. The current panel has been used to identify progeny and parents for selection and the application of this extended panel will further improve and help to design mango hybridization strategies for increased breeding efficiency.

  10. Genetic structure and distribution of pythium aphanidermatum populations in Pennsylvania greenhouses based on analysis of AFLP and SSR markers.

    Science.gov (United States)

    Lee, Seonghee; Garzón, Carla D; Moorman, Gary W

    2010-01-01

    Pythium aphanidermatum is one of the most aggressive species in the genus and has a wide host range, but little is known about its population genetic structure. We tested 123 P. aphanidermatum isolates with six AFLP primer combinations and four SSR markers. The genetic diversity of P. aphanidermatum was 0.34 with AFLP and 0.55 with SSR markers. SSR genotypes totaled 3-8 for each locus, and a total of 14 SSR genotypes were found among all isolates. Three major genetic groups were identified with the combination of AFLP and SSR marker data. The genetic structure observed among P. aphanidermatum isolates was related to location and mefenoxam fungicide resistance instead of host. Four genotypes (PA1, PA2, PA5 and PA7) were found in the population from a commercial greenhouse, and the genetic diversity of a greenhouse population was similar to that found in the whole sample. The molecular tools for P. aphanidermatum isolates identified the possible gene flow within and among populations in Pennsylvania greenhouses.

  11. Development of Soybean EST-SSR Markers and Their Use to Assess Genetic Diversity in the Subgenus Soja

    Institute of Scientific and Technical Information of China (English)

    LIU Yu-lin; LI Ying-hui; ZHOU Guo-an; Uzokwe N; CHANG Ru-zhen; CHEN Shou-yi; QIU Li-juan

    2010-01-01

    Developing expressed sequence tag-derived SSR (EST-SSR) markers is imperative in genetic research. In this paper, we reported 37 EST-SSR markers which were developed from 286 unigenes obtained from soybean eDNA library. Among the 286 markers designed for the 4 accessions of Glycine max and 6 of its wild progenitor (G. soja) within the subgenus Soja,209 markers amplified DNA fragments, taking 73.1% and 37 markers appeared to be polymorphic, which was 12.9% of the total. The 37 loci detected a total of 142 alleles, while the PIC values varied from 0.194 to 0.794. Both the number of alleles per locus and PIC value were significantly related to the SSR motif. Six EST-SSR loci may be fixed for different alleles between G. max and G. soja since they were particularly polymorphic among the 6 G. soja accessions. A neighbor-joining tree placed the G. max accessions together as a group within the G. soja, though the average genetic distance among G. soja accessions was much higher. These new EST-SSRs markers will be useful for genetic diversity analysis, genetic mapping construction and gene discovery in Soja subgenus.

  12. Analysis of Genetic Diversity in Cultivated and Wild Tomato Varieties in Chinese Market by RAPD and SSR

    Institute of Scientific and Technical Information of China (English)

    MENG Fan-juan; XU Xiang-yang; HUANG Feng-lan; LI Jing-fu

    2010-01-01

    RAPD and SSR were applied to assess genetic diversity in 61 tomato varieties from different species (Solanum lycopersicum L.,hirsutum.Humb L.,pimpinellifolium Miller L.,chilense Dun.L.,chmielenskii L.,peruvianum Miller L.,parvuflorum Miller L.).2062 and 869 clear fragments were amplified by RAPD and SSR,respectively.On the other hand,more polymorphic products were found by SSR as compared to RAPD,i.e.,100 and 43.84%,respectively.In addition,a higher value of the average similarity coefficient and lower PIC value were reflected in RAPD (0.79,0.407) compared to SSR (0.56,0.687).It can be inferred that SSR was a higher effective marker than RAPD to assess genetic diversity in tomato accessions.Similarly,the genetic base of tomato varieties in Chinese market was narrow.It is suggested that wild tomato varieties should be used to enrich the genetic base of the cultivated tomato varieties.

  13. Association analysis of grain traits with SSR markers between Aegilops tauschii and hexaploid wheat (Triticum aestivumL.)

    Institute of Scientific and Technical Information of China (English)

    ZHAO Jing-lan; WANG Hong-wei; ZHANG Xiao-cun; DU Xu-ye; LI An-fei; KONG Ling-rang

    2015-01-01

    Seven important grain traits, including grain length (GL), grain width (GW), grain perimeter (GP), grain area (GA), grain length/width ratio (GLW), roundness (GR), and thousand-grain weight (TGW), were analyzed using a set of 139 simple sequence repeat (SSR) markers in 130 hexaploid wheat varieties and 193Aegilops tauschiaccessions worldwide. In total, 1612 aleles inAe. tauschiand 1360 aleles in hexaploid wheat (Triticum aestivumL.) were detected throughout the D genome. 197 marker-trait associations inAe. tauschi were identiifed with 58 different SSR loci in 3 environments, and the average phenotypic variation value (R2) ranged from 0.68 to 15.12%. In contrast, 208 marker-trait associations were identiifed in wheat with 66 different SSR markers in 4 environments and the average phenotypicR2ranged from 0.90 to 19.92%. Further analysis indicated that there are 6 common SSR loci present in bothAe. tauschi and hexaploid wheat, which are signiifcantly associated with the 5 investigated grain traits (i.e., GA, GP, GR, GL, and TGW) and in total, 16 aleles derived from the 6 aforementioned SSR loci were shared byAe. tauschi and hexaploid wheat. These preliminary data suggest the existence of common aleles may explain the evolutionary process and the selection betweenAe. tauschi and hexaploid wheat. Furthermore, the genetic differentiation of grain shape and thousand-grain weight were observed in the evolutionary developmental process fromAe. tauschi to hexaploid wheat.

  14. Elaeis oleifera genomic-SSR markers: exploitation in oil palm germplasm diversity and cross-amplification in arecaceae.

    Science.gov (United States)

    Zaki, Noorhariza Mohd; Singh, Rajinder; Rosli, Rozana; Ismail, Ismanizan

    2012-01-01

    Species-specific simple sequence repeat (SSR) markers are favored for genetic studies and marker-assisted selection (MAS) breeding for oil palm genetic improvement. This report characterizes 20 SSR markers from an Elaeis oleifera genomic library (gSSR). Characterization of the repeat type in 2000 sequences revealed a high percentage of di-nucleotides (63.6%), followed by tri-nucleotides (24.2%). Primer pairs were successfully designed for 394 of the E. oleifera gSSRs. Subsequent analysis showed the ability of the 20 selected E. oleifera gSSR markers to reveal genetic diversity in the genus Elaeis. The average Polymorphism Information Content (PIC) value for the SSRs was 0.402, with the tri-repeats showing the highest average PIC (0.626). Low values of observed heterozygosity (H(o)) (0.164) and highly positive fixation indices (F(is)) in the E. oleifera germplasm collection, compared to the E. guineensis, indicated an excess of homozygosity in E. oleifera. The transferability of the markers to closely related palms, Elaeis guineensis, Cocos nucifera and ornamental palms is also reported. Sequencing the amplicons of three selected E. oleifera gSSRs across both species and palm taxa revealed variations in the repeat-units. The study showed the potential of E. oleifera gSSR markers to reveal genetic diversity in the genus Elaeis. The markers are also a valuable genetic resource for studying E. oleifera and other genus in the Arecaceae family.

  15. Elaeis oleifera Genomic-SSR Markers: Exploitation in Oil Palm Germplasm Diversity and Cross-Amplification in Arecaceae

    Directory of Open Access Journals (Sweden)

    Ismanizan Ismail

    2012-03-01

    Full Text Available Species-specific simple sequence repeat (SSR markers are favored for genetic studies and marker-assisted selection (MAS breeding for oil palm genetic improvement. This report characterizes 20 SSR markers from an Elaeis oleifera genomic library (gSSR. Characterization of the repeat type in 2000 sequences revealed a high percentage of di-nucleotides (63.6%, followed by tri-nucleotides (24.2%. Primer pairs were successfully designed for 394 of the E. oleifera gSSRs. Subsequent analysis showed the ability of the 20 selected E. oleifera gSSR markers to reveal genetic diversity in the genus Elaeis. The average Polymorphism Information Content (PIC value for the SSRs was 0.402, with the tri-repeats showing the highest average PIC (0.626. Low values of observed heterozygosity (Ho (0.164 and highly positive fixation indices (Fis in the E. oleifera germplasm collection, compared to the E. guineensis, indicated an excess of homozygosity in E. oleifera. The transferability of the markers to closely related palms, Elaeis guineensis, Cocos nucifera and ornamental palms is also reported. Sequencing the amplicons of three selected E. oleifera gSSRs across both species and palm taxa revealed variations in the repeat-units. The study showed the potential of E. oleifera gSSR markers to reveal genetic diversity in the genus Elaeis. The markers are also a valuable genetic resource for studying E. oleifera and other genus in the Arecaceae family.

  16. Molecular Assortment of Lens Species with Different Adaptations to Drought Conditions Using SSR Markers.

    Directory of Open Access Journals (Sweden)

    Dharmendra Singh

    Full Text Available The success of drought tolerance breeding programs can be enhanced through molecular assortment of germplasm. This study was designed to characterize molecular diversity within and between Lens species with different adaptations to drought stress conditions using SSR markers. Drought stress was applied at seedling stage to study the effects on morpho-physiological traits under controlled condition, where tolerant cultivars and wilds showed 12.8-27.6% and 9.5-23.2% reduction in seed yield per plant respectively. When juxtaposed to field conditions, the tolerant cultivars (PDL-1 and PDL-2 and wild (ILWL-314 and ILWL-436 accessions showed 10.5-26.5% and 7.5%-15.6% reduction in seed yield per plant, respectively under rain-fed conditions. The reductions in seed yield in the two tolerant cultivars and wilds under severe drought condition were 48-49% and 30.5-45.3% respectively. A set of 258 alleles were identified among 278 genotypes using 35 SSR markers. Genetic diversity and polymorphism information contents varied between 0.321-0.854 and 0.299-0.836, with mean value of 0.682 and 0.643, respectively. All the genotypes were clustered into 11 groups based on SSR markers. Tolerant genotypes were grouped in cluster 6 while sensitive ones were mainly grouped into cluster 7. Wild accessions were separated from cultivars on the basis of both population structure and cluster analysis. Cluster analysis has further grouped the wild accessions on the basis of species and sub-species into 5 clusters. Physiological and morphological characters under drought stress were significantly (P = 0.05 different among microsatellite clusters. These findings suggest that drought adaptation is variable among wild and cultivated genotypes. Also, genotypes from contrasting clusters can be selected for hybridization which could help in evolution of better segregants for improving drought tolerance in lentil.

  17. Molecular Assortment of Lens Species with Different Adaptations to Drought Conditions Using SSR Markers.

    Science.gov (United States)

    Singh, Dharmendra; Singh, Chandan Kumar; Tomar, Ram Sewak Singh; Taunk, Jyoti; Singh, Ranjeet; Maurya, Sadhana; Chaturvedi, Ashish Kumar; Pal, Madan; Singh, Rajendra; Dubey, Sarawan Kumar

    2016-01-01

    The success of drought tolerance breeding programs can be enhanced through molecular assortment of germplasm. This study was designed to characterize molecular diversity within and between Lens species with different adaptations to drought stress conditions using SSR markers. Drought stress was applied at seedling stage to study the effects on morpho-physiological traits under controlled condition, where tolerant cultivars and wilds showed 12.8-27.6% and 9.5-23.2% reduction in seed yield per plant respectively. When juxtaposed to field conditions, the tolerant cultivars (PDL-1 and PDL-2) and wild (ILWL-314 and ILWL-436) accessions showed 10.5-26.5% and 7.5%-15.6% reduction in seed yield per plant, respectively under rain-fed conditions. The reductions in seed yield in the two tolerant cultivars and wilds under severe drought condition were 48-49% and 30.5-45.3% respectively. A set of 258 alleles were identified among 278 genotypes using 35 SSR markers. Genetic diversity and polymorphism information contents varied between 0.321-0.854 and 0.299-0.836, with mean value of 0.682 and 0.643, respectively. All the genotypes were clustered into 11 groups based on SSR markers. Tolerant genotypes were grouped in cluster 6 while sensitive ones were mainly grouped into cluster 7. Wild accessions were separated from cultivars on the basis of both population structure and cluster analysis. Cluster analysis has further grouped the wild accessions on the basis of species and sub-species into 5 clusters. Physiological and morphological characters under drought stress were significantly (P = 0.05) different among microsatellite clusters. These findings suggest that drought adaptation is variable among wild and cultivated genotypes. Also, genotypes from contrasting clusters can be selected for hybridization which could help in evolution of better segregants for improving drought tolerance in lentil.

  18. SSR marker variations in Brassica species provide insight into the origin and evolution of Brassica amphidiploids.

    Science.gov (United States)

    Thakur, Ajay Kumar; Singh, Kunwar Harendra; Singh, Lal; Nanjundan, Joghee; Khan, Yasin Jeshima; Singh, Dhiraj

    2018-01-01

    Oilseed Brassica represents an important group of oilseed crops with a long history of evolution and cultivation. To understand the origin and evolution of Brassica amphidiploids, simple sequence repeat (SSR) markers were used to unravel genetic variations in three diploids and three amphidiploid Brassica species of U's triangle along with Eruca sativa as an outlier. Of 124 Brassica-derived SSR loci assayed, 100% cross-transferability was obtained for B. juncea and three subspecies of B. rapa, while lowest cross-transferability (91.93%) was obtained for Eruca sativa. The average % age of cross-transferability across all the seven species was 98.15%. The number of alleles detected at each locus ranged from one to six with an average of 3.41 alleles per primer pair. Neighbor-Joining-based dendrogram divided all the 40 accessions into two main groups composed of B. juncea/B. nigra/B. rapa and B. carinata/B. napus/B. oleracea. C-genome of oilseed Brassica species remained relatively more conserved than A- and B-genome. A- genome present in B. juncea and B. napus seems distinct from each other and hence provides great opportunity for generating diversity through synthesizing amphidiploids from different sources of A- genome. B. juncea had least intra-specific distance indicating narrow genetic base. B. rapa appears to be more primitive species from which other two diploid species might have evolved. The SSR marker set developed in this study will assist in DNA fingerprinting of various Brassica species cultivars, evaluating the genetic diversity in Brassica germplasm, genome mapping and construction of linkage maps, gene tagging and various other genomics-related studies in Brassica species. Further, the evolutionary relationship established among various Brassica species would assist in formulating suitable breeding strategies for widening the genetic base of Brassica amphidiploids by exploiting the genetic diversity present in diploid progenitor gene pools.

  19. Genetic diversity among some canola cultivars as revealed by RAPD, SSR and AFLP analyses.

    Science.gov (United States)

    Moghaieb, Reda E A; Mohammed, Etr H K; Youssief, Sawsan S

    2014-08-01

    To assess the genetic diversity among four canola cultivars (namely, Serw-3, Serw-4, Misser L-16 and Semu 249), random amplified polymorphic DNA (RAPD), simple sequence repeat polymorphism (SSR) and amplified fragment length polymorphism (AFLP) analyses were performed. The data indicated that all of the three molecular markers gave different levels of polymorphism. A total of 118, 31 and 338 markers that show 61, 67.7 and 81 % polymorphism percentages were resulted from the RAPD, SSR and AFLP analyses, respectively. Based on the data obtained the three markers can be used to differentiate between the four canola cultivars. The genotype-specific markers were determined, 18 out of the 72 polymorphic RAPD markers generated were found to be genotype-specific (25 %). The highest number of RAPD specific markers was scored for Semu 249 (15 markers), while Serw-4 scored two markers. On the other hand, Serw-3 scored one marker. The cultivar Semu 249 scored the highest number of unique AFLP markers, giving 57 unique markers, followed by Misser L-16 which was characterized by 40 unique AFLP markers, then Serw-3 giving 31 unique markers. While Serw-4 was characterized by the lowest number producing 14 unique positive markers. The dendrogram built on the basis of combined data from RAPD, SSR and AFLP analysis represents the genetic distances among the four canola cultivars. Understanding the genetic variability among the current canola cultivars opens up a possibility for developing a molecular genetic map that will lead to the application of marker-assisted selection tools in genetic improvement of canola.

  20. Analysis of genetic relationship among Arbutus unedo L.genotypes using RAPD and SSR markers

    Institute of Scientific and Technical Information of China (English)

    Filomena Gomes; Rita Costa; Maria M.Ribeiro; Elisa Figueiredo; Jorge M.Canhoto

    2013-01-01

    The strawberry tree (Arbutus unedo L.) is an underutilized,drought tolerant,fire resistant species with a south western distribution in Europe,and with ecological and putative socio-economical impact in Portugal and Mediterranean countries.Our aim was to develop an appropriate set of molecular markers to enable genetic diversity to be assessed and to fingerprint Arbutus unedo genotypes for breeding and conservation purposes in Portugal.Twenty-seven trees from a broad geographic range were screened with 20 random amplified polymorphic DNA(RAPD primers) and 11 microsatellite markers (SSR).The RAPDs generated 124 bands,57.3% of which were polymorphic,with an expected heterozygosity of 27%.We cross-amplified 11 SSR primers developed for Vaccinium spp.,and 5 were found to be polymorphic in A.unedo,with 75% of expected heterozygosity,a number of alleles of 11.6,a null allele frequency of 7.6% and a polymorphic information content of 71%.Although the SSRs were more polymorphic and informative than the RAPDs,both markers displayed high genetic variability with the gathered data.No geographic pattern was observed in the genetic variation distribution based on both marker systems,and the lack of correlation between genetic and geographical matrices was confirmed by Mantel tests.Likely,no correlation was found between pairwise SSR and RAPD band-sharing matrices.These results and their implications on A.unedo breeding and conservation programs are discussed.

  1. Desenho e validação de iniciadores microssatélites SSR para mamoneira

    Directory of Open Access Journals (Sweden)

    Edna Lôbo Machado

    2013-11-01

    Full Text Available O objetivo deste trabalho foi desenhar, validar e otimizar pares de iniciadores microssatélites SSR para mamoneira. O desenho dos pares de iniciadores foi feito por meio do aplicativo Websat, a partir de sequências depositadas no GenBank do National Center for Biotechnology Information (GenBank/NCBI, e a sua qualidade foi aferida com uso do aplicativo web NetPrimer. Foram utilizadas diferentes concentrações de DNA, cloreto de magnésio, pares de iniciadores, dNTPs e temperatura de anelamento para otimização das condições de PCR. Um total de 30 pares de iniciadores SSR foi desenhado, sintetizado e otimizado. O gel de agarose foi utilizado para detecção dos produtos amplificados, e o gel desnaturante de poliacrilamida, na otimização das condições de PCR e na identificação de polimorfismo. Os pares de iniciadores apresentaram percentagem média de guanina/citosina (GC igual a 47,29% e produtos amplificados com tamanhos entre 128 e 381 pb. Vinte e nove pares de iniciadores SSR (96,7% foram validados, dos quais nove foram polimórficos (23,3%. As concentrações otimizadas para amplificação são: DNA, 25 ng; cloreto de magnésio, 1,2 mmol L-1; iniciadores Forward e Reverse, 0,4 mmol L-1; dNTPs, 0,1 mmol L-1; e temperatura de anelamento, 62 a 64ºC. As ferramentas de bioinformática Websat e Net Primer podem ser utilizadas para desenvolver iniciadores microssatélites de qualidade, para a mamoneira, a partir de sequências depositadas no GenBank/NCBI.

  2. Characterization and Development of EST-SSR Markers Derived from Transcriptome of Yellow Catfish

    Directory of Open Access Journals (Sweden)

    Jin Zhang

    2014-10-01

    Full Text Available Yellow catfish (Pelteobagrus fulvidraco is one of the most important freshwater fish due to its delicious flesh and high nutritional value. However, lack of sufficient simple sequence repeat (SSR markers has hampered the progress of genetic selection breeding and molecular research for yellow catfish. To this end, we aimed to develop and characterize polymorphic expressed sequence tag (EST–SSRs from the 454 pyrosequencing transcriptome of yellow catfish. Totally, 82,794 potential EST-SSR markers were identified and distributed in the coding and non-coding regions. Di-nucleotide (53,933 is the most abundant motif type, and AC/GT, AAT/ATT, AAAT/ATTT are respective the most frequent di-, tri-, tetra-nucleotide repeats. We designed primer pairs for all of the identified EST-SSRs and randomly selected 300 of these pairs for further validation. Finally, 263 primer pairs were successfully amplified and 57 primer pairs were found to be consistently polymorphic when four populations of 48 individuals were tested. The number of alleles for the 57 loci ranged from 2 to 17, with an average of 8.23. The observed heterozygosity (HO, expected heterozygosity (HE, polymorphism information content (PIC and fixation index (fis values ranged from 0.04 to 1.00, 0.12 to 0.92, 0.12 to 0.91 and −0.83 to 0.93, respectively. These EST-SSR markers generated in this study could greatly facilitate future studies of genetic diversity and molecular breeding in yellow catfish.

  3. Chromosomal location of genomic SSR markers associated with yellow rust resistance in Turkish bread wheat (Triticum aestivum L.)

    Indian Academy of Sciences (India)

    F. Senturk Akfirat; F. Ertugrul; S. Hasancebi; Y. Aydin; K. Akan; Z. Mert; M. Cakir; A. Altinkut Uncuoglu

    2013-08-01

    We have previously reported Xgwm382 as a diagnostic marker for disease resistance against yellow rust in Izgi2001 × ES14 F2 population. Among the same earlier tested 230 primers, one SSR marker (Xgwm311) also amplified a fragment which is present in the resistant parent and in the resistant bulks, but absent in the susceptible parent and in the susceptible bulks. To understand the chromosome group location of these diagnostic markers, Xgwm382 and Xgwm311, in the same population, we selected 16 SSR markers mapped only in one genome of chromosome group 2 around 1–21 cM distance to these diagnostic markers based on the SSR consensus map of wheat. Out of 16 SSRs, Xwmc658 identified resistant F2 individuals as a diagnostic marker for yellow rust disease and provided the location of Xgwm382 and Xgwm311 on chromosome 2AL in our plant material.

  4. Genetic Diversity and Fingerprint Profiles of Commercial Lentinula edodes Cultivars Based on SSR Markers Developed from the Whole Genome Sequence

    Institute of Scientific and Technical Information of China (English)

    ZHANG Dan; SONG Chunyan; ZHANG Lujun; WU Ping; BAO Dapeng; SHANG Xiaodong; TAN Qi

    2014-01-01

    Lentinula edodes is an important cultivated mushroom in China, and accurate and reliable identification of individual cultivars is a prerequisite for successful cultivation and variety protection.In this study,the whole genome sequence of L.edodes was used to generate 200 simple sequence repeat (SSR) markers for delineating 25 commercial cultivars and for determining their genetic diversity.Our data revealed a relatively high level of genetic similarity among the cultivars,with average,minimum and maximum genetic similarity coefficient values of 0.776,0.567 and 1.000,respectively.Seven SSR primer pairs delineated eleven of the cultivars (Cr-02,Minfeng-1,Xianggu 241-4,Senyuan-1,Senyuan-8404,Xiang-9,Guangxiang-51,Huaxiang-5,L952,L9319 and L808)based on their unique multilocus SSR fingerprint profiles.

  5. Genetic Diversity of Chinese Temperate and Exotic Tropical,Subtropical Quality Protein Maize Inbreds by SSR Markers

    Institute of Scientific and Technical Information of China (English)

    FAN Xing-ming; TAN Jing; LI Ming-shun; YANG Jun-yun; CHEN Hong-mei

    2004-01-01

    Information on genetic relationship is of great value to maize (Zea mays L.) breeding. The objectives of this study were: 1) to classify 22 quality protein maize (QPM) inbreds into different groups by using simple sequence repeats (SSR) markers, which included exotic tropical, subtropical and domestic temperate QPM and normal maize inbreds; 2) to examine the consistency of grouping results obtained from SSR, specific combining ability (SCA) analysis,and genetic backgrounds of these inbreds. A set of 39 polymorphic SSR primers was selected from 70 primer pairs, which detected 136 alleles among the 22 lines. The mean polymorphism information content was 0.55. Based on analysis of genetic similarities, five groups were identified including Luda Red Cob, Sipingtou, Reid, Lancaster and a miscellaneous group with several tropical inbreds which could not be classified into the above four groups. The results generally agreed with previous results based on analysis of yield combining ability and pedigree data.

  6. Development of SSR Markers for a Phytopathogenic Fungus, Blumeria graminis f.sp. tritici, Using a FIASCO Protocol

    Institute of Scientific and Technical Information of China (English)

    WANG Meng; XUE Fei; YANG Peng; DUAN Xia-yu; ZHOU Yi-lin; SHEN Chong-yao; ZHANG Guo-zhen; WANG Bao-tong

    2014-01-01

    Simple sequence repeats (SSR) have been widely used as molecular markers due to their abundance and high polymorphism. However, up to now, the SSR markers had not been developed in the obligate biotrophic phytopathogenic fungus, Blumeria graminis f.sp. tritici. From (AC)10 and (AG)10 enriched genomic libraries for Bgt, 25 primer pairs were designed using the FIASCO (fast isolation by AFLP of sequences containing repeats) protocol. Five primer pairs exhibited polymorphism with allelic diversity from two to seven alleles and produced 29 alleles in a survey of 90 isolates collected from six provinces (cities) in China, while the others displayed monomorphic. Levels of observed heterozygosity ranged from 0.000-0.044 (mean 0.025) and expected heterozygosity ranged from 0.297-0.816 (mean 0.538). These molecular markers provide a novel source to genetic diversity assays and to genetic and physical mapping of Bgt. SSR markers of Bgt need to be further explored.

  7. Confamiliar transferability of simple sequence repeat (SSR) markers from cotton (Gossypium hirsutum L.) and jute (Corchorus olitorius L.) to twenty two Malvaceous species.

    Science.gov (United States)

    Satya, Pratik; Paswan, Pramod Kumar; Ghosh, Swagata; Majumdar, Snehalata; Ali, Nasim

    2016-06-01

    Cross-species transferability is a quick and economic method to enrich SSR database, particularly for minor crops where little genomic information is available. However, transferability of SSR markers varies greatly between species, genera and families of plant species. We assessed confamiliar transferability of SSR markers from cotton (Gossypium hirsutum) and jute (Corchorus olitorius) to 22 species distributed in different taxonomic groups of Malvaceae. All the species selected were potential industrial crop species having little or no genomic resources or SSR database. Of the 14 cotton SSR loci tested, 13 (92.86 %) amplified in G. arboreum and 71.43 % exhibited cross-genera transferability. Nine out of 11 jute SSRs (81.81 %) showed cross-transferability across genera. SSRs from both the species exhibited high polymorphism and resolving power in other species. The correlation between transferability of cotton and jute SSRs were highly significant (r = 0.813). The difference in transferability among species was also significant for both the marker groups. High transferability was observed at genus, tribe and subfamily level. At tribe level, transferability of jute SSRs (41.04 %) was higher than that of cotton SSRs (33.74 %). The tribe Byttnerieae exhibited highest SSR transferability (48.7 %). The high level of cross-genera transferability (>50 %) in ten species of Malvaceae, where no SSR resource is available, calls for large scale transferability testing from the enriched SSR databases of cotton and jute.

  8. Changes in allelic frequency over time in European bread wheat (Triticum aestivum L.) varieties revealed using DArT and SSR markers

    DEFF Research Database (Denmark)

    Orabi, Jihad; Jahoor, Ahmed; Backes, Gunter Martin

    2014-01-01

    A collection of 189 bread wheat landraces and cultivars, primarily of European origin, released between 1886 and 2009, was analyzed using two DNA marker systems. A set of 76 SSR markers and ~7,000 DArT markers distributed across the wheat genome were employed in these analyses. All of the SSR mar...

  9. A tetratricopeptide repeat domain-containing protein SSR1 located in mitochondria is involved in root development and auxin polar transport in Arabidopsis.

    Science.gov (United States)

    Zhang, Min; Wang, Cuiping; Lin, Qingfang; Liu, Aihua; Wang, Ting; Feng, Xuanjun; Liu, Jie; Han, Huiling; Ma, Yan; Bonea, Diana; Zhao, Rongmin; Hua, Xuejun

    2015-08-01

    Auxin polar transport mediated by a group of Pin-formed (PIN) transporters plays important roles in plant root development. However, the mechanism underlying the PIN expression and targeting in response to different developmental and environmental stimuli is still not fully understood. Here, we report a previously uncharacterized gene SSR1, which encodes a mitochondrial protein with tetratricopeptide repeat (TPR) domains, and show its function in root development in Arabidopsis thaliana. In ssr1-2, a SSR1 knock-out mutant, the primary root growth was dramatically inhibited due to severely impaired cell proliferation and cell elongation. Significantly lowered level of auxin was found in ssr1-2 roots by auxin measurement and was further supported by reduced expression of DR5-driven reporter gene. As a result, the maintenance of the root stem cell niche is compromised in ssr1-2. It is further revealed that the expression level of several PIN proteins, namely, PIN1, PIN2, PIN3, PIN4 and PIN7, were markedly reduced in ssr1-2 roots. In particular, we showed that the reduced protein level of PIN2 on cell membrane in ssr1-2 is due to impaired retrograde trafficking, possibly resulting from a defect in retromer sorting system, which destines PIN2 for degradation in vacuoles. In conclusion, our results indicated that SSR1 is functioning in root development in Arabidopsis, possibly by affecting PIN protein expression and subcellular targeting.

  10. Localized infusions of the partial alpha 7 nicotinic receptor agonist SSR180711 evoke rapid and transient increases in prefrontal glutamate release

    DEFF Research Database (Denmark)

    Bortz, D M; Mikkelsen, J D; Bruno, J P

    2013-01-01

    The ability of local infusions of the alpha 7 nicotinic acetycholine receptor (α7 nAChR) partial agonist SSR180711 to evoke glutamate release in prefrontal cortex was determined in awake rats using a microelectrode array. Infusions of SSR180711 produced dose-dependent increases in glutamate level...

  11. Molecular diversity and phylogeny of Triticum-Aegilops species possessing D genome revealed by SSR and ISSR markers

    Directory of Open Access Journals (Sweden)

    Moradkhani Hoda

    2015-12-01

    Full Text Available The aim of this study is investigation the applicability of SSR and ISSR markers in evaluating the genetic relationships in twenty accessions of Aegilops and Triticum species with D genome in different ploidy levels. Totally, 119 bands and 46 alleles were detected using ten primers for ISSR and SSR markers, respectively. Polymorphism Information Content values for all primers ranged from 0.345 to 0.375 with an average of 0.367 for SSR, and varied from 0.29 to 0.44 with the average 0.37 for ISSR marker. Analysis of molecular variance (AMOVA revealed that 81% (ISSR and 84% (SSR of variability was partitioned among individuals within populations. Comparing the genetic diversity of Aegilops and Triticum accessions, based on genetic parameters, shows that genetic variation of Ae. crassa and Ae. tauschii species are higher than other species, especially in terms of Nei’s gene diversity. Cluster analysis, based on both markers, separated total accessions in three groups. However, classification based on SSR marker data was not conformed to classification according to ISSR marker data. Principal co-ordinate analysis (PCoA for SSR and ISSR data showed that, the first two components clarified 53.48% and 49.91% of the total variation, respectively. This analysis (PCoA, also, indicated consistent patterns of genetic relationships for ISSR data sets, however, the grouping of accessions was not completely accorded to their own geographical origins. Consequently, a high level of genetic diversity was revealed from the accessions sampled from different eco-geographical regions of Iran.

  12. Exploiting EST databases for the development and characterization of EST-SSR markers in castor bean (Ricinus communis L.

    Directory of Open Access Journals (Sweden)

    Yang Jun-Bo

    2010-12-01

    Full Text Available Abstract Background The castor bean (Ricinus communis L., a monotypic species in the spurge family (Euphorbiaceae, 2n = 20, is an important non-edible oilseed crop widely cultivated in tropical, sub-tropical and temperate countries for its high economic value. Because of the high level of ricinoleic acid (over 85% in its seed oil, the castor bean seed derivatives are often used in aviation oil, lubricants, nylon, dyes, inks, soaps, adhesive and biodiesel. Due to lack of efficient molecular markers, little is known about the population genetic diversity and the genetic relationships among castor bean germplasm. Efficient and robust molecular markers are increasingly needed for breeding and improving varieties in castor bean. The advent of modern genomics has produced large amounts of publicly available DNA sequence data. In particular, expressed sequence tags (ESTs provide valuable resources to develop gene-associated SSR markers. Results In total, 18,928 publicly available non-redundant castor bean EST sequences, representing approximately 17.03 Mb, were evaluated and 7732 SSR sites in 5,122 ESTs were identified by data mining. Castor bean exhibited considerably high frequency of EST-SSRs. We developed and characterized 118 polymorphic EST-SSR markers from 379 primer pairs flanking repeats by screening 24 castor bean samples collected from different countries. A total of 350 alleles were identified from 118 polymorphic SSR loci, ranging from 2-6 per locus (A with an average of 2.97. The EST-SSR markers developed displayed moderate gene diversity (He with an average of 0.41. Genetic relationships among 24 germplasms were investigated using the genotypes of 350 alleles, showing geographic pattern of genotypes across genetic diversity centers of castor bean. Conclusion Castor bean EST sequences exhibited considerably high frequency of SSR sites, and were rich resources for developing EST-SSR markers. These EST-SSR markers would be particularly

  13. Exploiting EST databases for the development and characterization of EST-SSR markers in castor bean (Ricinus communis L.)

    Science.gov (United States)

    2010-01-01

    Background The castor bean (Ricinus communis L.), a monotypic species in the spurge family (Euphorbiaceae, 2n = 20), is an important non-edible oilseed crop widely cultivated in tropical, sub-tropical and temperate countries for its high economic value. Because of the high level of ricinoleic acid (over 85%) in its seed oil, the castor bean seed derivatives are often used in aviation oil, lubricants, nylon, dyes, inks, soaps, adhesive and biodiesel. Due to lack of efficient molecular markers, little is known about the population genetic diversity and the genetic relationships among castor bean germplasm. Efficient and robust molecular markers are increasingly needed for breeding and improving varieties in castor bean. The advent of modern genomics has produced large amounts of publicly available DNA sequence data. In particular, expressed sequence tags (ESTs) provide valuable resources to develop gene-associated SSR markers. Results In total, 18,928 publicly available non-redundant castor bean EST sequences, representing approximately 17.03 Mb, were evaluated and 7732 SSR sites in 5,122 ESTs were identified by data mining. Castor bean exhibited considerably high frequency of EST-SSRs. We developed and characterized 118 polymorphic EST-SSR markers from 379 primer pairs flanking repeats by screening 24 castor bean samples collected from different countries. A total of 350 alleles were identified from 118 polymorphic SSR loci, ranging from 2-6 per locus (A) with an average of 2.97. The EST-SSR markers developed displayed moderate gene diversity (He) with an average of 0.41. Genetic relationships among 24 germplasms were investigated using the genotypes of 350 alleles, showing geographic pattern of genotypes across genetic diversity centers of castor bean. Conclusion Castor bean EST sequences exhibited considerably high frequency of SSR sites, and were rich resources for developing EST-SSR markers. These EST-SSR markers would be particularly useful for both genetic

  14. Novel STATCOM Controller for Mitigating SSR and Damping Power System Oscillations in a Series Compensated Wind Parks

    DEFF Research Database (Denmark)

    Bak-Jensen, Birgitte; El-Moursi, M. S.; Abdel-Rahman, Mansour Hassan

    2010-01-01

    This paper addresses implementation issues associated with a novel damping control algorithm for a STATCOM in a series compensated wind park for mitigating SSR (subsynchronous resonance) and damping power system oscillations. The IEEE first benchmark model on subsynchronous resonance is adopted...... with integrating aggregated self excited induction generator based wind turbine to perform the studies. The potential occurrence and mitigation of the SSR caused by induction generator effects as well as torsional interactions, in a series compensated wind park are investigated. The auxiliary subsynchronous...

  15. Inheritance Analysis and Identification of SSR Markers Linked to Late Blight Resistant Gene in Tomato

    Institute of Scientific and Technical Information of China (English)

    ZHU Hai-shan; WU Tao; ZHANG Zhen-xian

    2006-01-01

    Late blight caused by Phytophthora infestans is the most serious disease of tomato production in China. Studies on the genetics of resistance and identification of molecular markers are very useful for breeding late blight resistant varieties.The objective of this paper was to study the inheritance of late blight resistance and identify simple sequence repeat (SSR)markers associated with resistance allele in tomato (Lycopersicon esculentum Mill). The results came from an F2 progeny of 241 plants derived from a cross between 5# inbred line that is susceptible to late blight and a resistant accession CLN2037E. The late blight responses of F2 plants were tested by artificially inoculation of detached-leaflets in plate and natural infection assayed under greenhouse conditions. Both methods showed that the resistance is dominant and inherited as monogenic trait. Genetic mapping and linkage analysis showed that the late blight resistance gene Ph-ROL was located on chromosome 9 with a genetic distance of 5.7 cM to the SSR marker TOM236.

  16. Transcriptome Analysis and Development of SSR Molecular Markers in Glycyrrhiza uralensis Fisch.

    Directory of Open Access Journals (Sweden)

    Yaling Liu

    Full Text Available Licorice is an important traditional Chinese medicine with clinical and industrial applications. Genetic resources of licorice are insufficient for analysis of molecular biology and genetic functions; as such, transcriptome sequencing must be conducted for functional characterization and development of molecular markers. In this study, transcriptome sequencing on the Illumina HiSeq 2500 sequencing platform generated a total of 5.41 Gb clean data. De novo assembly yielded a total of 46,641 unigenes. Comparison analysis using BLAST showed that the annotations of 29,614 unigenes were conserved. Further study revealed 773 genes related to biosynthesis of secondary metabolites of licorice, 40 genes involved in biosynthesis of the terpenoid backbone, and 16 genes associated with biosynthesis of glycyrrhizic acid. Analysis of unigenes larger than 1 Kb with a length of 11,702 nt presented 7,032 simple sequence repeats (SSR. Sixty-four of 69 randomly designed and synthesized SSR pairs were successfully amplified, 33 pairs of primers were polymorphism in in Glycyrrhiza uralensis Fisch., Glycyrrhiza inflata Bat., Glycyrrhiza glabra L. and Glycyrrhiza pallidiflora Maxim. This study not only presents the molecular biology data of licorice but also provides a basis for genetic diversity research and molecular marker-assisted breeding of licorice.

  17. Transferability of Newly Developed Pear SSR Markers to Other Rosaceae Species.

    Science.gov (United States)

    Fan, L; Zhang, M-Y; Liu, Q-Z; Li, L-T; Song, Y; Wang, L-F; Zhang, S-L; Wu, J

    2013-01-01

    A set of 120 simple sequence repeats (SSRs) was developed from the newly assembled pear sequence and evaluated for polymorphisms in seven genotypes of pear from different genetic backgrounds. Of these, 67 (55.8 %) primer pairs produced polymorphic amplifications. Together, the 67 SSRs detected 277 alleles with an average of 4.13 per locus. Sequencing of the amplification products from randomly picked loci NAUPy31a and NAUpy53a verified the presence of the SSR loci. When the 67 primer pairs were tested on 96 individual members of eight species in the Rosaceae family, 61.2 % (41/67) of the tested SSRs successfully amplified a PCR product in at least one of the Rosaceae genera. The transferability from pear to different species varied from 58.2 % (apple) to 11.9 % (cherry). The ratio of transferability also reflected the closer relationships within Maloideae over Prunoideae. Two pear SSR markers, NAUpy43c and NAUpy55k, could distinguish the 20 different apple genotypes thoroughly, and UPGMA cluster analysis grouped them into three groups at the similarity level of 0.56. The high level of polymorphism and good transferability of pear SSRs to Rosaceae species indicate their promise for application to future molecular screening, map construction, and comparative genomic studies among pears and other Rosaceae species.

  18. Molecular characterization of arabica and Conilon coffee plants genotypes by SSR and ISSR markers

    Directory of Open Access Journals (Sweden)

    Ludymila Brandão Motta

    2014-10-01

    Full Text Available The molecular characterization of ten genotypes of the Coffea arabica plants and of seven genotypes of C. canephora having interesting features for coffee breeding programs was carried to select the parents for breeding. A total of 40 SSR and 29 ISSR primers were used. The primers generated a total of 331 (307 polymorphic and 24 monomorphic bands. Analysis of genetic diversity presented dissimilarity intervals ranging from 0.22 to 0.44 between the Conilon genotypes, from 0.02 to 0.28 between the Arabica genotypes, and from 0.49 to 0.60 between the genotypes of the two species in the joint analysis. Four groups were formed: I = genotypes of C. arabica, II = four progenies of C. canephora, Conilon group, and one non defined C. canephora (Conilon or Robusta, III = one progeny of un-defined C. canephora (Conilon or Robusta and IV = one progeny of C. canephora of Robusta group. The grouping formed was consistent with the origins of each group. High stabilities of the bifurcations were found by bootstrap analysis. The use of molecular markers of the SSR and ISSR types in the diversity study was efficient in distinguishing genotypes between and within C. arabica and C. canephora.

  19. Mapping of Fertility Restoring Gene for Aegilops kotschyi Cytoplasmic Male Sterility in Wheat Using SSR Markers

    Institute of Scientific and Technical Information of China (English)

    LIU Bao-shen; SUN Qi-xin; GAO Qing-rong; SUN Lan-zhen; XIE Chao-jie; LI Chuan-you; NI Zhong-fu; DOU Bing-de

    2002-01-01

    LK783 was found to be a good fertility restorer for K-type male sterility of wheat. Microsatellite markers were employed to map the major restoring gene in LK783. Maintainer and restorer DNA pools were established using the extreme sterile and fertile plants among (KJ5418A//911289/LK783)F1 population,respectively. Seventy-nine sets of SSR primers were screened for polymorphism between the two pools, 6 of which were found polymorphic. Linkage analysis showed that Xgwm11, Xgwm18 , Xgwm264a and Xgwm273were linked to the restoring gene in LK783, while Xgwm11, Xgwm18 and Xgwm273 were co-segregated. The distance between the Rf gene in LK783 and the three co-segregated markers was 6.54±4.37 cM, the distance between Rf gene and Xgwm264a was 5.71±4.10 cM. The four SSR markers were located on chromosome 1BS by amplifying the DNA of nulli-tetrasomics and ditelosomics of CS with the 4 sets of primers, indicating that the major restoring gene in LK783 was located on 1BS, but the relative location of the gene was different from Rfv1, allelism of the two genes should be further investigated. The breeding for new fertility restorer lines of K-type cytoplasmic male sterility in wheat would be facilitated by using the four polymorphic markers.

  20. Chromosomal Location of Gene for Earbranching of Barley Natural Mutant "f151" Using SSR Markers

    Institute of Scientific and Technical Information of China (English)

    Feng Zongyun(冯宗云); Zhang Lili; Zhang Yizheng; Ling Hongqing

    2004-01-01

    f151, a natural earbranching mutant from naked barley landrace, has better structural characteristics of spike and is thought to be a very valuable germplasm to high-yield breeding of barley. Genetic analysis of earbranching trait is carried out in the populations of F1, F2, B1 and B2 which are produced by crossing including reciprocals and backcrossing between f151 and different barley varieties. The results show that earbranching trait of f151 is controlled by one pair of recessive genes without cytoplasm effects. The linkage between the earbranching gene and the SSR marker HVM40 on the short arm of chromosome 4H is found by bulked segregated analysis using SSR markers based on the F2 population of the hybrid "f151×Gateway". It can be inferred from the recombinant value of 0.087 between the gene and HVM40 that this gene is located on 4HS. The gene is temporarily named "mb".

  1. Fostering eGovernment as State Social Responsibility (SSR: Case Study of an Australian City Council

    Directory of Open Access Journals (Sweden)

    Sinara Rao Karna

    2012-12-01

    Full Text Available           Democracies around the world now face Citizen-apathy. This is a concern now more than ever faced by countries around the globe. eGovernment is undoubtedly a platform to deliberate and enable citizens regain confidence and faith in democratic  processes. Citizens now seek Verifiable, Open, Transparent, Empathetic, Responsive and Sensitive Electronic Democracy and Government (VOTERS EDG, Karna, 2012. Similar to corporate world, there are voices stressing on govenments for the need to understand the stakeholders, their involvement, relationships and responsibilities of a state in eGovernance. Citizens everywhere now demand Verifiable, Open, Transparent, Empathetic, Responsive and Sensitive Electronically Democratic Government as a State Social Responsibity (SSR. Peoples movements and outbursts against authorities with the help of Word of Mouse (Karna, 2012 have established that transparent and open governance is the need of the hour. This paper presents findings of the study conducted in an Australian City Council for preparing the city council for ‘City e-readiness’ to initiate e-Government activities. We propose the idea of ‘Centrality of Citizens’ in context of eGovernment. We further build upon the original concept of deeming eGovernment as ‘State Social Responsibility’ (SSR (Karna, 2010, by governments at all levels.  

  2. THE RELATIONSHIP BETWEEN HETEROSIS AND GENETIC DISTANCES BASED ON SSR MARKERS IN HELIANTHUS ANNUUS

    Directory of Open Access Journals (Sweden)

    A. V. Usatov

    2014-01-01

    Full Text Available Identifying the best inbred combinations for the development of commercial hybrid of sunflower remains the main challenge to sunflower breeders. In the present research the level of heterosis of F1 hybrids, genetic diversity of parental lines based on SSR markers, as well as its connection with specific combining ability of sunflower were studied. Ten sunflower elite inbred lines (3 restorer lines and 7 cytoplasmic male sterility lines and their hybrids were examined for plant height, seed yield, thousand seed mass, oil content and husk content. Field tests were carried out in 5-6 seasons. The level of heterosis was calculated using measurement of midparent heterosis. Genetic distance between pairs of tested sunflower inbred lines ranged from 0.45 to 0.74. Significant positive correlation was found between genetic distances among lines, measured using SSR markers and midparent heterosis for seed yield of hybrids (r = 0.79 p<0.05. The correlation between genetic distances and the level of midparent heterosis for other studied agronomic traits was not reliable. The dependence of seed yield of hybrids on genetic distances among parental lines may be used for planning of effective crossbreeding of sunflower. Further research is needed to determine the best inbred combinations for the development of commercial hybrid of sunflower.

  3. SSR characterization of Oryza glumaepatula populations from the Brazilian Amazon and Cerrado biomes.

    Science.gov (United States)

    Abreu, Aluana Gonçalves; Rosa, Thalita Marra; Borba, Tereza Cristina de Oliveira; Vianello, Rosana Pereira; Rangel, Paulo Hideo Nakano; Brondani, Claudio

    2015-08-01

    The level and distribution of the genetic variability in 18 natural populations of Oryza glumaepatula that were collected from two Brazilian states were estimated using a set of 23 highly informative SSR markers. Samples comprising 78 and 117 individuals from populations of the states of Tocantins and Roraima, respectively, were evaluated in order to integrate and support previous studies that were carried out with populations of O. glumaepatula from Brazil. A total of 189 alleles were identified with an average of 8.22 alleles per locus. The 11 populations from Roraima presented, in combination, a higher genetic diversity (HE = 0.245) compared with that of the seven populations from Tocantins (HE = 0.212). All of the populations showed high and significant inbreeding values (mean f = 0.59); however, the mean was higher in Tocantins populations, indicating a higher gene flow in Roraima populations. The overall coefficient of genetic differentiation (FST) among the populations was high and significant (0.59) and was higher in Tocantins due to the isolation of each population, in contrast to Roraima, where gene flow occurred more frequently. The SSR panel used in this work resulted to be informative (polymorphism information content = 0.201) for assessing genetic structure in O. glumaepatula populations.

  4. Genetic diversity of sweet sorghum germplasm in Mexico using AFLP and SSR markers

    Directory of Open Access Journals (Sweden)

    Víctor Pecina‑Quintero

    2012-08-01

    Full Text Available The objective of this work was to evaluate the diversity and genetic relationships between lines and varieties of the sweet sorghum (Sorghum bicolor germplasm bank of the National Institute for Forestry, Agriculture and Livestock Research, Mexico, using AFLP and SSR markers. The molecular markers revealed robust amplification profiles and were able to differentiate the 41 genotypes of sweet sorghum evaluated. Analysis of the frequency and distribution of polymorphic fragments allowed for the detection of unique (AFLP and rare (SSR alleles in several genotypes (RBSS‑8, RBSS‑9, RBSS‑25, RBSS‑32, and RBSS‑37, indicating that these markers may be associated with a feature that has not yet been determined or may be useful for the identification of these genotypes. The genetic relationships indicated the presence of at least two types of sweet sorghum: a group of modern genotypes used for sugar and biofuel production, and another group consisting of historic and modern genotypes used for the production of syrups. Sweet sorghum genotypes may be used to develop new varieties with higher sugar and juice contents.

  5. SSR Analysis on Diversity of AA Genome Oryza Species in the Southeast and South Asia

    Institute of Scientific and Technical Information of China (English)

    LU Jian-zhen; ZHANG Xiao-li; WANG Hai-gang; YUAN Xiao-ping; XU Qun; WANG Yi-ping; YU Han-yong; TANG Sheng-xiang; WEI Xing-hua

    2008-01-01

    To investigate genetic diversities among the AA genome Oryza species in the Southeast and South'Asia, a total of 428 accessions of the AA genome Oryza species were genotyped using 36 simple sequence repeats (SSR) markers distributed throughout the rice genome. All of the 36 SSR markers generated polymorphic bands, revealing 100% polymorphism. The number of alleles per locus ranged from 3 to 17 with the mean of 8.6. The Nei's genetic diversity index (He) ranged from 0.337 at RM455 to 0.865 at RM 169 with an average value of 0.650. The genetic diversity of the AA genome Oryza species in the Southeast Asia was obviously higher than that in the South Asia. Among the detected Oryza species in the South and Southeast Asia, O. rufipogon showed the highest genetic diversity. Meanwhile, a higher genetic differentiation (Fst) was found among the detected Oryza species in the Southeast Asia than in the South Asia. The Fst value between O. nivara and O. sativa was the highest. The results from the number of specific alleles, specific loci, and allele frequency confirmed the greater genetic variation among the detected species. In addition, the specific allele in RM161 displayed higher frequency (0.193), suggesting its important function in identifying Oryza species of AA genome.

  6. SSR Analysis on Diversity of AA Genome Oryza Species in the Southeast and South Asia

    Directory of Open Access Journals (Sweden)

    Jian-zhen LU

    2008-12-01

    Full Text Available To investigate genetic diversities among the AA genome Oryza species in the Southeast and South Asia, a total of 428 accessions of the AA genome Oryza species were genotyped using 36 simple sequence repeats (SSR markers distributed throughout the rice genome. All of the 36 SSR markers generated polymorphic bands, revealing 100% polymorphism. The number of alleles per locus ranged from 3 to 17 with the mean of 8.6. The Nei's genetic diversity index (He ranged from 0.337 at RM455 to 0.865 at RM169 with an average value of 0.650. The genetic diversity of the AA genome Oryza species in the Southeast Asia was obviously higher than that in the South Asia. Among the detected Oryza species in the South and Southeast Asia, O. rufipogon showed the highest genetic diversity. Meanwhile, a higher genetic differentiation (Fst was found among the detected Oryza species in the Southeast Asia than in the South Asia. The Fst value between O. nivara and O. sativa was the highest. The results from the number of specific alleles, specific loci, and allele frequency confirmed the greater genetic variation among the detected species. In addition, the specific allele in RM161 displayed higher frequency (0.193, suggesting its important function in identifying Oryza species of AA genome.

  7. Genetic Characterization of Green Bean (Phaseolus vulgaris L.) Accessions from Turkey with SCAR and SSR Markers.

    Science.gov (United States)

    Madakbaş, Seher Yıldız; Sarıkamış, Gölge; Başak, Hakan; Karadavut, Ufuk; Özmen, Canan Yüksel; Daşçı, Mete Gürhan; Çayan, Selin

    2016-08-01

    Characterization, conservation, and utilization of genetic resources is essential for the sustainability in agriculture. Plant genetic resources are important for breeding efforts designed for the generation of new cultivars or for the improvement of existing ones. Green bean has been cultivated extensively in Turkey giving rise to local accessions through selection over time and adaptation to various environmental conditions. The objective of the present study was to determine the genetic relationships of green bean accessions collected from Kırşehir Province of Turkey, located at the central Anatolia. Within a population of 275 green bean accessions, 50 accessions were selected on the basis of morphological observations for further evaluation with SSR and STS/SCAR markers together with 4 reference cultivars of Andean and Mesoamerican origin. SSR markers selected on the basis of high polymorphism information content revealed the genetic relatedness of selected green bean accessions. STS/SCAR markers associated with bean anthracnose, common bacterial blight, white mold, halo blight, and phaseolin protein demonstrated the inheritance of resistance traits of local accessions at the selected loci. These findings may help better utilize genetic resources and furthermore are expected to facilitate forthcoming breeding studies for the generation of novel cultivars well adapted to the region.

  8. SSR-based genetic diversity and structure of garlic accessions from Brazil.

    Science.gov (United States)

    da Cunha, Camila Pinto; Resende, Francisco Vilela; Zucchi, Maria Imaculada; Pinheiro, José Baldin

    2014-10-01

    Garlic is a spice and a medicinal plant; hence, there is an increasing interest in 'developing' new varieties with different culinary properties or with high content of nutraceutical compounds. Phenotypic traits and dominant molecular markers are predominantly used to evaluate the genetic diversity of garlic clones. However, 24 SSR markers (codominant) specific for garlic are available in the literature, fostering germplasm researches. In this study, we genotyped 130 garlic accessions from Brazil and abroad using 17 polymorphic SSR markers to assess the genetic diversity and structure. This is the first attempt to evaluate a large set of accessions maintained by Brazilian institutions. A high level of redundancy was detected in the collection (50 % of the accessions represented eight haplotypes). However, non-redundant accessions presented high genetic diversity. We detected on average five alleles per locus, Shannon index of 1.2, HO of 0.5, and HE of 0.6. A core collection was set with 17 accessions, covering 100 % of the alleles with minimum redundancy. Overall FST and D values indicate a strong genetic structure within accessions. Two major groups identified by both model-based (Bayesian approach) and hierarchical clustering (UPGMA dendrogram) techniques were coherent with the classification of accessions according to maturity time (growth cycle): early-late and midseason accessions. Assessing genetic diversity and structure of garlic collections is the first step towards an efficient management and conservation of accessions in genebanks, as well as to advance future genetic studies and improvement of garlic worldwide.

  9. Development of simple sequence repeat (SSR) markers of sesame (Sesamum indicum) from a genome survey.

    Science.gov (United States)

    Wei, Xin; Wang, Linhai; Zhang, Yanxin; Qi, Xiaoqiong; Wang, Xiaoling; Ding, Xia; Zhang, Jing; Zhang, Xiurong

    2014-04-22

    Sesame (Sesamum indicum), an important oil crop, is widely grown in tropical and subtropical regions. It provides part of the daily edible oil allowance for almost half of the world's population. A limited number of co-dominant markers has been developed and applied in sesame genetic diversity and germplasm identity studies. Here we report for the first time a whole genome survey used to develop simple sequence repeat (SSR) markers and to detect the genetic diversity of sesame germplasm. From the initial assembled sesame genome, 23,438 SSRs (≥5 repeats) were identified. The most common repeat motif was dinucleotide with a frequency of 84.24%, followed by 13.53% trinucleotide, 1.65% tetranucleotide, 0.3% pentanucleotide and 0.28% hexanucleotide motifs. From 1500 designed and synthesised primer pairs, 218 polymorphic SSRs were developed and used to screen 31 sesame accessions that from 12 countries. STRUCTURE and phylogenetic analyses indicated that all sesame accessions could be divided into two groups: one mainly from China and another from other countries. Cluster analysis classified Chinese major sesame varieties into three groups. These novel SSR markers are a useful tool for genetic linkage map construction, genetic diversity detection, and marker-assisted selective sesame breeding.

  10. A SSR-based composite genetic linkage map for the cultivated peanut (Arachis hypogaea L. genome

    Directory of Open Access Journals (Sweden)

    Li Shaoxiong

    2010-01-01

    Full Text Available Abstract Background The construction of genetic linkage maps for cultivated peanut (Arachis hypogaea L. has and continues to be an important research goal to facilitate quantitative trait locus (QTL analysis and gene tagging for use in a marker-assisted selection in breeding. Even though a few maps have been developed, they were constructed using diploid or interspecific tetraploid populations. The most recently published intra-specific map was constructed from the cross of cultivated peanuts, in which only 135 simple sequence repeat (SSR markers were sparsely populated in 22 linkage groups. The more detailed linkage map with sufficient markers is necessary to be feasible for QTL identification and marker-assisted selection. The objective of this study was to construct a genetic linkage map of cultivated peanut using simple sequence repeat (SSR markers derived primarily from peanut genomic sequences, expressed sequence tags (ESTs, and by "data mining" sequences released in GenBank. Results Three recombinant inbred lines (RILs populations were constructed from three crosses with one common female parental line Yueyou 13, a high yielding Spanish market type. The four parents were screened with 1044 primer pairs designed to amplify SSRs and 901 primer pairs produced clear PCR products. Of the 901 primer pairs, 146, 124 and 64 primer pairs (markers were polymorphic in these populations, respectively, and used in genotyping these RIL populations. Individual linkage maps were constructed from each of the three populations and a composite map based on 93 common loci were created using JoinMap. The composite linkage maps consist of 22 composite linkage groups (LG with 175 SSR markers (including 47 SSRs on the published AA genome maps, representing the 20 chromosomes of A. hypogaea. The total composite map length is 885.4 cM, with an average marker density of 5.8 cM. Segregation distortion in the 3 populations was 23.0%, 13.5% and 7.8% of the markers

  11. SSR Revisited.

    Science.gov (United States)

    Blake, Mary E.

    1979-01-01

    An experienced teacher presents guidelines for starting Sustained Silent Reading in a classroom, including explaining the program to the students and dealing with those who forget their books, disrupt the class, or fidget. A list of teacher background readings is included. (SJL)

  12. (SSR) markers

    African Journals Online (AJOL)

    SAM

    2014-07-30

    Jul 30, 2014 ... Simple sequence repeats (SSRs) are the most widely used marker system for plant variety characterization and ... gene tagging in marker assisted breeding and gene cloning in .... PLS-2 and PAU Selection Long) to 1.00 (between PC. 2062 and .... Comparative analyses of genetic diversities within tomato.

  13. (SSR) markers

    African Journals Online (AJOL)

    Yomi

    2012-04-03

    Apr 3, 2012 ... seeded and black-seeded cultivars and breeding lines. The group B included 70 ... maize, rice and tomatoes (Reif et al., 2006; Vigouroux et al., 2005; Warburton et ..... development of molecular markers for marker-assisted breeding. .... Selection under domestication: evidence for a sweep in the rice Waxy ...

  14. Genotype-specific microsatellite (SSR) markers for the sugarcane germplasm in the Karst region of Guizhou, China

    Science.gov (United States)

    It is the first report on SSR-based molecular evaluation of genetic variability among sugarcane genotypes from the Karst region of China that provides useful information for local sugarcane improvement. Eighteen sugarcane genotypes including 13 active cultivars and five elite QT-series clones bred l...

  15. Microsatellites for the genus Cucurbita and an SSR-based genetic linkage map of Cucurbita pepo L.

    Science.gov (United States)

    Gong, L; Stift, G; Kofler, R; Pachner, M; Lelley, T

    2008-06-01

    Until recently, only a few microsatellites have been available for Cucurbita, thus their development is highly desirable. The Austrian oil-pumpkin variety Gleisdorfer Olkürbis (C. pepo subsp. pepo) and the C. moschata cultivar Soler (Puerto Rico) were used for SSR development. SSR-enriched partial genomic libraries were established and 2,400 clones were sequenced. Of these 1,058 (44%) contained an SSR at least four repeats long. Primers were designed for 532 SSRs; 500 primer pairs produced fragments of expected size. Of these, 405 (81%) amplified polymorphic fragments in a set of 12 genotypes: three C. moschata, one C. ecuadorensis, and eight C. pepo representing all eight cultivar groups. On an average, C. pepo and C. moschata produced 3.3 alleles per primer pair, showing high inter-species transferability. There were 187 SSR markers detecting polymorphism between the USA oil-pumpkin variety "Lady Godiva" (O5) and the Italian crookneck variety "Bianco Friulano" (CN), which are the parents of our previous F(2) mapping population. It has been used to construct the first published C. pepo map, containing mainly RAPD and AFLP markers. Now the updated map comprises 178 SSRs, 244 AFLPs, 230 RAPDs, five SCARs, and two morphological traits (h and B). It contains 20 linkage groups with a map density of 2.9 cM. The observed genome coverage (Co) is 86.8%.

  16. 78 FR 17744 - Social Security Ruling, SSR 13-2p; Titles II and XVI: Evaluating Cases Involving Drug Addiction...

    Science.gov (United States)

    2013-03-22

    ... From the Federal Register Online via the Government Publishing Office SOCIAL SECURITY ADMINISTRATION Social Security Ruling, SSR 13-2p; Titles II and XVI: Evaluating Cases Involving Drug Addiction and Alcoholism (DAA); Correction AGENCY: Social Security Administration. ACTION: Notice of...

  17. Comparison of genetic diversity structure analyses of SSR molecular marker data within apple (Malus×domestica) genetic resources.

    Science.gov (United States)

    Patzak, Josef; Paprštein, František; Henychová, Alena; Sedlák, Jiří

    2012-09-01

    The aim of this study was to compare traditional hierarchical clustering techniques and principal coordinate analysis (PCoA) with the model-based Bayesian cluster analyses in relation to subpopulation differentiation based on breeding history and geographical origin of apple (Malus×domestica Borkh.) cultivars and landraces. We presented the use of a set of 10 microsatellite (SSR) loci for genetic diversity structure analyses of 273 apple accessions from national genetic resources. These SSR loci yielded a total of 113 polymorphic SSR alleles, with 5-18 alleles per locus. SSR molecular data were successfully used in binary and allelic input format for all genetic diversity analyses, but allelic molecular data did not reveal reliable results with the NTSYS-pc and BAPS softwares. A traditional cluster analysis still provided an easy and effective way for determining genetic diversity structure in the apple germplasm collection. A model-based Bayesian analysis also provided the clustering results in accordance to traditional cluster analysis, but the analyses were distorted by the presence of a dominant group of apple genetic resources owing to the narrow origin of the apple genome. PCoA confirmed that there were no noticeable differences in genetic diversity structure of apple genetic resources during the breeding history. The results of our analyses are useful in the context of enhancing apple collection management, sampling of core collections, and improving breeding processes.

  18. 77 FR 58604 - Social Security Ruling (SSR), 12-1p; Title II: Determining Whether Work Performed in Self...

    Science.gov (United States)

    2012-09-21

    ... ADMINISTRATION Social Security Ruling (SSR), 12-1p; Title II: Determining Whether Work Performed in Self..., Commissioner of Social Security. Policy Interpretation Ruling Title II: Determining whether work performed in... social programs to be SGA. See 20 CFR 404.1572. Policy Interpretation: For work activity performed...

  19. Development of 15 genic-ssr markers in oil-tea tree (Camellia oleifera based on transcriptome sequencing

    Directory of Open Access Journals (Sweden)

    Jia Baoguang

    2014-01-01

    Full Text Available Oil-tea tree is one of the most important woody edible oil plants; however, lack of useful molecular markers hinders current genetic research. We performed transcriptome sequencing of developing seeds and characterized microsatellites from transcriptome sequences to identify valuable markers for C. oleifera molecular genetics research. A total of 69,798 unigenes were identified, in which 6,949 putative SSR motifs from 6,042 SSR-containing unique putative transcripts were discovered. Twenty-nine primer pairs corresponding to 29 unigene loci were designed, of which 15 polymorphic genic-SSR markers were developed in 18 varieties and characterized by capillary electrophoresis. The number of alleles per locus (Na ranged from 2 to 14, the expected heterozygosity (He ranged from 0.374 to 0.876, and the polymorphism information content (PIC values ranged from 0.498 to 0.887, respectively. Cross-species amplification was also conducted in 15 varieties of C. japonica. All 15 markers successfully amplified PCR products with expected size in C. japonica and exhibited polymorphisms. The 15 polymorphic genic- SSR markers will have potential for applications in genetic diversity evaluation, molecular fingerprinting identification, comparative genome analysis, and genetic mapping in the C. oleifera and C. japonica.

  20. 77 FR 43640 - Social Security Ruling, SSR 12-2p; Titles II and XVI: Evaluation of Fibromyalgia

    Science.gov (United States)

    2012-07-25

    ... ADMINISTRATION Social Security Ruling, SSR 12-2p; Titles II and XVI: Evaluation of Fibromyalgia AGENCY: Social... determinable impairment of fibromyalgia, and how we evaluate fibromyalgia in disability claims and continuing... Interpretation Ruling Titles II and XVI: Evaluation of Fibromyalgia Purpose: This Social Security Ruling...

  1. Transcriptome Sequencing and Development of Genic SSR Markers of an Endangered Chinese Endemic Genus Dipteronia Oliver (Aceraceae

    Directory of Open Access Journals (Sweden)

    Tao Zhou

    2016-02-01

    Full Text Available Dipteronia Oliver (Aceraceae is an endangered Chinese endemic genus consisting of two living species, Dipteronia sinensis and Dipteronia dyeriana. However, studies on the population genetics and evolutionary analyses of Dipteronia have been hindered by limited genomic resources and genetic markers. Here, the generation, de novo assembly and annotation of transcriptome datasets, and a large set of microsatellite or simple sequence repeat (SSR markers derived from Dipteronia have been described. After Illumina pair-end sequencing, approximately 93.2 million reads were generated and assembled to yield a total of 99,358 unigenes. A majority of these unigenes (53%, 52,789 had at least one blast hit against the public protein databases. Further, 12,377 SSR loci were detected and 4179 primer pairs were designed for experimental validation. Of these 4179 primer pairs, 435 primer pairs were randomly selected to test polymorphism. Our results show that products from 132 primer pairs were polymorphic, in which 97 polymorphic SSR markers were further selected to analyze the genetic diversity of 10 natural populations of Dipteronia. The identification of SSR markers during our research will provide the much valuable data for population genetic analyses and evolutionary studies in Dipteronia.

  2. Genetic Variation in Triticum turgidum L.ssp.turgidum Landraces from China Assessed by EST-SSR Markers

    Institute of Scientific and Technical Information of China (English)

    LI Wei; DONG Pan; WEI Yu-ming; CHENG Guo-yue; ZHENG You-liang

    2008-01-01

    It was helpful for the wheat improvement to evaluate the genetic resources of Triticum turgidum L.ssp.turgidum landraces.In this study,68 turgidum landraces accessions,belonging to four geographic populations in China,were investigated by using EST-SSR markers.A total of 63 alleles were detected on 22 EST-SSR loci,and the number of alleles on each locus ranged from 1 to 5,with an average of 2.9.The results of the analysis of molecular variance (AMOVA)indicated that 92.5% of the total variations was attributed to the genetic variations within population,whereas only 7.5%variations among populations.Although the four populations had similar genetic diversity parameters,Sichuan population was yet distinguished from other populations when comparing the population samples in pairs.Significant correlations were detected by the statistic analysis among six genetic diversity parameters among each other.The selection difference between heterozygosty and homozygosty was also observed among different EST-SSR locus.The genetic similarity (GS)ranged from 0.18 to 0.98,with the mean of 0.72,and all accessions could be clustered into 7 groups.The dendrogram suggested that the genetic relationships among turgidum accessions evaluated by EST-SSR markers were unrelated to their geographic distributions.These results implied that turgidum landraces from China had the unique characters of genetic diversity.

  3. Fluorescence- and capillary electrophoresis (CE)-based SSR DNA fingerprinting and a molecular identity database for the Louisiana sugarcane industry

    Science.gov (United States)

    A database of Louisiana sugarcane molecular identity has been constructed and is being updated annually using FAM or HEX or NED fluorescence- and capillary electrophoresis (CE)-based microsatellite (SSR) fingerprinting information. The fingerprints are PCR-amplified from leaf DNA samples of current ...

  4. Development of polymorphic genic-SSR markers by cDNA library sequencing in boxwood, Buxus spp. (Buxaceae)

    Science.gov (United States)

    Genic microsatellites or simple sequence repeat (genic-SSR) markers were developed in boxwood (Buxus taxa) for genetic diversity analysis, identification of taxa, and to facilitate breeding. cDNA libraries were developed from mRNA extracted from leaves of Buxus sempervirens ‘Vardar Valley’ and seque...

  5. Genetic diversity among Brazilian soybean cultivars based on SSR loci and pedigree data

    Directory of Open Access Journals (Sweden)

    Regina Helena Geribello Priolli

    2010-06-01

    Full Text Available In this study, simple sequence repeats (SSR loci and pedigree data were used to investigate the genetic relationship in a group of 168 Brazilian soybean cultivars. Eighteen SSR loci produced an average of 5.06 alleles and a mean gene diversity of 0.58 for the cultivars studied. Genetic distance (GD was determined using the modified Roger's Wright distance, and a final dendrogram was in agreement with the cultivar pedigree. A distance matrix based on the coefficient of parentage scores was also generated for the cultivars, which ranged from 0 to 1, with a mean of 0.18, whereas SSR-based genetic similarity (1- GD ranged from 0.01 to 0.90, with a mean of 0.25. Mantel's Z test showed that the similarity matrices generated from both the data sets were low, but significantly correlated (r = 0.31, pLocos microssatélites e dados de genealogia foram utilizados para avaliar a diversidade genética de um grupo de 168 cultivares brasileiras de soja. Os dezoito locos utilizados apresentaram em média 5,06 alelos por loco e coeficiente de diversidade genética médio de 0,58. O dendrograma final resultante da matriz de distância genética de Roger modificado por Wright, apresentou boa concordância com a ancestralidade dos grupos formados. Também foi estimado os coeficientes de parentesco entre as cultivares, sendo observada variação de 0 a 1 com média de 0,18, enquanto que as similaridades para os locos microssatélites (1- GD variou de 0,01 a 0,90 com média de 0,25. A correlação entre as duas matrizes obtidas determinada pelo teste Z de Mantel apresentou valor baixo, 0,31, mas significativo (p<0,001. Os resultados obtidos sugerem que os locos microssatélites aliados às informações de genealogia proporcionam melhor análise da diversidade genética de cultivares de soja.

  6. Evaluation of Mungbean Mutant Lines to Drought Stress and Their Genetic Relationships Using SSR Markers

    Directory of Open Access Journals (Sweden)

    Yuliasti

    2015-12-01

    Full Text Available Development of mungbean cultivarstolerant to drought stress through mutation breeding approach would enable us to anticipate the crop yield-reducing effects of climate changes. The objective of this research was to evaluate the yield performance of mungbean mutant lines that showed tolerance to drought stress, and to analyze their genetic diversity and relationship among mutant lines using SSR markers. The study was conducted during the dry season of 2012 in the Muneng experimental farm, Probolinggo, East Java. The experiment was laid out in a randomized block design with four replications. Five mutant lines and two parental lines as control were tested for evaluation of yield and drought tolerance under twoenvironments of two irrigation systems as treatment. The two environmental conditions consisted of optimal irrigation (at least three times: at planting, flowering and during pod filling and suboptimal irrigation (two times at planting and flowering. To evaluate genetic variation among selected mutant lines and their discrimination from parental lines in molecular level, a cluster analysis was performed using Unweighted Pair Group Method with Arithmetic Mean (UPGMA in the NTSYS software. The results showed that three mutant lines, including PsJ30, PsJ31, PsJ32 produced the highest grain yields of 1.17, 1.01, and 1.04 ton/ha, respectively, compared to the other mutant lines and the parents Gelatik (0.85 ton/ha and Perkutut (0.87 ton/ha as control check. Of those mutant lines, PSJ31 was the most tolerant to drought with sensitivity index value of 0.47. The PSJ31 has now been officially released as a new variety ( 2013, named as Muri which was identified to have high yield and tolerant to drought. Based on 23 SSR markers used for clustering analysis of those 3 selected mutant lines,9SSR markers (MBSS R033; satt137; MBSSR008; MBSSR203; MBSSR013; MBSSR021; MBSSR016; MBSSR136; and DMBSSR013 were successfully identified the three mungbean mutant

  7. Analysis of simple sequence repeats in rice bean (Vigna umbellata) using an SSR-enriched library

    Institute of Scientific and Technical Information of China (English)

    Lixia Wang; Kyung Do Kim; Dongying Gao; Honglin Chen; Suhua Wang; SukHa Lee; Scott A. Jackson; Xuzhen Cheng

    2016-01-01

    Rice bean (Vigna umbellata Thunb.), a warm-season annual legume, is grown in Asia mainly for dried grain or fodder and plays an important role in human and animal nutrition because the grains are rich in protein and some essential fatty acids and minerals. With the aim of expediting the genetic improvement of rice bean, we initiated a project to develop genomic resources and tools for molecular breeding in this little-known but important crop. Here we report the construction of an SSR-enriched genomic library from DNA extracted from pooled young leaf tissues of 22 rice bean genotypes and developing SSR markers. In 433,562 reads generated by a Roche 454 GS-FLX sequencer, we identified 261,458 SSRs, of which 48.8% were of compound form. Dinucleotide repeats were predominant with an absolute proportion of 81.6%, followed by trinucleotides (17.8%). Other types together accounted for 0.6%. The motif AC/GT accounted for 77.7%of the total, followed by AAG/CTT (14.3%), and all others accounted for 12.0%. Among the flanking sequences, 2928 matched putative genes or gene models in the protein database of Arabidopsis thaliana, corresponding with 608 non-redundant Gene Ontology terms. Of these sequences, 11.2%were involved in cellular components, 24.2%were involved molecular functions, and 64.6%were associated with biological processes. Based on homolog analysis, 1595 flanking sequences were similar to mung bean and 500 to common bean genomic sequences. Comparative mapping was conducted using 350 sequences homologous to both mung bean and common bean sequences. Finally, a set of primer pairs were designed, and a validation test showed that 58 of 220 new primers can be used in rice bean and 53 can be transferred to mung bean. However, only 11 were polymorphic when tested on 32 rice bean varieties. We propose that this study lays the groundwork for developing novel SSR markers and will enhance the mapping of qualitative and quantitative traits and marker-assisted selection in

  8. Assessment of genetic diversity in Brassica juncea Brassicaceae genotypes using phenotypic differences and SSR markers

    Directory of Open Access Journals (Sweden)

    Vinu V.

    2013-12-01

    Full Text Available Las especies de mostaza del género Brassica representan uno de los cultivos de semillas oleaginosas más importantes en India, sin embargo, su diversidad genética es poco conocida. Para la utilización de genotipos en programas de cultivos resulta esencial un mayor conocimiento sobre este tema. Debido a ello, se evaluó la diversidad genética entre 44 genotipos de mostaza de la India Brassica juncea incluyendo variedades y líneas puras de diferentes zonas agro-climáticas de la India y algunos genotipos exóticos Australia, Polonia y China. Para ello, se utilizaron marcadores SSR específicos del genoma A y B y datos fenotípicos del rendimiento de 12 cosechas y sus características. De los 143 primers evaluados, 134 reportaron polimorfismo y un total de 355 alelos fueron amplificados. Se generaron dendrogramas a partir de los coeficientes de similitud de Jaccard y de disimilitud Manhattan, basados en un algoritmo de vinculación promedio UPGMA. Se utilizaron datos de marcadores genéticos y datos fenotípicos. Los genotipos se agruparon en cuatro grupos basados en las distancias genéticas. Ambos patrones de agrupamiento, tanto los basados en los coeficientes de similitud de Jaccard como los basados en los de disimilitud Manhattan, separaron independientemente los genotipos por su genealogía y origen, de una manera efectiva. El PCoA reveló que la agrupación de genotipos basada en datos de marcadores SSR, es más convincente que los datos fenotípicos, sin embargo, se observó que la correlación entre las matrices de distancia fenotípica y genética resultó muy baja r=0.11. Por lo tanto, para estudios de diversidad basados en marcadores moleculares es necesario realizar más pruebas. Los marcadores SSR constituyen herramientas más eficientes para discriminar entre genotipos de B. juncea, que las características cuantitativas.

  9. Analysis of simple sequence repeats in rice bean (Vigna umbellata using an SSR-enriched library

    Directory of Open Access Journals (Sweden)

    Lixia Wang

    2016-02-01

    Full Text Available Rice bean (Vigna umbellata Thunb., a warm-season annual legume, is grown in Asia mainly for dried grain or fodder and plays an important role in human and animal nutrition because the grains are rich in protein and some essential fatty acids and minerals. With the aim of expediting the genetic improvement of rice bean, we initiated a project to develop genomic resources and tools for molecular breeding in this little-known but important crop. Here we report the construction of an SSR-enriched genomic library from DNA extracted from pooled young leaf tissues of 22 rice bean genotypes and developing SSR markers. In 433,562 reads generated by a Roche 454 GS-FLX sequencer, we identified 261,458 SSRs, of which 48.8% were of compound form. Dinucleotide repeats were predominant with an absolute proportion of 81.6%, followed by trinucleotides (17.8%. Other types together accounted for 0.6%. The motif AC/GT accounted for 77.7% of the total, followed by AAG/CTT (14.3%, and all others accounted for 12.0%. Among the flanking sequences, 2928 matched putative genes or gene models in the protein database of Arabidopsis thaliana, corresponding with 608 non-redundant Gene Ontology terms. Of these sequences, 11.2% were involved in cellular components, 24.2% were involved molecular functions, and 64.6% were associated with biological processes. Based on homolog analysis, 1595 flanking sequences were similar to mung bean and 500 to common bean genomic sequences. Comparative mapping was conducted using 350 sequences homologous to both mung bean and common bean sequences. Finally, a set of primer pairs were designed, and a validation test showed that 58 of 220 new primers can be used in rice bean and 53 can be transferred to mung bean. However, only 11 were polymorphic when tested on 32 rice bean varieties. We propose that this study lays the groundwork for developing novel SSR markers and will enhance the mapping of qualitative and quantitative traits and marker

  10. Development of SSR markers by next-generation sequencing of Korean landraces of chamoe (Cucumis melo var. makuwa).

    Science.gov (United States)

    Park, Inkyu; Kim, Jungeun; Lee, Jeongyeo; Kim, Sewon; Cho, Okhee; Yang, Kyungbong; Ahn, Jongmoon; Nahm, Seokhyeon; Kim, Hyeran

    2013-12-01

    The oriental melon (Cucumis melo var. makuwa), called 'chamoe' in Korean, is a popular fruit crop cultivated mainly in Asia and a high-market value crop in Korea. To provide molecular breeding resources for chamoe, we developed and characterized genomic SSR markers from the preliminary Illumina read assemblies of Gotgam chamoe (one of the major landraces; KM) and SW3 (the breeding parent). Mononucleotide motifs were the most abundant type of markers, followed by di-, tri-, tetra-, and pentanucleotide motifs. The most abundant dinucleotide was AT, followed by AG and AC, and AAT was the most abundant trinucleotide motif in both assemblies. Following our SSR-marker development strategy, we designed a total of 370 primer sets. Of these, 236 primer sets were tested, exhibiting 93 % polymorphism between KM and SW3. Those polymorphic SSRs were successfully amplified in the netted and Kirkagac melons, which respectively exhibited 81 and 76 % polymorphism relative to KM, and 32 and 38 % polymorphism relative to SW3. Seven selected SSR markers with a total of 17 alleles (2-3 alleles per locus) were used to distinguish between KM, SW3, and four chamoe cultivars. Our results represent the first attempt to provide genomic resources for Korean landraces for the purposes of chamoe breeding, as well as to discover a set of SSR markers capable of discriminating chamoe varieties from Korea and the rest of Asia, which possess little genetic diversity. This study establishes a highly efficient strategy for developing SSR markers from preliminary Illumina assemblies of AT-rich genomes.

  11. Superconducting Focusing Lenses for the SSR1 Cryomodule of PXIE Test Stand at Fermilab

    Energy Technology Data Exchange (ETDEWEB)

    DiMarco, J. [Fermilab; Tartaglia, M. [Fermilab; Terechkine, I. [Fermilab

    2016-01-01

    Five solenoid-based focusing lenses designed for use inside the SSR1 cryomodule of the PXIE test stand at Fermilab have been fabricated and tested. In addition to a focusing solenoid, each lens is equipped with a set of windings that generate magnetic field in the transverse plane and can be used in the steering dipole mode or as a skew quadrupole corrector. The lenses will be installed between superconducting cavities in the cryomodule, so getting sufficiently low fringe magnetic field was one of the main design requirements. Beam dynamics simulations indicated a need for high accuracy positioning of the lenses in the cryomodule, which triggered a study towards understanding uncertainties of the magnetic axis position relative to the geometric features of the lens. This report summarizes the efforts towards certification of the lenses, including results of performance tests, fringe field data, and uncertainty of the magnetic axis position.

  12. Epidemiology of allergic diseases of the respiratory passages in the Kazakh SSR

    Energy Technology Data Exchange (ETDEWEB)

    Moshkevich, V.S.

    1985-01-01

    Over a period of 20 years, the authors have been studying the distribution, aetiology and causes of increasing incidence of allergic respiratory diseases in various climatogeographic zones of the Kazakh SSR. Large groups of people living in towns and in the country were examined by various methods. The number of patients seeking advice in health service establishments because of allergic rhinitis and bronchial asthma was found to increase every year. A number of factors influencing the incidence of disease were pointed out, such as the character of diet, duration of the person's stay, vaccination against brucellosis, pollution of the atmosphere, local flora, climate, and other factors. Morbidity also depended on the methods of studying the epidemiology of respiratory allergoses. The obtained results will help health service authorities in taking specific measures to reduce morbidity from the mentioned pathological condition.

  13. Genetic analysis and SSR mapping of stem rust resistance gene from wheat mutant D51

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Wheat (Triticum aestivum L.) stem rust caused by Puccinia graminis f.sp.tritici is one of the main diseases of wheat worldwide.Wheat mutant line D51,which forms a highly susceptive cultivar 'L6239' to the three races notated and cultured with immature embryos,shows resistance to prevailing races 21C3CPH,21C3CKH,and 21C3CTR of P.graminis f.sp.tritici in China.In this study,the number and the expression stages of the resistance genes in mutant D51 were studied using inoculation identification and microsatellite (SSR) marker analysis.Two F1 populations from the crosses of D51×L6239 (60 individuals) and D51 × Chinese Spring (60 individuals),their F2 populations (185 and 175 individuals respectively) at the seedling stage,and one F2 population derived from the cross of D51×L6239 (194 individuals) at the adult stage were inoculated with pathogen race 21C3CPH to test for resistance.All F1 individuals of the two crosses were immune to stem rust at both seedling and adult stages.The response pattern of the three F2 populations showed that the R:S segregation ratio was 3:1,suggesting that the stem rust resistance of D51 is controlled by a single dominant gene,and is expressed during the entire growth period.The identification of the stem rust resistance by the F3 progeny test confirmed the credibility of the F2 population test.Segregating populations and small population analyses were used to identify chromosomal regions and molecular markers linked to the gene by the SSR marker method.A total of 675 SSR markers and 185 individuals of the D51 x L6239 F2 population were used to search genetically linked markers to the target gene.Using Mapmaker 3.0 and Map-draw with Kosambi's function and other options set at default values,molecular mapping revealed that the gene was located on chromosome 5DS,linked with and flanked by two SSR markers,Xgwml90 and Xwmc150,at 18.58 and 21.33 cM,respectively.It has been reported that only one stem rust resistant gene,Sr30,is located on the

  14. A genetic linkage map of hexaploid naked oat constructed with SSR markers

    Institute of Scientific and Technical Information of China (English)

    Gaoyuan; Song; Pengjie; Huo; Bin; Wu; Zongwen; Zhang

    2015-01-01

    Naked oat is a unique health food crop in China. Using 202 F2 individuals derived from a hybrid between the variety 578 and the landrace Sanfensan, we constructed a genetic linkage map consisting of 22 linkage groups covering 2070.50 c M and including 208 simple sequence repeat(SSR) markers. The minimum distance between adjacent markers was0.01 c M and the average was 9.95 c M. Each linkage group contained 2–22 markers. The largest linkage group covered 174.40 c M and the shortest one covered 36.80 c M, with an average of 94.11 c M. Thirty-six markers(17.3%) showing distorted segregation were distributed across linkage groups LG5 to LG22. This map complements published oat genetic maps and is applicable for quantitative trait locus analysis, gene cloning and molecular marker-assisted selection.

  15. Hypermutability of genes in Homo sapiens due to the hosting of long mono-SSR.

    Science.gov (United States)

    Loire, Etienne; Praz, Françoise; Higuet, Dominique; Netter, Pierre; Achaz, Guillaume

    2009-01-01

    Simple sequence repeats (SSRs) are very common short repeats in eukaryotic genomes. "Long" SSRs are considered "hypermutable" sequences because they exhibit a high rate of expansion and contraction. Because they are potentially deleterious, long SSRs tend to be uncommon in coding sequences. However, several genes contain long SSRs in their exonic sequences. Here, we identify 1,291 human genes that host a mononucleotide SSR long enough to be prone to expansion or contraction, being called hypermutable hereafter. On the basis of Gene Ontology annotations, we show that only a restricted number of functions are overrepresented among those hypermutable genes including cell cycle and maintenance of DNA integrity. Using a probabilistic model, we show that genes involved in these functions are expected to host long SSRs because they tend to be long and/or are biased in nucleotide composition. Finally, we show that for almost all functions we observe fewer hypermutable sequences than expected under a neutral model. There are however interesting exceptions, for example, genes involved in protein and RNA transport, as well as meiosis and mismatch repair functions that have as many hypermutable genes as expected under neutrality. Conversely, there are functions (e.g., collagen-related genes) where hypermutable genes are more often avoided than in other functions. Our results show that, even though several functions harbor unusually long SSR in their exons, long SSRs are deleterious sequences in almost all functions and are removed by purifying selection. The strength of this purifying selection however greatly varies from function to function. We discuss possible explanations for this intriguing result.

  16. Assessment of Genetic Diversity and Population Genetic Structure of Corylus mandshurica in China Using SSR Markers.

    Directory of Open Access Journals (Sweden)

    Jian-Wei Zong

    Full Text Available Corylus mandshurica, also known as pilose hazelnut, is an economically and ecologically important species in China. In this study, ten polymorphic simple sequence repeat (SSR markers were applied to evaluate the genetic diversity and population structure of 348 C. mandshurica individuals among 12 populations in China. The SSR markers expressed a relatively high level of genetic diversity (Na = 15.3, Ne = 5.6604, I = 1.8853, Ho = 0.6668, and He = 0.7777. According to the coefficient of genetic differentiation (Fst = 0.1215, genetic variation within the populations (87.85% were remarkably higher than among populations (12.15%. The average gene flow (Nm = 1.8080 significantly impacts the genetic structure of C. mandshurica populations. The relatively high gene flow (Nm = 1.8080 among wild C. mandshurica may be caused by wind-pollinated flowers, highly nutritious seeds and self-incompatible mating system. The UPGMA (unweighted pair group method of arithmetic averages dendrogram was divided into two main clusters. Moreover, the results of STRUCTURE analysis suggested that C. mandshurica populations fell into two main clusters. Comparison of the UPGMA dendrogram and the Bayesian STRUCTURE analysis showed general agreement between the population subdivisions and the genetic relationships among populations of C. mandshurica. Group I accessions were located in Northeast China, while Group II accessions were in North China. It is worth noting that a number of genetically similar populations were located in the same geographic region. The results further showed that there was obvious genetic differentiation among populations from Northeast China to North China. Results from the Mantel test showed a weak but still significant positive correlation between Nei's genetic distance and geographic distance (km among populations (r = 0.419, P = 0.005, suggesting that genetic differentiation in the 12 C. mandshurica populations might be related to geographic

  17. Assessment of genetic diversity in the sorghum reference set using EST-SSR markers.

    Science.gov (United States)

    Ramu, P; Billot, C; Rami, J-F; Senthilvel, S; Upadhyaya, H D; Ananda Reddy, L; Hash, C T

    2013-08-01

    Selection and use of genetically diverse genotypes are key factors in any crop breeding program to develop cultivars with a broad genetic base. Molecular markers play a major role in selecting diverse genotypes. In the present study, a reference set representing a wide range of sorghum genetic diversity was screened with 40 EST-SSR markers to validate both the use of these markers for genetic structure analyses and the population structure of this set. Grouping of accessions is identical in distance-based and model-based clustering methods. Genotypes were grouped primarily based on race within the geographic origins. Accessions derived from the African continent contributed 88.6 % of alleles confirming the African origin of sorghum. In total, 360 alleles were detected in the reference set with an average of 9 alleles per marker. The average PIC value was 0.5230 with a range of 0.1379-0.9483. Sub-race, guinea margaritiferum (Gma) from West Africa formed a separate cluster in close proximity to wild accessions suggesting that the Gma group represents an independent domestication event. Guineas from India and Western Africa formed two distinct clusters. Accessions belongs to the kafir race formed the most homogeneous group as observed in earlier studies. This analysis suggests that the EST-SSR markers used in the present study have greater discriminating power than the genomic SSRs. Genetic variance within the subpopulations was very high (71.7 %) suggesting that the germplasm lines included in the set are more diverse. Thus, this reference set representing the global germplasm is an ideal material for the breeding community, serving as a community resource for trait-specific allele mining as well as genome-wide association mapping.

  18. Mapping of shoot fly tolerance loci in sorghum using SSR markers

    Indian Academy of Sciences (India)

    D. B. Apotikar; D. Venkateswarlu; R. B. Ghorade; R. M. Wadaskar; J. V. Patil; P. L. Kulwal

    2011-04-01

    Sorghum (Sorghum bicolor (L.) Moench) is one of the most important crops in the semiarid regions of the world. One of the important biotic constraints to sorghum production in India is the shoot fly which attacks sorghum at the seedling stage. Identification of the genomic regions containing quantitative trait loci (QTLs) for resistance to shoot fly and the linked markers can facilitate sorghum improvement programmes through marker-assisted selection. A simple sequence repeat (SSR) marker-based skeleton linkage map of two linkage groups of sorghum was constructed in a population of 135 recombinant inbred lines (RIL) derived from a cross between IS18551 (resistant to shoot fly) and 296B (susceptible to shoot fly). A total of 14 SSR markers, seven each on linkage groups A and C were mapped. Using data of different shoot fly resistance component traits, one QTL which is common for glossiness, oviposition and dead hearts was detected following composite interval mapping (CIM) on linkage group A. The phenotypic variation explained by this QTL ranged from 3.8%–6.3%. Besides the QTL detected by CIM, two more QTLs were detected following multi-trait composite interval mapping (MCIM), one each on linkage groups A and C for the combinations of traits which were correlated with each other. Results of the present study are novel as we could find out the QTLs governing more than one trait (pleiotropic QTLs). The identification of pleiotropic QTLs will help in improvement of more than one trait at a time with the help of the same linked markers. For all the QTLs, the resistant parent IS18551 contributed resistant alleles.

  19. Construction of intersubspecific molecular genetic map of lentil based on ISSR, RAPD and SSR markers

    Indian Academy of Sciences (India)

    Mamta Gupta; Bhawna Verma; Naresh Kumar; Rakesh K. Chahota; Rajeev Rathour; Shyam K. Sharma; Sabhyata Bhatia; Tilak R. Sharma

    2012-12-01

    Lentil (Lens culinaris ssp. culinaris), is a self-pollinating diploid ($2n = 2x = 14$), cool-season legume crop and is consumed worldwide as a rich source of protein (∼24.0%), largely in vegetarian diets. Here we report development of a genetic linkage map of Lens using 114 F2 plants derived from the intersubspecific cross between L 830 and ILWL 77. RAPD (random amplified polymorphic DNA) primers revealed more polymorphism than ISSR (intersimple sequence repeat) and SSR (simple sequence repeat) markers. The highest proportion (30.72%) of segregation distortion was observed in RAPD markers. Of the 235 markers (34 SSR, 9 ISSR and 192 RAPD) used in the mapping study, 199 (28 SSRs, 9 ISSRs and 162 RAPDs) were mapped into 11 linkage groups (LGs), varying between 17.3 and 433.8 cM and covering 3843.4 cM, with an average marker spacing of 19.3 cM. Linkage analysis revealed nine major groups with 15 or more markers each and two small LGs with two markers each, and 36 unlinked markers. The study reported assigning of 11 new SSRs on the linkage map. Of the 66 markers with aberrant segregation, 14 were unlinked and the remaining 52 were mapped. ISSR and RAPD markers were found to be useful in map construction and saturation. The current map represents maximum coverage of lentil genome and could be used for identification of QTL regions linked to agronomic traits, and for marker-assisted selection in lentil.

  20. SSR mining in oil palm EST database: application in oil palm germplasm diversity studies

    Indian Academy of Sciences (India)

    Ngoot-Chin Ting; Noorhariza Mohd Zaki; Rozana Rosli; Eng-Ti Leslie Low; Maizura Ithnin; Suan-Choo Cheah; Soon-Guan Tan; Rajinder Singh

    2010-08-01

    This study reports on the detection of additional expressed sequence tags (EST) derived simple sequence repeat (SSR) markers for the oil palm. A large collection of 19243 Elaeis guineensis ESTs were assembled to give 10258 unique sequences, of which 629 ESTs were found to contain 722 SSRs with a variety of motifs. Dinucleotide repeats formed the largest group (45.6%) consisting of 66.9% AG/CT, 21.9% AT/AT, 10.9% AC/GT and 0.3% CG/CG motifs. This was followed by trinucleotide repeats, which is the second most abundant repeat types (34.5%) consisting of AAG/CTT (23.3%), AGG/CCT (13.7%), CCG/CGG (11.2%), AAT/ATT (10.8%), AGC/GCT (10.0%), ACT/AGT (8.8%), ACG/CGT (7.6%), ACC/GGT (7.2%), AAC/GTT (3.6%) and AGT/ACT (3.6%) motifs. Primer pairs were designed for 405 unique EST-SSRs and 15 of these were used to genotype 105 E. guineensis and 30 E. oleifera accessions. Fourteen SSRs were polymorphic in at least one germplasm revealing a total of 101 alleles. The high percentage (78.0%) of alleles found to be specific for either E. guineensis or E. oleifera has increased the power for discriminating the two species. The estimates of genetic differentiation detected by EST-SSRs were compared to those reported previously. The transferability across palm taxa to two Cocos nucifera and six exotic palms is also presented. The polymerase chain reaction (PCR) products of three primer-pairs detected in E. guineensis, E. oleifera, C. nucifera and Jessinia bataua were cloned and sequenced. Sequence alignments showed mutations within the SSR site and the flanking regions. Phenetic analysis based on the sequence data revealed that C. nucifera is closer to oil palm compared to J. bataua; consistent with the taxanomic classification.

  1. Evaluation of rice germplasm under salt stress at the seedling stage through SSR markers

    Directory of Open Access Journals (Sweden)

    M. Al-Amin

    2013-06-01

    Full Text Available Twenty eight rice germplasms were used for identification of salt tolerant rice genotypes at the seedling stage at the experimental farm and Biotechnology laboratory of the Bangladesh Institute of Nuclear Agriculture (BINA, Mymensingh during February 2009 to October 2009. Phenotyping for salinity screening of the rice genotypes was done using salinized (EC level 12 dS m-1 nutrient solution in hydroponic system. Genotypes were evaluated for salinity tolerance on 1-9 scale based on seedling growth parameters following modified Standard Evaluation Scoring (SES of IRRI. Phenotypically, on the basis of SES and % total dry matter (TDM reduction of the genotypes viz. PBSAL-614, PBSAL-613, PBSAL-730, Horkuch, S-478/3 Pokkali and PBSAL (STL-15 were found to be salt tolerant; on the other hand Iratom-24, S-653/32, S-612/32, S-604/32, S-633/32, Charnock (DA6, BINA Dhan-6 and S-608/32 were identified as salt susceptible. For genotyping, ten SSR markers were used for polymorphism, where 3 primers (RM127, RM443 and RM140 were selected for evaluation of salt tolerance. In respect of Primer RM127, 7 lines were found salt tolerant and 11 lines were moderately tolerant and 10 lines were susceptible. Nine tolerant, 9 moderately tolerant and 10 susceptible lines were found when the primer RM140 was used and primer RM443 identified 8 lines as tolerant, 9 lines as moderately tolerant and 11 lines as susceptible. Thus, the salt tolerant lines can be used in further evaluation for salinity tolerance and the SSR markers used in this study are proving valuable for identifying salt tolerant genes in marker assisted breeding.

  2. 油梨基因组DNA提取、SSR-PCR反应体系优化及引物筛选%DNA Extraction,Optimization of SSR-PCR Reaction System and Primer Screening of Persea americana

    Institute of Scientific and Technical Information of China (English)

    周海兰; 李绍鹏; 李卫亮; 贺军虎; 包冬红; 李茂富

    2016-01-01

    旨在建立稳定可靠的油梨(Persea americana Mill)叶片DNA的提取方法和SSR-PCR反应体系及筛选出稳定的油梨SSR多态性引物,为开展油梨种质SSR分子标记提供遗传研究的基础。以油梨叶片为试材,比较3种油梨叶片DNA提取方法;利用L16(45)正交实验设计对油梨SSR-PCR反应体系进行优化;利用优化的反应体系筛选引物;同时,选取5对多态性引物对45份油梨种质进行PCR扩增,进一步检测该优化体系的稳定性。结果表明,常规2×CTAB法、改良2×CTAB法和植物DNA提取试剂盒法等3种DNA提取方法中,改良2×CTAB法对油梨基因组DNA的提取效果最佳;获得最优反应体系为:20μL总反应体系中,含约40 ng DNA模板、1.5 mmol/L Mg2+、0.15 mmol/L dNTPs、0.5 U Taq DNA聚合酶、0.5μmol/L引物;以此体系为基础进行引物筛选,从73对油梨SSR引物中筛选出了30对扩增条带清晰的多态性引物,说明该反应体系可用于油梨SSR标记的进一步研究;稳定性检测获得的谱带清晰,表明该优化反应体系是稳定可靠的。由此可见,改良的2×CTAB法可用于油梨叶片DNA的大量样本提取,优化后的SSR-PCR反应体系及筛选出的30对多态性引物可用于油梨SSR标记的进一步研究。%This study is to establish a stable and reliable DNA extraction method,optimize the SSR-PCR reaction system,and screen the stable polymorphism primers for avocado(Persea americana Mill)SSR for providing the genetic foundation to conduct the SSR molecular marker of germplasm in avocados. Taking avocado’leaves as the study material,3 avocado DNA extraction methods were compared,based on the L16(45)orthogonal experiment design,the SSR-PCR reaction system in avocados was optimized,and then by optimized reaction system the SSR primers were screened. To further test the stability of the optimized SSR-PCR system,the germplasms in 45 pieces of avocados were amplified by

  3. 12个玉米群体的 SSR 遗传多样性分析%Analyzing on SSR Genetic Diversity of 12 Maize Populations

    Institute of Scientific and Technical Information of China (English)

    孙峰成; 冯勇; 赵瑞霞; 苏二虎; 张来厚; 刘志雄; 石海波

    2013-01-01

    为明确玉米群体的遗传变异性,利用SSR分子标记技术,采用12株叶片混合、每个群体5个混合样本提取DNA的最优取样方法,对12个玉米群体及6个对照自交系进行遗传多样性分析,试验筛选出86对SSR适宜引物,共扩增出391条多态性带,每个位点上的等位基因数为2~11条,平均5.67条,以GD值0.67为基准,划分为6个类群。蒙A群、蒙B群、中综5号、黄早4为第一类,蒙C群、蒙群1、掖478为第二类,蒙群2、蒙群4、C群1、C群2、Mo17为第三类,蒙群3、C群3、中综7号、B73为第四类,丹340和齐319各单独为一类,该结果与产量SCA效应分析划分结果基本一致。%The widely genetic diversity in maize population is the important basis for maize breeding .To clear the genetic basis and genetic diversity is very important for germplasm enhancement and improvement of maize .In this research,SSR molecular marker technology and the best sampling method ,which DNA was extracted from five samples in each maize population and mixture of leaves of 12 plants, was adopted .The genetic diversity from 12 maize populations and 6 control inbred lines were analysed .86 pairs SSR primers were filtered in this experiment , 391 polymorphic bands were gained .The number of alleles ranged from 2 to 11,the average is 5.76.The studied 12 maize populations and 6 control inbred lines could be partitioned into 6 class groups on the basis of 0 .67 for the GD value.Meng A,Meng B,Zhongzong 5 and Huangzao 4 are belonged to one group ,Meng C,Mengqun 1 and Ye 478 are belonged to the second group ,Mengqun 2,Mengqun 4,C Qun 1,C Qun 2 and Mo17 are belonged to the third group,Mengqun 3,C Qun 3,Zhongzong 7 and B73 are belonged to the fourth group ,Dan 340 and Qi 319 are belonged to the fifth and sixth group ,respectively .The partition is similar with the partition based on the yield SCA effect .

  4. Molecular characterization of potato cultivars using SSR markers Caracterização molecular de cultivares de batata por marcadores SSR

    Directory of Open Access Journals (Sweden)

    Patrícia Favoretto

    2011-12-01

    Full Text Available The potato crop has a very narrow genetic base, so the use of molecular markers is a very important tool in the characterization of germplasm banks and evaluation of genetic divergence. The objective of this study was to identify, using microsatellite or simple sequence repeat (SSR markers, 38 accessions of potato from two collections of commercial cultivars. For the molecular characterization 10 loci were used, generating a total of 46 alleles, which were analyzed as binary data. A cluster analysis was performed with the Jaccard´s similarity coefficient and the UPGMA method, using the software NTSYSpc. On average, the number of alleles per locus was 4.6, ranging from two alleles for primers STM1049, STM 1053 and STM 1104 to 12 alleles per locus for primer STM0019a. Of the 46 alleles, only five were monomorphic, therefore presenting 89.1% polymorphism. The polymorphism information content (PIC varied from 0.13 to 0.86, with an average of 0.54. The Jaccard´s coefficient varied from 0.41 to 0.93, showing high genetic variability among accessions. Two possible duplicates [Atlantic (Canada and Atlantic (Chile, and Colorado and Ágata (EPAMIG (duplicates with these SSRs, which did not separate them] were identified. High similarity was also shown by cultivars Chipie and Melodie (EPAMIG, Voyager and Gourmandine (EPAMIG, Eole and Caesar (EPAMIG, and Cupido and Santé (Pirassu. The most genetically divergent accessions (Lady Rosetta and HPC-7B were also identified.A batata possui uma base genética estreita, sendo assim a utilização de marcadores moleculares é uma ferramenta muito importante no processo de caracterização de bancos de germoplasma e avaliação de divergência genética. O objetivo deste trabalho foi avaliar por meio de marcadores microssatélites ou Simple Sequence Repeats (SSR, 38 acessos de batata de duas coleções distintas contendo cultivares comerciais. Para a caracterização molecular foram analisados 10 loci, gerando um

  5. Genetic diversity analysis of Amomum tsao-ko in Jinping County of Yunnan Province using SSR markers

    Science.gov (United States)

    Ma, Mengli; Wang, Tiantao; Lei, En; Meng, Hengling; Xie, Linyan; Zhu, Kunlong; Duan, Shaoze; Li, Wenqiang; Lu, Bingyue

    2017-08-01

    Genetic diversity analysis is very important for germplasm resources conservation and utilization. The objective of this study was to assess the genetic diversity among 44 individuals of Amomum tsao-ko from Jinping County of Yunnan Province using 5 selected SSR (simple sequence repeat) markers. A total of 23 polymorphic loci were detected among these germplasms, with an average of 4.6 polymorphic loci per SSR primer combination. The percentage of polymorphic loci was 100%, whereas the mean effective number of alleles (Ne), observed heterozygosity(Ho), expected heterozygosity (He), Shannon's information index (I), and the mean polymorphism information content (PIC) were 3. 410, 0. 491, 0. 679, 1.266 and 0. 672, respectively, indicating that the Amomum tsao-ko germplasms from Jinping County had high genetic diversity.

  6. Selection and development of representative simple sequence repeat primers and multiplex SSR sets for high throughput automated genotyping in maize

    Institute of Scientific and Technical Information of China (English)

    WANG FengGe; ZHAO JiuRan; DAI JingRui; YI HongMei; KUANG Meng; SUN YanMei; YU XinYan; GUO JingLun; WANG Lu

    2007-01-01

    In the current study, 1900 maize simple sequence repeat (SSR) primers published in MaizeGDB were screened utilizing reference literature, 15 representative Chinese maize inbred lines and 15 Chinese maize hybrids from national regional testing. In total, 500 highly polymorphic primers were identified and used to construct a genetic map. 100 evenly distributed primers, 10 primers per chromosome, were further selected as a set of universal SSR core primers, recommended as preferred primers for general studies. These core primers were then redesigned and used to construct a high throughput multiplex PCR system based on a five-color fluorescence capillary detection system. We report here that two sets of ten-plex PCR combinations have been constructed, each consisting of 10 primers, with one primer per chromosome.

  7. Comparison of hybrid vigor based on parental distance in SSR markers and agronomic traits in mungbean (Vigna radiata (L. Wilczek

    Directory of Open Access Journals (Sweden)

    Worawit Sorajjapinun

    2012-02-01

    Full Text Available Heterosis of seed yield in mungbean (Vigna radiata (L. Wilczek has created an interest among plant breeders todevelop hybrid mungbean cultivars. The objective of this study was to compare levels of heterosis among four F1 hybrids ofmungbeans with different genetic distance. The hybrids were developed by using Sukhothai (SKT as the female parent andpollinated by male parents of different genetic distance as revealed by SSR markers. They were H192 (close distance, C357(moderate distance, TC1965 (high distance and W166 (very high distance. The results revealed that the F1 from the parentswith larger genetic distance showed higher heterosis in yield per plant and number of pods per plant. Thus SSR markerscombined with yield components can be used to identify parental lines with high genetic distance for hybrid seed productionin mungbean. This approach potentially helps to reduce the amount of fieldwork required for evaluation of F1 hybrids.

  8. Association of SSR markers with contents of fatty acids in olive oil and genetic diversity analysis of an olive core collection.

    Science.gov (United States)

    Ipek, M; Ipek, A; Seker, M; Gul, M K

    2015-03-27

    The purpose of this research was to characterize an olive core collection using some agronomic characters and simple sequence repeat (SSR) markers and to determine SSR markers associated with the content of fatty acids in olive oil. SSR marker analysis demonstrated the presence of a high amount of genetic variation between the olive cultivars analyzed. A UPGMA dendrogram demonstrated that olive cultivars did not cluster on the basis of their geographic origin. Fatty acid components of olive oil in these cultivars were determined. The results also showed that there was a great amount of variation between the olive cultivars in terms of fatty acid composition. For example, oleic acid content ranged from 57.76 to 76.9% with standard deviation of 5.10%. Significant correlations between fatty acids of olive oil were observed. For instance, a very high negative correlation (-0.812) between oleic and linoleic acids was detected. A structured association analysis between the content of fatty acids in olive oil and SSR markers was performed. STRUCTURE analysis assigned olive cultivars to two gene pools (K = 2). Assignment of olive cultivars to these gene pools was not based on geographical origin. Association between fatty acid traits and SSR markers was evaluated using the general linear model of TASSEL. Significant associations were determined between five SSR markers and stearic, oleic, linoleic, and linolenic acids of olive oil. Very high associations (P olive.

  9. 基于 SSR 分子标记的芥蓝遗传多样性分析%Genetic Diversity of Chinese Kale Based on SSR Markers

    Institute of Scientific and Technical Information of China (English)

    张德双; 卢桂香; 张娜; 于拴仓; 张凤兰; 隋光磊; 余阳俊; 赵岫云; 汪维红; 苏同兵

    2014-01-01

    Classification and genetic diversity of local varieties in Chinese kale were studied before .With the extending of Chinese kale hybrids ,they can show higher heterosis and better benefit .Therefore study on genetic di-versity of inbred lines is important now .In this research ,98 Chinese kale inbred lines were analyzed by 15 polymor-phic SSR markers which were selected from 55 pairs of primers locating on 9 chromosomes of cabbage .65 polymor-phic bands were detected by these 15 pairs of primers .UPGMA method was used to determine genetic diversities of 98 Chinese kale inbred lines .They were initially clustered intoⅠ,Ⅱ,Ⅲ,Ⅳ,Ⅴ groups with coefficient 0.71.Re-sults can be used to breed Chinese kale including selection and match of parents ,identification of hybrids and pro-tection of resources .%芥蓝的研究多集中在分类、常规种资源遗传多样性等方面。随着芥蓝杂交种的问世,杂交种的优势越来越突出,市场效果明显,因此,对芥蓝自交系的遗传多样性等研究尤为重要。选取分布在甘蓝9条染色体上的55对SSR引物,从中筛选出多态性好、分布均匀的15条SSR引物对98份芥蓝自交系进行分析,共得到65个多态性带型。采用UPGMA方法构建了一张聚类图,在相似系数为0.71时,将98份芥蓝自交系初步分为1,2,3,4,5组。研究结果为芥蓝育种中的亲本选配、杂交种鉴定和资源保护等提供了依据。在试配芥蓝新组合时,应选择遗传距离较远的自交系作为重点材料,后代的杂种优势会更显著。

  10. Genetic diversity, Population structure, parentage analysis, and construction of core collections in the French apple germplasm based on SSR markers

    OpenAIRE

    Lassois, Ludivine; Denancé, Caroline; Ravon, Elisa; Guyader, Arnaud; Guisnel, Rémi; Hibrand-Saint-Oyan, Laurence; Poncet, Charles; Lasserre - Zuber, Pauline; Feugey, Laurence; Durel, Charles-Eric

    2016-01-01

    In-depth characterization of apple genetic resources is a prerequisite for genetic improvement and for germplasm management. In this study, we fingerprinted a very large French collection of 2163 accessions with 24 SSR markers in order to evaluate its genetic diversity, population structure and genetic relationships, to link these features with cultivar selection date or usage (old or modern, dessert or cider cultivars), and to construct core collections. Most markers were highly discriminati...

  11. De Novo Transcriptome Assembly of the Chinese Swamp Buffalo by RNA Sequencing and SSR Marker Discovery.

    Directory of Open Access Journals (Sweden)

    Tingxian Deng

    Full Text Available The Chinese swamp buffalo (Bubalis bubalis is vital to the lives of small farmers and has tremendous economic importance. However, a lack of genomic information has hampered research on augmenting marker assisted breeding programs in this species. Thus, a high-throughput transcriptomic sequencing of B. bubalis was conducted to generate transcriptomic sequence dataset for gene discovery and molecular marker development. Illumina paired-end sequencing generated a total of 54,109,173 raw reads. After trimming, de novo assembly was performed, which yielded 86,017 unigenes, with an average length of 972.41 bp, an N50 of 1,505 bp, and an average GC content of 49.92%. A total of 62,337 unigenes were successfully annotated. Among the annotated unigenes, 27,025 (43.35% and 23,232 (37.27% unigenes showed significant similarity to known proteins in NCBI non-redundant protein and Swiss-Prot databases (E-value < 1.0E-5, respectively. Of these annotated unigenes, 14,439 and 15,813 unigenes were assigned to the Gene Ontology (GO categories and EuKaryotic Ortholog Group (KOG cluster, respectively. In addition, a total of 14,167 unigenes were assigned to 331 Kyoto Encyclopedia of Genes and Genomes (KEGG pathways. Furthermore, 17,401 simple sequence repeats (SSRs were identified as potential molecular markers. One hundred and fifteen primer pairs were randomly selected for amplification to detect polymorphisms. The results revealed that 110 primer pairs (95.65% yielded PCR amplicons and 69 primer pairs (60.00% presented polymorphisms in 35 individual buffaloes. A phylogenetic analysis showed that the five swamp buffalo populations were clustered together, whereas two river buffalo breeds clustered separately. In the present study, the Illumina RNA-seq technology was utilized to perform transcriptome analysis and SSR marker discovery in the swamp buffalo without using a reference genome. Our findings will enrich the current SSR markers resources and help spearhead

  12. Development of SSR Markers and Genetic Diversity in White Birch (Betula platyphylla.

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    Wei Hao

    Full Text Available In order to study genetic diversity of white birch (Betula platyphylla, 544 primer pairs were designed based on the genome-wide Solexa sequences. Among them, 215 primer pairs showed polymorphism between five genotypes and 111 primer pairs that presented clear visible bands in genotyping 41 white birch plants that were collected from 6 different geographical regions. A total of 717 alleles were obtained at 111 loci with a range of 2 to 12 alleles per locus. The results of statistic analysis showed that polymorphic frequency of the alleles ranged from 17% to 100% with a mean of 55.85%; polymorphism information content (PIC of the loci was from 0.09 to 0.58 with a mean of 0.30; and gene diversity between the tested genotypes was from 0.01 to 0.66 with a mean of 0.36. The results also indicated that major allele frequency ranged from 0.39 to 1.00 with an mean of 0.75; expected heterozygosity from 0.22 to 0.54 with a mean of 0.46; observed heterozygosity from 0.02 to 0.95 with a mean of 0.26; Nei's index from 0.21 to 0.54 with a mean of 0.46; and Shannon's Information from 0.26 to 0.87 with a mean of 0.66. The 41 white birch genotypes at the 111 selected SSR loci showed low to moderate similarity (0.025-0.610, indicating complicated genetic diversity among the white birch collections. The UPGMA-based clustering analysis of the allelic constitution of 41 white birch genotypes at 111 SSR loci suggested that the six different geographical regions can be further separated into four clusters at a similarity coefficient of 0.22. Genotypes from Huanren and Liangshui provenances were grouped into Cluster I, genotypes from Xiaobeihu and Qingyuan provenances into Cluster II, genotypes from Finland provenance into Cluster III, and genotypes from Maoershan into Cluster IV. The information provided in this study could help for genetic improvement and germplasm conservation, evaluation and utilization in white birch tree breeding program.

  13. Exploring the Transcriptome Landscape of Pomegranate Fruit Peel for Natural Product Biosynthetic Gene and SSR Marker Discovery(F).

    Science.gov (United States)

    Ono, Nadia Nicole; Britton, Monica Therese; Fass, Joseph Nathaniel; Nicolet, Charles Meyer; Lin, Dawei; Tian, Li

    2011-10-01

    Pomegranate fruit peel is rich in bioactive plant natural products, such as hydrolyzable tannins and anthocyanins. Despite their documented roles in human nutrition and fruit quality, genes involved in natural product biosynthesis have not been cloned from pomegranate and very little sequence information is available on pomegranate in the public domain. Shotgun transcriptome sequencing of pomegranate fruit peel cDNA was performed using RNA-Seq on the Illumina Genome Analyzer platform. Over 100 million raw sequence reads were obtained and assembled into 9,839 transcriptome assemblies (TAs) (>200 bp). Candidate genes for hydrolyzable tannin, anthocyanin, flavonoid, terpenoid and fatty acid biosynthesis and/or regulation were identified. Three lipid transfer proteins were obtained that may contribute to the previously reported IgE reactivity of pomegranate fruit extracts. In addition, 115 SSR markers were identified from the pomegranate fruit peel transcriptome and primers were designed for 77 SSR markers. The pomegranate fruit peel transcriptome set provides a valuable platform for natural product biosynthetic gene and SSR marker discovery in pomegranate. This work also demonstrates that next-generation transcriptome sequencing is an economical and effective approach for investigating natural product biosynthesis, identifying genes controlling important agronomic traits, and discovering molecular markers in non-model specialty crop species.

  14. Genetic Characterization of Turkish Snake Melon (Cucumis melo L. subsp. melo flexuosus Group) Accessions Revealed by SSR Markers.

    Science.gov (United States)

    Solmaz, Ilknur; Kacar, Yildiz Aka; Simsek, Ozhan; Sari, Nebahat

    2016-08-01

    Snake melon is an important cucurbit crop especially in the Southeastern and the Mediterranean region of Turkey. It is consumed as fresh or pickled. The production is mainly done with the local landraces in the country. Turkey is one of the secondary diversification centers of melon and possesses valuable genetic resources which have different morphological characteristics in case of snake melon. Genetic diversity of snake melon genotypes collected from different regions of Turkey and reference genotypes obtained from World Melon Gene Bank in Avignon-France was examined using 13 simple sequence repeat (SSR) markers. A total of 69 alleles were detected, with an average of 5.31 alleles per locus. The polymorphism information content of SSR markers ranged from 0.19 to 0.57 (average 0.38). Based on cluster analysis, two major groups were defined. The first major group included only one accession (61), while the rest of all accessions grouped in the second major group and separated into different sub-clusters. Based on SSR markers, cluster analysis indicated that considerably high genetic variability exists among the examined accessions; however, Turkish snake melon accessions were grouped together with the reference snake melon accessions.

  15. Development of EST-SSR markers for the study of population structure in lettuce (Lactuca sativa L.).

    Science.gov (United States)

    Simko, Ivan

    2009-01-01

    A set of 61 simple sequence repeat (SSR) markers was developed from the 19,523 Lactuca sativa and Lactuca serriola unigenes. Approximately 4.5% of the unigenes contained a perfect SSR at least 20 bp long, corresponding to roughly 1 perfect SSR per 14.7 kb. Marker polymorphism was tested on a set comprising 96 accessions representing all major horticultural types and 3 wild species (L. serriola, Lactuca saligna, and Lactuca virosa). Both the average marker heterozygosity (UHe = 0.32) and the number of different alleles per locus (Na = 3.56) were significantly reduced in expressed sequence tag (EST)-SSRs as compared with anonymous SSRs (UHe = 0.59, Na = 5.53). Marker transfer rate to the wild species corresponded to the decreasing sexual compatibility with L. sativa and was higher for EST-SSRs (100% L. serriola, 87% L. saligna, and 75% L. virosa) than for anonymous SSRs (93%, 66%, and 42%, respectively). Assessment of population structure among 90 L. sativa cultivars with SSRs was in good agreement with classification into the horticultural types. The average marker heterozygosity was smallest in iceberg (0.097), Latin (0.140), and romaine-type (0.151) cultivars while highest in leaf (green leaf 0.208 and red leaf 0.240) lettuces. The level of marker heterozygosity is in accord with morphological variability observed in different horticultural types.

  16. Genetic Diversity of Namibian Pennisetum glaucum (L.) R. BR. (Pearl Millet) Landraces Analyzed by SSR and Morphological Markers.

    Science.gov (United States)

    McBenedict, Billy; Chimwamurombe, Percy; Kwembeya, Ezekeil; Maggs-Kölling, Gillian

    2016-01-01

    Current Pennisetum glaucum (L.) R. BR. cultivars in Namibia have overall poor performance posing a threat to the nation's food security because this crop is staple for over 70% of the Namibian population. The crop suffers from undesirable production traits such as susceptibility to diseases, low yield, and prolonged reproductive cycle. This study aimed to understand the genetic diversity of the crop in Namibia by simple sequence repeats (SSRs) and morphology analysis. A total of 1441 genotypes were collected from the National Gene Bank representing all the Namibian landraces. A sample of 96 genotypes was further analyzed by SSR using Shannon-Wiener diversity index and revealed a value of 0.45 indicating low genetic diversity. Ordination using Principal Coordinate Analysis (PCoA) on SSR data confirmed clusters generated by UPGMA for the 96 P. glaucum accessions. UPGMA phenograms of 29 morphological characterized genotypes were generated for SSR and morphology data and the two trees revealed 78% resemblance. Lodging susceptibility, tillering attitude, spike density, fodder yield potential, early vigour, and spike shape were the phenotypic characters upon which some clusters were based in both datasets. It is recommended that efforts should be made to widen the current gene pool in Namibia.

  17. Genetic Diversity of Namibian Pennisetum glaucum (L. R. BR. (Pearl Millet Landraces Analyzed by SSR and Morphological Markers

    Directory of Open Access Journals (Sweden)

    Billy McBenedict

    2016-01-01

    Full Text Available Current Pennisetum glaucum (L. R. BR. cultivars in Namibia have overall poor performance posing a threat to the nation’s food security because this crop is staple for over 70% of the Namibian population. The crop suffers from undesirable production traits such as susceptibility to diseases, low yield, and prolonged reproductive cycle. This study aimed to understand the genetic diversity of the crop in Namibia by simple sequence repeats (SSRs and morphology analysis. A total of 1441 genotypes were collected from the National Gene Bank representing all the Namibian landraces. A sample of 96 genotypes was further analyzed by SSR using Shannon-Wiener diversity index and revealed a value of 0.45 indicating low genetic diversity. Ordination using Principal Coordinate Analysis (PCoA on SSR data confirmed clusters generated by UPGMA for the 96 P. glaucum accessions. UPGMA phenograms of 29 morphological characterized genotypes were generated for SSR and morphology data and the two trees revealed 78% resemblance. Lodging susceptibility, tillering attitude, spike density, fodder yield potential, early vigour, and spike shape were the phenotypic characters upon which some clusters were based in both datasets. It is recommended that efforts should be made to widen the current gene pool in Namibia.

  18. Transferability of simple sequence repeat (SSR) markers developed in guava (Psidium guajava L.) to four Myrtaceae species.

    Science.gov (United States)

    Rai, Manoj K; Phulwaria, Mahendra; Shekhawat, N S

    2013-08-01

    Present study demonstrated the cross-genera transferability of 23 simple sequence repeat (SSR) primer pairs developed for guava (Psidium guajava L.) to four new targets, two species of eucalypts (Eucalyptus citriodora, Eucalyptus camaldulensis), bottlebrush (Callistemon lanceolatus) and clove (Syzygium aromaticum), belonging to the family Myrtaceae and subfamily Myrtoideae. Off the 23 SSR loci assayed, 18 (78.2%) gave cross-amplification in E. citriodora, 14 (60.8%) in E. camaldulensis and 17-17 (73.9%) in C. lanceolatus and S. aromaticum. Eight primer pairs were found to be transferable to all four species. The number of alleles detected at each locus ranged from one to nine, with an average of 4.8, 2.6, 4.5 and 4.6 alleles in E. citriodora, E. camaldulensis, C. lanceolatus and S. aromaticum, respectively. The high levels of cross-genera transferability of guava SSRs may be applicable for the analysis of intra- and inter specific genetic diversity of target species, especially in E. citriodora, C. lanceolatus and S. aromaticum, for which till date no information about EST-derived as well as genomic SSR is available.

  19. Exploring the Transcriptome Landscape of Pomegranate Fruit Peel for Natural Product Biosynthetic Gene and SSR Marker Discovery

    Institute of Scientific and Technical Information of China (English)

    Nadia Nicole Ono; Monica Therese Britton; Joseph Nathaniel Fass; Charles Meyer Nicolet; Dawei Lin; Li Tian

    2011-01-01

    Pomegranate fruit peel is rich in bioactive plant natural products,such as hydrolyzable tannins and anthocyanins.Despite their documented roles in human nutrition and fruit quality,genes involved in natural product biosynthesis have not been cloned from pomegranate and very little sequence information is available on pomegranate in the public domain.Shotgun transcriptome sequencing of pomegranate fruit peel cDNA was performed using RNA-Seq on the Illumina Genome Analyzer platform.Over 100 million raw sequence reads were obtained and assembled into 9,839 transcriptome assemblies (TAs) (>200 bp).Candidate genes for hydrolyzable tannin,anthocyanin,flavonoid,terpenoid and fatty acid biosynthesis and/or regulation were identified.Three lipid transfer proteins were obtained that may contribute to the previously reported IgE reactivity of pomegranate fruit extracts.In addition,115 SSR markers were identified from the pomegranate fruit peel transcriptome and primers were designed for 77 SSR markers.The pomegranate fruit peel transcriptome set provides a valuable platform for natural product biosynthetic gene and SSR marker discovery in pomegranate.This work also demonstrates that next-generation transcriptome sequencing is an economical and effective approach for investigating natural product biosynthesis,identifying genes controlling important agronomic traits,and discovering molecular markers in non-model specialty crop species.

  20. Genetic map of triticale compiling DArT, SSR, and AFLP markers.

    Science.gov (United States)

    Tyrka, M; Bednarek, P T; Kilian, A; Wędzony, M; Hura, T; Bauer, E

    2011-05-01

    A set of 90 doubled haploid (DH) lines derived from F(1) plants that originated from a cross between × Triticosecale Wittm. 'Saka3006' and ×Triticosecale Wittm. 'Modus', via wide crossing with maize, were used to create a genetic linkage map of triticale. The map has 21 linkage groups assigned to the A, B, and R genomes including 155 simple sequence repeat (SSR), 1385 diversity array technology (DArT), and 28 amplified fragment length polymorphism (AFLP) markers covering 2397 cM with a mean distance between two markers of 4.1 cM. Comparative analysis with wheat consensus maps revealed that triticale chromosomes of the A and B genomes were represented by 15 chromosomes, including combinations of 2AS.2AL#, 2AL#2BL, 6AS.6AL#, and 2BS.6AL# instead of 2A, 2B, and 6A. In respect to published maps of rye, substantial rearrangements were found also for chromosomes 1R, 2R, and 3R of the rye genome. Chromosomes 1R and 2R were truncated and the latter was linked with 3R. A nonhomogeneous distribution of markers across the triticale genome was observed with evident bias (48%) towards the rye genome. This genetic map may serve as a reference linkage map of triticale for efficient studies of structural rearrangements, gene mapping, and marker-assisted selection.

  1. Genetic Diversity in Jatropha curcas L. Assessed with SSR and SNP Markers

    Directory of Open Access Journals (Sweden)

    Juan M. Montes

    2014-08-01

    Full Text Available Jatropha curcas L. (jatropha is an undomesticated plant that has recently received great attention for its utilization in biofuel production, rehabilitation of wasteland, and rural development. Knowledge of genetic diversity and marker-trait associations is urgently needed for the design of breeding strategies. The main goal of this study was to assess the genetic structure and diversity in jatropha germplasm with co-dominant markers (Simple Sequence Repeats (SSR and Single Nucleotide Polymorphism (SNP in a diverse, worldwide, germplasm panel of 70 accessions. We found a high level of homozygosis in the germplasm that does not correspond to the purely outcrossing mating system assumed to be present in jatropha. We hypothesize that the prevalent mating system of jatropha comprise a high level of self-fertilization and that the outcrossing rate is low. Genetic diversity in accessions from Central America and Mexico was higher than in accession from Africa, Asia, and South America. We identified makers associated with the presence of phorbol esters. We think that the utilization of molecular markers in breeding of jatropha will significantly accelerate the development of improved cultivars.

  2. Genetic Diversity Among Historical Olive (Olea europaea L.) Genotypes from Southern Anatolia Based on SSR Markers.

    Science.gov (United States)

    Sakar, Ebru; Unver, Hulya; Ercisli, Sezai

    2016-12-01

    Olive (Olea europaea) is an ancient and important crop in both olive oil production and table use. It is important to identify the genetic diversity of olive genetic resources for cultivar development and evaluation of olive germplasm. In the study, 14 microsatellite markers (UDO4, UDO8, UDO9, UDO11, UDO12, UDO22, UDO24, UDO26, UDO28, DCA9, DCA11, DCA13, DCA15, and DCA18) were used to assess the genetic variation on 76 olive (Olea europaea L.) genotypes from Mardin province together with 6 well-known Turkish and 4 well-known foreign reference cultivars. All microsatellite markers showed polymorphism and the number of alleles varied between 9 and 22, with an average of 14.57. The most informative loci were DCA 11 (22 alleles) and DCA 9 (21 alleles). Dendrogram based on genetic distances was constructed for the 86 olive genotypes/cultivars, which revealed the existence of different clusters. The high genetic similarity was evident between Bakırkire2 and Zinnar5 (0.74) genotypes, while the most genetically divergent genotypes were Gürmeşe5 and Yedikardeşler2 (0.19). It was concluded that there was abundant SSR polymorphism in olive germplasm in southern Anatolia in Turkey and could be important for future breeding activities.

  3. tropiTree: an NGS-based EST-SSR resource for 24 tropical tree species.

    Science.gov (United States)

    Russell, Joanne R; Hedley, Peter E; Cardle, Linda; Dancey, Siobhan; Morris, Jenny; Booth, Allan; Odee, David; Mwaura, Lucy; Omondi, William; Angaine, Peter; Machua, Joseph; Muchugi, Alice; Milne, Iain; Kindt, Roeland; Jamnadass, Ramni; Dawson, Ian K

    2014-01-01

    The development of genetic tools for non-model organisms has been hampered by cost, but advances in next-generation sequencing (NGS) have created new opportunities. In ecological research, this raises the prospect for developing molecular markers to simultaneously study important genetic processes such as gene flow in multiple non-model plant species within complex natural and anthropogenic landscapes. Here, we report the use of bar-coded multiplexed paired-end Illumina NGS for the de novo development of expressed sequence tag-derived simple sequence repeat (EST-SSR) markers at low cost for a range of 24 tree species. Each chosen tree species is important in complex tropical agroforestry systems where little is currently known about many genetic processes. An average of more than 5,000 EST-SSRs was identified for each of the 24 sequenced species, whereas prior to analysis 20 of the species had fewer than 100 nucleotide sequence citations. To make results available to potential users in a suitable format, we have developed an open-access, interactive online database, tropiTree (http://bioinf.hutton.ac.uk/tropiTree), which has a range of visualisation and search facilities, and which is a model for the efficient presentation and application of NGS data.

  4. Expressed sequence tags (ESTs and simple sequence repeat (SSR markers from octoploid strawberry (Fragaria × ananassa

    Directory of Open Access Journals (Sweden)

    Bies Dawn H

    2005-06-01

    Full Text Available Abstract Background Cultivated strawberry (Fragaria × ananassa represents one of the most valued fruit crops in the United States. Despite its economic importance, the octoploid genome presents a formidable barrier to efficient study of genome structure and molecular mechanisms that underlie agriculturally-relevant traits. Many potentially fruitful research avenues, especially large-scale gene expression surveys and development of molecular genetic markers have been limited by a lack of sequence information in public databases. As a first step to remedy this discrepancy a cDNA library has been developed from salicylate-treated, whole-plant tissues and over 1800 expressed sequence tags (EST's have been sequenced and analyzed. Results A putative unigene set of 1304 sequences – 133 contigs and 1171 singlets – has been developed, and the transcripts have been functionally annotated. Homology searches indicate that 89.5% of sequences share significant similarity to known/putative proteins or Rosaceae ESTs. The ESTs have been functionally characterized and genes relevant to specific physiological processes of economic importance have been identified. A set of tools useful for SSR development and mapping is presented. Conclusion Sequences derived from this effort may be used to speed gene discovery efforts in Fragaria and the Rosaceae in general and also open avenues of comparative mapping. This report represents a first step in expanding molecular-genetic analyses in strawberry and demonstrates how computational tools can be used to optimally mine a large body of useful information from a relatively small data set.

  5. Massive sorghum collection genotyped with SSR markers to enhance use of global genetic resources.

    Science.gov (United States)

    Billot, Claire; Ramu, Punna; Bouchet, Sophie; Chantereau, Jacques; Deu, Monique; Gardes, Laetitia; Noyer, Jean-Louis; Rami, Jean-François; Rivallan, Ronan; Li, Yu; Lu, Ping; Wang, Tianyu; Folkertsma, Rolf T; Arnaud, Elizabeth; Upadhyaya, Hari D; Glaszmann, Jean-Christophe; Hash, C Thomas

    2013-01-01

    Large ex situ collections require approaches for sampling manageable amounts of germplasm for in-depth characterization and use. We present here a large diversity survey in sorghum with 3367 accessions and 41 reference nuclear SSR markers. Of 19 alleles on average per locus, the largest numbers of alleles were concentrated in central and eastern Africa. Cultivated sorghum appeared structured according to geographic regions and race within region. A total of 13 groups of variable size were distinguished. The peripheral groups in western Africa, southern Africa and eastern Asia were the most homogeneous and clearly differentiated. Except for Kafir, there was little correspondence between races and marker-based groups. Bicolor, Caudatum, Durra and Guinea types were each dispersed in three groups or more. Races should therefore better be referred to as morphotypes. Wild and weedy accessions were very diverse and scattered among cultivated samples, reinforcing the idea that large gene-flow exists between the different compartments. Our study provides an entry to global sorghum germplasm collections. Our reference marker kit can serve to aggregate additional studies and enhance international collaboration. We propose a core reference set in order to facilitate integrated phenotyping experiments towards refined functional understanding of sorghum diversity.

  6. Massive sorghum collection genotyped with SSR markers to enhance use of global genetic resources.

    Directory of Open Access Journals (Sweden)

    Claire Billot

    Full Text Available Large ex situ collections require approaches for sampling manageable amounts of germplasm for in-depth characterization and use. We present here a large diversity survey in sorghum with 3367 accessions and 41 reference nuclear SSR markers. Of 19 alleles on average per locus, the largest numbers of alleles were concentrated in central and eastern Africa. Cultivated sorghum appeared structured according to geographic regions and race within region. A total of 13 groups of variable size were distinguished. The peripheral groups in western Africa, southern Africa and eastern Asia were the most homogeneous and clearly differentiated. Except for Kafir, there was little correspondence between races and marker-based groups. Bicolor, Caudatum, Durra and Guinea types were each dispersed in three groups or more. Races should therefore better be referred to as morphotypes. Wild and weedy accessions were very diverse and scattered among cultivated samples, reinforcing the idea that large gene-flow exists between the different compartments. Our study provides an entry to global sorghum germplasm collections. Our reference marker kit can serve to aggregate additional studies and enhance international collaboration. We propose a core reference set in order to facilitate integrated phenotyping experiments towards refined functional understanding of sorghum diversity.

  7. [Genetic analysis of gelatinization temperature in rice via microsatellite(SSR) markers].

    Science.gov (United States)

    Yan, C J; Xu, C W; Yi, C D; Liang, G H; Zhu, L H; Gu, M H

    2001-11-01

    Rice gelatinization temperature is an important character contributing to cooking quality. Here the inheritance of gelatinization temperature (GT), which was represented by alkali spreading value (ASV), was reported. Two parents, Balilla (japonica variety) and Nantehao (indica variety), which were significantly different on GT-ASV, were selected to construct a backcross population Balilla/Nantehao//Balilla containing 142 individuals. And ASV was investigated in the population, a continuous distribution with two obvious peaks was observed. It indicated that GT-ASV was controlled by one major gene, also modified by some minor genes. In order to map the major and minor genes and estimate the effects of genes. A total of 119 SSR markers were employed to construct a linkage map; further a genome-wide detection was carried out by interval mapping method. The results showed that 6 QTLs were detected, of which, qASV6-1 located on chromosome 6 was a major gene with 87.6% variance explained, and alleles from parent Nantehao could decrease the value. It shoud be the same locus as the alkali degeneration gene (alk). The other QTLs (qASV2, qASV3, qASV6-2, qASV9, and qASV11) all belong to minor genes, which were located on chromosome 2,3,6,9 and 11, respectively. In two parents, they carried the positive and negative alleles simultaneously. These results will be helpful for rice quality breeding and improvement.

  8. A Set of 20 New SSR Markers Developed and Evaluated in Mandevilla Lindl.

    Directory of Open Access Journals (Sweden)

    Alev Oder

    2016-09-01

    Full Text Available Mandevilla is an ornamental crop with a bright future worldwide because of its high commercial acceptance and added value. However, as with most ornamental species, there are few molecular tools to support cultivar breeding and innovation. In this work, we report the development and analysis of 20 new Simple Sequence Repeat (SSR markers in Mandevilla. Microsatellites were isolated from two enriched small-insert genomic libraries of Mandevilla × amabilis. The diversity parameters estimated after their amplification in a group of 11 commercial genotypes illustrate the effect of two opposite drifts: the high relatedness of cultivars belonging to the same commercial group and the high divergence of other cultivars, especially M. × amabilis. Based on their different band patterns, six genotypes were uniquely distinguished, and two groups of sport mutations remained undistinguishable. The amplification of the SSRs in three wild species suggested the existence of unexploited diversity available to be introgressed into the commercial pool. This is the first report of available microsatellites in Mandevilla. The development process has provided some clues concerning the genome structure of the species, and the SSRs obtained will help to create new products and to protect existing and upcoming plant innovations.

  9. Assessment of genetic variation in tomato (Solanum lycopersicum L.) inbred lines using SSR molecular markers

    Institute of Scientific and Technical Information of China (English)

    Solomon Benor; Mengyu Zhang; Zhoufei Wang; Hongsheng Zhang

    2008-01-01

    A study was conducted to determine the genetic diversity of 39 determinate and indeterminate tomato inbred lines collected from China, Japan, S. Korea, and USA. Using 35 SSR polymorphic markers, a total of 150 alleles were found with moderate levels of diversity, and a high number of unique alleles existing in these tomato lines. The mean number of alleles per locus was 4.3 and the average polymorphism information content (PIC) was 0.31. Unweighted Pair Group Method with Arithmetic Mean (UPGMA) clustering at genetic similarity value of 0.85 grouped the inbred lines into four groups, where one USA cultivar formed a separate and more distant cluster. The most similar inbred lines are from USA, both with determinate type, whereas the most different lines are from USA (Us-16) and Japan (Ja-2) with determinate and indeterminate growth habit, respectively. Clustering was consistent with the known information regarding geographical location and growth habit. The genetic distance information reported in this study might be used by breeders when planning future crosses among these inbred lines.

  10. Nuclear safety enhancement of the Instrumentation and Control System at TRIGA SSR 14 MW-Romania

    Energy Technology Data Exchange (ETDEWEB)

    Preda, Marin; Ciocanescu, Marin; Mugurel Ana, Emil; Barbalata, Eugenia [Institute for Nuclear Research, Pitesti (Romania)

    2008-10-29

    In order to comply with the IAEA safety standards and national regulations and to enhance the nuclear safety at TRIGA SSR 14 MW Romanian reactor in 2006 has began a process of instrumentation and control system modifications. By taking account of the operation experience and IAEA guides, the basic requirement for instrumentation and control system modification is the separation between safety and operating components in order to decrease the human error consequences and avoid the common cause failures. Beside that system modernization consists in TRIGA 14 MW console replacement. New instrumentation and control system consists in: - a new reactor operation console, that contains all the necessary modules for reactor operation and parameter display, - three racks for control system that contains all the necessary modules for safety parameter measurement and in scram logic the required redundancy, data acquisition, annunciators, - a terminal boundary rack for connections between field transducers and control room equipments. Modernization did not cover any sensor replacement but keep the actual scram logic and enhance the reactor safety features. The instrumentation and control system is designed, manufactured by INVAP Argentina and will be delivered, installed and tested by the end of 2008. Following to these activities safety documentation will be completed and issued to National Regulatory Body in order to obtain the operation license. Financially the Project is supported by IAEA Vienna and Romanian Government in the framework of a technical cooperation program. (authors)

  11. EVALUATION OF GENETIC DIVERSITY IN CACAO COLLECTED FROM KOLAKA, SOUTHEAST SULAWESI, USING SSR MARKERS

    Directory of Open Access Journals (Sweden)

    Rubiyo Rubiyo

    2016-02-01

    Full Text Available Kolaka, which is located in Southeast Sulawesi, has long been known as one of cacao production centers in Indonesia. Therefore, many different cacao germplasms can be found in this region. The study aimed to evaluate genetic diversity and relationships of 12 cacao genotypes collected from Kolaka. Genomic DNA was extracted by using a modified CTAB method. Meanwhile, genetic diversity was analyzed based on 16 SSR markers, which then separated by 6% non-denaturing polyacryl-amide gel electrophoresis. The result showed that all of those markers, 14 markers exhibited polymorphism and subsequently used for data analysis using NTSYS and PowerMarker program. About 70 different alleles were generated from 12 cacao genotypes analyzed with an average of 5 alleles per locus. Average value of polymorphism information content (PIC resulted in this study was 0.59. The cluster analysis using UPGMA method based on the genetic similarity coefficient revealed that all cacao genotypes were separated into three major groups. The first group consisted of five cacao genotypes, the second one held four cacao genotypes, whereas the third group contained three genotypes. This result indicates that three genotypes that clustered separately from the others could be used as a good clonal candidate for cacao breeding program. The information resulted from this present study would be useful for future cacao breeding program, especially in efforts to release a new variety.

  12. SSR Mapping of QTLs Conferring Cold Tolerance in an Interspecific Cross of Tomato

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    Yang Liu

    2016-01-01

    Full Text Available A population of 146 RILs (Recombinant Inbred Line was derived from the cross between a cold-sensitive cultivated Solanum lycopersicum L. XF98-7 and a cold-tolerant wild Solanum pimpinellifolium LA2184. Relative germination ratio (RGR and chilling index (CI were used to evaluate the cold tolerance of the parental lines and RILs. It was found that the RGR and CI were significantly different between S. lycopersicum XF98-7 and S. pimpinellifolium LA2184 under cold treatment, indicating that wild species was more adapted to chilling temperature. The continuous and normal distribution of RGR and CI in RIL population suggested that the trait of cold tolerance was a typically quantitative trait controlled by multigenes. The molecular linkage map was constructed by using 120 simple-sequence repeat (SSR markers, resulting in 15 linkage groups, with a total distance of 256.8 cM and average interval of 2.14 cM. Five QTLs controlling RGR and four QTLs for CI were detected with genetic contribution ranging from 0.95% to 19.55%. Thus, the nine QTLs will provide references for further fine position mapping for cold tolerance. The polymorphic markers could be used as a way of indirectly selecting the plant trait of interest and would promote developing new tomato variety by marker-assisted selection.

  13. A Set of 20 New SSR Markers Developed and Evaluated in Mandevilla Lindl.

    Science.gov (United States)

    Oder, Alev; Lannes, Robert; Viruel, Maria Angeles

    2016-09-30

    Mandevilla is an ornamental crop with a bright future worldwide because of its high commercial acceptance and added value. However, as with most ornamental species, there are few molecular tools to support cultivar breeding and innovation. In this work, we report the development and analysis of 20 new Simple Sequence Repeat (SSR) markers in Mandevilla. Microsatellites were isolated from two enriched small-insert genomic libraries of Mandevilla × amabilis. The diversity parameters estimated after their amplification in a group of 11 commercial genotypes illustrate the effect of two opposite drifts: the high relatedness of cultivars belonging to the same commercial group and the high divergence of other cultivars, especially M. × amabilis. Based on their different band patterns, six genotypes were uniquely distinguished, and two groups of sport mutations remained undistinguishable. The amplification of the SSRs in three wild species suggested the existence of unexploited diversity available to be introgressed into the commercial pool. This is the first report of available microsatellites in Mandevilla. The development process has provided some clues concerning the genome structure of the species, and the SSRs obtained will help to create new products and to protect existing and upcoming plant innovations.

  14. New Hypervariable SSR Markers for Diversity Analysis, Hybrid Purity Testing and Trait Mapping in Pigeonpea [Cajanus cajan (L.) Millspaugh].

    Science.gov (United States)

    Bohra, Abhishek; Jha, Rintu; Pandey, Gaurav; Patil, Prakash G; Saxena, Rachit K; Singh, Indra P; Singh, D; Mishra, R K; Mishra, Ankita; Singh, F; Varshney, Rajeev K; Singh, N P

    2017-01-01

    Draft genome sequence in pigeonpea offers unprecedented opportunities for genomics assisted crop improvement via enabling access to genome-wide genetic markers. In the present study, 421 hypervariable simple sequence repeat (SSR) markers from the pigeonpea genome were screened on a panel of eight pigeonpea genotypes yielding marker validation and polymorphism percentages of 95.24 and 54.11%, respectively. The SSR marker assay uncovered a total of 570 alleles with three as an average number of alleles per marker. Similarly, the mean values for gene diversity and PIC were 0.44 and 0.37, respectively. The number of polymorphic markers ranged from 39 to 89 for different parental combinations. Further, 60 of these SSRs were assayed on 94 genotypes, and model based clustering using STRUCTURE resulted in the identification of the two subpopulations (K = 2). This remained in close agreement with the clustering patterns inferred from genetic distance (GD)-based approaches i.e., dendrogram, factorial and principal coordinate analysis (PCoA). The AMOVA accounted majority of the genetic variation within groups (89%) in comparison to the variation existing between the groups (11%). A subset of these markers was implicated for hybrid purity testing. We also demonstrated utility of these SSR markers in trait mapping through association and bi-parental linkage analyses. The general linear (GLM) and mixed linear (MLM) models both detected a single SSR marker (CcGM03681) with R(2) = 16.4 as associated with the resistance to Fusarium wilt variant 2. Similarly, by using SSR data in a segregating backcross population, the corresponding restorer-of-fertility (Rf) locus was putatively mapped at 39 cM with the marker CcGM08896. However, The marker-trait associations (MTAs) detected here represent a very preliminary type and hence demand deeper investigations for conclusive evidence. Given their ability to reveal polymorphism in simple agarose gels, the hypervariable SSRs are valuable

  15. Genetic linkage maps for Asian and American lotus constructed using novel SSR markers derived from the genome of sequenced cultivar

    Directory of Open Access Journals (Sweden)

    Yang Mei

    2012-11-01

    Full Text Available Abstract Background The genus Nelumbo Adans. comprises two living species, N. nucifera Gaertan. (Asian lotus and N. lutea Pers. (American lotus. A genetic linkage map is an essential resource for plant genetic studies and crop improvement but has not been generated for Nelumbo. We aimed to develop genomic simple sequence repeat (SSR markers from the genome sequence and construct two genetic maps for Nelumbo to assist genome assembly and integration of a genetic map with the genome sequence. Results A total of 86,089 SSR motifs were identified from the genome sequences. Di- and tri-nucleotide repeat motifs were the most abundant, and accounted for 60.73% and 31.66% of all SSRs, respectively. AG/GA repeats constituted 51.17% of dinucleotide repeat motifs, followed by AT/TA (44.29%. Of 500 SSR primers tested, 386 (77.20% produced scorable alleles with an average of 2.59 per primer, and 185 (37.00% showed polymorphism among two parental genotypes, N. nucifera ‘Chinese Antique’ and N. lutea ‘AL1’, and six progenies of their F1 population. The normally segregating markers, which comprised 268 newly developed SSRs, 37 previously published SSRs and 53 sequence-related amplified polymorphism markers, were used for genetic map construction. The map for Asian lotus was 365.67 cM with 47 markers distributed in seven linkage groups. The map for American lotus was 524.51 cM, and contained 177 markers distributed in 11 genetic linkage groups. The number of markers per linkage group ranged from three to 34 with an average genetic distance of 3.97 cM between adjacent markers. Moreover, 171 SSR markers contained in linkage groups were anchored to 97 genomic DNA sequence contigs of ‘Chinese Antique’. The 97 contigs were merged into 60 scaffolds. Conclusion Genetic mapping of SSR markers derived from sequenced contigs in Nelumbo enabled the associated contigs to be anchored in the linkage map and facilitated assembly of the genome sequences of

  16. Comparison of similarity coefficients used for cluster analysis based on SSR markers in sister line wheat cultivars

    Directory of Open Access Journals (Sweden)

    Denčić Srbislav

    2016-01-01

    Full Text Available The objective of this study was to compared fourteen different similarity coefficients and their influence in sister line wheat cultivars clustering. Seventeen sister cultivars developed from two crosses were used and fingerprinted with 19 wheat microsatellite markers. Comparisons among the similarity coefficients were made using the Sperman correlation analysis, dendogram evaluation (visual inspection and consensus fork index - CIc, projection efficiency in a two-dimensional space, and groups formed by the Tocher optimization procedure. The Sperman correlation coefficients among the fourteen similarity coefficients were all high showing a strong association between them. The correlation coefficient between Dice and Kulczinski and Ochiai I as well as between Hamann and Simple matching and between Kulczinski and Ochiai I was equal to 1. Although visual estimation of the dendograms shows almost identical clustering structures, CIc indexes indicate that all coefficients are not identical. [Projekat Ministarstva nauke Republike Srbije, br. TR 31066

  17. An overview of SSR149415, a selective nonpeptide vasopressin V(1b) receptor antagonist for the treatment of stress-related disorders.

    Science.gov (United States)

    Serradeil-Le Gal, Claudine; Wagnon, Jean; Tonnerre, Bernard; Roux, Richard; Garcia, Georges; Griebel, Guy; Aulombard, Alain

    2005-01-01

    Vasopressin (AVP) and corticotropin-releasing factor (CRF) are key mediators in the organism's neuro-adaptive response to stress. Through pituitary and central vasopressin V(1b) receptors, AVP participates in the control of the hypothalamic-pituitary-adrenal axis (HPA) and is involved in various emotional processes. SSR149415 is the first selective, orally active vasopressin V(1b) receptor antagonist yet described. It is a competitive antagonist with nanomolar affinity for animal and human V(1b) receptors and displays a highly selective profile with regard to a large number of receptors or enzymes. In vitro, SSR149415 potently antagonizes functional cellular events associated with V(1b) receptor activation by AVP, such as intracellular Ca(2+) increase or proliferation in various cell systems. Pharmacological studies, performed by measuring ACTH secretion induced by various stimulants such as hormones (AVP or AVP + CRF) or physical stress (restraint or forced swimming stress and dehydration) in conscious rats or mice, confirm the antagonist profile of SSR149415 and its efficacy in normalizing ACTH secretion in vivo. SSR149415 is active by the oral route, at doses from 3 mg/kg, it potentiates CRF effect and displays a long-lasting oral effect in the different models. At 10 mg/kg p.o. its duration of action is longer than 4 h. This molecule also decreases anxiety and exerts marked antidepressant-like activity in several predictive animal models. The anxiolytic effects of SSR149415 have been demonstrated in various Generalized Anxiety Disorders (GAD) models (four-plate, punished drinking, elevated plus-maze, light dark, mouse defense test battery, fear-potentiated startle and social interaction tests). It is as effective as the benzodiazepine diazepam in the acute stress exposure test. SSR149415 has similar efficacy to the reference antidepressant drug, fluoxetine, in acute (forced-swimming) and chronic (chronic mild stress and subordination stress) situations in

  18. Identification and characterization of gene-based SSR markers in date palm (Phoenix dactylifera L.

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    Zhao Yongli

    2012-12-01

    Full Text Available Abstract Background Date palm (Phoenix dactylifera L. is an important tree in the Middle East and North Africa due to the nutritional value of its fruit. Molecular Breeding would accelerate genetic improvement of fruit tree through marker assisted selection. However, the lack of molecular markers in date palm restricts the application of molecular breeding. Results In this study, we analyzed 28,889 EST sequences from the date palm genome database to identify simple-sequence repeats (SSRs and to develop gene-based markers, i.e. expressed sequence tag-SSRs (EST-SSRs. We identified 4,609 ESTs as containing SSRs, among which, trinucleotide motifs (69.7% were the most common, followed by tetranucleotide (10.4% and dinucleotide motifs (9.6%. The motif AG (85.7% was most abundant in dinucleotides, while motifs AGG (26.8%, AAG (19.3%, and AGC (16.1% were most common among trinucleotides. A total of 4,967 primer pairs were designed for EST-SSR markers from the computational data. In a follow up laboratory study, we tested a sample of 20 random selected primer pairs for amplification and polymorphism detection using genomic DNA from date palm cultivars. Nearly one-third of these primer pairs detected DNA polymorphism to differentiate the twelve date palm cultivars used. Functional categorization of EST sequences containing SSRs revealed that 3,108 (67.4% of such ESTs had homology with known proteins. Conclusion Date palm EST sequences exhibits a good resource for developing gene-based markers. These genic markers identified in our study may provide a valuable genetic and genomic tool for further genetic research and varietal development in date palm, such as diversity study, QTL mapping, and molecular breeding.

  19. Association mapping of seed oil and protein content in Sesamum indicum L. using SSR markers.

    Science.gov (United States)

    Li, Chun; Miao, Hongmei; Wei, Libin; Zhang, Tide; Han, Xiuhua; Zhang, Haiyang

    2014-01-01

    Sesame is an important oil crop for the high oil content and quality. The seed oil and protein contents are two important traits in sesame. To identify the molecular markers associated with the seed oil and protein contents in sesame, we systematically performed the association mapping among 369 worldwide germplasm accessions under 5 environments using 112 polymorphic SSR markers. The general linear model (GLM) was applied with the criteria of logP ≥ 3.0 and high stability under all 5 environments. Among the 369 sesame accessions, the oil content ranged from 27.89%-58.73% and the protein content ranged from 16.72%-27.79%. A significant negative correlation of the oil content with the protein content was found in the population. A total of 19 markers for oil content were detected with a R2 value range from 4% to 29%; 24 markers for protein content were detected with a R2 value range from 3% to 29%, of which 19 markers were associated with both traits. Moreover, partial markers were confirmed using mixed linear model (MLM) method, which suggested that the oil and protein contents are controlled mostly by major genes. Allele effect analysis showed that the allele associated with high oil content was always associated with low protein content, and vice versa. Of the 19 markers associated with oil content, 17 presented near the locations of the plant lipid pathway genes and 2 were located just next to a fatty acid elongation gene and a gene encoding Stearoyl-ACP Desaturase, respectively. The findings provided a valuable foundation for oil synthesis gene identification and molecular marker assistant selection (MAS) breeding in sesame.

  20. A saturated SSR/DArT linkage map of Musa acuminata addressing genome rearrangements among bananas

    Directory of Open Access Journals (Sweden)

    Matsumoto Takashi

    2010-04-01

    Full Text Available Abstract Background The genus Musa is a large species complex which includes cultivars at diploid and triploid levels. These sterile and vegetatively propagated cultivars are based on the A genome from Musa acuminata, exclusively for sweet bananas such as Cavendish, or associated with the B genome (Musa balbisiana in cooking bananas such as Plantain varieties. In M. acuminata cultivars, structural heterozygosity is thought to be one of the main causes of sterility, which is essential for obtaining seedless fruits but hampers breeding. Only partial genetic maps are presently available due to chromosomal rearrangements within the parents of the mapping populations. This causes large segregation distortions inducing pseudo-linkages and difficulties in ordering markers in the linkage groups. The present study aims at producing a saturated linkage map of M. acuminata, taking into account hypotheses on the structural heterozygosity of the parents. Results An F1 progeny of 180 individuals was obtained from a cross between two genetically distant accessions of M. acuminata, 'Borneo' and 'Pisang Lilin' (P. Lilin. Based on the gametic recombination of each parent, two parental maps composed of SSR and DArT markers were established. A significant proportion of the markers (21.7% deviated (p Conclusions We propose a synthetic map with 11 linkage groups containing 489 markers (167 SSRs and 322 DArTs covering 1197 cM. This first saturated map is proposed as a "reference Musa map" for further analyses. We also propose two complete parental maps with interpretations of structural rearrangements localized on the linkage groups. The structural heterozygosity in P. Lilin is hypothesized to result from a duplication likely accompanied by an inversion on another chromosome. This paper also illustrates a methodological approach, transferable to other species, to investigate the mapping of structural rearrangements and determine their consequences on marker

  1. An EST-derived SNP and SSR genetic linkage map of cassava (Manihot esculenta Crantz).

    Science.gov (United States)

    Rabbi, Ismail Yusuf; Kulembeka, Heneriko Philbert; Masumba, Esther; Marri, Pradeep Reddy; Ferguson, Morag

    2012-07-01

    Cassava (Manihot esculenta Crantz) is one of the most important food security crops in the tropics and increasingly being adopted for agro-industrial processing. Genetic improvement of cassava can be enhanced through marker-assisted breeding. For this, appropriate genomic tools are required to dissect the genetic architecture of economically important traits. Here, a genome-wide SNP-based genetic map of cassava anchored in SSRs is presented. An outbreeder full-sib (F1) family was genotyped on two independent SNP assay platforms: an array of 1,536 SNPs on Illumina's GoldenGate platform was used to genotype a first batch of 60 F1. Of the 1,358 successfully converted SNPs, 600 which were polymorphic in at least one of the parents and was subsequently converted to KBiosciences' KASPar assay platform for genotyping 70 additional F1. High-precision genotyping of 163 informative SSRs using capillary electrophoresis was also carried out. Linkage analysis resulted in a final linkage map of 1,837 centi-Morgans (cM) containing 568 markers (434 SNPs and 134 SSRs) distributed across 19 linkage groups. The average distance between adjacent markers was 3.4 cM. About 94.2% of the mapped SNPs and SSRs have also been localized on scaffolds of version 4.1 assembly of the cassava draft genome sequence. This more saturated genetic linkage map of cassava that combines SSR and SNP markers should find several applications in the improvement of cassava including aligning scaffolds of the cassava genome sequence, genetic analyses of important agro-morphological traits, studying the linkage disequilibrium landscape and comparative genomics.

  2. In vivo imaging of neuroinflammation in the rodent brain with [{sup 11}C]SSR180575, a novel indoleacetamide radioligand of the translocator protein (18 kDa)

    Energy Technology Data Exchange (ETDEWEB)

    Chauveau, Fabien [CEA, DSV, IBM, Service Hospitalier Frederic Joliot, Orsay (France); Universite Paris Sud, INSERM U1023, Orsay (France); Universite Lyon 1, Creatis, CNRS UMR 5220, INSERM U630, INSA Lyon, Lyon (France); Boutin, Herve [CEA, DSV, IBM, Service Hospitalier Frederic Joliot, Orsay (France); Universite Paris Sud, INSERM U1023, Orsay (France); University of Manchester, Faculty of Life Sciences, Manchester (United Kingdom); Camp, Nadja van; Tavitian, Bertrand [CEA, DSV, IBM, Service Hospitalier Frederic Joliot, Orsay (France); Universite Paris Sud, INSERM U1023, Orsay (France); Thominiaux, Cyrille; Dolle, Frederic [CEA, DSV, IBM, Service Hospitalier Frederic Joliot, Orsay (France); Hantraye, Philippe [CEA, DSV, IBM, MIRCEN, Fontenay-aux-Roses (France); Rivron, Luc [Sanofi-Aventis, GMPK-Global Isotope Chemistry and Metabolite Synthesis Department (ICMS), Paris (France); Marguet, Frank; Castel, Marie-Noelle; Rooney, Thomas; Benavides, Jesus [Sanofi-Aventis, CNS Department, Paris (France)

    2011-03-15

    Neuroinflammation is involved in neurological disorders through the activation of microglial cells. Imaging of neuroinflammation with radioligands for the translocator protein (18 kDa) (TSPO) could prove to be an attractive biomarker for disease diagnosis and therapeutic evaluation. The indoleacetamide-derived 7-chloro-N,N,5-trimethyl-4-oxo-3-phenyl-3,5-dihydro-4H-pyridazino[4,5-b]indole-1-acetamide, SSR180575, is a selective high-affinity TSPO ligand in human and rodents with neuroprotective effects. Here we report the radiolabelling of SSR180575 with {sup 11}C and in vitro and in vivo imaging in an acute model of neuroinflammation in rats. The image contrast and the binding of [{sup 11}C]SSR180575 are higher than that obtained with the isoquinoline-based TSPO radioligand, [{sup 11}C]PK11195. Competition studies demonstrate that [{sup 11}C]SSR180575 has high specific binding for the TSPO. [{sup 11}C]SSR180575 is the first PET radioligand for the TSPO based on an indoleacetamide scaffold designed for imaging neuroinflammation in animal models and in the clinic. (orig.)

  3. Exploiting Illumina Sequencing for the Development of 95 Novel Polymorphic EST-SSR Markers in Common Vetch (Vicia sativa subsp. sativa

    Directory of Open Access Journals (Sweden)

    Zhipeng Liu

    2014-05-01

    Full Text Available The common vetch (Vicia sativa subsp. sativa, a self-pollinating and diploid species, is one of the most important annual legumes in the world due to its short growth period, high nutritional value, and multiple usages as hay, grain, silage, and green manure. The available simple sequence repeat (SSR markers for common vetch, however, are insufficient to meet the developing demand for genetic and molecular research on this important species. Here, we aimed to develop and characterise several polymorphic EST-SSR markers from the vetch Illumina transcriptome. A total number of 1,071 potential EST-SSR markers were identified from 1025 unigenes whose lengths were greater than 1,000 bp, and 450 primer pairs were then designed and synthesized. Finally, 95 polymorphic primer pairs were developed for the 10 common vetch accessions, which included 50 individuals. Among the 95 EST-SSR markers, the number of alleles ranged from three to 13, and the polymorphism information content values ranged from 0.09 to 0.98. The observed heterozygosity values ranged from 0.00 to 1.00, and the expected heterozygosity values ranged from 0.11 to 0.98. These 95 EST-SSR markers developed from the vetch Illumina transcriptome could greatly promote the development of genetic and molecular breeding studies pertaining to in this species.

  4. Determination of genetic relationships among elite thermosensitive genic male sterile lines (TGMS) of rice (Oryza sativa L.) employing morphological and simple sequence repeat (SSR) markers

    Indian Academy of Sciences (India)

    Vikas Kumar Singh; Priti Upadhyay; Pallavi Sinha; Ashish Kumar Mall; Sanjay Kumar Jaiswal; Atul Singh; Ranjith Kumar Ellur; Sunil Biradar; R. M. Sundaram; Sukhpal Singh; Ilyas Ahmed; B. Mishra; A. K. Singh; C. Kole

    2011-04-01

    A set of morphological traits and SSR markers were used to determine the genetic relationship among 12 elite thermosensitive genic male sterile (TGMS) lines developed at three different research institutions of India. Agro-morphological data recorded on 20 morphological traits revealed a wide base of genetic variation and a set of four morphological traits could distinguish most of the TGMS lines. Analysis with 30 SSR markers (20 EST-SSRs and 10 genomic SSRs) revealed 27 markers to be polymorphic, amplifying a total of 83 alleles. Each SSR marker amplified 2–6 alleles with an average of 2.76 alleles per marker and a PIC value varying from 0.54 to 0.96. Cluster analysis based on SSR and morphological data clearly differentiated the lines according to their source of origin. Correlation analysis between morphological and molecular data revealed a very poor association ($r = 0.06$), which could be attributed to selection pressure, genetic drift, sampling error and unknown relationship among related lines. The SSR markers discriminated the genotypes distinctly and quantified the genetic diversity precisely among the TGMS lines. Data on the yield per plant indicated that the genotypes grouping under a similar cluster showed same heterotic behaviour as compared to the genotypes from different clusters when crossed to similar pollinators.

  5. Development and characterization of novel EST-SSR markers and their application for genetic diversity analysis of Jerusalem artichoke (Helianthus tuberosus L.).

    Science.gov (United States)

    Mornkham, T; Wangsomnuk, P P; Mo, X C; Francisco, F O; Gao, L Z; Kurzweil, H

    2016-10-24

    Jerusalem artichoke (Helianthus tuberosus L.) is a perennial tuberous plant and a traditional inulin-rich crop in Thailand. It has become the most important source of inulin and has great potential for use in chemical and food industries. In this study, expressed sequence tag (EST)-based simple sequence repeat (SSR) markers were developed from 40,362 Jerusalem artichoke ESTs retrieved from the NCBI database. Among 23,691 non-redundant identified ESTs, 1949 SSR motifs harboring 2 to 6 nucleotides with varied repeat motifs were discovered from 1676 assembled sequences. Seventy-nine primer pairs were generated from EST sequences harboring SSR motifs. Our results show that 43 primers are polymorphic for the six studied populations, while the remaining 36 were either monomorphic or failed to amplify. These 43 SSR loci exhibited a high level of genetic diversity among populations, with allele numbers varying from 2 to 7, with an average of 3.95 alleles per loci. Heterozygosity ranged from 0.096 to 0.774, with an average of 0.536; polymorphic index content ranged from 0.096 to 0.854, with an average of 0.568. Principal component analysis and neighbor-joining analysis revealed that the six populations could be divided into six clusters. Our results indicate that these newly characterized EST-SSR markers may be useful in the exploration of genetic diversity and range expansion of the Jerusalem artichoke, and in cross-species application for the genus Helianthus.

  6. Assessment of genetic diversity among Chinese upland cottons with Fusarium and/or Verticillium wilts resistance by AFLP and SSR markers

    Institute of Scientific and Technical Information of China (English)

    WANG Xingfen; MA Jun; YANG Shuo; ZHANG Guiyin; MA Zhiying

    2007-01-01

    Genetic diversity among 95 Chinese upland cottons with Fusarium and/or Verticillium wilts resistance was estimated using Amplified Fragment Length Polymorphism (AFLP) and Simple Sequence Repeat (SSR) markers.Twenty EcoRI-MseI AFLP and 19 SSR primers with polymorphism were selected to perform the fingerprinting.The results showed that 20 AFLP primer pairs produced a total of 1 480 major bands among 95 genotypes,and 214 were polymorphic bands.The number of total bands per primer pair ranged from 47 to 109,with an average of 74.0.The polymorphism information content (PIC) values for the 20 primer pairs varied from 0.01 (E-ACT/M-CAT) to 0.24 (E-ACA/MCTA),and the average value was 0.09.Nineteen SSR primers generated 89 DNA bands,of which 61 were polymorphic.The total number of alleles per locus varied from 3 to 8,with an average of 4.7.The average PIC value for the SSR amplification products was 0.69.Genetic similarity estimates for the entire data set ranged from 0.978 to 0.998 based on AFLP and SSR bands.It was proved that the close genetic relationship and narrow genetic diversity existed in the tested cultivars.The clustering patterns could not be correlated to the geographic origin,the pedigree and common parentage of the cultivars.

  7. Leaf Transcriptome Sequencing for Identifying Genic-SSR Markers and SNP Heterozygosity in Crossbred Mango Variety ‘Amrapali’ (Mangifera indica L.)

    Science.gov (United States)

    Mahato, Ajay Kumar; Sharma, Nimisha; Singh, Akshay; Srivastav, Manish; Jaiprakash; Singh, Sanjay Kumar; Singh, Anand Kumar; Sharma, Tilak Raj; Singh, Nagendra Kumar

    2016-01-01

    Mango (Mangifera indica L.) is called “king of fruits” due to its sweetness, richness of taste, diversity, large production volume and a variety of end usage. Despite its huge economic importance genomic resources in mango are scarce and genetics of useful horticultural traits are poorly understood. Here we generated deep coverage leaf RNA sequence data for mango parental varieties ‘Neelam’, ‘Dashehari’ and their hybrid ‘Amrapali’ using next generation sequencing technologies. De-novo sequence assembly generated 27,528, 20,771 and 35,182 transcripts for the three genotypes, respectively. The transcripts were further assembled into a non-redundant set of 70,057 unigenes that were used for SSR and SNP identification and annotation. Total 5,465 SSR loci were identified in 4,912 unigenes with 288 type I SSR (n ≥ 20 bp). One hundred type I SSR markers were randomly selected of which 43 yielded PCR amplicons of expected size in the first round of validation and were designated as validated genic-SSR markers. Further, 22,306 SNPs were identified by aligning high quality sequence reads of the three mango varieties to the reference unigene set, revealing significantly enhanced SNP heterozygosity in the hybrid Amrapali. The present study on leaf RNA sequencing of mango varieties and their hybrid provides useful genomic resource for genetic improvement of mango. PMID:27736892

  8. Assessment of EST-SSR markers for genetic analisys on coffee Potencial de marcadores EST-SSR para análise genética em café

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    Robson Fernando Missio

    2009-09-01

    Full Text Available EST-SSR markers were used to investigate the genetic diversity among and within coffee populations, to explore the possibility of their use for fingerprinting of cultivars and to assist breeding programs. Seventeen markers, developed from ESTs (Expressed Sequence Tags from the Brazilian Coffee Genome Project, were used. All markers showed polymorphism among the genotypes assessed. The average number of allele per primer was 5.1. The highest polymorphisms were found within C. canephora (88.2% and rust-resistant varieties (35.3%. About 29.4% of the markers differentiated C. arabica from Híbrido de Timor; it was also possible to identify those closest and farthest from C. arabica . The analysis of population-grouped genotypes revealed a 64.0% genetic diversity among and a 36.0% genetic diversity within populations. The differentiation index was 0.637. Six markers distinguished four rust-resistance varieties, showing their fingerprinting potential. These results demonstrate the usefulness of EST-SSR markers for cross orientation, in diversity and introgression studies, and in genetic mapping.No estudo da diversidade genética entre e dentro de populações de café, foram usados marcadores EST-SSR, visando avaliar seu potencial para identificar cultivares comerciais e assistir programas de melhoramento. Os 17 marcadores utilizados foram desenvolvidos a partir das seqüências ESTs do Projeto Brasileiro do Genoma Café. Em todos os marcadores observou-se polimorfismo entre os genótipos avaliados, com um número médio de 5,1 alelos por primer. Os maiores polimorfismos foram constatados dentro de C. canephora (88,2% e em variedades resistentes à ferrugem (35,3%. Dos marcadores analisados, 29,4% distinguiram C. arabica dos Híbridos de Timor (HDT, sendo possível identificar os mais próximos e os mais distantes de C. arabica . A análise dos genótipos agrupados por população revelou diversidade genética de 64% entre populações e 36% dentro

  9. Species-specific SSR alleles for studies of hybrid cattails (Typha latifolia x T. angustifolia; Typhaceae) in North America.

    Science.gov (United States)

    Snow, Allison A; Travis, Steven E; Wildová, Radka; Fér, Tomás; Sweeney, Patricia M; Marburger, Joy E; Windels, Steven; Kubátová, Barbora; Goldberg, Deborah E; Mutegi, Evans

    2010-12-01

    Studies of hybridizing species are facilitated by the availability of species-specific molecular markers for identifying early- and later-generation hybrids. Cattails are a dominant feature of wetland communities, and a better understanding of the prevalence of hybrids is needed to assess the ecological and evolutionary effects of hybridization. Hybridization between Typha angustifolia and T. latifolia produce long-lived clones, known as Typha ×glauca, which are considered to be invasive. Although morphological variation in cattails makes it difficult to recognize early- and later-generation hybrids, several dominant, species-specific RAPD markers are available. Our goal was to find codominant, species-specific markers with greater polymorphism than RAPDs, to identify later-generation hybrids more efficiently. • We screened nine SSR (simple sequence repeat) loci that were described from populations in Ukraine, and we surveyed 31 cattail populations from the upper Midwest and eastern USA. • Seven SSR loci distinguished the parent taxa and were consistent with known species-specific RAPD markers, allowing easier detection of backcrossing. We used linear discriminant analysis to show that F(1) hybrid phenotypes were intermediate between the parent taxa, while those of backcrossed plants overlapped with the hybrids and their parents. Log(leaf length/leaf width), spike gap length, spike length, and stem diameter explained much of the variation among groups. • We provide the first documentation of backcrossed plants in hybridizing cattail populations in Michigan. The diagnostic SSR loci we identified should be extremely useful for examining the evolutionary and ecology interactions of hybridizing cattails in North America.

  10. Characterization of flower-bud transcriptome and development of genic SSR markers in Asian lotus (Nelumbo nucifera Gaertn..

    Directory of Open Access Journals (Sweden)

    Weiwei Zhang

    Full Text Available Asian lotus (Nelumbo nucifera Gaertn. is the national flower of India, Vietnam, and one of the top ten traditional Chinese flowers. Although lotus is highly valued for its ornamental, economic and cultural uses, genomic information, particularly the expressed sequence based (genic markers is limited. High-throughput transcriptome sequencing provides large amounts of transcriptome data for promoting gene discovery and development of molecular markers.In this study, 68,593 unigenes were assembled from 1.34 million 454 GS-FLX sequence reads of a mixed flower-bud cDNA pool derived from three accessions of N. nucifera. A total of 5,226 SSR loci were identified, and 3,059 primer pairs were designed for marker development. Di-nucleotide repeat motifs were the most abundant type identified with a frequency of 65.2%, followed by tri- (31.7%, tetra- (2.1%, penta- (0.5% and hexa-nucleotide repeats (0.5%. A total of 575 primer pairs were synthesized, of which 514 (89.4% yielded PCR amplification products. In eight Nelumbo accessions, 109 markers were polymorphic. They were used to genotype a sample of 44 accessions representing diverse wild and cultivated genotypes of Nelumbo. The number of alleles per locus varied from 2 to 9 alleles and the polymorphism information content values ranged from 0.6 to 0.9. We performed genetic diversity analysis using 109 polymorphic markers. A UPGMA dendrogram was constructed based on Jaccard's similarity coefficients revealing distinct clusters among the 44 accessions.Deep transcriptome sequencing of lotus flower buds developed 3,059 genic SSRs, making a significant addition to the existing SSR markers in lotus. Among them, 109 polymorphic markers were successfully validated in 44 accessions of Nelumbo. This comprehensive set of genic SSR markers developed in our study will facilitate analyses of genetic diversity, construction of linkage maps, gene mapping, and marker-assisted selection breeding for lotus.

  11. Phylogenetic inference and SSR characterization of tropical woody bamboos tribe Bambuseae (Poaceae: Bambusoideae) based on complete plastid genome sequences.

    Science.gov (United States)

    Vieira, Leila do Nascimento; Dos Anjos, Karina Goulart; Faoro, Helisson; Fraga, Hugo Pacheco de Freitas; Greco, Thiago Machado; Pedrosa, Fábio de Oliveira; de Souza, Emanuel Maltempi; Rogalski, Marcelo; de Souza, Robson Francisco; Guerra, Miguel Pedro

    2016-05-01

    The complete plastome sequencing is an efficient option for increasing phylogenetic resolution and evolutionary studies, as well as may greatly facilitate the use of plastid DNA markers in plant population genetic studies. Merostachys and Guadua stand out as the most common and the highest potential utilization bamboos indigenous of Brazil. Here, we sequenced the complete plastome sequences of the Brazilian Guadua chacoensis and Merostachys sp. to perform full plastome phylogeny and characterize the occurrence, type, and distribution of SRRs using 20 Bambuseae species. The determined plastome sequence of Merostachys sp. and G. chacoensis is 136,334 and 135,403 bp in size, respectively, with an identical gene content and typical quadripartite structure consisting of a pair of IRs separated by the LSC and SSC regions. The Maximum Likelihood and Bayesian Inference analyses produced phylogenomic trees identical in topology. These trees supported monophyly of Paleotropical and Neotropical Bamboos clades. The Neotropical bamboos segregated into three well-supported lineages, Chusqueinae, Guaduinae, and Arthrostylidiinae, with the last two forming a well-supported sister relationship. Paleotropical bamboos segregated into two well-supported lineages, Hickeliinae and Bambusinae + Melocanninae. We identified 141.8 cpSSR in Bambuseae plastomes and an inferior value (38.15) for plastome coding sequences. Among them, we identified 16 polymorphic SSR loci, with number of alleles varying from 3 to 10. These 16 polymorphic cpSSR loci in Bambuseae plastome can be assessed for the intraspecific level of polymorphism, leading to innovative highly sensitive phylogeographic and population genetics studies for this tribe.

  12. De novo assembly of transcriptome sequencing in Caragana korshinskii Kom. and characterization of EST-SSR markers.

    Directory of Open Access Journals (Sweden)

    Yan Long

    Full Text Available Caragana korshinskii Kom. is widely distributed in various habitats, including gravel desert, clay desert, fixed and semi-fixed sand, and saline land in the Asian and African deserts. To date, no previous genomic information or EST-SSR marker has been reported in Caragana Fabr. genus. In this study, more than two billion bases of high-quality sequence of C. korshinskii were generated by using illumina sequencing technology and demonstrated the de novo assembly and annotation of genes without prior genome information. These reads were assembled into 86,265 unigenes (mean length = 709 bp. The similarity search indicated that 33,955 and 21,978 unigenes showed significant similarities to known proteins from NCBI non-redundant and Swissprot protein databases, respectively. Among these annotated unigenes, 26,232 a unigenes were separately assigned to Gene Ontology (GO database. When 22,756 unigenes searched against the Kyoto Encyclopedia of Genes and Genomes Pathway (KEGG database, 5,598 unigenes were assigned to 5 main categories including 32 KEGG pathways. Among the main KEGG categories, metabolism was the biggest category (2,862, 43.7%, suggesting the active metabolic processes in the desert tree. In addition, a total of 19,150 EST-SSRs were identified from 15,484 unigenes, and the characterizations of EST-SSRs were further compared with other four species in Fabraceae. 126 potential marker sites were randomly selected to validate the assembly quality and develop EST-SSR markers. Among the 9 germplasms in Caranaga Fabr. genus, PCR success rate were 93.7% and the phylogenic tree was constructed based on the genotypic data. This research generated a substantial fraction of transcriptome sequences, which were very useful resources for gene annotation and discovery, molecular markers development, genome assembly and annotation. The EST-SSR markers identified and developed in this study will facilitate marker-assisted selection breeding.

  13. Bulked Segregant Analysis to Detect QTL Related to Heat Tolerance in Rice(Oryza sativa L.)Using SSR Markers

    Institute of Scientific and Technical Information of China (English)

    ZHANG Gui-lian; CHEN Li-yun; XIAO Guo-ying; XIAO Ying-hui; CHEN Xin-bo; ZHANG Shun-tang

    2009-01-01

    The study was undertaken to assess the genetic effect of quantitative trait loci(QTLs)conferring heat tolerance at flowering stage in rice.A population consisting of 279 F2 individuals from the cross between 996,a heat tolerant cultivar and 4628,a heat-sensitive cultivar,was analyzed for their segregation pattern of the difference of seed set rate under optimal temperature condition and high temperature condition.The difference of seed set rate under optimal temperature condition and high temperature condition showed normal distribution,indicating the polygenic control over the trait.To identify main effect of QTL for heat tolerance,the parents were surveyed with 200 primer pairs of simple sequence repeats(SSR).The parental survey revealed 30% polymorphism between parents.In order to detect the main QTL association with heat tolerance,a strategy of combining the DNA pooling from selected segregants and genotyping was adopted.The association of putative markers identified based on DNA pooling from selected segregants was established by single marker analysis(SMA).The results of SMA revealed that SSR markers,RM3735 on chromosome 4 and RM3586 on chromosome 3 showed significant association with heat tolerance respectively.accounted for 17 and 3% of the total variation respectively.The heat tolerance during flowering stage in rice was controlled by multiple gene.The SSR markers,RM3735 on chromosome 4 and RM3586 on chromosome 3 showed significant association with heat tolerance respectively,accounted for 17 and 3% of the total variation respectively.The two genetic loci,especially for RM3735 on chromosome 4,can be used in marker-assistant-selected method in heat tolerance breeding in rice.

  14. Development of Gene-Based SSR Markers in Rice Bean (Vigna umbellata L. Based on Transcriptome Data.

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    Honglin Chen

    Full Text Available Rice bean (Vigna umbellata (Thunb. Ohwi & Ohashi is a warm season annual legume mainly grown in East Asia. Only scarce genomic resources are currently available for this legume crop species and no simple sequence repeat (SSR markers have been specifically developed for rice bean yet. In this study, approximately 26 million high quality cDNA sequence reads were obtained from rice bean using Illumina paired-end sequencing technology and assembled into 71,929 unigenes with an average length of 986 bp. Of these unigenes, 38,840 (33.2% showed significant similarity to proteins in the NCBI non-redundant protein and nucleotide sequence databases. Furthermore, 30,170 (76.3% could be classified into gene ontology categories, 25,451 (64.4% into Swiss-Prot categories and 21,982 (55.6% into KOG database categories (E-value < 1.0E-5. A total of 9,301 (23.5% were mapped onto 118 pathways using the Kyoto Encyclopedia of Genes and Genome (KEGG pathway database. A total of 3,011 genic SSRs were identified as potential molecular markers. AG/CT (30.3%, AAG/CTT (8.1% and AGAA/TTCT (20.0% are the three main repeat motifs. A total of 300 SSR loci were randomly selected for validation by using PCR amplification. Of these loci, 23 primer pairs were polymorphic among 32 rice bean accessions. A UPGMA dendrogram revealed three major clusters among 32 rice bean accessions. The large number of SSR-containing sequences and genic SSRs in this study will be valuable for the construction of high-resolution genetic linkage maps, association or comparative mapping and genetic analyses of various Vigna species.

  15. Development of EST-SSR Markers in (Citrus aurantium L.)%积壳EST-SSR标记的开发

    Institute of Scientific and Technical Information of China (English)

    杨春霞; 温强; 叶金山; 朱培林

    2011-01-01

    The big collection of expressed sequence tags (ESTs) from Citrus aurantium L. is available in public database, and offers an opportunity to identify simple sequence repeats (SSR) in ESTs by data mining. These sequences may provide an estimate of diversity in the expressed portion of the genome and may be useful for comparative mapping, for tagging important traits of interest, and for additional map-based cloning of important genes.We analyzed fiontal 11 029 Unigene sequences fi.om C. aurantium database using online SSR identified software SSRIT. Totally, 327 ESTs with 348 SSRs were identified, and accounted for 2.96% of the total number of EST sequences. Trinucleotide repeats (a total of 161) were the most abundant repeat class, and accounted for 46.26% of all found SSRs. According to these EST sequences containing SSR, 58 primer pairs were designed using Primer 3.0. of these, 36 primer pairs amplified DNA fragments and 6 primer pairs exhibited polymorphism, account for 62.07% and 10.34% of the total designed 58 pairs. The development of new EST-SSR markers from C. aurantium has potential important implication for genetic analysis and exploitation of genetic resources of C. aurantium and would provide a more direct estimate of functional diversity.%GenBank上己公布的积壳EST序列为开发新的SSR标记提供了宝贵的数据资源.本研究利用在线SSR鉴定软件SSRIT分析来自积壳EST数据库的11029条Unigene序列.分析结果共发现327条EST序列含有348个SSR位点,占总数的2.96%.其中,三核苷酸重复的SSR类型最多,共有161个,占检索总数的46.26%. Primer 3.0设计合成58对EST-SSR引物,其中36对能扩增出产物,6对引物产生多态性分离,分别占所设计引物总数的62.07%和10.34%.本文研究成果为今后积壳遗传多样性分析、遗传图谱构建及比较基因组等研究方面奠定了基础.

  16. Construction of a genetic map and localization of QTLs for yield traits in tomato by SSR markers

    Institute of Scientific and Technical Information of China (English)

    LIU Yang; CHEN Huoying; WEI Yutang; ZHUANG Tianming

    2005-01-01

    Using an F2 population derived from the hybrid of Lycopersicon esculentum Mill. 'XF 98-7' × Lycopersicon pimpinellifolium LA2184, a SSR genetic linkage map of tomato is constructed. The map contains 112 markers and spans 808.4 cM with an average distance of 7.22 cM between loci. Two quantitative trait loci (QTLs) for first flower node on chromosomes 5 and 11, two QTLs for number of flowers per truss on chromosomes 2 and 5, and five QTLs for fruit weight on chromosomes 1, 2, 3, 9 and 12 are identified.

  17. 豌豆基因组SSR标记在蚕豆中的通用性分析%Transferability of Pea SSR Markers in Horsebean

    Institute of Scientific and Technical Information of China (English)

    侯万伟; 刘玉皎

    2012-01-01

    分析了21对豌豆(Pisum sativum)基因组SSR引物在10个蚕豆(Vicia faba)品种中的通用性.结果表明,豌豆基因组SSR引物在蚕豆中的通用性达38.10%,有效引物在蚕豆品种中的多态性比例为100%.%Transferability of 21 pairs of SSR markers of pea (Pisum sativum) in horsebean (Vicia faba) was tested. Results showed that the transferability rate of pea SSR in horsebean was 38.10%, and polymorphism rate of effective SSR in horse-bean was 100%.

  18. 马铃薯致病疫霉EST-SSR PCR反应体系的优化%Optimization of PCR system in EST-SSR analysis of Phytophthora infestans

    Institute of Scientific and Technical Information of China (English)

    王佳楠; 吕文河; 金光辉; 白雅梅; 李文霞; 韩英鹏

    2009-01-01

    由致病疫霉(Phytophthora infestans Montagne de Bary)引起的马铃薯晚疫病是危害马铃薯生产的最严重病害.试验以致病疫霉茵株HHO6-23为模板,以Pi08N为引物,研究致病疫霉EST-SSR PCR反应体系中各主要成分和退火温度对扩增结果的影响.优化后的PCR反应体系为:25 ng模板DNA,0.5 mmol·L-1dNTPs,2μL10×Buffer(Mg2+Free),1.75 mmol·L-1MgCl2,15 pmol引物,1.2 UTaq DNA聚合酶,加ddH2O至20μL;同时确定引物退火温度为63℃.PCR体系稳定性试验结果表明,优化后的致病疫霉EST-SSR PCR反应体系稳定、可靠,适合进行致病疫霉群体遗传多样性研究.

  19. High resolution melting analysis is a more sensitive and effective alternative to gel-based platforms in analysis of SSR--an example in citrus.

    Science.gov (United States)

    Distefano, Gaetano; Caruso, Marco; La Malfa, Stefano; Gentile, Alessandra; Wu, Shu-Biao

    2012-01-01

    High resolution melting curve analysis (HRM) has been used as an efficient, accurate and cost-effective tool to detect single nucleotide polymorphisms (SNPs) or insertions or deletions (INDELs). However, its efficiency, accuracy and applicability to discriminate microsatellite polymorphism have not been extensively assessed. The traditional protocols used for SSR genotyping include PCR amplification of the DNA fragment and the separation of the fragments on electrophoresis-based platform. However, post-PCR handling processes are laborious and costly. Furthermore, SNPs present in the sequences flanking repeat motif cannot be detected by polyacrylamide-gel-electrophoresis based methods. In the present study, we compared the discriminating power of HRM with the traditional electrophoresis-based methods and provided a panel of primers for HRM genotyping in Citrus. The results showed that sixteen SSR markers produced distinct polymorphic melting curves among the Citrus spp investigated through HRM analysis. Among those, 10 showed more genotypes by HRM analysis than capillary electrophoresis owing to the presence of SNPs in the amplicons. For the SSR markers without SNPs present in the flanking region, HRM also gave distinct melting curves which detected same genotypes as were shown in capillary electrophoresis (CE) analysis. Moreover, HRM analysis allowed the discrimination of most of the 15 citrus genotypes and the resulting genetic distance analysis clustered them into three main branches. In conclusion, it has been approved that HRM is not only an efficient and cost-effective alternative of electrophoresis-based method for SSR markers, but also a method to uncover more polymorphisms contributed by SNPs present in SSRs. It was therefore suggested that the panel of SSR markers could be used in a variety of applications in the citrus biodiversity and breeding programs using HRM analysis. Furthermore, we speculate that the HRM analysis can be employed to analyse SSR

  20. High resolution melting analysis is a more sensitive and effective alternative to gel-based platforms in analysis of SSR--an example in citrus.

    Directory of Open Access Journals (Sweden)

    Gaetano Distefano

    Full Text Available High resolution melting curve analysis (HRM has been used as an efficient, accurate and cost-effective tool to detect single nucleotide polymorphisms (SNPs or insertions or deletions (INDELs. However, its efficiency, accuracy and applicability to discriminate microsatellite polymorphism have not been extensively assessed. The traditional protocols used for SSR genotyping include PCR amplification of the DNA fragment and the separation of the fragments on electrophoresis-based platform. However, post-PCR handling processes are laborious and costly. Furthermore, SNPs present in the sequences flanking repeat motif cannot be detected by polyacrylamide-gel-electrophoresis based methods. In the present study, we compared the discriminating power of HRM with the traditional electrophoresis-based methods and provided a panel of primers for HRM genotyping in Citrus. The results showed that sixteen SSR markers produced distinct polymorphic melting curves among the Citrus spp investigated through HRM analysis. Among those, 10 showed more genotypes by HRM analysis than capillary electrophoresis owing to the presence of SNPs in the amplicons. For the SSR markers without SNPs present in the flanking region, HRM also gave distinct melting curves which detected same genotypes as were shown in capillary electrophoresis (CE analysis. Moreover, HRM analysis allowed the discrimination of most of the 15 citrus genotypes and the resulting genetic distance analysis clustered them into three main branches. In conclusion, it has been approved that HRM is not only an efficient and cost-effective alternative of electrophoresis-based method for SSR markers, but also a method to uncover more polymorphisms contributed by SNPs present in SSRs. It was therefore suggested that the panel of SSR markers could be used in a variety of applications in the citrus biodiversity and breeding programs using HRM analysis. Furthermore, we speculate that the HRM analysis can be employed to

  1. High Resolution Melting Analysis Is a More Sensitive and Effective Alternative to Gel-Based Platforms in Analysis of SSR – An Example in Citrus

    Science.gov (United States)

    Distefano, Gaetano; Caruso, Marco; La Malfa, Stefano; Gentile, Alessandra; Wu, Shu-Biao

    2012-01-01

    High resolution melting curve analysis (HRM) has been used as an efficient, accurate and cost-effective tool to detect single nucleotide polymorphisms (SNPs) or insertions or deletions (INDELs). However, its efficiency, accuracy and applicability to discriminate microsatellite polymorphism have not been extensively assessed. The traditional protocols used for SSR genotyping include PCR amplification of the DNA fragment and the separation of the fragments on electrophoresis-based platform. However, post-PCR handling processes are laborious and costly. Furthermore, SNPs present in the sequences flanking repeat motif cannot be detected by polyacrylamide-gel-electrophoresis based methods. In the present study, we compared the discriminating power of HRM with the traditional electrophoresis-based methods and provided a panel of primers for HRM genotyping in Citrus. The results showed that sixteen SSR markers produced distinct polymorphic melting curves among the Citrus spp investigated through HRM analysis. Among those, 10 showed more genotypes by HRM analysis than capillary electrophoresis owing to the presence of SNPs in the amplicons. For the SSR markers without SNPs present in the flanking region, HRM also gave distinct melting curves which detected same genotypes as were shown in capillary electrophoresis (CE) analysis. Moreover, HRM analysis allowed the discrimination of most of the 15 citrus genotypes and the resulting genetic distance analysis clustered them into three main branches. In conclusion, it has been approved that HRM is not only an efficient and cost-effective alternative of electrophoresis-based method for SSR markers, but also a method to uncover more polymorphisms contributed by SNPs present in SSRs. It was therefore suggested that the panel of SSR markers could be used in a variety of applications in the citrus biodiversity and breeding programs using HRM analysis. Furthermore, we speculate that the HRM analysis can be employed to analyse SSR

  2. Molecular genetic alterations in egfr CA-SSR-1 microsatellite and egfr copy number changes are associated with aggressiveness in thymoma

    Science.gov (United States)

    Conti, Salvatore; Gallo, Enzo; Sioletic, Stefano; Facciolo, Francesco; Palmieri, Giovannella; Lauriola, Libero; Evoli, Amelia; Martucci, Robert; Di Benedetto, Anna; Novelli, Flavia; Giannarelli, Diana; Deriu, Gloria; Granone, Pierluigi; Ottaviano, Margaret; Muti, Paola; Pescarmona, Edoardo

    2016-01-01

    Background The key role of egfr in thymoma pathogenesis has been questioned following the failure in identifying recurrent genetic alterations of egfr coding sequences and relevant egfr amplification rate. We investigated the role of the non-coding egfr CA simple sequence repeat 1 (CA-SSR-1) in a thymoma case series. Methods We used sequencing and egfr-fluorescence in situ hybridization (FISH) to genotype 43 thymomas; (I) for polymorphisms and somatic loss of heterozygosity of the non-coding egfr CA-SSR-1 microsatellite and (II) for egfr gene copy number changes. Results We found two prevalent CA-SSR-1 genotypes: a homozygous 16 CA repeat and a heterozygous genotype, bearing alleles with 16 and 20 CA repeats. The average combined allele length was correlated with tumor subtype: shorter sequences were significantly associated with the more aggressive WHO thymoma subtype group including B2/B3, B3 and B3/C histotypes. Four out of 29 informative cases analysed for somatic CA-SSR-1 loss of heterozygosity showed allelic imbalance (AI), 3/4 with loss of the longer allele. By egfr-FISH analysis, 9 out of 33 cases were FISH positive. Moreover, the two integrated techniques demonstrated that 3 out of 4 CA-SSR-1-AI positive cases with short allele relative prevalence showed significantly low or high chromosome 7 “polysomy”/increased gene copy number by egfr-FISH. Conclusions Our molecular and genetic and follow up data indicated that CA-SSR-1-allelic imbalance with short allele relative prevalence significantly correlated with EGFR 3+ immunohistochemical score, increased egfr Gene Copy Number, advanced stage and with relapsing/metastatic behaviour in thymomas. PMID:27076933

  3. Identification of SSR markers closely linked to the yellow seed coat color gene in heading Chinese cabbage (Brassica rapa L. ssp. pekinensis)

    Science.gov (United States)

    Ren, Yanjing; Wu, Junqing; Zhao, Jing; Hao, Lingyu

    2017-01-01

    ABSTRACT Research on the yellow-seeded variety of heading Chinese cabbage will aid in broadening its germplasm resources and lay a foundation for AA genome research in Brassica crops. Here, an F2 segregating population of 1575 individuals was constructed from two inbred lines (brown-seeded ‘92S105’ and yellow-seeded ‘91-125’). This population was used to identify the linkage molecular markers of the yellow seed coat trait using simple sequence repeat (SSR) techniques combined with a bulk segregant analysis (BSA). Of the 144 SSR primer pairs on the A01-A10 chromosomes from the Brassica database (http://brassicadb.org/brad/), two pairs located on the A06 chromosome showed polymorphic bands between the bulk DNA pools of eight brown-seeded and eight yellow-seeded F2 progeny. Based on the genome sequence, 454 SSR markers were designed to A06 to detect these polymorphic bands and were synthesized. Six SSR markers linked to the seed coat color gene were successfully selected for fine linkage genetic map construction, in which the two closest flanking markers, SSR449a and SSR317, mapped the Brsc-ye gene to a 40.2 kb region with distances of 0.07 and 0.06 cM, respectively. The molecular markers obtained in this report will assist in the marker-assisted selection and breeding of yellow-seeded lines in Brassica rapa L. and other close species. PMID:28069590

  4. Exploiting transcriptome data for the development and characterization of gene-based SSR markers related to cold tolerance in oil palm (Elaeis guineensis).

    Science.gov (United States)

    Xiao, Yong; Zhou, Lixia; Xia, Wei; Mason, Annaliese S; Yang, Yaodong; Ma, Zilong; Peng, Ming

    2014-12-19

    The oil palm (Elaeis guineensis, 2n = 32) has the highest oil yield of any crop species, as well as comprising the richest dietary source of provitamin A. For the tropical species, the best mean growth temperature is about 27°C, with a minimal growth temperature of 15°C. Hence, the plantation area is limited into the geographical ranges of 10°N to 10°S. Enhancing cold tolerance capability will increase the total cultivation area and subsequently oil productivity of this tropical species. Developing molecular markers related to cold tolerance would be helpful for molecular breeding of cold tolerant Elaeis guineensis. In total, 5791 gene-based SSRs were identified in 51,452 expressed sequences from Elaeis guineensis transcriptome data: approximately one SSR was detected per 10 expressed sequences. Of these 5791 gene-based SSRs, 916 were derived from expressed sequences up- or down-regulated at least two-fold in response to cold stress. A total of 182 polymorphic markers were developed and characterized from 442 primer pairs flanking these cold-responsive SSR repeats. The polymorphic information content (PIC) of these polymorphic SSR markers across 24 lines of Elaeis guineensis varied from 0.08 to 0.65 (mean = 0.31 ± 0.12). Using in-silico mapping, 137 (75.3%) of the 182 polymorphic SSR markers were located onto the 16 Elaeis guineensis chromosomes. Total coverage of 473 Mbp was achieved, with an average physical distance of 3.4 Mbp between adjacent markers (range 96 bp - 20.8 Mbp). Meanwhile, Comparative analysis of transcriptome under cold stress revealed that one ICE1 putative ortholog, five CBF putative orthologs, 19 NAC transcription factors and four cold-induced orhologs were up-regulated at least two fold in response to cold stress. Interestingly, 5' untranslated region of both Unigene21287 (ICE1) and CL2628.Contig1 (NAC) both contained an SSR markers. In the present study, a series of SSR markers were developed based on sequences

  5. Anodizing Effect on the Wear and Corrosion Behavior of EN AC-46500 Components Produced by Semi-Solid Rheocasting (SSR)

    Science.gov (United States)

    Forn, A.; Baile, M. T.; Picas, J. A.; Martín, E.; Menargues, S.

    2011-05-01

    In this work the effect of the anodizing process on the surface properties of SSR components was investigated. EN AC-46500 aluminium alloy components were formed using a 700 Ton high pressure machine and an Idra Semi Solid Rheocasting Station (SSR). The samples were heat treated with the aim of modifying the form and distribution of the eutectic silicon phase and after the heat treatment they were shotpeened in different conditions to obtain different surface roughness. Finally, the components were anodized with the purpose of improving the tribological properties and corrosion resistance. Surface modifications were investigated as they might have beneficial effects on the wear and corrosion behaviour. Experiments using a tribometer (ball on disc configuration) were performed in order to evaluate the tribological properties of the material and salt spray corrosion tests were used to study the corrosion resistance. These studies were carried out before and after the anodizing process. The anodized components show a significant improvement of the corrosion and wear resistance under the tested conditions, in spite of the high percentage of intermetallics compounds present in the AC-46500 alloy.

  6. SSR Marker Analysis on indica-japonica Differentiation of Natural Population of Oryza rufipogon in Yuanjiang, Yunnan Province

    Institute of Scientific and Technical Information of China (English)

    LI Ya-li; YANG Xiao-xi; ZHAO Feng-ping; XU Ming-hui

    2006-01-01

    By using 19 pairs of primers that could identify two subspecies (indica and japonica) of cultivated rice (Oryza sativa L.), the indica-japonica differentiation of 56 individuals from the natural population of common wild rice (Oryza rufipogon Griff.) in Yuanjiang was analyzed by SSR (microsatellite DNAs, or simple sequence repeat). Of the 19 pairs of primers, 17 pairs (89.47%) could amplify only one kind of band type among ail of the individuals, but primers RM251 and RM18 could amplify polymorphic band types. The bands amplified by 16 pairs of primers (84.21%) were identical to the indica-japonica diagnostic bands of relevant locus in cultivated rice, including 11 japonica-like loci and 4 indica-like loci. The bands amplified by the other three pairs of primers (RM18, RM202,RM205) were different from indica or japonica diagnostic bands of cultivated rice. The results showed that according to 19 loci analyzed, 84.21% of SSR loci in genomic DNA of common wild rice in Yuanjiang displayed indica-japonica differentiation and 13.79% of the loci still kept primitive, and most of the detected loci were homogenetic in the natural population.

  7. Molecular analysis of cultivated naked barley (Hordeum vulgare L.) from Qinghai-Tibet Plateau in China using SSR markers

    Institute of Scientific and Technical Information of China (English)

    Zhifen PAN; Guangbing DENG; Xuguang ZHAI; Hai LONG; Yawei TANG; Xiaolin QIANG; Maoqun YU

    2008-01-01

    Naked barley is widely planted in Qinghai-Tibet Plateau in China and is essential for the daily life of Tibetans in those regions. In this study, the genetic diversity of 64 cultivated naked barley accessions from Qinghai-Tibet Plateau in China was analyzed using 30 mapped SSRs linked with the important traits of barley improvement. A total of 132 alleles were identified at 22 polymorphic SSR loci, with the number of each locus ranging from 2 to 15, the polymorphism information con-tent (PIC) values ranging from 0.16 to 0.91, and with an average of 0.65. Of the selected SSRs, 13 SSR markers with high PIC value were highly efficient for the genetic analysis of Chinese barley. The accessions were divided into five main groups by cluster analysis and could be differentiated from each other. The genetic diversity in the Tibet accessions was slightly higher than in the Sichuan accessions. It is found that there were specific genes linked with the collecting sites. These results indi-cate the cultivated naked barley from Qinghai-Tibet Plateau in China are highly polymorphic and could be considered as an important resource bank for cultivated naked barley breeding in the future.

  8. Identification of QTLs associated with callogenesis and embryogenesis in oil palm using genetic linkage maps improved with SSR markers.

    Directory of Open Access Journals (Sweden)

    Ngoot-Chin Ting

    Full Text Available Clonal reproduction of oil palm by means of tissue culture is a very inefficient process. Tissue culturability is known to be genotype dependent with some genotypes being more amenable to tissue culture than others. In this study, genetic linkage maps enriched with simple sequence repeat (SSR markers were developed for dura (ENL48 and pisifera (ML161, the two fruit forms of oil palm, Elaeis guineensis. The SSR markers were mapped onto earlier reported parental maps based on amplified fragment length polymorphism (AFLP and restriction fragment length polymorphism (RFLP markers. The new linkage map of ENL48 contains 148 markers (33 AFLPs, 38 RFLPs and 77 SSRs in 23 linkage groups (LGs, covering a total map length of 798.0 cM. The ML161 map contains 240 markers (50 AFLPs, 71 RFLPs and 119 SSRs in 24 LGs covering a total of 1,328.1 cM. Using the improved maps, two quantitative trait loci (QTLs associated with tissue culturability were identified each for callusing rate and embryogenesis rate. A QTL for callogenesis was identified in LGD4b of ENL48 and explained 17.5% of the phenotypic variation. For embryogenesis rate, a QTL was detected on LGP16b in ML161 and explained 20.1% of the variation. This study is the first attempt to identify QTL associated with tissue culture amenity in oil palm which is an important step towards understanding the molecular processes underlying clonal regeneration of oil palm.

  9. Development and Characterization of 1,906 EST-SSR Markers from Unigenes in Jute (Corchorus spp.).

    Science.gov (United States)

    Zhang, Liwu; Li, Yanru; Tao, Aifen; Fang, Pingping; Qi, Jianmin

    2015-01-01

    Jute, comprising white and dark jute, is the second important natural fiber crop after cotton worldwide. However, the lack of expressed sequence tag-derived simple sequence repeat (EST-SSR) markers has resulted in a large gap in the improvement of jute. Previously, de novo 48,914 unigenes from white jute were assembled. In this study, 1,906 EST-SSRs were identified from these assembled uingenes. Among these markers, di-, tri- and tetra-nucleotide repeat types were the abundant types (12.0%, 56.9% and 21.6% respectively). The AG-rich or GA-rich nucleotide repeats were the predominant. Subsequently, a sample of 116 SSRs, located in genes encoding transcription factors and cellulose synthases, were selected to survey polymorphisms among12 diverse jute accessions. Of these, 83.6% successfully amplified at least one fragment and detected polymorphism among the 12diverse genotypes, indicating that the newly developed SSRs are of good quality. Furthermore, the genetic similarity coefficients of all the 12 accessions were evaluated using 97 polymorphic SSRs. The cluster analysis divided the jute accessions into two main groups with genetic similarity coefficient of 0.61. These EST-SSR markers not only enrich molecular markers of jute genome, but also facilitate genetic and genomic researches in jute.

  10. Development and Characterization of 1,906 EST-SSR Markers from Unigenes in Jute (Corchorus spp..

    Directory of Open Access Journals (Sweden)

    Liwu Zhang

    Full Text Available Jute, comprising white and dark jute, is the second important natural fiber crop after cotton worldwide. However, the lack of expressed sequence tag-derived simple sequence repeat (EST-SSR markers has resulted in a large gap in the improvement of jute. Previously, de novo 48,914 unigenes from white jute were assembled. In this study, 1,906 EST-SSRs were identified from these assembled uingenes. Among these markers, di-, tri- and tetra-nucleotide repeat types were the abundant types (12.0%, 56.9% and 21.6% respectively. The AG-rich or GA-rich nucleotide repeats were the predominant. Subsequently, a sample of 116 SSRs, located in genes encoding transcription factors and cellulose synthases, were selected to survey polymorphisms among12 diverse jute accessions. Of these, 83.6% successfully amplified at least one fragment and detected polymorphism among the 12diverse genotypes, indicating that the newly developed SSRs are of good quality. Furthermore, the genetic similarity coefficients of all the 12 accessions were evaluated using 97 polymorphic SSRs. The cluster analysis divided the jute accessions into two main groups with genetic similarity coefficient of 0.61. These EST-SSR markers not only enrich molecular markers of jute genome, but also facilitate genetic and genomic researches in jute.

  11. Development of Gene-Based SSR Markers in Winged Bean (Psophocarpus tetragonolobus (L.) DC.) for Diversity Assessment

    Science.gov (United States)

    Wong, Quin Nee; Tanzi, Alberto Stefano; Ho, Wai Kuan; Malla, Sunir; Blythe, Martin; Karunaratne, Asha; Massawe, Festo; Mayes, Sean

    2017-01-01

    Winged bean (Psophocarpus tetragonolobus) is an herbaceous multipurpose legume grown in hot and humid countries as a pulse, vegetable (leaves and pods), or root tuber crop depending on local consumption preferences. In addition to its different nutrient-rich edible parts which could contribute to food and nutritional security, it is an efficient nitrogen fixer as a component of sustainable agricultural systems. Generating genetic resources and improved lines would help to accelerate the breeding improvement of this crop, as the lack of improved cultivars adapted to specific environments has been one of the limitations preventing wider use. A transcriptomic de novo assembly was constructed from four tissues: leaf, root, pod, and reproductive tissues from Malaysian accessions, comprising of 198,554 contigs with a N50 of 1462 bp. Of these, 138,958 (70.0%) could be annotated. Among 9682 genic simple sequence repeat (SSR) motifs identified (excluding monomer repeats), trinucleotide-repeats were the most abundant (4855), followed by di-nucleotide (4500) repeats. A total of 18 SSR markers targeting di- and tri-nucleotide repeats have been validated as polymorphic markers based on an initial assessment of nine genotypes originated from five countries. A cluster analysis revealed provisional clusters among this limited, yet diverse selection of germplasm. The developed assembly and validated genic SSRs in this study provide a foundation for a better understanding of the plant breeding system for the genetic improvement of winged bean. PMID:28282950

  12. Genetic diversity of the black gram [Vigna mungo (L.) Hepper] gene pool as revealed by SSR markers.

    Science.gov (United States)

    Kaewwongwal, Anochar; Kongjaimun, Alisa; Somta, Prakit; Chankaew, Sompong; Yimram, Tarikar; Srinives, Peerasak

    2015-03-01

    In this study, 520 cultivated and 14 wild accessions of black gram (Vigna mungo (L.) Hepper) were assessed for diversity using 22 SSR markers. Totally, 199 alleles were detected with a mean of 9.05 alleles per locus. Wild black gram showed higher gene diversity than cultivated black gram. Gene diversity of cultivated accessions among regions was comparable, while allelic richness of South Asia was higher than that of other regions. 78.67% of the wild gene diversity presented in cultivated accessions, indicating that the domestication bottleneck effect in black gram is relatively low. Genetic distance analysis revealed that cultivated black gram was more closely related to wild black gram from South Asia than that from Southeast Asia. STRUCTURE, principal coordinate and neighbor-joining analyses consistently revealed that 534 black gram accessions were grouped into three major subpopulations. The analyses also revealed that cultivated black gram from South Asia was genetically distinct from that from West Asia. Comparison by SSR analysis with other closely related Vigna species, including mungbean, azuki bean, and rice bean, revealed that level of gene diversity of black gram is comparable to that of mungbean and rice bean but lower than that of azuki bean.

  13. Disomic Inheritance and Segregation Distortion of SSR Markers in Two Populations of Cynodon dactylon (L. Pers. var. dactylon.

    Directory of Open Access Journals (Sweden)

    Yuanwen Guo

    Full Text Available Common bermudagrass [C. dactylon (L. Pers. var. dactylon] is economically and environmentally the most important member among Cynodon species because of its extensive use for turf, forage and soil erosion control in the world. However, information regarding the inheritance within the taxon is limited. Accordingly, the objective of this study was to determine qualitative inheritance mode in common bermudagrass. Two tetraploid (2n = 4x = 36, first-generation selfed (S1 populations, 228 progenies of 'Zebra' and 273 from A12359, were analyzed for segregation with 21 and 12 simple sequence repeat (SSR markers, respectively. It is concluded that the inheritance mode of tetraploid bermudagrass was complete or near complete disomic. It is evident that the two bermudagrass parents had an allotetraploid genome with two distinct subgenomes since 33 SSR primer pairs amplified 34 loci, each having two alleles. Severe transmission ratio distortions occurred in the Zebra population while less so in the A12359 population. The findings of disomic inheritance and segregation ratio distortion in common bermudagrass is significant in subsequent linkage map construction, quantitative trait locus mapping and marker-assisted selection in the species.

  14. SSR_pipeline: a bioinformatic infrastructure for identifying microsatellites from paired-end Illumina high-throughput DNA sequencing data

    Science.gov (United States)

    Miller, Mark P.; Knaus, Brian J.; Mullins, Thomas D.; Haig, Susan M.

    2013-01-01

    SSR_pipeline is a flexible set of programs designed to efficiently identify simple sequence repeats (e.g., microsatellites) from paired-end high-throughput Illumina DNA sequencing data. The program suite contains 3 analysis modules along with a fourth control module that can automate analyses of large volumes of data. The modules are used to 1) identify the subset of paired-end sequences that pass Illumina quality standards, 2) align paired-end reads into a single composite DNA sequence, and 3) identify sequences that possess microsatellites (both simple and compound) conforming to user-specified parameters. The microsatellite search algorithm is extremely efficient, and we have used it to identify repeats with motifs from 2 to 25bp in length. Each of the 3 analysis modules can also be used independently to provide greater flexibility or to work with FASTQ or FASTA files generated from other sequencing platforms (Roche 454, Ion Torrent, etc.). We demonstrate use of the program with data from the brine fly Ephydra packardi (Diptera: Ephydridae) and provide empirical timing benchmarks to illustrate program performance on a common desktop computer environment. We further show that the Illumina platform is capable of identifying large numbers of microsatellites, even when using unenriched sample libraries and a very small percentage of the sequencing capacity from a single DNA sequencing run. All modules from SSR_pipeline are implemented in the Python programming language and can therefore be used from nearly any computer operating system (Linux, Macintosh, and Windows).

  15. Construction of an integrated pepper map using RFLP, SSR, CAPS, AFLP, WRKY, rRAMP, and BAC end sequences.

    Science.gov (United States)

    Lee, Heung-Ryul; Bae, Ik-Hyun; Park, Soung-Woo; Kim, Hyoun-Joung; Min, Woong-Ki; Han, Jung-Heon; Kim, Ki-Taek; Kim, Byung-Dong

    2009-01-31

    Map-based cloning to find genes of interest, markerassisted selection (MAS), and marker-assisted breeding (MAB) all require good genetic maps with high reproducible markers. For map construction as well as chromosome assignment, development of single copy PCR-based markers and map integration process are necessary. In this study, the 132 markers (57 STS from BAC-end sequences, 13 STS from RFLP, and 62 SSR) were newly developed as single copy type PCR-based markers. They were used together with 1830 markers previously developed in our lab to construct an integrated map with the Joinmap 3.0 program. This integrated map contained 169 SSR, 354 RFLP, 23 STS from BAC-end sequences, 6 STS from RFLP, 152 AFLP, 51 WRKY, and 99 rRAMP markers on 12 chromosomes. The integrated map contained four genetic maps of two interspecific (Capsicum annuum 'TF68' and C. chinense 'Habanero') and two intraspecific (C. annuum 'CM334' and C. annuum 'Chilsungcho') populations of peppers. This constructed integrated map consisted of 805 markers (map distance of 1858 cM) in interspecific populations and 745 markers (map distance of 1892 cM) in intraspecific populations. The used pepper STS were first developed from end sequences of BAC clones from Capsicum annuum 'CM334'. This integrated map will provide useful information for construction of future pepper genetic maps and for assignment of linkage groups to pepper chromosomes.

  16. A SNP and SSR based genetic map of asparagus bean (Vigna. unguiculata ssp. sesquipedialis) and comparison with the broader species.

    Science.gov (United States)

    Xu, Pei; Wu, Xiaohua; Wang, Baogen; Liu, Yonghua; Ehlers, Jeffery D; Close, Timothy J; Roberts, Philip A; Diop, Ndeye-Ndack; Qin, Dehui; Hu, Tingting; Lu, Zhongfu; Li, Guojing

    2011-01-06

    Asparagus bean (Vigna. unguiculata ssp. sesquipedialis) is a distinctive subspecies of cowpea [Vigna. unguiculata (L.) Walp.] that apparently originated in East Asia and is characterized by extremely long and thin pods and an aggressive climbing growth habit. The crop is widely cultivated throughout Asia for the production of immature pods known as 'long beans' or 'asparagus beans'. While the genome of cowpea ssp. unguiculata has been characterized recently by high-density genetic mapping and partial sequencing, little is known about the genome of asparagus bean. We report here the first genetic map of asparagus bean based on SNP and SSR markers. The current map consists of 375 loci mapped onto 11 linkage groups (LGs), with 191 loci detected by SNP markers and 184 loci by SSR markers. The overall map length is 745 cM, with an average marker distance of 1.98 cM. There are four high marker-density blocks distributed on three LGs and three regions of segregation distortion (SDRs) identified on two other LGs, two of which co-locate in chromosomal regions syntenic to SDRs in soybean. Synteny between asparagus bean and the model legume Lotus. japonica was also established. This work provides the basis for mapping and functional analysis of genes/QTLs of particular interest in asparagus bean, as well as for comparative genomics study of cowpea at the subspecies level.

  17. A SNP and SSR based genetic map of asparagus bean (Vigna. unguiculata ssp. sesquipedialis and comparison with the broader species.

    Directory of Open Access Journals (Sweden)

    Pei Xu

    Full Text Available Asparagus bean (Vigna. unguiculata ssp. sesquipedialis is a distinctive subspecies of cowpea [Vigna. unguiculata (L. Walp.] that apparently originated in East Asia and is characterized by extremely long and thin pods and an aggressive climbing growth habit. The crop is widely cultivated throughout Asia for the production of immature pods known as 'long beans' or 'asparagus beans'. While the genome of cowpea ssp. unguiculata has been characterized recently by high-density genetic mapping and partial sequencing, little is known about the genome of asparagus bean. We report here the first genetic map of asparagus bean based on SNP and SSR markers. The current map consists of 375 loci mapped onto 11 linkage groups (LGs, with 191 loci detected by SNP markers and 184 loci by SSR markers. The overall map length is 745 cM, with an average marker distance of 1.98 cM. There are four high marker-density blocks distributed on three LGs and three regions of segregation distortion (SDRs identified on two other LGs, two of which co-locate in chromosomal regions syntenic to SDRs in soybean. Synteny between asparagus bean and the model legume Lotus. japonica was also established. This work provides the basis for mapping and functional analysis of genes/QTLs of particular interest in asparagus bean, as well as for comparative genomics study of cowpea at the subspecies level.

  18. Genome-Wide Analysis of Simple Sequence Repeats and Efficient Development of Polymorphic SSR Markers Based on Whole Genome Re-Sequencing of Multiple Isolates of the Wheat Stripe Rust Fungus.

    Directory of Open Access Journals (Sweden)

    Huaiyong Luo

    Full Text Available The biotrophic parasitic fungus Puccinia striiformis f. sp. tritici (Pst causes stripe rust, a devastating disease of wheat, endangering global food security. Because the Pst population is highly dynamic, it is difficult to develop wheat cultivars with durable and highly effective resistance. Simple sequence repeats (SSRs are widely used as molecular markers in genetic studies to determine population structure in many organisms. However, only a small number of SSR markers have been developed for Pst. In this study, a total of 4,792 SSR loci were identified using the whole genome sequences of six isolates from different regions of the world, with a marker density of one SSR per 22.95 kb. The majority of the SSRs were di- and tri-nucleotide repeats. A database containing 1,113 SSR markers were established. Through in silico comparison, the previously reported SSR markers were found mainly in exons, whereas the SSR markers in the database were mostly in intergenic regions. Furthermore, 105 polymorphic SSR markers were confirmed in silico by their identical positions and nucleotide variations with INDELs identified among the six isolates. When 104 in silico polymorphic SSR markers were used to genotype 21 Pst isolates, 84 produced the target bands, and 82 of them were polymorphic and revealed the genetic relationships among the isolates. The results show that whole genome re-sequencing of multiple isolates provides an ideal resource for developing SSR markers, and the newly developed SSR markers are useful for genetic and population studies of the wheat stripe rust fungus.

  19. 美国黑核桃SSR反应体系优化%Optimization of SSR Reaction System in Juglans nigra

    Institute of Scientific and Technical Information of China (English)

    赵鹏; Keith E.Wosete; 程飞; 张硕新

    2012-01-01

    The optimization of the SSR-PCR ( simple sequence repeat-polymerase chain reaction) reaction system is an important basic protocol when SSRs are used for pedigree construction, genotyping or population genetics research in black walnut (Juglans nigra L. ). We systematically tested the concentrations of Taq DNA pdlymerase, BSA, dNTPs, Mg2+ , primers, and template DNA concentration in the PCR reaction to determine.the optimal reaction system. The results indicated that the optimal SSR-PCR reaction conditions for black walnut (J. Nigra L. ) included a total volume of 10 (iL containing 1 μL of 10 ng · μL-1 DNA, 1 μL of 10 X Taq DNA polymerase reaction buffer (1.5 mmol · L-1 Mg2+ ) , 1. 25 μL of 200 mmol · L-1 dNTPs (0. 3 mmol · L-1 ) , 1 μL of 1 mg · mL-1 BSA ( Bovine Serum Albumin, 0. 1 mg · mL-1) , 1.0 μL of 10 μmol · L-1 each primer (when using one pair primer in each PCR reaction) or 0. 5 μL of 10 μmol · L-1 each primer (when using three pairs primer in each PCR reaction) , 0. 5 units Taq polymerase, and 4. 5 μL sterilized distilled water. The thermal cycling conditions were as follows; denaturation 3 min at 94℃ ; 32 cycles of 15 s at 93℃, 1 min at the annealing temperature for the primer, 30 s at 72℃ ; and a final extension of 10 min at 72℃ at the end of the amplification. The results showed that this SSR-PCR protocol resulted in clear, reproducible results suitable for the analysis of population genetics, genotyping, and for molecular ecology.%优化SSR-PCR反应体系是黑核桃(Juglans nigra L.)SSR基因鉴定和群体遗传等研究的基础.本研究通过对PCR反应中Mg2+浓度、牛血清白蛋白(Bovine Serum Albumin,BSA)浓度、Taq聚合酶用量、dNTPs浓度、引物浓度和模板DNA量的组合以及PCR程序组合试验,确定了黑核桃SSR的最佳反应体系,即在10 μL的PCR反应体系中,含10 ng模板DNA,0.1 mg·mL-1牛血清蛋白(BSA),0.25 mmol·L-1 dNTPs,1.5 mmol·L-1 Mg2+1 μL 10XTaq DNA

  20. Construction of a genetic linkage map for tetraploid hybrid wheatgrass using a SSR molecular marker%利用 SSR 分子标记构建四倍体杂交冰草的遗传连锁图谱

    Institute of Scientific and Technical Information of China (English)

    姜志艳; 于肖夏; 于卓; 张志成; 石悦; 姜超

    2016-01-01

    为构建四倍体杂交冰草分子遗传连锁图谱,对深入开展冰草产量、抗性等重要性状的 QTL 定位及分子标记辅助育种提供依据,以四倍体杂种 F2分离群体的347个单株及亲本蒙古冰草和航道冰草为材料,采用 SSR 分子标记技术和 Joinmap 4.0软件进行了遗传作图研究。试验从256对 SSR 引物中筛选出条带清晰稳定、多态性丰富的适宜引物30对,PCR 扩增得到224个 SSR 标记位点,平均每对引物扩增出7.47个位点,其中多态性标记位点185个,占82.6%。偏分离分析显示,在185个 SSR 多态性标记位点中有24个标记产生偏分离,占13.0%,符合植物遗传作图时通常偏分离标记比率<30%的要求,可用于遗传作图。构建了1张四倍体杂交冰草的分子遗传连锁框架图谱,该图谱包含14个连锁群、185个标记,其长度范围在123.0~202.6 cM 之间,连锁群 LG4最长、LG12最短,各连锁群的平均长度167.32 cM,覆盖基因组总长度2342.5 cM,标记间的平均距离12.66 cM。%To establish a genetic linkage map in tetraploid hybrid wheatgrass genetic mapping was conducted u-sing a simple sequence repeats (SSR)molecular marker technique with ‘Joinmap’4.0 software.347 individu-als from the F2 segregating population and their parents were utilized,this helped lay the foundation for further study of marker-assisted breeding,and quantitative trait locus (QTL)location of important traits in wheat-grass,such as disease resistance and yield.Thirty optimal primers with clear,stable and high polymorphic bands were screened from 256 tested SSR primers.A total of 224 SSR loci were obtained from polymerase chain reaction (PCR)amplification with an average of 7.47 loci per primer,of which 185 were polymorphic lo-ci,accounting for 82.6% of all loci.Segregation distortion analysis showed that a total of 24 loci were distort-ed,accounted for 13.0% of all (185)polymorphic

  1. SSR标记在甜瓜中的研究进展%The Advances of the Application of SSR Markers in Cucumis melo L.

    Institute of Scientific and Technical Information of China (English)

    盛云燕; 侯莉华; 刘芳

    2011-01-01

    SSR (simple sequence repeat) markers are one of DNA markers based on the polymerase chain reaction (PCR).SSRs (simple sequence repeats) show much higher level polymorphism and randomly distribute along the linkage map in melon (Cucumis melo L.), and the SSR markers are inherited in a codominant manner.The utilization of SSR markers in genetic diversity, genome mapping, gene location, and marker assisted selection in melon genetics and breeding are summarized in this paper.%SSR(simple sequence repeat)标记是建立在PCR基础上的一种新型DNA分子标记.由于SSR具有丰富的多态性,随机分布于甜瓜的整个基因组中,并表现为共显性,所以它是进行甜瓜遗传研究的理想工具.笔者就SSR标记在甜瓜遗传多样性分析,构建遗传连锁图谱、标记和定位目的基因及标记辅助选择等方面的研究进展进行了综述.

  2. An integrated genetic linkage map of watermelon and genetic diversity based on single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers

    Science.gov (United States)

    Watermelon (Citrullus lanatus var. lanatus) is an important vegetable fruit throughout the world. A high number of single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers should provide large coverage of the watermelon genome and high phylogenetic resolution of germplasm acces...

  3. 棉花遗传作图用SSR标记的开发%Development of SSR Markers towards Genetic Mapping in Cotton (GossyPium hirsutum L. )

    Institute of Scientific and Technical Information of China (English)

    Siva P. KUMPATLA; Erin C. HORNE; Manali R. SHAH; Manju GUPTA; Steven A. THOMPSON

    2002-01-01

    @@ Availability of informative molecular markers is a prerequisite for genetic mapping and marker assisted selection projects. Micro-satellites or Simple Sequence Repeat (SSR) markers are PCR-based and currently the most widely used marker system in the plant molecular genetics community due to their high degree of polymorphism, random distribution throughout the genome and their suitability for high throughput genotyping formats.

  4. High-Throughput Development of SSR Markers from Pea (Pisum sativum L.) Based on Next Generation Sequencing of a Purified Chinese Commercial Variety.

    Science.gov (United States)

    Yang, Tao; Fang, Li; Zhang, Xiaoyan; Hu, Jinguo; Bao, Shiying; Hao, Junjie; Li, Ling; He, Yuhua; Jiang, Junye; Wang, Fang; Tian, Shufang; Zong, Xuxiao

    2015-01-01

    Pea (Pisum sativum L.) is an important food legume globally, and is the plant species that J.G. Mendel used to lay the foundation of modern genetics. However, genomics resources of pea are limited comparing to other crop species. Application of marker assisted selection (MAS) in pea breeding has lagged behind many other crops. Development of a large number of novel and reliable SSR (simple sequence repeat) or microsatellite markers will help both basic and applied genomics research of this crop. The Illumina HiSeq 2500 System was used to uncover 8,899 putative SSR containing sequences, and 3,275 non-redundant primers were designed to amplify these SSRs. Among the 1,644 SSRs that were randomly selected for primer validation, 841 yielded reliable amplifications of detectable polymorphisms among 24 genotypes of cultivated pea (Pisum sativum L.) and wild relatives (P. fulvum Sm.) originated from diverse geographical locations. The dataset indicated that the allele number per locus ranged from 2 to 10, and that the polymorphism information content (PIC) ranged from 0.08 to 0.82 with an average of 0.38. These 1,644 novel SSR markers were also tested for polymorphism between genotypes G0003973 and G0005527. Finally, 33 polymorphic SSR markers were anchored on the genetic linkage map of G0003973 × G0005527 F2 population.

  5. Association Analysis of SSR Markers with Phenology, Grain, and Stover-Yield Related Traits in Pearl Millet (Pennisetum glaucum (L. R. Br.

    Directory of Open Access Journals (Sweden)

    Baskaran Kannan

    2014-01-01

    Full Text Available Pearl millet is a staple food crop for millions of people living in the arid and semi-arid tropics. Molecular markers have been used to identify genomic regions linked to traits of interest by conventional QTL mapping and association analysis. Phenotypic recurrent selection is known to increase frequencies of favorable alleles and decrease those unfavorable for the traits under selection. This study was undertaken (i to quantify the response to recurrent selection for phenotypic traits during breeding of the pearl millet open-pollinated cultivar “CO (Cu 9” and its four immediate progenitor populations and (ii to assess the ability of simple sequence repeat (SSR marker alleles to identify genomic regions linked to grain and stover yield-related traits in these populations by association analysis. A total of 159 SSR alleles were detected across 34 selected single-copy SSR loci. SSR marker data revealed presence of subpopulations. Association analysis identified genomic regions associated with flowering time located on linkage group (LG 6 and plant height on LG4, LG6, and LG7. Marker alleles on LG6 were associated with stover yield, and those on LG7 were associated with grain yield. Findings of this study would give an opportunity to develop marker-assisted recurrent selection (MARS or marker-assisted population improvement (MAPI strategies to increase the rate of gain for pearl millet populations undergoing recurrent selection.

  6. Open reading frame ssr2016 is required for antimycin A-sensitive photosystem I-driven cyclic electron flow in the cyanobacterium Synechocystis sp. PCC 6803

    NARCIS (Netherlands)

    Yeremenko, N.; Jeanjean, R.; Prommeenate, P.; Krasikov, V.; Nixon, P.J.; Vermaas, W.F.J.; Havaux, M.; Matthijs, H.C.P.

    2005-01-01

    Open reading frame ssr2016 encodes a protein with substantial sequence similarities to PGR5 identified as a component of the antimycin A-sensitive ferredoxin:plastoquinone reductase (FQR) in PSI cyclic photophosphorylation in Arabidopsis thaliana. We studied cyclic electron flow in Synechocystis sp.

  7. Analysis of simple sequence repeats in rice bean(Vigna umbellata) using an SSR-enriched library

    Institute of Scientific and Technical Information of China (English)

    Lixia Wang; Kyung Do Kim; Dongying Gao; Honglin Chen; Suhua Wang; Suk Ha Lee; Scott A. Jackson; Xuzhen Cheng

    2016-01-01

    Rice bean(Vigna umbellata Thunb.), a warm-season annual legume, is grown in Asia mainly for dried grain or fodder and plays an important role in human and animal nutrition because the grains are rich in protein and some essential fatty acids and minerals. With the aim of expediting the genetic improvement of rice bean, we initiated a project to develop genomic resources and tools for molecular breeding in this little-known but important crop.Here we report the construction of an SSR-enriched genomic library from DNA extracted from pooled young leaf tissues of 22 rice bean genotypes and developing SSR markers.In 433,562 reads generated by a Roche 454 GS-FLX sequencer, we identified 261,458 SSRs, of which 48.8% were of compound form. Dinucleotide repeats were predominant with an absolute proportion of 81.6%, followed by trinucleotides(17.8%). Other types together accounted for 0.6%. The motif AC/GT accounted for 77.7% of the total, followed by AAG/CTT(14.3%), and all others accounted for 12.0%. Among the flanking sequences, 2928 matched putative genes or gene models in the protein database of Arabidopsis thaliana, corresponding with 608 non-redundant Gene Ontology terms. Of these sequences, 11.2% were involved in cellular components, 24.2% were involved molecular functions, and 64.6% were associated with biological processes. Based on homolog analysis, 1595 flanking sequences were similar to mung bean and 500 to common bean genomic sequences. Comparative mapping was conducted using 350 sequences homologous to both mung bean and common bean sequences. Finally, a set of primer pairs were designed, and a validation test showed that58 of 220 new primers can be used in rice bean and 53 can be transferred to mung bean.However, only 11 were polymorphic when tested on 32 rice bean varieties. We propose that this study lays the groundwork for developing novel SSR markers and will enhance the mapping of qualitative and quantitative traits and marker-assisted selection in rice

  8. Development and Identification of SSR Markers Associated with Starch Properties and β-Carotene Content in the Storage Root of Sweet Potato (Ipomoea batatas L.)

    Science.gov (United States)

    Zhang, Kai; Wu, Zhengdan; Tang, Daobin; Lv, Changwen; Luo, Kai; Zhao, Yong; Liu, Xun; Huang, Yuanxin; Wang, Jichun

    2016-01-01

    Sweet potato (Ipomoea batatas L.) is a nutritious food crop and, based on the high starch content of its storage root, a potential bioethanol feedstock. Enhancing the nutritional value and starch quantity of storage roots are important goals of sweet potato breeding programs aimed at developing improved varieties for direct consumption, processing, and industrial uses. However, developing improved lines of sweet potato is challenging due to the genetic complexity of this plant and the lack of genome information. Short sequence repeat (SSR) markers are powerful molecular tools for tracking important loci in crops and for molecular-based breeding strategies; however, few SSR markers and marker-trait associations have hitherto been identified in sweet potato. In this study, we identified 1824 SSRs by using a de novo assembly of publicly available ESTs and mRNAs in sweet potato, and designed 1476 primer pairs based on SSR-containing sequences. We mapped 214 pairs of primers in a natural population comprised of 239 germplasms, and identified 1278 alleles with an average of 5.972 alleles per locus and a major allele frequency of 0.7702. Population structure analysis revealed two subpopulations in this panel of germplasms, and phenotypic characterization demonstrated that this panel is suitable for association mapping of starch-related traits. We identified 32, 16, and 17 SSR markers associated with starch content, β-carotene content, and starch composition in the storage root, respectively, using association analysis and further evaluation of a subset of sweet potato genotypes with various characteristics. The SSR markers identified here can be used to select varieties with desired traits and to investigate the genetic mechanism underlying starch and carotenoid formation in the starchy roots of sweet potato. PMID:26973669

  9. Application of SSR marker in genetics experimental teaching%SSR分子标记技术在遗传学实验教学中的应用

    Institute of Scientific and Technical Information of China (English)

    夏曦中; 车婧; 章志宏; 王建波

    2012-01-01

    该实验是科研成果转化为实验教学的一个案例.选择位于水稻不同连锁群上的6对SSR引物构建了2个杂交稻及其亲本的SSR指纹图谱,建立了一套适合于本科生实验的杂交水稻亲本鉴定的稳定的SSR技术体系.筛选的6对引物进行PCR扩增得到的杂交稻均有2条带.由SSR指纹图谱分析可得:杂交稻P5的亲本是P2和P4,P6的亲本是P1和P3.通过本实验巩固了学生关于分离定律的学习,并有所延伸.%This is a case to turn an achievement in scientific research into the teaching experiment. It helps students to learn the theory and method of SSR marker from the experiment, and helps them grasp the technology how to identify the genetic relatives based on SSR fingerprint. It is adapted to teaching experiment that the technology of the six SSR primers in different chromosomes in hybrid rice is selected to distribute the SSR fingerprint of two hybrid rice combinations and their parents. The two bands of hybrid rice are complement types of their parents. Baaed on the SSR fingerprint, it can conclude that P2 and P4 are the parents of P5, and P1 and P3 are the parents of P6. Mendel's law of segragation and other knowledge can be consolidated by this experiment.

  10. Isolation and Characterization of Simple Sequence Repeats (SSR) Markers from the Moss Genus Orthotrichum Using a Small Throughput Pyrosequencing Machine

    Science.gov (United States)

    Sawicki, Jakub; Kwaśniewski, Mirosław; Szczecińska, Monika; Chwiałkowska, Karolina; Milewicz, Monika; Plášek, Vítězslav

    2012-01-01

    Here, we report the results of next-generation sequencing on the GS Junior system to identify a large number of microsatellites from the epiphytic moss Orthotrichum speciosum. Using a combination of a total (non-enrichment) genomic library and small-scale 454 pyrosequencing, we determined 5382 contigs whose length ranged from 103 to 5445 bp. In this dataset we identified 92 SSR (simple sequence repeats) motifs in 89 contigs. Forty-six of these had flanking regions suitable for primer design. We tested PCR amplification, reproducibility, and the level of polymorphism of 46 primer pairs for Orthotrichum speciosum using 40 individuals from two populations. As a result, the designed primers revealed 35 polymorphic loci with more than two alleles detected. This method is cost- and time-effective in comparison with traditional approaches involving cloning and sequencing. PMID:22837714

  11. Cluster and principal component analysis based on SSR markers of Amomum tsao-ko in Jinping County of Yunnan Province

    Science.gov (United States)

    Ma, Mengli; Lei, En; Meng, Hengling; Wang, Tiantao; Xie, Linyan; Shen, Dong; Xianwang, Zhou; Lu, Bingyue

    2017-08-01

    Amomum tsao-ko is a commercial plant that used for various purposes in medicinal and food industries. For the present investigation, 44 germplasm samples were collected from Jinping County of Yunnan Province. Clusters analysis and 2-dimensional principal component analysis (PCA) was used to represent the genetic relations among Amomum tsao-ko by using simple sequence repeat (SSR) markers. Clustering analysis clearly distinguished the samples groups. Two major clusters were formed; first (Cluster I) consisted of 34 individuals, the second (Cluster II) consisted of 10 individuals, Cluster I as the main group contained multiple sub-clusters. PCA also showed 2 groups: PCA Group 1 included 29 individuals, PCA Group 2 included 12 individuals, consistent with the results of cluster analysis. The purpose of the present investigation was to provide information on genetic relationship of Amomum tsao-ko germplasm resources in main producing areas, also provide a theoretical basis for the protection and utilization of Amomum tsao-ko resources.

  12. High-density Linkage Map of Cultivated Allotetraploid Cotton Based on SSR, TRAP, SRAP and AFLP Markers

    Institute of Scientific and Technical Information of China (English)

    Jiwen Yu; Shuxun Yu; Cairui Lu; Wu Wang; Shuli Fan; Meizhen Song; Zhongxu Lin; Xianlong Zhang; Jinfa Zhang

    2007-01-01

    A high-density linkage map was constructed for an F2 population derived from an interspecific cross of cultivated allotetraploid species between Gossyplum hirsutum L. and G. barbadense L. A total of 186 F2 individuals from the interspecific cross of "CRI 36 × Hai 7124" were genotyped at 1 252 polymorphic loci including a novel marker system,target region amplification polymorphism (TRAP). The map consists of 1 097 markers, including 697 simple sequence repeats (SSRs), 171 TRAPs, 129 sequence-related amplified polymorphisms, 98 amplified fragment length polymorphisms, and two morphological markers, and spanned 4 536.7 cM with an average genetic distance of 4.1 cM per marker. Using 45 duplicated SSR loci among chromosomes, 11 of the 13 pairs of homologous chromosomes were identified in tetraplold cotton. This map will provide an essential resource for high resolution mapping of quantitative trait loci and molecular breeding in cotton.

  13. Genetic diversity studies and identification of SSR markers associated with Fusarium wilt (Fusarium udum) resistance in cultivated pigeonpea (Cajanus cajan)

    Indian Academy of Sciences (India)

    A. K. Singh; V. P. Rai; R. Chand; R. P. Singh; M. N. Singh

    2013-08-01

    Genetic diversity and identification of simple sequence repeat markers correlated with Fusarium wilt resistance was performed in a set of 36 elite cultivated pigeonpea genotypes differing in levels of resistance to Fusarium wilt. Twenty-four polymorphic sequence repeat markers were screened across these genotypes, and amplified a total of 59 alleles with an average high polymorphic information content value of 0.52. Cluster analysis, done by UPGMA and PCA, grouped the 36 pigeonpea genotypes into two main clusters according to their Fusarium wilt reaction. Based on the Kruskal–Wallis ANOVA and simple regression analysis, six simple sequence repeat markers were found to be significantly associated with Fusarium wilt resistance. The phenotypic variation explained by these markers ranged from 23.7 to 56.4%. The present study helps in finding out feasibility of prescreened SSR markers to be used in genetic diversity analysis and their potential association with disease resistance.

  14. Genetic Diversity of Maize Populations Developed by Two Kinds of Recurrent Selection Methods Investigated with SSR Markers

    Institute of Scientific and Technical Information of China (English)

    LI Lu-jiang; YANG Ke-cheng; PAN Guang-tang; RONG Ting-zhao

    2008-01-01

    Two cycles of biparental mass selection (MS) and one cycle of half-sib-S3 family combining selection (HS-S3) for yield were carried out in 2 synthetic maize populations P4C0 and P5C0 synchronously.The genetic diversity of 8 maize populations,including both the basic populations and their developed populations,were evaluated by 30 SSR primers.On the 30 SSR loci,a total of 184 alleles had been detected in these populations.At each locus,the number of alleles varied from 2 to 14,with an average of 6.13.The number and ratio of polymorphic loci in both the basic populations were higher than those of their developed populations,respectively.There was nearly no difference after MS but decreased after HS-S3 in both the basic populations in the mean gene heterozygosity.The mean genetic distance changed slightly after MS but decreased in a bigger degree after HS-S3 in both the basic populations.Analyses on the distribution of genetic distances showed that the ranges of the genetic distance were wider after MS and most of the genetic distances in populations developed by HS-S3 were smaller than those in both the basic populations.The number of genotypes increased after MS but decreased after HS-S3 in both the basic populations.The genetic diversity of intra-population was much more than genetic diversity of inter-population in both the basic populations.All these indexes demonstrated that the genetic diversity of populations after MS was similar to their basic populations,and the genetic diversity was maintained during MS,whereas the genetic diversity of populations decreased after HS-S3.This result indicated that heterogeneity between some of the individuals in the developed populations increased after MS,whereas the populations become more homozygotic after HS-S3.

  15. Unraveling the efficiency of RAPD and SSR markers in diversity analysis and population structure estimation in common bean.

    Science.gov (United States)

    Zargar, Sajad Majeed; Farhat, Sufia; Mahajan, Reetika; Bhakhri, Ayushi; Sharma, Arjun

    2016-01-01

    Increase in food production viz-a-viz quality of food is important to feed the growing human population to attain food as well as nutritional security. The availability of diverse germplasm of any crop is an important genetic resource to mine the genes that may assist in attaining food as well as nutritional security. Here we used 15 RAPD and 23 SSR markers to elucidate diversity among 51 common bean genotypes mostly landraces collected from the Himalayan region of Jammu and Kashmir, India. We observed that both the markers are highly polymorphic. The discriminatory power of these markers was determined using various parameters like; percent polymorphism, PIC, resolving power and marker index. 15 RAPDs produced 171 polymorphic bands, while 23 SSRs produced 268 polymorphic bands. SSRs showed a higher PIC value (0.300) compared to RAPDs (0.243). Further the resolving power of SSRs was 5.241 compared to 3.86 for RAPDs. However, RAPDs showed a higher marker index (2.69) compared to SSRs (1.279) that may be attributed to their higher multiplex ratio. The dendrograms generated with hierarchical UPGMA cluster analysis grouped genotypes into two main clusters with various degrees of sub clustering within the cluster. Here we observed that both the marker systems showed comparable accuracy in grouping genotypes of common bean according to their area of cultivation. The model based STRUCTURE analysis using 15 RAPD and 23 SSR markers identified a population with 3 sub-populations which corresponds to distance based groupings. High level of genetic diversity was observed within the population. These findings have further implications in common bean breeding as well as conservation programs.

  16. Development of SSR Markers in Hickory (Carya cathayensis Sarg.) and Their Transferability to Other Species of Carya.

    Science.gov (United States)

    Li, Juan; Zeng, Yanru; Shen, Dengfeng; Xia, Guohua; Huang, Yinzhi; Huang, Youjun; Chang, Jun; Huang, Jianqin; Wang, Zhengjia

    2014-10-01

    Hickory (Carya cathayensis Sarg.), an important nut-producing species in Southeastern China, has high economic value, but so far there has been no cultivar bred under species although it is mostly propagated by seeding and some elite individuals have been found. It has been found recently that this species has a certain rate of apomixis and poor knowledge of its genetic background has influenced development of a feasible breeding strategy. Here in this paper we first release SSR (Simple sequence repeat) markers developed in this species and their transferability to other three species of the same genus, Carya. A total of 311 pairs of SSR primers in hickory were developed based on sequenced cDNAs of a fruit development-associated cDNA library and RNA-seq data of developing female floral buds and could be used to distinguish hickory, C. hunanensis Cheng et R. H. Chang ex R. H. Chang et Lu, C. illinoensis K. Koch (pecan) and C. dabieshanensis M. C. Liu et Z. J. Li, but they were monomorphic in both hickory and C. hunanensis although multi-alleles have been identified in all the four species. There is a transferability rate of 63.02% observed between hickory and pecan and the markers can be applied to study genetic diversity of accessions in pecan. When used in C. dabieshanensis, it was revealed that C. dabieshanensis had the number of alleles per locus ranging from 2 to 4, observed heterozygosity from 0 to 0.6667 and expected heterozygosity from 0.333 to 0.8667, respectively, which supports the existence of C. dabieshanensis as a separate species different from hickory and indicates that there is potential for selection and breeding in this species.

  17. Transcriptome sequencing of lentil based on second-generation technology permits large-scale unigene assembly and SSR marker discovery

    Directory of Open Access Journals (Sweden)

    Materne Michael

    2011-05-01

    Full Text Available Abstract Background Lentil (Lens culinaris Medik. is a cool-season grain legume which provides a rich source of protein for human consumption. In terms of genomic resources, lentil is relatively underdeveloped, in comparison to other Fabaceae species, with limited available data. There is hence a significant need to enhance such resources in order to identify novel genes and alleles for molecular breeding to increase crop productivity and quality. Results Tissue-specific cDNA samples from six distinct lentil genotypes were sequenced using Roche 454 GS-FLX Titanium technology, generating c. 1.38 × 106 expressed sequence tags (ESTs. De novo assembly generated a total of 15,354 contigs and 68,715 singletons. The complete unigene set was sequence-analysed against genome drafts of the model legume species Medicago truncatula and Arabidopsis thaliana to identify 12,639, and 7,476 unique matches, respectively. When compared to the genome of Glycine max, a total of 20,419 unique hits were observed corresponding to c. 31% of the known gene space. A total of 25,592 lentil unigenes were subsequently annoated from GenBank. Simple sequence repeat (SSR-containing ESTs were identified from consensus sequences and a total of 2,393 primer pairs were designed. A subset of 192 EST-SSR markers was screened for validation across a panel 12 cultivated lentil genotypes and one wild relative species. A total of 166 primer pairs obtained successful amplification, of which 47.5% detected genetic polymorphism. Conclusions A substantial collection of ESTs has been developed from sequence analysis of lentil genotypes using second-generation technology, permitting unigene definition across a broad range of functional categories. As well as providing resources for functional genomics studies, the unigene set has permitted significant enhancement of the number of publicly-available molecular genetic markers as tools for improvement of this species.

  18. De novo transcriptomic analysis and development of EST-SSR markers in the Siberian tiger (Panthera tigris altaica).

    Science.gov (United States)

    Lu, Taofeng; Sun, Yujiao; Ma, Qin; Zhu, Minghao; Liu, Dan; Ma, Jianzhang; Ma, Yuehui; Chen, Hongyan; Guan, Weijun

    2016-12-01

    The Siberian tiger, Panthera tigris altaica, is an endangered species, and much more work is needed to protect this species, which is still vulnerable to extinction. Conservation efforts may be supported by the genetic assessment of wild populations, for which highly specific microsatellite markers are required. However, only a limited amount of genetic sequence data is available for this species. To identify the genes involved in the lung transcriptome and to develop additional simple sequence repeat (SSR) markers for the Siberian tiger, we used high-throughput RNA-Seq to characterize the Siberian tiger transcriptome in lung tissue (designated 'PTA-lung') and a pooled tissue sample (designated 'PTA'). Approximately 47.5 % (33,187/69,836) of the lung transcriptome was annotated in four public databases (Nr, Swiss-Prot, KEGG, and COG). The annotated genes formed a potential pool for gene identification in the tiger. An analysis of the genes differentially expressed in the PTA lung, and PTA samples revealed that the tiger may have suffered a series of diseases before death. In total, 1062 non-redundant SSRs were identified in the Siberian tiger transcriptome. Forty-three primer pairs were randomly selected for amplification reactions, and 26 of the 43 pairs were also used to evaluate the levels of genetic polymorphism. Fourteen primer pairs (32.56 %) amplified products that were polymorphic in size in P. tigris altaica. In conclusion, the transcriptome sequences will provide a valuable genomic resource for genetic research, and these new SSR markers comprise a reasonable number of loci for the genetic analysis of wild and captive populations of P. tigris altaica.

  19. Genetic diversity and structure of the zombi pea (Vigna vexillata (L.) A. Rich) gene pool based on SSR marker analysis.

    Science.gov (United States)

    Dachapak, Sujinna; Somta, Prakit; Poonchaivilaisak, Supalak; Yimram, Tarika; Srinives, Peerasak

    2017-04-01

    Zombi pea (Vigna vexillata (L.) A. Rich) is an underutilized legume species and a useful gene source for resistance to biotic and abiotic stresses, although there is little understanding on its genetic diversity and structure. In this study, 422 (408 wild and 14 cultivated) accessions of zombi pea from diverse origins (201 from Africa, 126 from America, 85 from Australia, 5 from Asia and 5 from unknown origin) were analyzed with 20 simple sequence repeat (SSR) markers to determine its genetic diversity and genetic structure. The SSR markers detected 273 alleles in total with a mean of 13.6 alleles per locus. Polymorphism information content values of the markers varied from 0.58 to 0.90 with an average of 0.76. Overall gene diversity was 0.715. Gene diversity and average allelic richness was highest in Africa (0.749 and 8.08, respectively) and lowest in America (0.435 and 4.10, respectively). Nei's genetic distance analysis revealed that the highest distance was between wild Australia and cultivated Africa (0.559), followed by wild West Africa and wild Australia (0.415). STRUCTURE, neighbor-joining (NJ), and principal coordinate analyses consistently showed that these zombi pea accessions were clustered into three major groups, viz. America, Africa and Asia, and Australia. NJ tree also suggested that American and Australian accessions are originated from East African zombi peas, and that the cultivated accessions from Africa and Asia were genetically distinct, while those from America were clustered with some cultivated accessions from Africa. These results suggest that Africa is the center of origin and diversity of zombi pea, and that domestication of this pea took place more than once in different regions.

  20. Assessing the Genetic Diversity and Genealogical Reconstruction of Cypress (Cupressus funebris Endl. Breeding Parents Using SSR Markers

    Directory of Open Access Journals (Sweden)

    Hanbo Yang

    2016-07-01

    Full Text Available To identify genetic diversity, genetic structure and the relationship among accessions, and further establish a core collection for the long-term breeding of cypress (Cupressus funebris Endl., the genealogy of breeding parents was reconstructed using simple sequence repeat (SSR molecular markers. Seventeen SSR markers were used to detect molecular polymorphisms among 290 cypress accessions from five provinces and 53 accessions with unknown origin in China. A total of 92 alleles (Na were detected with 5.412 alleles per locus and an average polymorphism information content (PIC of 0.593. The haplotype diversity (H ranged from 0.021 to 0.832, with an average of 0.406. The number of alleles (Na and the effective number of alleles (Ne ranged from 4.294 to 5.176 and from 2.488 to 2.817 among five populations, respectively. The pairwise population matrix of Nei’s genetic distance ranged from 0.008 to 0.023. Based on the results of unweighted pair group method average (UPGMA cluster and population structure analyses, 343 breeding parents were divided into two major groups. Lower genetic differentiation coefficients and closer genetic relationships were observed among cypress breeding parents, suggesting that the genetic basis was narrow, and the genetic relationship was confused by frequent introduction and wide cultivation. Moreover, we reconstructed the genealogy between breeding parents and 30 accessions of breeding parents from an identified core collection. According to the present study, not only geographic origin but also the relationship of the individuals should be considered in future crossbreeding work.

  1. Analysis of SSR characteristics in EST sequences of oil palm (Elaeis guineensis Jacg.)%油棕EST序列中SSR的分布特征分析

    Institute of Scientific and Technical Information of China (English)

    吴春太; 陈青; 刘锐; 李维国

    2012-01-01

    In order to make full use of the EST resources in the present public database to develop the EST -SSR primers, in this study, 39 227 ESTs of oil palm (Elaeis guineensis Jacg. ) from GenBank database were downloaded and analyzed, resulting in 15 716 non - redundant sequences with total length about 7 977. 734 kb. 699 SSRs were discovered, the frequency of these EST - SSRs was 4.45% and the mean distance was 11.41 kb in non - redundant ESTs. Among them the dinucleotide and trinucleotide repeats were dominant types, accounting for 38.48% and 25. 32% respectively. AG/CT was repeated most in all nucleotide repeat motifs, accounting for 27. 47% . Blast analysis showed that 44. 95% of SSR - ESTs were homologous with functional gene in non - redundant protein sequences databases ( Nr database). The homology with known functions from Vitis vinifera had the greatest proportion and reached up to 4.42%. Simultaneously, the functional classification of 54 SSR -ESTs as made by GO system, of which 46 were found in the Nr and EST database, and the other 8 showed no homology. These ESTs can be divided into 18 functional subclasses, and the functional items and SSR -ESTs relevant to binding presented higher quantity than all other functional subclasses. The function of other 580 ESTs was not researched.%为充分利用现有公共数据库中的EST资源开发EST - SSR引物,本研究从GenBank数据库获取39 227条油棕EST,通过聚类拼接和处理,得到全长为7 977.734 kb的无冗余序列15 716条.在这些序列中共检索出699个SSRs,检出率为4.45%,平均11.41 kb出现1个SSR,包括99种重复基元.其中,二核苷酸和三核苷酸重复是主要的类型,分别占总SSRs的38.48%和25.32%.在所有的核苷酸重复基序中,二核苷酸重复序列AG/CT所占比例最高,约占27.47%.Blastx分析发现44.95%的SSR - ESTs与非冗余蛋白质序列数据库(nr)中功能基因同源,功能已知的蛋白质中葡萄来源的SSR - ESTs

  2. Development, cross-species/genera transferability of novel EST-SSR markers and their utility in revealing population structure and genetic diversity in sugarcane

    KAUST Repository

    Singh, Ram K.

    2013-07-01

    Sugarcane (Saccharum spp. hybrid) with complex polyploid genome requires a large number of informative DNA markers for various applications in genetics and breeding. Despite the great advances in genomic technology, it is observed in several crop species, especially in sugarcane, the availability of molecular tools such as microsatellite markers are limited. Now-a-days EST-SSR markers are preferred to genomic SSR (gSSR) as they represent only the functional part of the genome, which can be easily associated with desired trait. The present study was taken up with a new set of 351 EST-SSRs developed from the 4085 non redundant EST sequences of two Indian sugarcane cultivars. Among these EST-SSRs, TNR containing motifs were predominant with a frequency of 51.6%. Thirty percent EST-SSRs showed homology with annotated protein. A high frequency of SSRs was found in the 5\\'UTR and in the ORF (about 27%) and a low frequency was observed in the 3\\'UTR (about 8%). Two hundred twenty-seven EST-SSRs were evaluated, in sugarcane, allied genera of sugarcane and cereals, and 134 of these have revealed polymorphism with a range of PIC value 0.12 to 0.99. The cross transferability rate ranged from 87.0% to 93.4% in Saccharum complex, 80.0% to 87.0% in allied genera, and 76.0% to 80.0% in cereals. Cloning and sequencing of EST-SSR size variant amplicons revealed that the variation in the number of repeat-units was the main source of EST-SSR fragment polymorphism. When 124 sugarcane accessions were analyzed for population structure using model-based approach, seven genetically distinct groups or admixtures thereof were observed in sugarcane. Results of principal coordinate analysis or UPGMA to evaluate genetic relationships delineated also the 124 accessions into seven groups. Thus, a high level of polymorphism adequate genetic diversity and population structure assayed with the EST-SSR markers not only suggested their utility in various applications in genetics and genomics in

  3. Comparative evaluation of genetic diversity using RAPD, SSR and cytochrome P450 gene based markers with respect to calcium content in finger millet (Eleusine coracana L. Gaertn.)

    Indian Academy of Sciences (India)

    Preety Panwar; Manoj Nath; Vijay Kumar Yadav; Anil Kumar

    2010-08-01

    Genetic relationships among 52 Eleusine coracana (finger millet) genotypes collected from different districts of Uttarakhand were investigated by using randomly amplified polymorphic DNA (RAPD), simple sequence repeat (SSR) and cytochrome P450 gene based markers. A total of 18 RAPD primers, 10 SSR primers, and 10 pairs of cytochrome P450 gene based markers, respectively, revealed 49.4%, 50.2% and 58.7% polymorphism in 52 genotypes of E. coracana. Mean polymorphic information content (PIC) for each of these marker systems (0.351 for RAPD, 0.505 for SSR and 0.406 for cyt P450 gene based markers) suggested that all the marker systems were effective in determining polymorphisms. Pair-wise similarity index values ranged from 0.011 to 0.999 (RAPD), 0.010 to 0.999 (SSR) and 0.001 to 0.998 (cyt P450 gene based markers) and mean similarity index value of 0.505, 0.504 and 0.499, respectively. The dendrogram developed by RAPD, SSR and cytochrome P450 gene based primers analyses revealed that the genotypes are grouped in different clusters according to high calcium (300–450 mg/100 g), medium calcium (200–300 mg/100 g) and low calcium (100–200 mg/100 g). Mantel test employed for detection of goodness of fit established cophenetic correlation values above 0.95 for all the three marker systems. The dendrograms and principal coordinate analysis (PCA) plots derived from the binary data matrices of the three marker systems are highly concordant. High bootstrap values were obtained at major nodes of phenograms through WINBOOT software. Comparison of RAPD, SSR and cytochrome P450 gene based markers, in terms of the quality of data output, indicated that SSRs and cyt P450 gene based markers are particularly promising for the analysis of plant genome diversity. The genotypes of finger millet collected from different districts of Uttarakhand constitute a wide genetic base and clustered according to calcium contents. The identified genotypes could be used in breeding programmes and

  4. 万寿菊SS-PCR反应体系的优化%Optimization in SSR-PCR Reaction System of Marigold

    Institute of Scientific and Technical Information of China (English)

    杨帆; 曾丽; 赵子刚; 张嫔; 龚霄雯

    2011-01-01

    实验材料为色素万寿菊雄性不育两用系'9901AB',通过对SSR-PCR反应体系中的主要因素dNTPs、引物及模板DNA进行最优条件筛选,建立了适合于万寿菊雄性不育两用系的SSRPCR反应体系:2.5μL 10×buffer、40 ng模板DNA、2μL 10μmol·μL1引物、1.0 U Taq酶、1.2μL2.5 mmol·μL-1dNTP,ddH2()补足体系至25μL;P(R循环程序为:94℃预变性2 min;38个循环(94℃变性30 s、56℃退火30 s、72℃延伸1 min),72℃延伸10 min.采用优化后的SSR-PCR体系,将已公布的向日葵15对引物运用于万寿菊雄性不育两用系材料上,结果表明万寿菊与向日葵之间可以共享部分SSR引物信息.%The experimental material is marigold yellow pigment male sterile line '9901AB'. The SSR-PCR was established within 25 μL reaction volumes containing 2. 5 μL 10 × PCR amplification buffer, 40 ng template DNA,2 μL 10 μmol · μL-1 primers, 1.0 U Taq DNA polymerase, 1.2 μL 2. 5 mmol ·μL-1 dNTP and made to volume with sterile double-distilled water by screening the optimal main factors that dNTP,primers and template DNA in SSR-PCR reaction system. The SSR-PCR was built using the conditions: 94 ℃ for 2 min; 38 cycles of 94 ℃ for 30 s,56 ℃ for 30 s,72 ℃ for 1 min; 72 ℃ for 10 min. Results show that some of the SSR primers developed from sunflower (Helianthus annuus ) could be directly used in marigold genome study.

  5. Novye ateisticheskie podkhody v kognitivnoi nauke o religii

    DEFF Research Database (Denmark)

    Geertz, Armin W.

    2013-01-01

    En russisk oversættelse af et kapitel i bogen Contemporary Theories of Religion: A Critical Companion, red. af Michael Stausberg (Abingdon: Routledge, 2009) på engelsk. Det russiske tidsskrift har titlen State, Religion and Church in Russia and Worldwide....

  6. Association Analysis of Simple Sequence Repeat (SSR Markers with Agronomic Traits in Tall Fescue (Festuca arundinacea Schreb..

    Directory of Open Access Journals (Sweden)

    Yanhong Lou

    Full Text Available Tall fescue is widely used in temperate regions throughout the world as a dominant forage grass as well as a turfgrass, in pastoral and turf industry. However, the utilization of tall fescue was limited because of its leaf roughness, poor regeneration ability and poor stress resistance. New cultivars were desirable in modern pastoral industries exceed the potential of existing cultivars. Therefore, well understanding the agronomic traits and describing germplasms would help to overcome these constraints, and morphological evaluation of tall fescue germplasm is the key component in selecting rational parents for hybridization breeding. However, describing the morphological traits of tall fescue germplasm is costly and time-consuming. Fortunately, biotechnology approaches can supplement conventional breeding efforts for tall fescue improvement. Association mapping, as a powerful approach to identify association between agronomic traits and molecular markers has been widely used for enhancing the utilization, conservation and management of the tall fescue germplasms. Therefore, in the present research, 115 tall fescue accessions from different origins (25 accessions are cultivars; 31 accessions from America; 32 accessions from European; 7 accessions from Africa; 20 accessions from Asia, were evaluated for agronomic traits and genetic diversity with 90 simple sequence repeat (SSR markers. The panel displayed significant variation in spike count per plant (SCP and spike weight (SW. However, BCS performed the lowest CV among all the observed agronomic traits. Three subpopulations were identified within the collections but no obvious relative kinship (K was found. The GLM model was used to describe the association between SSR and agronomic traits. Fifty-one SSR markers associated with agronomic traits were observed. Twelve single-associated markers were associated with PH; six single-associated markers were associated with BCS; eight single

  7. Optimization of SSR Reaction System for Pinus sylvestris var. mongolica%樟子松SSR反应体系优化

    Institute of Scientific and Technical Information of China (English)

    方攀; 张运城; 袁虎威; 刘玉林; 李伟

    2013-01-01

      In order to research the genetic structure diversity of Pinus sylvestris var. mongolica, SSR reaction sys-tem was optimized in this study. At first, for the sake of determining a suitable reaction system, single factor tests with multi-level were designed respectively under six factors (DNA template, Taq DNA polymerase, dNTP, primer, annealing temperature, cycles). On the basis of above, the 4 factors which were DNA template, Taq DNA poly-merase, dNTP, Primer were further optimized in 4 levels using L16(45) orthogonal test. The obtained optimal reaction system for Pinus sylvestris var. mongolica was as follows:25μL volume of reaction system cotains DNA template 50 ng, Taq DNA polymerase 1.0 U, dNTP 0.3 mmol/L, Primer 0.15μmol/L, 10íTaq Buffer (including Mg2+) 2.5μL. The optimization of SSR reaction system for Pinus sylvestris var. mongolica contributes to the development of SSR markers, and lays the foundation for analyzing the genetic structure diversity of Pinus sylvestris var. mongolica in natural populations and artificial populations, constructing the genetic map, and mapping function genes.%  从模板DNA、Taq酶含量、dNTP浓度、引物浓度、退火温度、循环次数6个方面,分别设置单因素多水平试验,观察条带的亮度及清晰度,以确定合适的反应体系。然后利用L16(45)正交试验,对DNA模板浓度、Taq酶含量、dNTP浓度、引物浓度这4个因素在4个水平上做进一步优化。建立了樟子松SSR最佳反应体系:25滋L的反应体系中包含模板DNA 50 ng,Taq 酶1.0 U,dNTP 0.3 mmol/L,引物0.15滋mol/L,10×Taq Buffer (含Mg2+)2.5滋L。樟子松SSR反应体系的优化,有助于对樟子松SSR分子标记的研究,为分析樟子松天然群体和人工群体的遗传结构多样性,构建遗传图谱和定位功能基因奠定了基础。

  8. Genetic analysis and molecular mapping of a new fertility restorer gene Rf8 for Triticum timopheevi cytoplasm in wheat (Triticum aestivum L.) using SSR markers.

    Science.gov (United States)

    Sinha, Pallavi; Tomar, S M S; Vinod; Singh, Vikas K; Balyan, H S

    2013-12-01

    A study on mode of inheritance and mapping of fertility restorer (Rf) gene(s) using simple sequence repeat (SSR) markers was conducted in a cross of male sterile line 2041A having Triticum timopheevi cytoplasm and a restorer line PWR4099 of common wheat (Triticum aestivum L.). The F1 hybrid was completely fertile indicating that fertility restoration is a dominant trait. Based on the pollen fertility and seed set of bagged spikes in F2 generation, the individual plants were classified into fertile and sterile groups. Out of 120 F2 plants, 97 were fertile and 23 sterile (based on pollen fertility) while 98 plants set ≥ 5 seeds/spike and 22 produced ≤ 4 or no seed. The observed frequency fits well into Mendelian ratio of 3 fertile: 1 sterile with χ(2) value of 2.84 for pollen fertility and 2.17 for seed setting indicating that the fertility restoration is governed by a single dominant gene in PWR4099. The three linked SSR markers, Xwmc503, Xgwm296 and Xwmc112 located on the chromosome 2DS were placed at a distance of 3.3, 5.8 and 6.7 cM, respectively, from the Rf gene. Since, no known Rf gene is located on the chromosome arm 2DS, the Rf gene in PWR4099 is a new gene and proposed as Rf8. The closest SSR marker, Xwmc503, linked to the Rf8 was validated in a set of Rf, maintainer and cytoplasmic male sterile lines. The closely linked SSR marker Xwmc503 may be used in marker-assisted backcross breeding facilitating the transfer of fertility restoration gene Rf8 into elite backgrounds with ease.

  9. 板栗品种线粒体SSR遗传多样性分析%Genetic Diversity of Castanea mollissima Variety Based on Mitochondrial SSR Markers

    Institute of Scientific and Technical Information of China (English)

    张先启; 郭献平; 刘玉芬; 张国庆; 王珊珊; 刘妍; 秦岭; 曹庆芹

    2012-01-01

    本试验通过对来自水稻和马铃薯的16对具有多态性的线粒体SSR引物进行筛选,得到2对适用于板栗的具有多态性条带的线粒体SSR引物.利用这2对多态性引物对76个板栗品种进行遗传多样性分析.结果表明2个多态性SSR位点检测到4个等位基因,平均每个位点产生2.0个等位基因.应用NTSYS2.10软件中的UPGMA方法,对数据进行聚类分析,获得板栗资源线粒体SSR聚类图.结果表明:在相似系数0.15处可以将板栗种质资源按亲缘关系分成3组.%The genetic diversity of 76 Castanea mollissima accesions was analyzed by mitochondrial SSR. Two polymorphic mtSSR primers were obtained by testing universal 16 primers from rice and potato. Two polymorphic mtSSR primers generated 4 alleles with an average of 2. 0 alleles per primer among 76 C. mollissima accessions. Unweighted pair-group arithematic averages method (UPGMA) was applied to construct a cluster tree of C. mollissima resources based on mitochondrial SSR data by NTSYS2.10 software was. The results showed that 76 C. mollissima cultivars were classified into three groups at the level of similarity 0.15.

  10. EST-derived SSR markers used as anchor loci for the construction of a consensus linkage map in ryegrass (Lolium spp.

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    Studer Bruno

    2010-08-01

    Full Text Available Abstract Background Genetic markers and linkage mapping are basic prerequisites for marker-assisted selection and map-based cloning. In the case of the key grassland species Lolium spp., numerous mapping populations have been developed and characterised for various traits. Although some genetic linkage maps of these populations have been aligned with each other using publicly available DNA markers, the number of common markers among genetic maps is still low, limiting the ability to compare candidate gene and QTL locations across germplasm. Results A set of 204 expressed sequence tag (EST-derived simple sequence repeat (SSR markers has been assigned to map positions using eight different ryegrass mapping populations. Marker properties of a subset of 64 EST-SSRs were assessed in six to eight individuals of each mapping population and revealed 83% of the markers to be polymorphic in at least one population and an average number of alleles of 4.88. EST-SSR markers polymorphic in multiple populations served as anchor markers and allowed the construction of the first comprehensive consensus map for ryegrass. The integrated map was complemented with 97 SSRs from previously published linkage maps and finally contained 284 EST-derived and genomic SSR markers. The total map length was 742 centiMorgan (cM, ranging for individual chromosomes from 70 cM of linkage group (LG 6 to 171 cM of LG 2. Conclusions The consensus linkage map for ryegrass based on eight mapping populations and constructed using a large set of publicly available Lolium EST-SSRs mapped for the first time together with previously mapped SSR markers will allow for consolidating existing mapping and QTL information in ryegrass. Map and markers presented here will prove to be an asset in the development for both molecular breeding of ryegrass as well as comparative genetics and genomics within grass species.

  11. Pro-cognitive and antipsychotic efficacy of the alpha7 nicotinic partial agonist SSR180711 in pharmacological and neurodevelopmental latent inhibition models of schizophrenia.

    Science.gov (United States)

    Barak, Segev; Arad, Michal; De Levie, Amaya; Black, Mark D; Griebel, Guy; Weiner, Ina

    2009-06-01

    Schizophrenia symptoms can be segregated into positive, negative and cognitive, which exhibit differential sensitivity to drug treatments. Accumulating evidence points to efficacy of alpha7 nicotinic receptor (nAChR) agonists for cognitive deficits in schizophrenia but their activity against positive symptoms is thought to be minimal. The present study examined potential pro-cognitive and antipsychotic activity of the novel selective alpha7 nAChR partial agonist SSR180711 using the latent inhibition (LI) model. LI is the reduced efficacy of a previously non-reinforced stimulus to gain behavioral control when paired with reinforcement, compared with a novel stimulus. Here, no-drug controls displayed LI if non-reinforced pre-exposure to a tone was followed by weak but not strong conditioning (2 vs 5 tone-shock pairings). MK801 (0.05 mg/kg, i.p.) -treated rats as well as rats neonatally treated with nitric oxide synthase inhibitor L-NoArg (10 mg/kg, s.c.) on postnatal days 4-5, persisted in displaying LI with strong conditioning, whereas amphetamine (1 mg/kg) -treated rats failed to show LI with weak conditioning. SSR180711 (0.3, 1, 3 mg/kg, i.p.) was able to alleviate abnormally persistent LI produced by acute MK801 and neonatal L-NoArg; these models are believed to model cognitive aspects of schizophrenia and activity here was consistent with previous findings with alpha7-nAChR agonists. In addition, unexpectedly, SSR180711 (1, 3 mg/kg, i.p.) potentiated LI with strong conditioning in no-drug controls and reversed amphetamine-induced LI disruption, two effects considered predictive of activity against positive symptoms of schizophrenia. These findings suggest that SSR180711 may be beneficial not only for the treatment of cognitive symptoms in schizophrenia, as reported multiple times previously, but also positive symptoms.

  12. Genetic architecture of purple pigmentation and tagging of some loci to SSR markers in pearl millet, Pennisetum glaucum (L. R. Br.

    Directory of Open Access Journals (Sweden)

    Pusapati Varalakshmi

    2012-01-01

    Full Text Available This report describes the construction of integrated genetic maps in pearl millet involving certain purple phenotype and simple sequence repeat (SSR markers. These maps provide a direct means of implementing DNA marker-assisted selection and of facilitating "map-based cloning" for engineering novel traits. The purple pigmentation of leaf sheath, midrib and leaf margin was inherited together 'en bloc' under the control of a single dominant locus (the 'midrib complex' and was inseparably associated with the locus governing the purple coloration of the internode. The purple panicle was caused by a single dominant locus. Each of the three characters (purple lamina, purple stigma and purple seed was governed by two complementary loci. One of the two loci governing purple seed was associated with the SSR locus Xpsmp2090 in linkage group 1, with a linkage value of 22 cM, while the other locus was associated with the SSR locus Xpsmp2270 in linkage group 6, with a linkage value of 23 cM. The locus for purple pigmentation of the midrib complex was either responsible for pigmentation of the panicle in a pleiotropic manner or was linked to it very closely and associated with the SSR locus Xpsmp2086 in linkage group 4, with a suggestive linkage value of 21 cM. A dominant allele at this locus seems to be a prerequisite for the development of purple pigmentation in the lamina, stigma and seed. These findings suggest that the locus for pigmentation of the midrib complex might regulate the basic steps in anthocyanin pigment development by acting as a structural gene while other loci regulate the formation of color in specific plant parts.

  13. An efficient and rapid DNA minipreparation procedure suitable for PCR/SSR and RAPD analyses in tropical forest tree species

    Directory of Open Access Journals (Sweden)

    Ana Lilia Alzate-Marin

    2009-10-01

    Full Text Available An efficient and rapid DNA minipreparation modified method for frozen samples was developed for five tropical tree species: Copaifera langsdorffii, Hymenaea courbaril, Eugenia uniflora, Tabebuia roseo alba and Cariniana estrellensis. This procedure that dispenses the use of liquid nitrogen, phenol and the addition of proteinase K, is an adaptation of the CTAB-based DNA extraction method. The modifications included the use of PVP to eliminate the polyphenols, only one chloroform-isoamyl alcohol step and the addition of RNase immediately after extraction with chloroform. The yields of the DNA samples ranged from 25.7 to 42.1 µg from 100 mg leaf tissue. The DNA samples extracted by this method were successfully used for PCR (SSR and RAPD analyses in these five and other twelve tropical tree species.Este trabalho teve como objetivo otimizar um protocolo econômico, rápido e eficaz de minipreparação de DNA genômico, para as espécies florestais Copaifera langsdorffii (Óleo de Copaíba, Hymenaea courbaril (Jatobá, Eugenia uniflora (Pitanga, Tabebuia roseo alba (Ipê Branco e Cariniana estrellensis (Jequitibá Branco. Este método é uma adaptação da técnica de extração CTAB de Doyle e Doyle (1990, o qual consiste principalmente na adição de PVP para eliminar polifenoles, somente uma etapa de extração com clorofórmio-álcool isoamílico e a adição da RNase A imediatamente após a extração com clorofórmio. O método também dispensa o uso de nitrogênio líquido, o uso do fenol e a adição de proteinase K. Os DNAs das espécies florestais extraídos apresentaram alto rendimento e boa qualidade, com rendimento de 25.7 a 42.1 µg de DNA a partir de 100 mg de tecido foliar congelado. Com este protocolo, em apenas 1 dia de trabalho, uma pessoa pode completar o isolamento do DNA de aproximadamente 50 amostras de folhas (dependendo da capacidade da centrífuga. O DNA obtido pode ser usado para métodos de análise baseados em PCR (SSR e

  14. A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study

    Directory of Open Access Journals (Sweden)

    Cherubini Marcello

    2010-10-01

    Full Text Available Abstract Background Expressed Sequence Tags (ESTs are a source of simple sequence repeats (SSRs that can be used to develop molecular markers for genetic studies. The availability of ESTs for Quercus robur and Quercus petraea provided a unique opportunity to develop microsatellite markers to accelerate research aimed at studying adaptation of these long-lived species to their environment. As a first step toward the construction of a SSR-based linkage map of oak for quantitative trait locus (QTL mapping, we describe the mining and survey of EST-SSRs as well as a fast and cost-effective approach (bin mapping to assign these markers to an approximate map position. We also compared the level of polymorphism between genomic and EST-derived SSRs and address the transferability of EST-SSRs in Castanea sativa (chestnut. Results A catalogue of 103,000 Sanger ESTs was assembled into 28,024 unigenes from which 18.6% presented one or more SSR motifs. More than 42% of these SSRs corresponded to trinucleotides. Primer pairs were designed for 748 putative unigenes. Overall 37.7% (283 were found to amplify a single polymorphic locus in a reference full-sib pedigree of Quercus robur. The usefulness of these loci for establishing a genetic map was assessed using a bin mapping approach. Bin maps were constructed for the male and female parental tree for which framework linkage maps based on AFLP markers were available. The bin set consisting of 14 highly informative offspring selected based on the number and position of crossover sites. The female and male maps comprised 44 and 37 bins, with an average bin length of 16.5 cM and 20.99 cM, respectively. A total of 256 EST-SSRs were assigned to bins and their map position was further validated by linkage mapping. EST-SSRs were found to be less polymorphic than genomic SSRs, but their transferability rate to chestnut, a phylogenetically related species to oak, was higher. Conclusion We have generated a bin map for oak

  15. A comparison between SSR-PCR and normal PCR technology in detection of Paragonimus in different areas%SSR-PCR和常规PCR检测不同地区并殖吸虫遗专变异的比较研究

    Institute of Scientific and Technical Information of China (English)

    单小云; 楼宏强; 胡野; 楼景; 屠平光; 方萍

    2011-01-01

    目的 以SSR-PCR和常规PCR对浙江省和福建省5个不同地区并殖吸虫进行遗传变异检测,比较两者对并殖吸虫的基因水平分类的差异.方法 采用微卫星锚定PCR (SSR-PCR)对基因组DNA进行PCR扩增,扩增产物按Nei的方法计算遗传距离,并应用SPSS软件构建系统进化树;采用常规PCR扩增线粒体细胞色素C氧化酶亚单位(C()I)及核糖体DNA第二间区(ITS2)的基因序列,测序后用BoiEdit软件分析同源性,用MEGA软件构建种系发生树.结果 不同地区并殖吸虫标本的SSR-PCR产物呈多态性,浙江金华、浙江永嘉、福建周宁与福建平和、福建政和的标本存在明显的差异.前两者的遗传距离最近,为0.3333,浙江金华与福建平和的标本遗传距离最远,为0.8667.常规PCR基因序列分析显示浙江金华、浙江永嘉、福建周宁的标本之间在种系发生树上比较接近,浙江金华和浙江永嘉的标本最为接近.结论 利用SSR-PCR和常规PCR进行并殖吸虫的遗传变异分析结果基本一致.SSR-PCR是一种比常规PCR更方便的并殖吸虫遗传变异研究方法.%The aim was to detect the genetic variation of Paragonimus in 5 areas in Zhejiang Province and Fujian Province with technologies of SSR-PCR and normal PCR, so as to compare the differences on the gene horizontal classification. Our method was to amplify the genome DNA with the technology of simple sequence repeat-anchored PCR(SSR-PCR), and count the genetic distance with the method of Nei, and construct the dendrogram with SPSS software. This study was also corduct to amplify COI gene and ITS2 gene by normal PCR, analyze homology through BoiEdit, and construct stammbaum through MEGA. The SSR-PCR product of the Paragonimus speciman in different areas was polymorphic. There were obvious differences between Jinhua in Zhejiang Province, Yongjia in Zhejiang Province, Zhouning in Fujian Province and pinghe and zhenghe in Fujian province. The genetic distance

  16. Development of a gene-centered ssr atlas as a resource for papaya (Carica papaya marker-assisted selection and population genetic studies.

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    Newton Medeiros Vidal

    Full Text Available Carica papaya (papaya is an economically important tropical fruit. Molecular marker-assisted selection is an inexpensive and reliable tool that has been widely used to improve fruit quality traits and resistance against diseases. In the present study we report the development and validation of an atlas of papaya simple sequence repeat (SSR markers. We integrated gene predictions and functional annotations to provide a gene-centered perspective for marker-assisted selection studies. Our atlas comprises 160,318 SSRs, from which 21,231 were located in genic regions (i.e. inside exons, exon-intron junctions or introns. A total of 116,453 (72.6% of all identified repeats were successfully mapped to one of the nine papaya linkage groups. Primer pairs were designed for markers from 9,594 genes (34.5% of the papaya gene complement. Using papaya-tomato orthology assessments, we assembled a list of 300 genes (comprising 785 SSRs potentially involved in fruit ripening. We validated our atlas by screening 73 SSR markers (including 25 fruit ripening genes, achieving 100% amplification rate and uncovering 26% polymorphism rate between the parental genotypes (Sekati and JS12. The SSR atlas presented here is the first comprehensive gene-centered collection of annotated and genome positioned papaya SSRs. These features combined with thousands of high-quality primer pairs make the atlas an important resource for the papaya research community.

  17. Identification of SSR and RAPD markers linked to a resistance allele for angular leaf spot in the common bean (Phaseolus vulgaris line ESAL 550

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    Gilvan Ferreira da Silva

    2003-12-01

    Full Text Available The objective of this study was to identify RAPD and SSR markers associated with a resistant allele for angular leaf spot (Phaeoisariopsis griseola from the line 'ESAL 550', derived from the Andean 'Jalo EEP 558' cultivar, to assist selection of resistant genotypes. The resistant line 'ESAL 550' and the susceptible cultivar 'Carioca MG' were crossed to generate F1 and F2 populations. One hundred and twenty F2:3 families were evaluated. The DNA of the 12 most resistant families was bulked and the same was done with the DNA of the 10 most susceptible, generating two contrasting bulks. One RAPD and one SSR marker was found to be linked in coupling phase to the resistant allele. The SSR marker was amplified by the primer PV-atct001(282C, and its distance from the resistant allele was 7.6 cM. This is the most useful marker for indirect selection of resistant plants in segregating populations. The RAPD marker was amplified by the primer OPP07(857C linked in coupling phase to the resistant allele, and distant 24.4 cM. Therefore, this RAPD marker is not so useful in assisting selection because it is too far from the resistant allele.

  18. Development of a gene-centered ssr atlas as a resource for papaya (Carica papaya) marker-assisted selection and population genetic studies.

    Science.gov (United States)

    Vidal, Newton Medeiros; Grazziotin, Ana Laura; Ramos, Helaine Christine Cancela; Pereira, Messias Gonzaga; Venancio, Thiago Motta

    2014-01-01

    Carica papaya (papaya) is an economically important tropical fruit. Molecular marker-assisted selection is an inexpensive and reliable tool that has been widely used to improve fruit quality traits and resistance against diseases. In the present study we report the development and validation of an atlas of papaya simple sequence repeat (SSR) markers. We integrated gene predictions and functional annotations to provide a gene-centered perspective for marker-assisted selection studies. Our atlas comprises 160,318 SSRs, from which 21,231 were located in genic regions (i.e. inside exons, exon-intron junctions or introns). A total of 116,453 (72.6%) of all identified repeats were successfully mapped to one of the nine papaya linkage groups. Primer pairs were designed for markers from 9,594 genes (34.5% of the papaya gene complement). Using papaya-tomato orthology assessments, we assembled a list of 300 genes (comprising 785 SSRs) potentially involved in fruit ripening. We validated our atlas by screening 73 SSR markers (including 25 fruit ripening genes), achieving 100% amplification rate and uncovering 26% polymorphism rate between the parental genotypes (Sekati and JS12). The SSR atlas presented here is the first comprehensive gene-centered collection of annotated and genome positioned papaya SSRs. These features combined with thousands of high-quality primer pairs make the atlas an important resource for the papaya research community.

  19. A comparative analysis of distribution and conservation of microsatellites in the transcripts of sequenced Fusarium species and development of genic-SSR markers for polymorphism analysis.

    Science.gov (United States)

    Mahfooz, Sahil; Srivastava, Arpita; Srivastava, Alok K; Arora, Dilip K

    2015-09-01

    We used an in silico approach to survey and compare microsatellites in transcript sequences of four sequenced members of genus Fusarium. G + C content of transcripts was found to be positively correlated with the frequency of SSRs. Our analysis revealed that, in all the four transcript sequences studied, the occurrence, relative abundance and density of microsatellites varied and was not influenced by transcript sizes. No correlation between relative abundance and transcript sizes was observed. The relative abundance and density of microsatellites were highest in the transcripts of Fusarium solani when compared with F. graminearum, F. verticillioides and F. oxysporum. The maximum frequency of SSRs among all four sequence sets was of trinucleotide repeats (67.8%), whereas the dinucleotide repeat represents Fusarium species. In order to study polymorphism within Fusarium isolates, 11 polymorphic genic-SSR markers were developed. Of the 11 markers, 5 were from F. oxysporum and remaining 6 belongs to F. solani. SSR markers from F. oxysporum were found to be more polymorphic (38%) as compared to F. solani (26%). Eleven polymorphic markers obtained in this study clearly demonstrate the utility of newly developed SSR markers in establishing genetic relationships among different isolates of Fusarium. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  20. Transcriptome Sequencing Analysis and Development of EST-SSR Markers for Pinus koraiensis%红松转录组SSR分析及EST-SSR标记开发

    Institute of Scientific and Technical Information of China (English)

    张振; 张含国; 莫迟; 张磊

    2015-01-01

    【目的】红松已开发的分子标记缺乏共显性的遗传标记,尚不能满足分子标记辅助育种的需要。利用转录组数据开发 SSR标记目前仍然是较为经济高效的 DNA分子标记开发策略,本研究利用高通量测序技术开发红松 EST-SSR标记,掌握其在转录组序列中的分布类型及特征,为红松的 SSR多样性分析及变异分析提供基础。【方法】利用 SSR检索程序从红松转录组41476条 Unigenes中筛选得到1757个 SSR 位点,并对 SSR 位点的数量、分布特征进行统计分析。设计合成101对 SSR引物,采用琼脂糖电泳初步检查和聚丙烯酰胺凝胶电泳分离检测方法确定引物的多态性,并收集扩增产物,送测序验证,最终开发出16对 SSR引物。合成6对荧光引物,采用荧光标记技术对来自黑龙江省鹤岗、林口、铁力、苇河4个种子园的53份自由授粉子代进行遗传多样性分析。【结果】基于转录组序列开发出的 EST-SSR的分布频率( SSR 的个数与总 Unigene 的数量比)为4.24%。单、二、三核苷酸重复单元分别占总SSR的46.90%,17.12%和34.66%; SSR重复单元的重复次数分布在5~24次之间。参试的101对引物中有21对引物扩增可检测出多态性位点,占引物总数的20.8%;重测序验证,有16对引物能够扩增出目标序列。6对荧光引物共检测出18个等位基因,多态性信息量(PIC)为0.0363~0.6674,平均为0.325。【结论】红松属于基因组序列比较庞大的裸子植物,本研究可扩增出多态性位点的引物重复单元以二、三核苷酸重复为主。所研究红松种子园子代属于中等多态性水平。本研究印证了利用红松转录组数据开发 SSR标记的可行性,同时采用荧光标记技术检测红松自由授粉子代材料,为红松种质资源的多样性水平分析及变异水平的研究提供基础。%Objective]In Korean pine ( Pinus koraiensis

  1. Comparative analyses of fungicide sensitivity and SSR marker variations indicate a low risk of developing azoxystrobin resistance in Phytophthora infestans.

    Science.gov (United States)

    Qin, Chun-Fang; He, Meng-Han; Chen, Feng-Ping; Zhu, Wen; Yang, Li-Na; Wu, E-Jiao; Guo, Zheng-Liang; Shang, Li-Ping; Zhan, Jiasui

    2016-02-08

    Knowledge of the evolution of fungicide resistance is important in securing sustainable disease management in agricultural systems. In this study, we analyzed and compared the spatial distribution of genetic variation in azoxystrobin sensitivity and SSR markers in 140 Phytophthora infestans isolates sampled from seven geographic locations in China. Sensitivity to azoxystrobin and its genetic variation in the pathogen populations was measured by the relative growth rate (RGR) at four fungicide concentrations and determination of the effective concentration for 50% inhibition (EC50). We found that all isolates in the current study were sensitive to azoxystrobin and their EC50 was similar to that detected from a European population about 20 years ago, suggesting the risk of developing azoxystrobin resistance in P. infestans populations is low. Further analyses indicate that reduced genetic variation and high fitness cost in resistant mutations are the likely causes for the low evolutionary likelihood of developing azoxystrobin resistance in the pathogen. We also found a negative correlation between azoxystrobin tolerance in P. infestans populations and the mean annual temperature of collection sites, suggesting that global warming may increase the efficiency of using the fungicide to control the late blight.

  2. Patterns of genetic structure and evidence of gene flow among Tunisian Citrus species based on informative nSSR markers.

    Science.gov (United States)

    Ben Romdhane, Meriam; Riahi, Leila; Selmi, Ayet; Zoghlami, Nejia

    2016-01-01

    This study investigates the extent of genetic diversity, phylogenetic relationships and the amount of gene flow among Tunisian Citrus species based on a set of 15 informative nuclear SSR molecular markers. Genotyping data highlighted an allelic richness among Tunisian Citrus species and has allowed the detection of 168 alleles among them 104.19 were effective. The partition of the total genetic diversity (HT=0.832) showed that the highest amount of variation within the Citrus species is HS=0.550, while the relative amount of the between-species genetic diversity GST does not exceed 0.338. This pattern of genetic structure was supported by low-to-moderate FST pairwise values and the presence of a gene flow (Nm) among the eight Citrus species. The lowest genetic differentiation was revealed between the species C. sinensis and C. insitorum (FST=0.111, Nm=1.99), while the highest genetic differentiation was recorded between the species C. aurantifolia and C. paradisi (FST=0.367, Nm=0.43). The established Neighbor Joining analysis showed that all genotypes were widely discriminated and clearly pooled according to their species of origin, with minor exceptions. Copyright © 2016 Académie des sciences. Published by Elsevier SAS. All rights reserved.

  3. Genome evolution of intermediate wheatgrass as revealed by EST-SSR markers developed from its three progenitor diploid species.

    Science.gov (United States)

    Wang, Richard R-C; Larson, Steve R; Jensen, Kevin B; Bushman, B Shaun; DeHaan, Lee R; Wang, Shuwen; Yan, Xuebing

    2015-02-01

    Intermediate wheatgrass (Thinopyrum intermedium (Host) Barkworth & D.R. Dewey), a segmental autoallohexaploid (2n = 6x = 42), is not only an important forage crop but also a valuable gene reservoir for wheat (Triticum aestivum L.) improvement. Throughout the scientific literature, there continues to be disagreement as to the origin of the different genomes in intermediate wheatgrass. Genotypic data obtained from newly developed EST-SSR primers derived from the putative progenitor diploid species Pseudoroegneria spicata (Pursh) Á. Löve (St genome), Thinopyrum bessarabicum (Savul. & Rayss) Á. Löve (J = J(b) = E(b)), and Thinopyrum elongatum (Host) D. Dewey (E = J(e) = E(e)) indicate that the V genome of Dasypyrum (Coss. & Durieu) T. Durand is not one of the three genomes in intermediate wheatgrass. Based on all available information in the literature and findings in this study, the genomic designation of intermediate wheatgrass should be changed to J(vs)J(r)St, where J(vs) and J(r) represent ancestral genomes of present-day J(b) of Th. bessarabicum and J(e) of Th. elongatum, with J(vs) being more ancient. Furthermore, the information suggests that the St genome in intermediate wheatgrass is most similar to the present-day St found in diploid species of Pseudoroegneria from Eurasia.

  4. Genetic diversity and breeding history of Winter Mushroom (Flammulina velutipes) in China uncovered by genomic SSR markers.

    Science.gov (United States)

    Liu, Xiao Bin; Feng, Bang; Li, Jing; Yan, Chen; Yang, Zhu L

    2016-10-10

    Flammulina velutipes is one of the most widely cultivated mushroom species in China. However, its genetic background remains poorly understood due to the limited sampling and poor molecular markers used. In this study, 124 F. velutipes strains were employed, including 110 cultivars and 14 wild strains, and 25 new SSR markers were developed based on the genome of F. velutipes. A total of 153 alleles were detected in 124 strains to investigate the improper cultivar naming, genetic diversity and breeding history of F. velutipes in China. Our fingerprinting analyses indicated that 65 strains can be differentiated from the total of 124 strains, and over 53% of the strains are labeled with improper commercial names. The genetic diversities of wild strains are higher than those of the cultivars, suggesting that wild strains may harbor a large "arsenal" gene pool in nature available for strain breeding. The white cultivars in China were originally introduced from Japan, while the yellow cultivars were directly domesticated from wild strains isolated from southeastern China or hybridized between the white cultivars and yellow strains. Copyright © 2016 Elsevier B.V. All rights reserved.

  5. Deletion of the RluD pseudouridine synthase promotes SsrA peptide tagging of ribosomal protein S7.

    Science.gov (United States)

    Schaub, Ryan E; Hayes, Christopher S

    2011-01-01

    RluD catalyses formation of three pseudouridine residues within helix 69 of the 50S ribosome subunit. Helix 69 makes important contacts with the decoding centre on the 30S subunit and deletion of rluD was recently shown to interfere with translation termination in Escherichia coli. Here, we show that deletion of rluD increases tmRNA activity on ribosomes undergoing release factor 2 (RF2)-mediated termination at UGA stop codons. Strikingly, tmRNA-mediated SsrA peptide tagging of two proteins, ribosomal protein S7 and LacI, was dramatically increased in ΔrluD cells. S7 tagging was due to a unique C-terminal peptide extension found in E. coli K-12 strains. Introduction of the rpsG gene (encoding S7) from an E. coli B strain abrogated S7 tagging in the ΔrluD background, and partially complemented the mutant's slow-growth phenotype. Additionally, exchange of the K-12 prfB gene (encoding RF2) with the B strain allele greatly reduced tagging in ΔrluD cells. In contrast to E. coli K-12 cells, deletion of rluD in an E. coli B strain resulted in no growth phenotype. These findings indicate that the originally observed rluD phenotypes result from synthetic interactions with rpsG and prfB alleles found within E. coli K-12 strains.

  6. Development and Validation of 697 Novel Polymorphic Genomic and EST-SSR Markers in the American Cranberry (Vaccinium macrocarpon Ait.

    Directory of Open Access Journals (Sweden)

    Brandon Schlautman

    2015-01-01

    Full Text Available The American cranberry, Vaccinium macrocarpon Ait., is an economically important North American fruit crop that is consumed because of its unique flavor and potential health benefits. However, a lack of abundant, genome-wide molecular markers has limited the adoption of modern molecular assisted selection approaches in cranberry breeding programs. To increase the number of available markers in the species, this study identified, tested, and validated microsatellite markers from existing nuclear and transcriptome sequencing data. In total, new primers were designed, synthesized, and tested for 979 SSR loci; 697 of the markers amplified allele patterns consistent with single locus segregation in a diploid organism and were considered polymorphic. Of the 697 polymorphic loci, 507 were selected for additional genetic diversity and segregation analyses in 29 cranberry genotypes. More than 95% of the 507 loci did not display segregation distortion at the p < 0.05 level, and contained moderate to high levels of polymorphism with a polymorphic information content >0.25. This comprehensive collection of developed and validated microsatellite loci represents a substantial addition to the molecular tools available for geneticists, genomicists, and breeders in cranberry and Vaccinium.

  7. Development of a panel of unigene-derived polymorphic EST-SSR markers in lentil using public database information

    Institute of Scientific and Technical Information of China (English)

    Debjyoti Sen Gupta; Peng Cheng; Gaurav Sablok; Dil Thavarajah; Pushparajah Thavarajah; Clarice J Coyne; Shiv Kumar; Michael Baum; Rebecca J McGee

    2016-01-01

    Lentil (Lens culinaris Medik.), a diploid (2n=14) with a genome size greater than 4000 Mbp, is an important cool season food legume grown worldwide. The availability of genomic resources is limited in this crop species. The objective of this study was to develop polymorphic markers in lentil using publicly available curated expressed sequence tag information (ESTs). In this study, 9513 ESTs were downloaded from the National Center for Biotechnology Information (NCBI) database to develop unigene-based simple sequence repeat (SSR) markers. The ESTs were assembled into 4053 unigenes and then analyzed to identify 374 SSRs using the MISA microsatellite identification tool. Among the 374 SSRs, 26 compound SSRs were observed. Primer pairs for these SSRs were designed using Primer3 version 1.14. To classify the functional annotation of ESTs and EST–SSRs, BLASTx searches (using E-value 1 × 10−5) against the public UniProt (http://www.uniprot.org/) and NCBI (http://www.ncbi.nlh.nih.gov/) data-bases were performed. Further functional annotation was performed using PLAZA (version 3.0) comparative genomics and GO annotation was summarized using the Plant GO slim category. Among the synthesized 312 primers, 219 successfully amplified Lens DNA. A diverse panel of 24 Lens genotypes was used to identify polymorphic markers. A polymorphic set of 57 markers successfully discriminated the test genotypes. This set of polymorphic markers with functional annotation data could be used as molecular tools in lentil breeding.

  8. A deep sequencing analysis of transcriptomes and the development of EST-SSR markers in mungbean (Vigna radiata)

    Indian Academy of Sciences (India)

    CHANGYOU LIU; BAOJIE FAN; ZHIMIN CAO; QIUZHU SU; YAN WANG; ZHIXIAO ZHANG; JING WU; JING TIAN

    2016-09-01

    Mungbean (Vigna radiata L. Wilczek) is one of the most important leguminous food crops in Asia. We employed Illumina paired-end sequencing to analyse transcriptomes of three different mungbean genotypes. A total of 38.3–39.8 million paired-end reads with 73 bp lengths were generated. The pooled reads from the three libraries were assembled into 56,471 transcripts. Following a cluster analysis, 43,293 unigenes were obtained with an average length of 739 bp and N50 length of 1176 bp. Of the unigenes, 34,903 (80.6%) had significant similarity to known proteins in the NCBI nonredundant protein database (Nr), while 21,450 (58.4%) had BLAST hits in the Swiss-Prot database (E-value < 10⁻⁵). Further, 1245 differential expression genes were detected among three mungbean genotypes. In addition, we identified 3788 expressed sequence tag-simple sequence repeat (EST-SSR) motifs that could be used as potential molecular markers. Among 320 tested loci, 310 (96.5%) yielded amplification products, and 151 (47.0%) exhibited polymorphisms among six mungbean accessions. These transcriptome data and mungbean EST-SSRs could serve as a valuable resource for novel gene discovery and the marker-assisted selective breeding of this specie

  9. De novo characterization of Larimichthys crocea transcriptome for growth-/immune-related gene identification and massive microsatellite (SSR) marker development

    Science.gov (United States)

    Han, Zhaofang; Xiao, Shijun; Liu, Xiande; Liu, Yang; Li, Jiakai; Xie, Yangjie; Wang, Zhi Yong

    2016-04-01

    The large yellow croaker, Larimichthys crocea is an important marine fish in China with a high economic value. In the last decade, the stock conservation and aquaculture industry of this species have been facing severe challenges because of wild population collapse and degeneration of important economic traits. However, genes contributing to growth and immunity in L. crocea have not been thoroughly analyzed, and available molecular markers are still not sufficient for genetic resource management and molecular selection. In this work, we sequenced the transcriptome in L. crocea liver tissue with a Roche 454 sequencing platform and assembled the transcriptome into 93 801 transcripts. Of them, 38 856 transcripts were successfully annotated in nt, nr, Swiss-Prot, InterPro, COG, GO and KEGG databases. Based on the annotation information, 3 165 unigenes related to growth and immunity were identified. Additionally, a total of 6 391 simple sequence repeats (SSRs) were identified from the transcriptome, among which 4 498 SSRs had enough flanking regions to design primers for polymerase chain reactions (PCR). To access the polymorphism of these markers, 30 primer pairs were randomly selected for PCR amplification and validation in 30 individuals, and 12 primer pairs (40.0%) exhibited obvious length polymorphisms. This work applied RNA-Seq to assemble and analyze a live transcriptome in L. crocea. With gene annotation and sequence information, genes related to growth and immunity were identified and massive SSR markers were developed, providing valuable genetic resources for future gene functional analysis and selective breeding of L. crocea.

  10. De novo characterization of Larimichthys crocea transcriptome for growth-/immune-related gene identification and massive microsatellite (SSR) marker development

    Science.gov (United States)

    Han, Zhaofang; Xiao, Shijun; Liu, Xiande; Liu, Yang; Li, Jiakai; Xie, Yangjie; Wang, Zhiyong

    2017-03-01

    The large yellow croaker, Larimichthys crocea is an important marine fish in China with a high economic value. In the last decade, the stock conservation and aquaculture industry of this species have been facing severe challenges because of wild population collapse and degeneration of important economic traits. However, genes contributing to growth and immunity in L. crocea have not been thoroughly analyzed, and available molecular markers are still not sufficient for genetic resource management and molecular selection. In this work, we sequenced the transcriptome in L. crocea liver tissue with a Roche 454 sequencing platform and assembled the transcriptome into 93 801 transcripts. Of them, 38 856 transcripts were successfully annotated in nt, nr, Swiss-Prot, InterPro, COG, GO and KEGG databases. Based on the annotation information, 3 165 unigenes related to growth and immunity were identified. Additionally, a total of 6 391 simple sequence repeats (SSRs) were identified from the transcriptome, among which 4 498 SSRs had enough flanking regions to design primers for polymerase chain reactions (PCR). To access the polymorphism of these markers, 30 primer pairs were randomly selected for PCR amplification and validation in 30 individuals, and 12 primer pairs (40.0%) exhibited obvious length polymorphisms. This work applied RNA-Seq to assemble and analyze a live transcriptome in L. crocea. With gene annotation and sequence information, genes related to growth and immunity were identified and massive SSR markers were developed, providing valuable genetic resources for future gene functional analysis and selective breeding of L. crocea.

  11. Comparative Analysis of Genetic Diversity in Landraces of Waxy Maize from Yunnan and Guizhou Using SSR Markers

    Institute of Scientific and Technical Information of China (English)

    LIU Yong-jian; HUANG Yu-bi; RONG Ting-zhao; TIAN Meng-liang; YANG Jun-pin

    2005-01-01

    Waxy maize landraces are abundant in Yunnan and Guizhou of China. Genetic diversity of waxy maize landraces from Yunnan and Guizhou were analyzed using SSR markers. We screened 38 landraces with 50 primers that generated 3 to 6 polymorphic bands, with an average of 4.13 bands. Shannon's information indices for genetic diversity of the 14 waxy maize landraces from Yunnan varied from 4.9571 to 42.1138 and averaged 26.5252; Shannon's information indices for genetic diversity of the 24 waxy maize landraces from Guizhou varied from 22.0066 to 40.6320 and averaged 32.3156. For the 14 waxy maize landraces from Yunnan, the within-landrace genetic diversity accounted for 45.40% and the among-landrace genetic diversity accounted for 54.60% of the total genetic diversity observed. For the 24 waxy maize landraces from Guizhou, the within-landrace genetic diversity accounted for 50.76% and the among-landrace genetic diversity accounted for 49.24% of the total observed. Some individual landraces possessed as much as 96.86% of the total genetic diversity occurring among landraces within origins. Differentiation between geographic origins accounted for only 3.14% of the total genetic diversity. Both Yunnan and Guizhou would be the diversity centers and the original centers of waxy maize.

  12. Assessment of Plasmodium falciparum resistance to ferroquine (SSR97193 in field isolates and in W2 strain under pressure

    Directory of Open Access Journals (Sweden)

    Pradines Bruno

    2006-02-01

    Full Text Available Abstract Background Ferroquine (FQ, or SSR97193, is a novel antimalarial drug currently in phase I clinical trials. FQ is a unique organometallic compound designed to overcome the chloroquine (CQ resistance problem. FQ revealed to be equally active on CQ-sensitive and CQ-resistant Plasmodium falciparum laboratory strains and field isolates. FQ is also curative on rodent malaria parasites. As FQ will be tested in patients, the potential for resistance to this drug was evaluated. Methods The relationship between CQ-resistant transporter gene genotype and susceptibility to FQ were studied in 33 Cambodian P. falciparum field isolates previously studied for their in vitro response to CQ. In parallel, the ability of the CQ-resistant strain W2, to become resistant to FQ under drug pressure was assessed. Results The IC50 values for FQ in field isolates were found to be unrelated to mutations occurring in the P. falciparum chloroquine resistance transporter (PfCRT or to the level of expression of the corresponding mRNA. In vitro, under a drug pressure of 100 nM of FQ, transient survival was observed in only one of two experiments. Conclusion Field isolates studies and experimental drug pressure experiments showed that FQ overcomes CQ resistance, which reinforces the potential of this compound as a new antimalarial drug.

  13. De novo Assembly, Characterization of Immature Seed Transcriptome and Development of Genic-SSR Markers in Black Gram [Vigna mungo (L. Hepper].

    Directory of Open Access Journals (Sweden)

    J Souframanien

    Full Text Available Black gram [V. mungo (L. Hepper] is an important legume crop extensively grown in south and south-east Asia, where it is a major source of dietary protein for its predominantly vegetarian population. However, lack of genomic information and markers has become a limitation for genetic improvement of this crop. Here, we report the transcriptome sequencing of the immature seeds of black gram cv. TU94-2, by Illumina paired end sequencing technology to generate transcriptome sequences for gene discovery and genic-SSR marker development. A total of 17.2 million paired-end reads were generated and 48,291 transcript contigs (TCS were assembled with an average length of 443 bp. Based on sequence similarity search, 33,766 TCS showed significant similarity to known proteins. Among these, only 29,564 TCS were annotated with gene ontology (GO functional categories. A total number of 138 unique KEGG (Kyoto Encyclopedia of Genes and Genomes pathways were identified, of which majority of TCS are grouped into purine metabolism (678 followed by pyrimidine metabolism (263. A total of 48,291 TCS were searched for SSRs and 1,840 SSRs were identified in 1,572 TCS with an average frequency of one SSR per 11.9 kb. The tri-nucleotide repeats were most abundant (35% followed by di-nucleotide repeats (32%. PCR primer pairs were successfully designed for 933 SSR loci. Sequences analyses indicate that about 64.4% and 35.6% of the SSR motifs were present in the coding sequences (CDS and untranslated regions (UTRs respectively. Tri-nucleotide repeats (57.3% were preferentially present in the CDS. The rate of successful amplification and polymorphism were investigated using selected primers among 18 black gram accessions. Genic-SSR markers developed from the Illumina paired end sequencing of black gram immature seed transcriptome will provide a valuable resource for genetic diversity, evolution, linkage mapping, comparative genomics and marker-assisted selection in black gram.

  14. De novo Assembly, Characterization of Immature Seed Transcriptome and Development of Genic-SSR Markers in Black Gram [Vigna mungo (L.) Hepper].

    Science.gov (United States)

    Souframanien, J; Reddy, Kandali Sreenivasulu

    2015-01-01

    Black gram [V. mungo (L.) Hepper] is an important legume crop extensively grown in south and south-east Asia, where it is a major source of dietary protein for its predominantly vegetarian population. However, lack of genomic information and markers has become a limitation for genetic improvement of this crop. Here, we report the transcriptome sequencing of the immature seeds of black gram cv. TU94-2, by Illumina paired end sequencing technology to generate transcriptome sequences for gene discovery and genic-SSR marker development. A total of 17.2 million paired-end reads were generated and 48,291 transcript contigs (TCS) were assembled with an average length of 443 bp. Based on sequence similarity search, 33,766 TCS showed significant similarity to known proteins. Among these, only 29,564 TCS were annotated with gene ontology (GO) functional categories. A total number of 138 unique KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways were identified, of which majority of TCS are grouped into purine metabolism (678) followed by pyrimidine metabolism (263). A total of 48,291 TCS were searched for SSRs and 1,840 SSRs were identified in 1,572 TCS with an average frequency of one SSR per 11.9 kb. The tri-nucleotide repeats were most abundant (35%) followed by di-nucleotide repeats (32%). PCR primer pairs were successfully designed for 933 SSR loci. Sequences analyses indicate that about 64.4% and 35.6% of the SSR motifs were present in the coding sequences (CDS) and untranslated regions (UTRs) respectively. Tri-nucleotide repeats (57.3%) were preferentially present in the CDS. The rate of successful amplification and polymorphism were investigated using selected primers among 18 black gram accessions. Genic-SSR markers developed from the Illumina paired end sequencing of black gram immature seed transcriptome will provide a valuable resource for genetic diversity, evolution, linkage mapping, comparative genomics and marker-assisted selection in black gram.

  15. Integration of novel SSR and gene-based SNP marker loci in the chickpea genetic map and establishment of new anchor points with Medicago truncatula genome

    Science.gov (United States)

    Nayak, Spurthi N.; Zhu, Hongyan; Varghese, Nicy; Datta, Subhojit; Choi, Hong-Kyu; Horres, Ralf; Jüngling, Ruth; Singh, Jagbir; Kavi Kishor, P. B.; Sivaramakrishnan, S.; Hoisington, Dave A.; Kahl, Günter; Winter, Peter; Cook, Douglas R.

    2010-01-01

    This study presents the development and mapping of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers in chickpea. The mapping population is based on an inter-specific cross between domesticated and non-domesticated genotypes of chickpea (Cicer arietinum ICC 4958 × C. reticulatum PI 489777). This same population has been the focus of previous studies, permitting integration of new and legacy genetic markers into a single genetic map. We report a set of 311 novel SSR markers (designated ICCM—ICRISAT chickpea microsatellite), obtained from an SSR-enriched genomic library of ICC 4958. Screening of these SSR markers on a diverse panel of 48 chickpea accessions provided 147 polymorphic markers with 2–21 alleles and polymorphic information content value 0.04–0.92. Fifty-two of these markers were polymorphic between parental genotypes of the inter-specific population. We also analyzed 233 previously published (H-series) SSR markers that provided another set of 52 polymorphic markers. An additional 71 gene-based SNP markers were developed from transcript sequences that are highly conserved between chickpea and its near relative Medicago truncatula. By using these three approaches, 175 new marker loci along with 407 previously reported marker loci were integrated to yield an improved genetic map of chickpea. The integrated map contains 521 loci organized into eight linkage groups that span 2,602 cM, with an average inter-marker distance of 4.99 cM. Gene-based markers provide anchor points for comparing the genomes of Medicago and chickpea, and reveal extended synteny between these two species. The combined set of genetic markers and their integration into an improved genetic map should facilitate chickpea genetics and breeding, as well as translational studies between chickpea and Medicago. Electronic supplementary material The online version of this article (doi:10.1007/s00122-010-1265-1) contains supplementary material, which is

  16. Partial agonist properties of the antipsychotics SSR181507, aripiprazole and bifeprunox at dopamine D2 receptors: G protein activation and prolactin release.

    Science.gov (United States)

    Cosi, Cristina; Carilla-Durand, Elisabeth; Assié, Marie Bernadette; Ormiere, Anne Marie; Maraval, Mireille; Leduc, Nathalie; Newman-Tancredi, Adrian

    2006-03-27

    Dopamine D2 receptor antagonists induce hyperprolactinemia depending on the extent of D2 receptor blockade. We compared the effects of the new antipsychotic agents SSR181507 ((3-exo)-8-benzoyl-N-[[(2 s)7-chloro-2,3-dihydro-1,4-benzodioxin-1-yl]methyl]-8-azabicyclo[3.2.1]octane-3-methanamine monohydrochloride), bifeprunox (DU127090: 1-(2-Oxo-benzoxazolin-7-yl)-4-(3-biphenyl)methylpiperazinemesylate) and SLV313 (1-(2,3-dihydro-benzo[1,4]dioxin-5-yl)-4-[5-(4-fluorophenyl)-pyridin-3-ylmethyl]-piperazine) with those of aripiprazole (7-{4-[4-(2,3-dichlorophenyl)-1-piperazinyl]-butyloxy)-3,4-dihydro-2(1 H)-quinolinone), clozapine and haloperidol, on functional measures of dopamine D2 receptor activity in vitro and in vivo: [35S]-GTPgammaS binding to membranes from Sf9 insect cells expressing human dopamine D2 Long (hD2 L) receptors, and serum prolactin levels in the rat. All compounds antagonized apomorphine-induced G protein activation at dopamine hD2 L receptors. Antagonist potencies of aripiprazole, bifeprunox and SLV313 were similar to haloperidol (pK(b) = 9.12), whereas SSR181507 (8.16) and clozapine (7.35) were less potent. Haloperidol, SLV313 and clozapine were silent antagonists but SSR181507, bifeprunox and aripiprazole stimulated [35S]-GTPgammaS binding by 17.5%, 26.3% and 25.6%, respectively, relative to 100 microM apomorphine (Emax = 100%). pEC50s were: SSR181507, 8.08; bifeprunox, 8.97; aripiprazole, 8.56. These effects were antagonized by raclopride. Following oral administration in vivo, the drugs increased prolactin release to different extents. SLV313 and haloperidol potently (ED50 0.12 and 0.22 mg/kg p.o., respectively) stimulated prolactin release up to 86 and 83 ng/ml. Aripiprazole potently (ED50 0.66 mg/kg p.o.) but partially (32 ng/ml) induced prolactin release. SSR181507 (ED50 4.9 mg/kg p.o.) also partially (23 ng/ml) enhanced prolactin release. Bifeprunox only weakly increased prolactin at high doses (13 ng/ml at 40 mg/kg) and clozapine only

  17. A method for high throughput DNA extraction from crop materials for SSR-PCR amplification%适于SSR-PCR的农作物基因组总DNA高通量提取方法的建立

    Institute of Scientific and Technical Information of China (English)

    梁俊; 张妍; 陈忠良; 莫璋红; 范业赓; 吴凯朝; 李鸣; 李杨瑞

    2012-01-01

    [目的]建立一种新的、通用、快速的农作物基因组总DNA提取方法,为应用分子标记技术研究遗传多样性及变异提供方便.[方法]分别从甘蔗、水稻、玉米、花生和大豆5种作物中提取基因组DNA,用琼脂糖凝胶电泳对所提取的DNA质量进行检测,然后每种作物分别选取两对SSR引物进行PCR扩增,用聚丙烯酰胺凝胶电泳检测扩增结果.[结果]采用该提取方法,不同作物产生的纯DNA在100.0~160.0 g/g,提取DNA的A260/A280比率在1.80~1.95.此外,电泳凝胶未出现可见的RNA污染,每个作物基因组DNA单一条带非常清晰,DNA结构完整,质量较高,适用于分子标记的研究.应用SSR分子标记进行PCR扩增,重复性、稳定性好,经琼脂糖凝胶电泳检测,条带清晰且分辨率较高.[结论]建立的DNA提取方法为直接将叶片剪碎后装入EP管中,加入提取缓冲液进行DNA提取,省去了用液氮研磨的过程.与传统的DNA分离方法相比,新建立的DNA提取方法具有高通量、简单、快速、经济效益高等优点.%[Objective]A novel,rapid,and universal method for DNA extraction from crops was developed to accelerate the studies on the genetic diversities and variations using various molecular markers.[Method] The DNA isolated from five crop varieties,viz.,sugarcane,rice,maize,peanut,and soybean using the method this paper account,and the total DNA was detected by agarose gel electrophoresis.Then PCR was performed using 2 pairs of SSR primer for each crop and the products were visualized on polyacrylamide gel electrophoresis.[Result]The presented method yielded pure DNA ranged from 100.0-160.0 g per gram of material depending upon the plant type.DNA samples with A260/A280 ratio ranged from 1.80 to 1.95.Furthermore,there was no visible RNA contamination in electrophoresed gels and the single bands of genomic DNA isolated from each crop were highly distinct.The DNA extracted from different crops showed high quality

  18. Characterization of the transcriptome and EST-SSR development in Boea clarkeana, a desiccation-tolerant plant endemic to China

    Directory of Open Access Journals (Sweden)

    Ying Wang

    2017-06-01

    Full Text Available Background Desiccation-tolerant (DT plants can recover full metabolic competence upon rehydration after losing most of their cellular water (>95% for extended periods of time. Functional genomic approaches such as transcriptome sequencing can help us understand how DT plants survive and respond to dehydration, which has great significance for plant biology and improving the drought tolerance of crops. Boea clarkeana Hemsl. (Gesneriaceae is a DT dicotyledonous herb. Its genomic sequences characteristics remain unknown. Based on transcriptomic analyses, polymorphic EST-SSR (simple sequence repeats in expressed sequence tags molecular primers can be designed, which will greatly facilitate further investigations of the population genetics and demographic histories of DT plants. Methods In the present study, we used the platform Illumina HiSeq™2000 and de novo assembly technology to obtain leaf transcriptomes of B. clarkeana and conducted a BLASTX alignment of the sequencing data and protein databases for sequence classification and annotation. Then, based on the sequence information, the EST-SSR markers were developed, and the functional annotation of ESTs containing polymorphic SSRs were obtained through BLASTX. Results A total of 91,449 unigenes were generated from the leaf cDNA library of B. clarkeana. Based on a sequence similarity search with a known protein database, 72,087 unigenes were annotated. Among the annotated unigenes, a total of 71,170 unigenes showed significant similarity to the known proteins of 463 popular model species in the Nr database, and 59,962 unigenes and 32,336 unigenes were assigned to Gene Ontology (GO classifications and Cluster of Orthologous Groups (COG, respectively. In addition, 44,924 unigenes were mapped in 128 KEGG pathways. Furthermore, a total of 7,610 unigenes with 8,563 microsatellites were found. Seventy-four primer pairs were selected from 436 primer pairs designed for polymorphism validation. SSRs with

  19. Characterization of the transcriptome and EST-SSR development in Boea clarkeana, a desiccation-tolerant plant endemic to China.

    Science.gov (United States)

    Wang, Ying; Liu, Kun; Bi, De; Zhou, Shoubiao; Shao, Jianwen

    2017-01-01

    Desiccation-tolerant (DT) plants can recover full metabolic competence upon rehydration after losing most of their cellular water (>95%) for extended periods of time. Functional genomic approaches such as transcriptome sequencing can help us understand how DT plants survive and respond to dehydration, which has great significance for plant biology and improving the drought tolerance of crops. Boea clarkeana Hemsl. (Gesneriaceae) is a DT dicotyledonous herb. Its genomic sequences characteristics remain unknown. Based on transcriptomic analyses, polymorphic EST-SSR (simple sequence repeats in expressed sequence tags) molecular primers can be designed, which will greatly facilitate further investigations of the population genetics and demographic histories of DT plants. In the present study, we used the platform Illumina HiSeq™2000 and de novo assembly technology to obtain leaf transcriptomes of B. clarkeana and conducted a BLASTX alignment of the sequencing data and protein databases for sequence classification and annotation. Then, based on the sequence information, the EST-SSR markers were developed, and the functional annotation of ESTs containing polymorphic SSRs were obtained through BLASTX. A total of 91,449 unigenes were generated from the leaf cDNA library of B. clarkeana. Based on a sequence similarity search with a known protein database, 72,087 unigenes were annotated. Among the annotated unigenes, a total of 71,170 unigenes showed significant similarity to the known proteins of 463 popular model species in the Nr database, and 59,962 unigenes and 32,336 unigenes were assigned to Gene Ontology (GO) classifications and Cluster of Orthologous Groups (COG), respectively. In addition, 44,924 unigenes were mapped in 128 KEGG pathways. Furthermore, a total of 7,610 unigenes with 8,563 microsatellites were found. Seventy-four primer pairs were selected from 436 primer pairs designed for polymorphism validation. SSRs with higher polymorphism rates were

  20. Genetic Diversity and Population Structure of Tetraploid Wheats (Triticum turgidum L. Estimated by SSR, DArT and Pedigree Data.

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    Giovanni Laidò

    Full Text Available Levels of genetic diversity and population genetic structure of a collection of 230 accessions of seven tetraploid Triticum turgidum L. subspecies were investigated using six morphological, nine seed storage protein loci, 26 SSRs and 970 DArT markers. The genetic diversity of the morphological traits and seed storage proteins was always lower in the durum wheat compared to the wild and domesticated emmer. Using Bayesian clustering (K = 2, both of the sets of molecular markers distinguished the durum wheat cultivars from the other tetraploid subspecies, and two distinct subgroups were detected within the durum wheat subspecies, which is in agreement with their origin and year of release. The genetic diversity of morphological traits and seed storage proteins was always lower in the improved durum cultivars registered after 1990, than in the intermediate and older ones. This marked effect on diversity was not observed for molecular markers, where there was only a weak reduction. At K >2, the SSR markers showed a greater degree of resolution than for DArT, with their identification of a greater number of groups within each subspecies. Analysis of DArT marker differentiation between the wheat subspecies indicated outlier loci that are potentially linked to genes controlling some important agronomic traits. Among the 211 loci identified under selection, 109 markers were recently mapped, and some of these markers were clustered into specific regions on chromosome arms 2BL, 3BS and 4AL, where several genes/quantitative trait loci (QTLs are involved in the domestication of tetraploid wheats, such as the tenacious glumes (Tg and brittle rachis (Br characteristics. On the basis of these results, it can be assumed that the population structure of the tetraploid wheat collection partially reflects the evolutionary history of Triticum turgidum L. subspecies and the genetic potential of landraces and wild accessions for the detection of unexplored alleles.

  1. Genetic diversity and population structure assessed by SSR and SNP markers in a large germplasm collection of grape

    Science.gov (United States)

    2013-01-01

    Background The economic importance of grapevine has driven significant efforts in genomics to accelerate the exploitation of Vitis resources for development of new cultivars. However, although a large number of clonally propagated accessions are maintained in grape germplasm collections worldwide, their use for crop improvement is limited by the scarcity of information on genetic diversity, population structure and proper phenotypic assessment. The identification of representative and manageable subset of accessions would facilitate access to the diversity available in large collections. A genome-wide germplasm characterization using molecular markers can offer reliable tools for adjusting the quality and representativeness of such core samples. Results We investigated patterns of molecular diversity at 22 common microsatellite loci and 384 single nucleotide polymorphisms (SNPs) in 2273 accessions of domesticated grapevine V. vinifera ssp. sativa, its wild relative V. vinifera ssp. sylvestris, interspecific hybrid cultivars and rootstocks. Despite the large number of putative duplicates and extensive clonal relationships among the accessions, we observed high level of genetic variation. In the total germplasm collection the average genetic diversity, as quantified by the expected heterozygosity, was higher for SSR loci (0.81) than for SNPs (0.34). The analysis of the genetic structure in the grape germplasm collection revealed several levels of stratification. The primary division was between accessions of V. vinifera and non-vinifera, followed by the distinction between wild and domesticated grapevine. Intra-specific subgroups were detected within cultivated grapevine representing different eco-geographic groups. The comparison of a phenological core collection and genetic core collections showed that the latter retained more genetic diversity, while maintaining a similar phenotypic variability. Conclusions The comprehensive molecular characterization of our grape

  2. Construction of a SSR-based genetic map and identification of QTLs for catechins content in tea plant (Camellia sinensis).

    Science.gov (United States)

    Ma, Jian-Qiang; Yao, Ming-Zhe; Ma, Chun-Lei; Wang, Xin-Chao; Jin, Ji-Qiang; Wang, Xue-Min; Chen, Liang

    2014-01-01

    Catechins are the most important bioactive compounds in tea, and have been demonstrated to possess a wide variety of pharmacological activities. To characterize quantitative trait loci (QTLs) for catechins content in the tender shoots of tea plant, we constructed a moderately saturated genetic map using 406 simple sequence repeat (SSR) markers, based on a pseudo-testcross population of 183 individuals derived from an intraspecific cross of two Camellia sinensis varieties with diverse catechins composition. The map consisted of fifteen linkage groups (LGs), corresponding to the haploid chromosome number of tea plant (2n = 2x = 30). The total map length was 1,143.5 cM, with an average locus spacing of 2.9 cM. A total of 25 QTLs associated with catechins content were identified over two measurement years. Of these, nine stable QTLs were validated across years, and clustered into four main chromosome regions on LG03, LG11, LG12 and LG15. The population variability explained by each QTL was predominantly at moderate-to-high levels and ranged from 2.4% to 71.0%, with an average of 17.7%. The total number of QTL for each trait varied from four to eight, while the total population variability explained by all QTLs for a trait ranged between 38.4% and 79.7%. This is the first report on the identification of QTL for catechins content in tea plant. The results of this study provide a foundation for further cloning and functional characterization of catechin QTLs for utilization in improvement of tea plant.

  3. Construction of a SSR-based genetic map and identification of QTLs for catechins content in tea plant (Camellia sinensis.

    Directory of Open Access Journals (Sweden)

    Jian-Qiang Ma

    Full Text Available Catechins are the most important bioactive compounds in tea, and have been demonstrated to possess a wide variety of pharmacological activities. To characterize quantitative trait loci (QTLs for catechins content in the tender shoots of tea plant, we constructed a moderately saturated genetic map using 406 simple sequence repeat (SSR markers, based on a pseudo-testcross population of 183 individuals derived from an intraspecific cross of two Camellia sinensis varieties with diverse catechins composition. The map consisted of fifteen linkage groups (LGs, corresponding to the haploid chromosome number of tea plant (2n = 2x = 30. The total map length was 1,143.5 cM, with an average locus spacing of 2.9 cM. A total of 25 QTLs associated with catechins content were identified over two measurement years. Of these, nine stable QTLs were validated across years, and clustered into four main chromosome regions on LG03, LG11, LG12 and LG15. The population variability explained by each QTL was predominantly at moderate-to-high levels and ranged from 2.4% to 71.0%, with an average of 17.7%. The total number of QTL for each trait varied from four to eight, while the total population variability explained by all QTLs for a trait ranged between 38.4% and 79.7%. This is the first report on the identification of QTL for catechins content in tea plant. The results of this study provide a foundation for further cloning and functional characterization of catechin QTLs for utilization in improvement of tea plant.

  4. Determination of the genetic diversity of vegetable soybean [Glycine max (L.) Merr.] using EST-SSR markers

    Institute of Scientific and Technical Information of China (English)

    Gu-wen ZHANG; Sheng-chun XU; Wei-hua MAO; Qi-zan HU; Ya-ming GONG

    2013-01-01

    The development of expressed sequence tag-derived simple sequence repeats (EST-SSRs) provided a useful tool for investigating plant genetic diversity.In the present study,22 polymorphic EST-SSRs from grain soybean were identified and used to assess the genetic diversity in 48 vegetable soybean accessions.Among the 22 EST-SSR loci,tri-nucleotides were the most abundant repeats,accounting for 50.00% of the total motifs.GAA was the most common motif among tri-nucleotide repeats,with a frequency of 18.18%.Polymorphic analysis identified a total of 71 alleles,with an average of 3.23 per locus.The polymorphism information content (PIC) values ranged from 0.144 to 0.630,with a mean of 0.386.Observed heterozygosity (Ho) values varied from 0.0196 to 1.0000,with an average of 0.6092,while the expected heterozygosity (He) values ranged from 0.1502 to 0.6840,with a mean value of 0.4616.Principal coordinate analysis and phylogenetic tree analysis indicated that the accessions could be assigned to different groups based to a large extent on their geographic distribution,and most accessions from China were clustered into the same groups.These results suggest that Chinese vegetable soybean accessions have a narrow genetic base.The results of this study indicate that EST-SSRs from grain soybean have high transferability to vegetable soybean,and that these new markers would be helpful in taxonomy,molecular breeding,and comparative mapping studies of vegetable soybean in the future.

  5. Black Locust (Robinia pseudoacacia L. Root Cuttings: Diversity and Identity Revealed by SSR Genotyping: A Case Study

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    Maria Emilia Malvolti

    2015-10-01

    Full Text Available Background and Purpose: Black locust (Robinia pseudoacacia L. is a valuable species native to North America and today widely planted throughout the world for biomass production. In Hungary, where Robinia has great importance in the forest management, the clones have been selected for plantations on good, medium and poor quality sites. To conserve the identity, superior clones are vegetatively propagated by root cuttings. At times the collection of root cuttings can cause uncertainty for clonal identity because of the overlap of roots from neighboring plants. This can occur especially when the repository is damaged from severe environmental accidents and the planting layout has been lost. The aim of this study has been to verify by molecular markers the diversity or identity of black locust clones by root cuttings harvested in a damaged trial. Materials and Methods: Root cuttings of 91 clones belonging to five cultivars were collected in a trial severely damaged by storms and flooding periods. The obtained plantlets were analyzed with nine microsatellite (SSR markers and the genetic identity/diversity within and among the plants was tested using the software GenAlEx version 6. Results: Multilocus genotypes (MLG and the Paetkau’s assignation test (1985 revealed genetic variability among the samples: the analyzed plantlets were grouped in four classes instead of the five expected. In addition, 6 unique genotypes have been detected. Conclusions: This study remarks problems that may arise during the harvest of Robinia’s root cuttings, especially when the planting layout has been confused. Molecular analyses can be successfully used to control the germplasm before its sale as guaranty for nurseries, farmers and stakeholders.

  6. Studies on Classification and Identification based on Morphological Markers and SSR Markers for Elite Varieties of Cucumis melo L.%基于形态学标记及 SSR 标记的甜瓜主栽品种分类鉴定研究

    Institute of Scientific and Technical Information of China (English)

    李瑞峰; 高鹏; 朱子成; 栾非时

    2014-01-01

    Studies on classification and identification of 60 melon(Cucumis melo L.)materials were conducted by SSR marker and Morphological marker. Based on morphological cluster analysis the genetic similarity coefficient of the 60 materials ranged from 0.73-0.94,and at the genetic similarity coefficient of 0.74 these melons could be classified into 2 categories:Cucumis melo ssp. conomon and C. melo ssp. melo. Cucumis melo ssp. conomon could be subdivided into 4 groups,which are preliminarily classified by single fruit weight,peel color,aroma,maturity. The result of SSR cluster analysis showed that the genetic similarity coefficient of the 60 accessions ranged from 0.75-0.95. Also,the test materials could be divided into 6 categories at the genetic similarity coefficient of 0.77. 18 pairs of the SSR primers could detect 4-11 polymorphic bands with an average of 8 bands. The average polymorphism information content(PIC)was 0.71 with the changing range of 0.58-0.88. The fingerprinting effectively distinguished the 60 materials and every accession had unique fingerprinting using QR code.%利用形态学标记、SSR 分子标记技术对市场上广泛种植的甜瓜品种进行分类鉴定。利用形态学聚类分析,得到60份材料间的相似系数为0.73~0.94,在相似系数为0.74处,60份甜瓜材料被分为2类,为薄皮甜瓜和厚皮甜瓜;在相似系数为0.77处,薄皮甜瓜按照单果质量、熟性、果皮底色、芳香气分为4组,实现初步分类。经过 SSR 标记聚类分析,得到60份材料间的相似系数为0.75~0.95,当相似系数为0.77时,可以将所有供试材料分为6类。利用 SSR 分子标记技术,为60份不同甜瓜品种构建唯一的指纹图谱。18对 SSR 引物,每对引物可以检测到4~11条数目不等的多态性条带,平均为8条。多态性信息含量(PIC)平均为0.71,变化范围为0.58~0.88。采用 QR 编码为60份甜瓜材料构建了唯一的指纹图谱。试验

  7. Analysis of SSRs in grape genome and development of SSR database%葡萄全基因组SSR分析和数据库构建

    Institute of Scientific and Technical Information of China (English)

    蔡斌; 李成慧; 姚泉洪; 周军; 陶建敏; 章镇

    2009-01-01

    We developed a Perl script-SSRFinder to detect SSRs in grape genome sequence. A total of 114 520 SSRs were isolated from publicly available Vitis vinifera L. ' Pinor Nori PN40024' genomic DNA sequence. Among them, 37 648 mononucleotide repeats, 30 123 dinucleotide repeats, 18 705 trinucleotide repeats, 14 566 tetranucleotide repeats, 3 492 pentanucleotide repeats, and 9 986 hexanucleotide repeats were found, accounting for 32. 9% , 26. 3% , 16. 3% , 12. 7% , 3. 0% , and 8. 7% of the total SSRs respectively. SSRs with poly ( A/T)_n repeats represented the most abundant type, whereas C/G-rich motifs were the rarest type. We also assessed the distribution of SSRs on genome fragment. The results showed that the SSRs distributed mainly in inter-genic region and were moderately abundant in UTRs. In coding region, the distribution of all repeat types was less frequent except tri- and hexa-nucleotide repeats. To make use of these SSRs, we developed a database on the Internet. The database of grape SSRs ( DGSSR) is a database comprehensively collecting and annotating grape SSRs. The DGSSR contains all the SSRs with their related information detected in the study. It provides flexible query interface and detailed annotations for individual SSR. It also contains SSRs detected from Vitis vinifera L. ESTs dataset. The DGSSR is available at http: //www. yaolab. sh. cn/ssr.%利用Perl语言开发了用于探寻基因组SSR的程序SSRFinder,并利用其从法国国家基因测序中心(Genoscope)公布的欧亚种葡萄(Vitis vinifera L.)黑比诺品系PN40024的基因组序列中检索到114 520个SSR.其中含单核苷酸、二核苷酸、三核苷酸、四核苷酸、五核苷酸和六核苷酸重复单元的SSR数目分别为37 648(329%)、30 123(263%)、18 705(163%)、14 566(127%)、3 492(30%)和9 986(87%)个.在各类SSR中,不同核苷酸组成的重复单元频率间存在较大的差异,其中富含A/T重复单元的SSR频率最高,而富含C/G重复单元的SSR频率

  8. Sequence-based SSR marker development and their application in defining the Introgressions of LA0716 (Solanum pennellii in the background of cv. M82 (Solanum lycopersicum.

    Directory of Open Access Journals (Sweden)

    Wenbo Long

    Full Text Available The introgression lines (ILs from cv. M82 (Solanum lycopersicum × LA0716 (S. pennellii have been proven to be exceptionally useful for genetic analysis and gene cloning. The introgressions were originally defined by RFLP markers at their development. The objectives of this study are to develop polymorphic SSR markers, and to re-define the DNA introgression from LA0716 in the ILs. Tomato sequence data was scanned by software to generate SSR markers. In total, 829 SSRs, which could be robustly amplified by PCR, were developed. Among them, 658 SSRs were dinucleotide repeats, 162 were trinucleotide repeats, and nine were tetranucleotide repeats. The 829 SSRs together with 96 published RFLPs were integrated into the physical linkage map of S. lycopersicum. Introgressions of DNA fragments from LA0716 were re-defined among the 75 ILs using the newly developed SSRs. A specific introgression of DNA fragment from LA0716 was identified in 72 ILs as described previously by RFLP, whereas the specific DNA introgression described previously were not detected in the ILs LA4035, LA4059 and LA4091. The physical location of each investigated DNA introgression was finely determined by SSR mapping. Among the 72 ILs, eight ILs showed a shorter and three ILs (IL3-2, IL12-3 and IL12-3-1 revealed a longer DNA introgression than that framed by RFLPs. Furthermore, 54 previously undefined segments were found in 21 ILs, ranging from 1 to 11 DNA introgressions per IL. Generally, the newly developed SSRs provide additional markers for genetic studies of tomatoes, and the fine definition of DNA introgressions from LA0716 would facilitate the use of the ILs for genetic analysis and gene cloning.

  9. Construction of an integrated genetic linkage map for the A genome of Brassica napus using SSR markers derived from sequenced BACs in B. rapa

    Directory of Open Access Journals (Sweden)

    King Graham J

    2010-10-01

    Full Text Available Abstract Background The Multinational Brassica rapa Genome Sequencing Project (BrGSP has developed valuable genomic resources, including BAC libraries, BAC-end sequences, genetic and physical maps, and seed BAC sequences for Brassica rapa. An integrated linkage map between the amphidiploid B. napus and diploid B. rapa will facilitate the rapid transfer of these valuable resources from B. rapa to B. napus (Oilseed rape, Canola. Results In this study, we identified over 23,000 simple sequence repeats (SSRs from 536 sequenced BACs. 890 SSR markers (designated as BrGMS were developed and used for the construction of an integrated linkage map for the A genome in B. rapa and B. napus. Two hundred and nineteen BrGMS markers were integrated to an existing B. napus linkage map (BnaNZDH. Among these mapped BrGMS markers, 168 were only distributed on the A genome linkage groups (LGs, 18 distrubuted both on the A and C genome LGs, and 33 only distributed on the C genome LGs. Most of the A genome LGs in B. napus were collinear with the homoeologous LGs in B. rapa, although minor inversions or rearrangements occurred on A2 and A9. The mapping of these BAC-specific SSR markers enabled assignment of 161 sequenced B. rapa BACs, as well as the associated BAC contigs to the A genome LGs of B. napus. Conclusion The genetic mapping of SSR markers derived from sequenced BACs in B. rapa enabled direct links to be established between the B. napus linkage map and a B. rapa physical map, and thus the assignment of B. rapa BACs and the associated BAC contigs to the B. napus linkage map. This integrated genetic linkage map will facilitate exploitation of the B. rapa annotated genomic resources for gene tagging and map-based cloning in B. napus, and for comparative analysis of the A genome within Brassica species.

  10. A combined functional and structural genomics approach identified an EST-SSR marker with complete linkage to the Ligon lintless-2 genetic locus in cotton (Gossypium hirsutum L.

    Directory of Open Access Journals (Sweden)

    Tang Yuhong

    2011-09-01

    Full Text Available Abstract Background Cotton fiber length is an important quality attribute to the textile industry and longer fibers can be more efficiently spun into yarns to produce superior fabrics. There is typically a negative correlation between yield and fiber quality traits such as length. An understanding of the regulatory mechanisms controlling fiber length can potentially provide a valuable tool for cotton breeders to improve fiber length while maintaining high yields. The cotton (Gossypium hirsutum L. fiber mutation Ligon lintless-2 is controlled by a single dominant gene (Li2 that results in significantly shorter fibers than a wild-type. In a near-isogenic state with a wild-type cotton line, Li2 is a model system with which to study fiber elongation. Results Two near-isogenic lines of Ligon lintless-2 (Li2 cotton, one mutant and one wild-type, were developed through five generations of backcrosses (BC5. An F2 population was developed from a cross between the two Li2 near-isogenic lines and used to develop a linkage map of the Li2 locus on chromosome 18. Five simple sequence repeat (SSR markers were closely mapped around the Li2 locus region with two of the markers flanking the Li2 locus at 0.87 and 0.52 centimorgan. No apparent differences in fiber initiation and early fiber elongation were observed between the mutant ovules and the wild-type ones. Gene expression profiling using microarrays suggested roles of reactive oxygen species (ROS homeostasis and cytokinin regulation in the Li2 mutant phenotype. Microarray gene expression data led to successful identification of an EST-SSR marker (NAU3991 that displayed complete linkage to the Li2 locus. Conclusions In the field of cotton genomics, we report the first successful conversion of gene expression data into an SSR marker that is associated with a genomic region harboring a gene responsible for a fiber trait. The EST-derived SSR marker NAU3991 displayed complete linkage to the Li2 locus on

  11. Novel SSR markers from BAC-end sequences, DArT arrays and a comprehensive genetic map with 1,291 marker loci for chickpea (Cicer arietinum L..

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    Mahendar Thudi

    Full Text Available Chickpea (Cicer arietinum L. is the third most important cool season food legume, cultivated in arid and semi-arid regions of the world. The goal of this study was to develop novel molecular markers such as microsatellite or simple sequence repeat (SSR markers from bacterial artificial chromosome (BAC-end sequences (BESs and diversity arrays technology (DArT markers, and to construct a high-density genetic map based on recombinant inbred line (RIL population ICC 4958 (C. arietinum×PI 489777 (C. reticulatum. A BAC-library comprising 55,680 clones was constructed and 46,270 BESs were generated. Mining of these BESs provided 6,845 SSRs, and primer pairs were designed for 1,344 SSRs. In parallel, DArT arrays with ca. 15,000 clones were developed, and 5,397 clones were found polymorphic among 94 genotypes tested. Screening of newly developed BES-SSR markers and DArT arrays on the parental genotypes of the RIL mapping population showed polymorphism with 253 BES-SSR markers and 675 DArT markers. Segregation data obtained for these polymorphic markers and 494 markers data compiled from published reports or collaborators were used for constructing the genetic map. As a result, a comprehensive genetic map comprising 1,291 markers on eight linkage groups (LGs spanning a total of 845.56 cM distance was developed (http://cmap.icrisat.ac.in/cmap/sm/cp/thudi/. The number of markers per linkage group ranged from 68 (LG 8 to 218 (LG 3 with an average inter-marker distance of 0.65 cM. While the developed resource of molecular markers will be useful for genetic diversity, genetic mapping and molecular breeding applications, the comprehensive genetic map with integrated BES-SSR markers will facilitate its anchoring to the physical map (under construction to accelerate map-based cloning of genes in chickpea and comparative genome evolution studies in legumes.

  12. Bioinformatic Analysis of Microsatellites in the Genome of Sporisorium reilianum and the Design of SSR Primers%玉米丝黑穗病菌基因组SSR信息分析及其引物设计

    Institute of Scientific and Technical Information of China (English)

    王雪梅; 李新凤; 路平; 王建明

    2015-01-01

    探讨玉米丝黑穗病菌(Sporisorium reilianum)基因组序列中 SSR 位点的分布与组成特点,为开发可用于玉米丝黑穗病菌遗传多样性分析的 Genomic‐SSR 标记奠定基础。从 NCBI 公共数据库下载玉米丝黑穗病菌的23条染色体基因组序列,利用 SSRIT 在线软件对第4、5、6、7条染色体进行 SSR 位点的搜索,并且利用 Primer 3.0软件设计Genomic‐SSR 引物。结果表明:在玉米丝黑穗病菌基因组序列的第4、5、6、7条染色体中,共搜索到317个 SSR 位点,平均每条染色体出现79个 SSR 位点,其总长度为6.89 kb ,占这四条染色体基因组总长的0.21%,大约每10.3 kb 中就有一个大于18 bp 的 SSR 序列。其中,主要的重复类型是三核苷酸重复单元,占全部 SSR 的53.94%(171个),其次为二核苷酸重复单元,占全部 SSR 的16.09%(51个)。数量最少的是六碱基重复单元,为17个(5.36%)。出现频率最高的的重复基序为(GCA /TGC)n(13.25%),其次是(AGC/GCT )n 和(CAG/CTG)n ,出现频率分别为8.52%、8.20%。并在此基础上,利用 Primer3.0在线软件设计了40对 SSR 引物。玉米丝黑穗病菌基因组序列中 SSR 位点丰富,具有发掘玉米丝黑穗病菌 SSR 标记的潜力。%The objective of this study is to investigate the distribution and components of Sporisorium reilianum SSRs derived from Genomics. These researches could lay the foundation for the development of Genomic‐SSR markers that would be useful for the genetic diversity analysis of Sporisorium reilianum. The whole genome sequence of Sporisorium reilianum were obtained from NCBI.SSRIT (simple sequence repeat identification tool) was used to search SSRs in fourth ,fifth ,sixth and seventh chromosome and Primer3.0 was used to design Genomic‐SSR primers. A total of 171 SSRs were observed in fourth ,fifth ,sixth and seventh chromosome ,with an average of 79

  13. The Ssr protein (T1E_1405) from Pseudomonas putida DOT-T1E enables oligonucleotide-based recombineering in platform strain P. putida EM42

    DEFF Research Database (Denmark)

    Aparicio, Tomás; Ingemann Jensen, Sheila; Nielsen, Alex Toftgaard

    2016-01-01

    of reference strain KT2440) is still a time-consuming endeavor. In this work we have investigated the in vivo activity of the Ssr protein encoded by the open reading frame T1E_1405 from Pseudomonas putida DOT-T1E, a plausible functional homologue of the β protein of the Red recombination system of λ phage...... of Escherichia coli. A test based on the phenotypes of pyrF mutants of P. putida (the yeast’s URA3 ortholog) was developed for quantifying the ability of Ssr to promote invasion of the genomic DNA replication fork by synthetic oligonucleotides. The efficiency of the process was measured by monitoring...

  14. Transcriptomic Identification of Drought-Related Genes and SSR Markers in Sudan Grass Based on RNA-Seq

    Directory of Open Access Journals (Sweden)

    Yongqun Zhu

    2017-05-01

    Full Text Available Sudan grass (Sorghum sudanense is an annual warm-season gramineous forage grass that is widely used as pasture, hay, and silage. However, drought stress severely impacts its yield, and there is limited information about the mechanisms of drought tolerance in Sudan grass. In this study, we used next-generation sequencing to identify differentially expressed genes (DEGs in the Sudan grass variety Wulate No.1, and we developed simple sequence repeat (SSR markers associated with drought stress. From 852,543,826 raw reads, nearly 816,854,366 clean reads were identified and used for analysis. A total of 80,686 unigenes were obtained via de novo assembly of the clean reads including 45,065 unigenes (55.9% that were identified as coding sequences (CDSs. According to Gene Ontology analysis, 31,444 unigenes were annotated, 11,778 unigenes were identified to 25 categories in the clusters of orthologous groups of proteins (KOG classification, and 11,223 unigenes were assigned to 280 Kyoto Encyclopedia of Genes and Genomes (KEGG pathways. Additionally, there were 2,329 DEGs under a short-term of 25% polyethylene glycol (PEG treatment, while 5,101 DEGs were identified under the long-term of 25% PEG treatment. DEGs were enriched in pathways of carbon fixation in photosynthetic organisms and plant hormone signal transduction which played a leading role in short-term of drought stress. However, DEGs were mainly enriched in pathway of plant hormone signal transduction that played an important role under long-term of drought stress. To increase accuracy, we excluded all the DEGs of all controls, specifically, five DEGs that were associated with high PEG concentrations were found through RNA-Seq. All five genes were up-regulated under drought stress, but the functions of the genes remain unclear. In addition, we identified 17,548 SSRs obtained from 80,686 unigenes. The newly identified drought tolerance DEGs will contribute to transgenic breeding efforts, while

  15. De novo transcriptome assembly, development of EST-SSR markers and population genetic analyses for the desert biomass willow, Salix psammophila.

    Science.gov (United States)

    Jia, Huixia; Yang, Haifeng; Sun, Pei; Li, Jianbo; Zhang, Jin; Guo, Yinghua; Han, Xiaojiao; Zhang, Guosheng; Lu, Mengzhu; Hu, Jianjun

    2016-12-20

    Salix psammophila, a sandy shrub known as desert willow, is regarded as a potential biomass feedstock and plays an important role in maintaining local ecosystems. However, a lack of genomic data and efficient molecular markers limit the study of its population evolution and genetic breeding. In this study, chromosome counts, flow cytometry and SSR analyses indicated that S. psammophila is tetraploid. A total of 6,346 EST-SSRs were detected based on 71,458 de novo assembled unigenes from transcriptome data. Twenty-seven EST-SSR markers were developed to evaluate the genetic diversity and population structure of S. psammophila from eight natural populations in Northern China. High levels of genetic diversity (mean 10.63 alleles per locus; mean HE 0.689) were dectected in S. psammophila. The weak population structure and little genetic differentiation (pairwise FST = 0.006-0.016) were found among Population 1-Population 7 (Pop1-Pop7; Inner Mongolia and Shaanxi), but Pop8 (Ningxia) was clearly separated from Pop1-Pop7 and moderate differentiation (pairwise FST = 0.045-0.055) was detected between them, which may be influenced by local habitat conditions. Molecular variance analyses indicated that most of the genetic variation (94.27%) existed within populations. These results provide valuable genetic informations for natural resource conservation and breeding programme optimisation of S. psammophila.

  16. Characterization of Global Transcriptome Using Illumina Paired-End Sequencing and Development of EST-SSR Markers in Two Species of Gynostemma (Cucurbitaceae).

    Science.gov (United States)

    Zhao, Yue-Mei; Zhou, Tao; Li, Zhong-Hu; Zhao, Gui-Fang

    2015-11-30

    Gynostemma pentaphyllum is an important medicinal herb of the Cucurbitaceae family, but limited genomic data have hindered genetic studies. In this study, transcriptomes of two closely-related Gynostemma species, Gynostemma cardiospermum and G. pentaphyllum, were sequenced using Illumina paired-end sequencing technology. A total of 71,607 nonredundant unigenes were assembled. Of these unigenes, 60.45% (43,288) were annotated based on sequence similarity search with known proteins. A total of 11,059 unigenes were identified in the Kyoto Encyclopedia of Genes and Genomes Pathway (KEGG) database. A total of 3891 simple sequence repeats (SSRs) were detected in 3526 nonredundant unigenes, 2596 primer pairs were designed and 360 of them were randomly selected for validation. Of these, 268 primer pairs yielded clear products among six G. pentaphyllum samples. Thirty polymorphic SSR markers were used to test polymorphism and transferability in Gynostemma. Finally, 15 SSR makers that amplified in all 12 Gynostemma species were used to assess genetic diversity. Our results generated a comprehensive sequence resource for Gynostemma research.

  17. Characterization of Global Transcriptome Using Illumina Paired-End Sequencing and Development of EST-SSR Markers in Two Species of Gynostemma (Cucurbitaceae

    Directory of Open Access Journals (Sweden)

    Yue-Mei Zhao

    2015-11-01

    Full Text Available Gynostemma pentaphyllum is an important medicinal herb of the Cucurbitaceae family, but limited genomic data have hindered genetic studies. In this study, transcriptomes of two closely-related Gynostemma species, Gynostemma cardiospermum and G. pentaphyllum, were sequenced using Illumina paired-end sequencing technology. A total of 71,607 nonredundant unigenes were assembled. Of these unigenes, 60.45% (43,288 were annotated based on sequence similarity search with known proteins. A total of 11,059 unigenes were identified in the Kyoto Encyclopedia of Genes and Genomes Pathway (KEGG database. A total of 3891 simple sequence repeats (SSRs were detected in 3526 nonredundant unigenes, 2596 primer pairs were designed and 360 of them were randomly selected for validation. Of these, 268 primer pairs yielded clear products among six G. pentaphyllum samples. Thirty polymorphic SSR markers were used to test polymorphism and transferability in Gynostemma. Finally, 15 SSR makers that amplified in all 12 Gynostemma species were used to assess genetic diversity. Our results generated a comprehensive sequence resource for Gynostemma research.

  18. Diverse pore loops of the AAA+ ClpX machine mediate unassisted and adaptor-dependent recognition of ssrA-tagged substrates.

    Science.gov (United States)

    Martin, Andreas; Baker, Tania A; Sauer, Robert T

    2008-02-29

    ClpX, an archetypal proteolytic AAA+ unfoldase, must engage the ssrA tags of appropriate substrates prior to ATP-dependent unfolding and translocation of the denatured polypeptide into ClpP for degradation. Here, specificity-transplant and disulfide-crosslinking experiments reveal that the ssrA tag interacts with different loops that form the top, middle, and lower portions of the central channel of the ClpX hexamer. Our results support a two-step binding mechanism, in which the top loop serves as a specificity filter and the remaining loops form a binding site for the peptide tag relatively deep within the pore. Crosslinking experiments suggest a staggered arrangement of pore loops in the hexamer and nucleotide-dependent changes in pore-loop conformations. This mechanism of initial tag binding would allow ATP-dependent conformational changes in one or more pore loops to drive peptide translocation, force unfolding, and mediate threading of the denatured protein through the ClpX pore.

  19. The pituitary mediates the anxiolytic-like effects of the vasopressin V1B receptor antagonist, SSR149415, in a social interaction test in rats.

    Science.gov (United States)

    Shimazaki, Toshiharu; Iijima, Michihiko; Chaki, Shigeyuki

    2006-08-14

    A vasopressin V(1B) receptor antagonist has been shown to exhibit anxiolytic effects in a variety of animal models of anxiety. In the present study, we examined the involvement of the pituitary in the anxiolytic effects of a vasopressin V(1B) receptor antagonist by conducting a social interaction test in rats. In the sham-operated rats, both the vasopressin V(1B) receptor antagonist SSR149415 and the benzodiazepine chlordiazepoxide significantly increased the social behavior of a pair of unfamiliar rats, and the blood adrenocorticotropic hormone levels were markedly increased during the social interaction test. Hypophysectomy also increased the length of time that the animals engaged in social behavior to the same extent as that observed after treatment of the sham-operated rats with anxiolytics. However, while chlordiazepoxide further increased the duration of social interaction in the hypophysectomized rats, the anxiolytic effects of SSR149415 was no longer observed in these animals. These results suggest that the anxiolytic effects of the vasopressin V(1B) receptor antagonist in the social interaction test are mediated through blockade of the vasopressin V(1B) receptor in the pituitary.

  20. Genetic diversity and population structure in natural populations of Moroccan Atlas cedar (Cedrus atlantica; Pinaceae) determined with cpSSR markers.

    Science.gov (United States)

    Terrab, Anass; Paun, Ovidiu; Talavera, Salvador; Tremetsberger, Karin; Arista, Montserrat; Stuessy, Tod F

    2006-09-01

    Atlas cedar (Cedrus atlantica) is an ecologically and economically important forest tree species of northern Africa and is considered one of the endangered conifer species in the region. Chloroplast microsatellites (cpSSR) were used to study genetic variation within and among populations and geographical structure in natural populations of C. atlantica throughout its entire distribution range in Morocco. A total of 25 chloroplast haplotypes and 66 cpSSR alleles were found among 162 individuals. The cpSSRs indicate that C. atlantica appears to maintain a high level of genetic diversity (mean H(e) = 0.95), as observed in most coniferous species. Values of mean pairwise distance within a population (D(2)(SH)) were related to the size and location of the populations. AMOVA analysis showed that most of the variation in C. atlantica occurs within populations and confirmed the general tendency of gymnosperms to display lower values of population differentiation than angiosperms. The distance-based clustering method (PCoA and neighbor-joining analysis) and the geographical structure revealed a poor structure among the six populations of Cedrus atlantica. Also, a Mantel test indicated a weak correlation between geographic and genetic distances (P = 0.106, r = 0.363). These results are also interpreted in the context of postglacial history of the region plus human impacts.

  1. Discrimination Capacity of RAPD, ISSR and SSR Markers and of their Effectiveness in Establishing Genetic Relationship and Diversity among Egyptian and Saudi Wheat Cultivars

    Directory of Open Access Journals (Sweden)

    Salah E.D. El-Assal

    2012-01-01

    Full Text Available Problem statement: Yield crop cultivars and landraces are valuable sources of genetic variations that the knowledge and implication of these variations are critical in the plant breeding programs. our major objective of this study is investigating the discriminating capacity of RAPD, ISSR and SSR markers and of their effectiveness in establishing genetic relationship and diversity among Egyptian and Saudi wheat cultivars. Approach: Eleven wheat cultivars and landraces collected from Egypt and Saudi Arabia, five Egyptian wheat (Sakha 93, Sods 1, Sods 4, Gmiza 9 and Sohag 3 and six Saudi wheat landrace cultivars (Hmees, Al-Kaseem, Hegazi, Abo-Sakr, Dubai 1 and Nagran were characterized using RAPD, ISSR and SSR molecular markers as efficient tools. Ten and nine oligonucleotide primers of RAPD and ISSR respectively and four primer pairs of SSR were used in wheat samples analysis. Only clear and repeatable band profile of 6 RAPD, 8 ISSR and 2 SSR primers were obtained. In RAPD analyses, 74 out of 141 bands (52% were polymorphic. Results: The number of alleles ranged from 8-21 per primer, with an average of 14.1 per primer. In ISSR analyses, a total of 78 alleles were detected, along with 36 alleles (46% were polymorphic. The number of alleles per primer ranged from 5-10 with an average of 8.6 alleles per ISSR primer. SSR reactions recorded 6 alleles, of which 5 alleles (83% were polymorphic. Cluster analysis was conducted using Unweighted Pair Group Method that depends on Arithmetic Average (UPGMA. The dendrogram cluster diagram classified the evaluated genotypes in three major clusters corresponding to the cultivation regions. The first group contains Sakha 93, Sods 1 and Sods 4 with more than 80% Genetic Similarity (GS. The GS between Sakha 93 and Sods 1, Sakha 93 and Sods 4 or Sods 1 and Sods 4 were 83.6%, 83.9 and 85.4 respectively. The second group contains Gmiza 9 and Sohag 3 with GS 83.1%. The third group contains most of the Saudi landrace

  2. 洋葱转录组SSR信息分析及其多态性研究%Analysis on SSR Information in Transcriptome of Onion and the Polymorphism

    Institute of Scientific and Technical Information of China (English)

    李满堂; 张仕林; 邓鹏; 侯喜林; 王建军

    2015-01-01

    Bioinformatics methods were used to analyze the onion(Allium cepa L.)transcriptome SSR loci information and designed simple sequence repeat (SSR) primers,so as to provide a powerful tool for screening onion molecular marker assisted breeding.Five thousand nine hundred and fifty-nine SSR loci (5.10%) were obtained from 106 932 unigenes (84.04 Mb) by using MISA software to screen the onion transcriptome sequencing,and its frequency was 1/14.1 kb.Trinucleotide repeat was the main type,accounted for as much as 37.27% of all SSRs.The AAG/CTT were the predominant repeat types (10.20%),followed by mononucleotide repeat motif (30.91%) and dinucleotide repeat motif (24.75%).Five thousand two hundred and fifty-eight pairs of SSR primers were designed using Primer 5.Randomly 20 pairs of primers were selected for PCR amplification,12 amplified on clear and reproducible bands,9 in 24 different types showed polymorphism in onion material.Twenty-four onions plants were divided into 4 groups by UPGMA.%采用生物信息学方法分析洋葱(Allium cepa L.)转录组中的SSR位点信息,并设计简单重复序列(SSR)引物,以期为洋葱分子标记辅助育种提供有力工具.利用MISA工具筛选了洋葱转录组测序获得的106 932条unigenes (84.04 Mb),并对其SSR位点信息进行了分析,共筛选得到5 959个SSR位点(占总unigenes的5.10%),其发生频率为1/14.1 kb.SSRs位点中主导类型是以AAG/CTT(占总SSRs的10.20%)为主的三核苷酸重复,占总SSRs的37.27%;其次是单、二核苷酸重复,其出现频率分别为30.91%和24.75%.利用Primer5共设计出5 258对SSR引物.随机选择20对引物进行PCR扩增,其中12对扩增出清晰可重复的条带,9对在24个不同类型洋葱材料中表现出多态性.利用UPGMA作图,将24个洋葱材料分为4类.

  3. SSR和ISSR分子标记及其在桑树遗传育种研究中的应用前景%SSR and ISSR Molecular Markers and Their Usage in Genetics and Breeding of Mulberry Tress

    Institute of Scientific and Technical Information of China (English)

    赵卫国; 苗雪霞; 潘一乐; 黄勇平

    2006-01-01

    本文对SSR(simple sequence repeat)和ISSR(inter-simple sequence repeat)分子标记的定义和各自优点进行了综述,并展望这两种分子标记技术在桑树遗传育种研究中的应用前景.

  4. Development of SSR Molecular Markers Based on Expressed Sequence Tags from Seeds of Fagopyrum esculentum%基于微卫星标记普通荞麦种子序列表达标签的开发

    Institute of Scientific and Technical Information of China (English)

    石桃雄; 黎瑞源; 郭菊卉; 李月; 李光; 陈庆富

    2014-01-01

    为丰富普通荞麦(Fagopyrum esculentum Moench)的序列信息,挖掘有效的 SSR 标记,基于Hiseq 2000测序平台对普通荞麦的种子转录谱进行测序、分析,利用 Misa 软件进行 SSR 位点扫描,采用Primer 5.0引物设计程序对其中的300个 SSR 位点设计引物,随机挑选40对引物对19个普通荞麦品系进行遗传多样性分析。结果表明:测序共产生20508824条高质量的短序列(read),总长度为1889111004 bp,通过拼接最终获得54947条转录本(transcript)和36133个独立基因(unigene)。在2226个独立基因中发现了2666个 SSR 位点。有20对引物(占50%)能扩增出目标产物,其中,12对有多态性,多态性信息量(PIC)范围为0.10~0.93,平均为0.57,多态性程度高。%To enrich sequences information and develop mass SSR marker,the authors used Hiseq2000 to sequence and de novo assemble the seed transcriptome of F.esculentum.SSR motifs were identified using MISA 1.0 software and 300 primer pairs flanking EST-SSR loci were designed using Primer 5.0 software.A total of 20 508 824 high quality reads (total length 1,889,111,004 bp)were obtained comprising 54 947 transcripts and 36 133 unigenes.In total,2 666 SSRs were identified from 2 226 unigenes.Twenty (50%)out of 40 primer pairs selected at random yielded amplification products,of which 12 primer pairs showed polymorphism among 19 different common buckwheat varieties,and the PIC ranged from 0.10 to 0.93 with the mean value of 0.57.

  5. Transferability of Mungbean Genomic-SSR Markers in Other Vigna Species%绿豆基因组SSR引物在豇豆属作物中的通用性

    Institute of Scientific and Technical Information of China (English)

    钟敏; 程须珍; 王丽侠; 王素华; 王小宝

    2012-01-01

    Cowpea (Vigna unguiculata L. Walp.), mungbean (V. Radiata L. Wilczek), rice bean [V. Umbellate (Thunb.) Ohwi & Ohashi], and adzuki bean (V; angularis Willd. Ohwi and Ohashi) are major food legumes in China. At present, SSR markers for genetic analysis of these legumes are much limited. Transferability analysis of primers has the vital significance to reduce their development cost and improve their development efficiency. In this study, 1 205 SSR primers were tested for their transferability and polymorphism by PCR amplification with the genomic DNA of four Vigna species, cowpea, adzuki bean, mungbean and rice bean. The results indicated that the transferability rate of mungbean genomic-SSR in cowpea, adzuki bean and rice bean was 50.0%, 73.3%, and 81.6%, and the ratio of polymorphism SSR primers in these crops was 4.1%, 1.7%, and 1.5%, whereas 32.0% in mungbean. A total of 469 mungbean genomic-SSR primers were detected to be highly transferable among different species of Vigna. The transferability of mungbean genomic-SSR was higher in adzuki bean and rice bean than in cowpea. These transferable markers are useful for further genetic and breeding studies in these species.%分子标记的种间通用性可降低其开发成本,提高利用效率,也有助于促进遗传研究较薄弱物种的分子遗传学研究.本文选取绿豆、小豆、豇豆及饭豆材料各3份,分析1205对新开发的绿豆基因组SSR引物在这些材料中的扩增效果,结果显示绿豆基因组SSR引物在豇豆、小豆和饭豆中的通用性比率分别为50.0%、73.3%和81.6%;多态性比率分别为4.1%、1.7%和1.5%;在4个种间均通用的引物469对.这些通用性SSR引物将有助于这4种食用豆类在多样性评价、连锁图谱的构建、基因定位及比较基因组学等方面的研究.

  6. Analysis of SSR information in EST resource of saffron crocus (Crocus sativus)%番红花EST资源的SSR信息分析

    Institute of Scientific and Technical Information of China (English)

    陈国庆

    2011-01-01

    6745 ESTs of saffron crocus in the public database of NCBI were downloaded and analysed, resulting in 1431 non-redundant ESTs with total length about 612.01 kb. A total of 108 SSRs distributed in 103 ESTs were detected,accouting for 7.55% of the non-redundant ESTs. The average distribution distance of these EST-SSRs was about 5.67 kb. Dinucleotide and trinucleotide repeats were the main types in Crocus sativus, accouting for 30.56% and 37. 96% of all the SSRs,respectively. AG/CT and AAG/CTT are the most frequent motifs,accounting for 66. 67%and 29. 27 % in dinucleotide and trinucleotide repeats, respectively. The present study provides a base for the development and further applification of EST-SSR markers in saffron crocus.%从NCBI公共数据库下载得到6745条番红花EST,通过前处理得到全长为612.01 kb的无冗余EST 1431条.在这些序列中搜索出108个SSR,分布于103条EST中,出现频率为7.55%.这些EST-SSR的平均分布距离是5.67 kb.二核苷酸重复和三核苷酸重复是番红花主要的重复类型,分别占总EST-SSR的30.56%和37.96%.AG/CT和AAG/CTT是二、三核苷酸重复中的优势基元,分别占二、三核苷酸重复的66.67%和29.27%.本研究为番红花EST-SSR标记的建立和进一步应用奠定了基础.

  7. SSR Marker of the Gene Conferring Sethoxydim Resistance in Setaria italica (L .)Beauv%谷子抗“拿捕净”基因的SSR标记

    Institute of Scientific and Technical Information of China (English)

    2013-01-01

      为探究谷子抗病育种的理论基础,采用Blast比对的方法,利用已知的谷子抗“拿捕净”除草剂的基因组序列,对谷子抗“拿捕净”基因进行SSR分子连锁标记筛选研究。利用抗“拿捕净”基因的已知序列找到了在谷子基因组中第7和第9条染色体上均存在同源序列,分别在这些同源序列上下游寻找SSR引物,在谷子F2群体中进行SSR标记的筛选,进行共分离分析。结果表明:位于第7染色体上的2个SSR标记SIMS13569和SIMS13512与谷子抗“拿捕净”基因性状共分离,即表现为连锁遗传,该标记可用于分子标记辅助选择,对谷子抗“拿捕净”基因育种具有重要的现实意义;而第9染色体上的序列不具有抗“拿捕净”的作用。%Utilizing the known genome sequence of herbicide-resistant to Sethoxydim in foxtail millet ,selection SSR markers which was linkage of herbicide-resistant to Sethoxydim was studied .Using Blast alignment meth-od ,the homologous sequences of herbicide-resistant to Sethoxydim gene was found in the seventh and the ninth chromosomes in foxtail millet .In the upstream and downstream of homologous sequences ,primers were de-signed to select SSR molecular markers .In the F2 population of foxtail millet ,the herbicide-resistant to Se-thoxydim gene was linkage of two SSR markers ,SIMS13569 and SIMS13512 which were in the seventh chro-mosome ,and could be used for molecular marker assisted selection .It is important to the genetic breeding of herbicide-resistant to Sethoxydim in foxtail millet .However ,the homologous sequence in the ninth chromosome was not own the effect of herbicide-resistant to Sethoxydim .

  8. Highly informative single-copy nuclear microsatellite DNA markers developed using an AFLP-SSR approach in black spruce (Picea mariana and red spruce (P. rubens.

    Directory of Open Access Journals (Sweden)

    Yong-Zhong Shi

    Full Text Available Microsatellites or simple sequence repeats (SSRs are highly informative molecular markers for various biological studies in plants. In spruce (Picea and other conifers, the development of single-copy polymorphic genomic microsatellite markers is quite difficult, owing primarily to the large genome size and predominance of repetitive DNA sequences throughout the genome. We have developed highly informative single-locus genomic microsatellite markers in black spruce (Picea mariana and red spruce (Picea rubens using a simple but efficient method based on a combination of AFLP and microsatellite technologies.A microsatellite-enriched library was constructed from genomic AFLP DNA fragments of black spruce. Sequencing of the 108 putative SSR-containing clones provided 94 unique sequences with microsatellites. Twenty-two of the designed 34 primer pairs yielded scorable amplicons, with single-locus patterns. Fourteen of these microsatellite markers were characterized in 30 black spruce and 30 red spruce individuals drawn from many populations. The number of alleles at a polymorphic locus ranged from 2 to 18, with a mean of 9.3 in black spruce, and from 3 to 15, with a mean of 6.2 alleles in red spruce. The polymorphic information content or expected heterozygosity ranged from 0.340 to 0.909 (mean = 0.67 in black spruce and from 0.161 to 0.851 (mean = 0.62 in red spruce. Ten SSR markers showing inter-parental polymorphism inherited in a single-locus Mendelian mode, with two cases of distorted segregation. Primer pairs for almost all polymorphic SSR loci resolved microsatellites of comparable size in Picea glauca, P. engelmannii, P. sitchensis, and P. abies.The AFLP-based microsatellite-enriched library appears to be a rapid, cost-effective approach for isolating and developing single-locus informative genomic microsatellite markers in black spruce. The markers developed should be useful in black spruce, red spruce and other Picea species for

  9. Identification of microsatellite markers (SSR linked to a new bacterial blight resistance gene xa33(t in rice cultivar ‘Ba7’

    Directory of Open Access Journals (Sweden)

    Theerayut Toojinda

    2009-05-01

    Full Text Available This study attempts to identify a new source of bacterial blight (BB resistance gene and microsatellite makers (SSR linked to it. A total number of 139 F2 progenies generated from a cross between the resistant donor ‘Ba7’and ‘Pin Kaset’ were developed and used for this study. A Thai Xoo isolate, TXO16, collected from Phitsanulok province, was used to evaluate the resistance reaction in the F2 population. The segregation ratio of resistance (R and susceptibility (S was statistically fitted to 1R:3S model indicating single recessive gene segregation. Twenty F2 individuals consisting of 10 resistant and 10 susceptible plants were chosen for DNA analysis. Sixty-two polymorphic markers covering all rice chromosomes were used to identify the location and linked markers of the resistance gene. Four SSR markers, viz. RM30, RM7243, RM5509 and RM400, located on the long arm of rice chromosome 6, could clearly discriminate between resistant and susceptible phenotypes, and 161 BC2F2:3 individuals carrying BB resistance gene were developed through MAS using these SSR markers. This population was inoculated with TXO16 to validate and confirm the location of the gene and linked markers. The segregation ratio was statistically fitted to 1R:3S model confirming a recessive nature of the gene action in this germplasm. Phenotypic-genotypic association including five additional markers suggested that RM20590 was tightly linked to this resistance gene (R2=59.12 %. The BB phenotype was controlled by a recessive gene with incomplete dominance of susceptible allele providing intermediate resistance to Xoo pathogen in heterozygotes. The location of the gene was in the vicinity of a dominant gene, Xa7, which was previously reported. However, the resistance gene identified here was different from Xa7 because of the different nature of gene action. Consequently, this gene was tentatively designated as xa33(t. The resistance gene from rice cultivar ‘Ba7’ and the

  10. Utilização de marcadores moleculares RAPD e EST's SSR para estudo da variabilidade genética em cana-de-açúcar¹ Use of molecular markers RAPD, and ESTs SSR to study genetic variability in sugarcane

    Directory of Open Access Journals (Sweden)

    João Andrade Dutra Filho

    2013-03-01

    Full Text Available Marcadores moleculares dos tipos RAPD e EST's SSR foram utilizados como ferramentas para avaliar a variabilidade bem como estimar a divergência genética entre variedades comerciais e clones de cana-de-açúcar oriundos via autofecundação. Vinte e três genótipos foram utilizados neste estudo oriundos do Programa de Melhoramento Genético da Cana-de-açúcar da Rede Interuniversitária para o Desenvolvimento do Setor Sucroalcooleiro (PMGCA/RIDESA. A extração do DNA genômico seguiu a metodologia CTAB com modificações para cana-de-açúcar. Foram utilizados 11 oligonucleotídeos RAPD da operon Technologies e 7 EST's SRR obtidos através de uma extensa revisão de literatura. As análises da divergência genética foram realizadas com o auxílio do Programa GENES. Os marcadores RAPD detectaram um alto grau de polimorfismo genético, produzindo 61 bandas, das quais 58 foram polimórficas. Os marcadores EST's SSR amplificaram 38 alelos, sendo 34 polimórficos. Havendo a formação de três grupos, com a população estudada. A maior parte da variação genética foi mantida dentro das progênies, evidenciando a ocorrência de um alto grau de variabilidade genética entre os genótipos de cada progênie para fins de melhoramento. Através da divergência genética estimada foi possível identificar parentais divergentes para trabalhos de hibridação, visando a obtenção de clones superiores com caracteres de interesse à agroindústria canavieira. Os marcadores molecuares RAPD e EST's SSR foram igualmente eficientes para estimar a variabilidade genética nos genótipos testados e elaborar os cruzamentos a serem realizados nos programas de melhoramento.Molecular markers of the type RAPD and ESTs SSR were used as tools to evaluate the variability, and estimate the genetic divergence between commercial varieties and sugarcane clones from self-pollination. Twenty-three genotypes from the Program for the Genetic Improvement of Sugarcane of the

  11. SSR Inheritance Analysis and Screening for Linked Marker of Powdery Mildew Resistance in Cucumber(Cucumis sativus L.)%黄瓜白粉病抗性遗传分析与连锁标记筛选

    Institute of Scientific and Technical Information of China (English)

    聂京涛; 潘俊松; 何欢乐; 司龙亭; 蔡润

    2011-01-01

    In order to accelerate molecular marker assisted breeding process of powdery mildew resistance in cucumber ( Cucumis sativus L.) , in this paper, high susceptible cucumber inbred line M 12,abd high resistant inbred line M3 to powdery mildew were taken as parent and their hybrid, F2 populations and BC1 populations were used as experimental materials.We identified the seedlings inoculated with powdery mildew fungus and probed into the genetic regulation of powdery mildew resistance in cucumber.Combing with BSA method and SSR technology, SSR markers linked to the major resistant gene of powdery mildew in cucumber was obtained.The results showed that the resistance to powdery mildew was mainly controlled by a single recessive gene.By analyzing F2 single plant with SSR technique, a marker SSR15592 linked to the resistant gene was identified.The genetic distance between this marker and resistant gene was 7.62 cM.%以黄瓜高感、高抗白粉病自交系M12、M3为亲本组合得到的F2群体和BC1群体为试材,采用苗期接种鉴定,探讨了黄瓜白粉病抗性的遗传规律;结合BSA法和SSR技术,获得了与黄瓜白粉病抗性主效基因连锁的SSR标记.结果表明,供试亲本间白粉病抗性主要受一隐性单基因控制.对F2单株进行SSR分析,鉴定出1个与黄瓜白粉病抗性基因连锁的标记SSR15592,该标记与抗性基因间的遗传距离为7.62 cM.

  12. Isolation and Characterization of Simple Sequence Repeats (SSR Markers from the Moss Genus Orthotrichum Using a Small Throughput Pyrosequencing Machine

    Directory of Open Access Journals (Sweden)

    Vítězslav Plášek

    2012-06-01

    Full Text Available Here, we report the results of next-generation sequencing on the GS Junior system to identify a large number of microsatellites from the epiphytic moss Orthotrichum speciosum. Using a combination of a total (non-enrichment genomic library and small-scale 454 pyrosequencing, we determined 5382 contigs whose length ranged from 103 to 5445 bp. In this dataset we identified 92 SSR (simple sequence repeats motifs in 89 contigs. Forty-six of these had flanking regions suitable for primer design. We tested PCR amplification, reproducibility, and the level of polymorphism of 46 primer pairs for Orthotrichum speciosum using 40 individuals from two populations. As a result, the designed primers revealed 35 polymorphic loci with more than two alleles detected. This method is cost- and time-effective in comparison with traditional approaches involving cloning and sequencing.

  13. EST-derived SSR markers used as anchor loci for the construction of a consensus linkage map in ryegrass (Lolium spp.)

    DEFF Research Database (Denmark)

    Studer, Bruno; Kölliker, Roland; Muylle, Hilde;

    2010-01-01

    of publicly available Lolium EST-SSRs mapped for the first time together with previously mapped SSR markers will allow for consolidating existing mapping and QTL information in ryegrass. Map and markers presented here will prove to be an asset in the development for both molecular breeding of ryegrass as well......Background Genetic markers and linkage mapping are basic prerequisites for marker-assisted selection and map-based cloning. In the case of the key grassland species Lolium spp., numerous mapping populations have been developed and characterised for various traits. Although some genetic linkage maps...... of these populations have been aligned with each other using publicly available DNA markers, the number of common markers among genetic maps is still low, limiting the ability to compare candidate gene and QTL locations across germplasm. Results A set of 204 expressed sequence tag (EST)-derived simple sequence repeat...

  14. Genetic Analysis and Preliminary Mapping of a Highly Male-Sterile Gene in Foxtail Millet (Setaria italica L. Beauv.) Using SSR Markers

    Institute of Scientific and Technical Information of China (English)

    WANG Jun; DIAO Xian-min; GUO Ping-yi; WANG Zhi-lan; YANG Hui-qing; YUAN Feng; GUO Er-hu; TIAN Gang; AN Yuan-huai; LI Hui-xia; WANG Yu-wen

    2013-01-01

    Breeding of male-sterile lines has become the mainstream for the heterosis utilization in foxtail millet, but the genetic basis of most male-sterile lines used for the hybrid is still an area to be elucidated. In this study, a highly male-sterile line Gao146A was investigated. Genetic analysis indicated that the highly male-sterile phenotype was controlled by a single recessive gene a single recessive gene. Using F2 population derived from cross Gao146A/K103, one gene controlling the highly male-sterility, tentatively named asms1, which linked to SSR marker b234 with genetic distance of 16.7 cM, was mapped on the chromosome VI. These results not only laid the foundation for ifne mapping of this highly male-sterile gene, but also helped to accelerate the improvement of highly male-sterile lines by using molecular marker assisted breeding method.

  15. PRELIMINARY STUDY ON FINGERPRINT ON SSR AND ISSR OF APOSTICHOPUS JAPONICUS%扩增仿刺参SSR和ISSR指纹技术的初步研究

    Institute of Scientific and Technical Information of China (English)

    闫晗; 侯林; 毕相东; 王雪

    2006-01-01

    利用SSR(Simple Sequence Repeats)技术和ISSR(Inter Simple Sequence Repeats)技术对仿刺参(Apostichopus Japonicus)进行了PCR扩增.探索了刺参基因组DNA的提取方法.为了得到更好的PCR扩增结果,对引物浓度、Mg2+浓度、dNTP浓度、模板浓度、Taq浓度和退火温度及循环数等方面进行了研究,从而摸索出一个适合刺参SSR和ISSR分析的反应体系和反应条件,并对PCR反应中的一些特定影响因子进行了分析.

  16. Ultrastructure and ssrRNA sequencing of Myxidium amazonense n. sp. a myxosporean parasite of Corydoras melini from the Rio Negro river, Amazonas state, Brazil.

    Science.gov (United States)

    Mathews, Patrick D; Silva, Marcia R M; Maia, Antônio A M; Adriano, Edson A

    2015-12-01

    In a survey of myxozoan parasites of ornamental freshwater fish from the Rio Negro river, it was found that seven of 30 (23.3 %) Corydoras melini specimens examined had plasmodia of a new Myxidium species (Myxidium amazonense n. sp.) in the gallbladder. The fish were caught in the Rio Negro river, in the municipality of Santa Isabel do Rio Negro, in the state of Amazonas, Brazil. The plasmodia had a tubular shape, which was organized as a spiral spring with several turns in the gallbladder. The development of the myxospores was asynchronic, with disporic pansporoblasts. Mature myxospores were elongated, with 17.0 ± 0.9 (16.1-17.9) μm in length and 3.7 ± 0.7 (3.0-4.4) μm in width, and lightly arcuate from the valval view, with their bodies tapering slowly until ending in rounded extremities. The valval surface had nine to ten grooves in each valve. The polar capsules, one at either end of the spore, had a length of 5.4 ± 0.5 (4.9-5.9) μm and a width of 3.4 ± 0.6 (2.8-4.0) μm. Ultrastructural analysis showed that the wall of the plasmodia had numerous microvilli-like structures, pinocytotic canals, and cytoplasmic bridges connecting the pansporoblasts to each other and to the ectoplasm zone. Phylogenetic analysis, based on a small subunit ribosomal RNA (ssrRNA), identified the new species as a sister species of Myxidiumceccarelli, the unique South American Myxidium species whose ssrRNA sequence is available in the NCBI database. This study is the first description of Myxidium species in ornamental freshwater fish from Amazon.

  17. Comparison of PCR-RFLP Based on Ribosomal Regions and SSR Markers in Genetic Diversity of Pistachio Die-Back Caused by Paecilomyces variotii

    Directory of Open Access Journals (Sweden)

    Rostami

    2015-01-01

    Full Text Available Background In recent years, die-back of pistachio has become one of the most important diseases in Kerman gardens. With regard to the importance of this disease and the lack of comprehensive information regarding the population genetic structure of the pathogen, it is necessary to set an appropriate indicator in the study of genetic diversity. Objectives In the present study, we examined simple sequence repeats (SSRs and restriction fragment length polymorphism (PCR-RFLPs (two PCR-based marker assays to determine Paecilomyces variotti genetic diversity. Materials and Methods The utility of SSRs and PCR-RFLPs was examined to determine genetic diversity using 20 isolates of Paecilomyces variotii. In order to determine the performance of indicators, effective multiplex ratio (EMR, polymorphism information content (PIC, and marker index (MI were calculated. Results Both systems discriminated 20 isolates of P. variotii successfully but were different in the amount of detectable polymorphism. Using cluster analysis of digestion reaction, SSR based on UPGMA algorithm, and Jaccard similarity coefficient, the isolates with 70% similarity level were divided into 7 and 3 groups, respectively. Reviewed indicators were at higher level for PCR-RFLPs marker. Four restriction endonucleases enzymes in RFLP produced 20 loci that 90% of them were polymorphic; and for SSR it was 32 loci that 37.5% were polymorphic. Conclusions This is the first research in comparing two genetic marker systems in P. variotti. We were prompted to explore polymorphisms utility in P. variotti with a look at using germplasm screening mapping of genome and strain improvement programs.

  18. 咖啡叶锈病菌转录组SSR信息分析%Transcriptome Sequences SSR Information Analysis of Coffee Leaf Rust

    Institute of Scientific and Technical Information of China (English)

    吴伟怀; 邹海娟; 贺春萍; 梁艳琼; 习金根; 郑肖兰; 郑金龙; 李锐; 易克贤

    2014-01-01

    咖啡叶锈病是咖啡一种毁灭性病害.利用GRAMENE网站提供的SSR鉴定工具SSRIT(Simple Sequence Repeat Identification Tool),对咖啡叶锈病菌8 310条无冗余的EST分别进行SSR鉴定.结果共搜查到1 292个1~6碱基SSR,出现频率最高的为三碱基重复基元类型,其次为二碱基重复基元类型与六碱基重复基元类型.分别为459、321与214个,其出现频率分别为35.5%、24.8%与16.6%.AT/AT为二核苷酸中优势重复类型,占其总数的49.8%;而ATC/ATG与AAG/CTr则为三核苷酸中优势重复类型,二者分别占三核苷酸SSR总数的23.5%与23.3%.进一步对SSR多态性进行了预测,从而筛选出长度在22 bp以上具有潜在多态性的SSR 223个.此结果对于咖啡叶锈病菌群体遗传变异、多样性和进化等研究提供了分子标记.

  19. Development of a genome-wide multiple duplex-SSR protocol and its applications for the identification of selfed progeny in switchgrass

    Directory of Open Access Journals (Sweden)

    Liu Linglong

    2012-10-01

    Full Text Available Abstract Background Switchgrass (Panicum virgatum is a herbaceous crop for the cellulosic biofuel feedstock development in the USA and Europe. As switchgrass is a naturally outcrossing species, accurate identification of selfed progeny is important to producing inbreds, which can be used in the production of heterotic hybrids. Development of a technically reliable, time-saving and easily used marker system is needed to quantify and characterize breeding origin of progeny plants of targeted parents. Results Genome-wide screening of 915 mapped microsatellite (simple sequence repeat, SSR markers was conducted, and 842 (92.0% produced clear and scorable bands on a pooled DNA sample of eight switchgrass varieties. A total of 166 primer pairs were selected on the basis of their relatively even distribution in switchgrass genome and PCR amplification quality on 16 tetraploid genotypes. Mean polymorphic information content value for the 166 markers was 0.810 ranging from 0.116 to 0.959. From them, a core set of 48 loci, which had been mapped on 17 linkage groups, was further tested and optimized to develop 24 sets of duplex markers. Most of (up to 87.5% targeted, but non-allelic amplicons within each duplex were separated by more than 10-bp. Using the established duplex PCR protocol, selfing ratio (i.e., selfed/all progeny x100% was identified as 0% for a randomly selected open-pollinated ‘Kanlow’ genotype grown in the field, 15.4% for 22 field-grown plants of bagged inflorescences, and 77.3% for a selected plant grown in a growth chamber. Conclusions The study developed a duplex SSR-based PCR protocol consisting of 48 markers, providing ample choices of non-tightly-linked loci in switchgrass whole genome, and representing a powerful, time-saving and easily used method for the identification of selfed progeny in switchgrass. The protocol should be a valuable tool in switchgrass breeding efforts.

  20. Construction of an interspecific genetic map based on InDel and SSR for mapping the QTLs affecting the initiation of flower primordia in pepper (Capsicum spp..

    Directory of Open Access Journals (Sweden)

    Shu Tan

    Full Text Available Re-sequencing permits the mining of genome-wide variations on a large scale and provides excellent resources for the research community. To accelerate the development and application of molecular markers and identify the QTLs affecting the flowering time-related trait in pepper, a total of 1,038 pairs of InDel and 674 SSR primers from different sources were used for genetic mapping using the F2 population (n = 154 derived from a cross between BA3 (C. annuum and YNXML (C. frutescens. Of these, a total of 224 simple PCR-based markers, including 129 InDels and 95 SSRs, were validated and integrated into a map, which was designated as the BY map. The BY map consisted of 13 linkage groups (LGs and spanned a total genetic distance of 1,249.77 cM with an average marker distance of 5.60 cM. Comparative analysis of the genetic and physical map based on the anchored markers showed that the BY map covered nearly the whole pepper genome. Based on the BY map, one major and five minor QTLs affecting the number of leaves on the primary axis (Nle were detected on chromosomes P2, P7, P10 and P11 in 2012. The major QTL on P2 was confirmed based on another subset of the same F2 population (n = 147 in 2014 with selective genotyping of markers from the BY map. With the accomplishment of pepper whole genome sequencing and annotations (release 2.0, 153 candidate genes were predicted to embed in the Nle2.2 region, of which 12 important flowering related genes were obtained. The InDel/SSR-based interspecific genetic map, QTLs and candidate genes obtained by the present study will be useful for the downstream isolation of flowering time-related gene and other genetic applications for pepper.

  1. An SSR-based linkage map of yardlong bean (Vigna unguiculata (L.) Walp. subsp. unguiculata Sesquipedalis Group) and QTL analysis of pod length.

    Science.gov (United States)

    Kongjaimun, Alisa; Kaga, Akito; Tomooka, Norihiko; Somta, Prakit; Shimizu, Takehiko; Shu, Yujian; Isemura, Takehisa; Vaughan, Duncan A; Srinives, Peerasak

    2012-02-01

    Yardlong bean (Vigna unguiculata (L.) Walp. subsp. unguiculata Sesquipedalis Group) (2n = 2x = 22) is one of the most important vegetable legumes of Asia. The objectives of this study were to develop a genetic linkage map of yardlong bean using SSR makers from related Vigna species and to identify QTLs for pod length. The map was constructed from 226 simple sequence repeat (SSR) markers from cowpea (Vigna unguiculata (L.) Walp. subsp. unguiculata Unguiculata Group), azuki bean (Vigna angularis (Willd.) Ohwi & Ohashi), and mungbean (Vigna radiata (L.) Wilczek) in a BC(1)F(1) ((JP81610 × TVnu457) × JP81610) population derived from the cross between yardlong bean accession JP81610 and wild cowpea (Vigna unguiculata subsp. unguiculata var. spontanea) accession TVnu457. The markers were clustered into 11 linkage groups (LGs) spanning 852.4 cM in total length with a mean distance between adjacent markers of 3.96 cM. All markers on LG11 showed segregation distortion towards the homozygous yardlong bean JP81610 genotype. The markers on LG11 were also distorted in the rice bean (Vigna umbellata (Thunb.) Ohwi & Ohashi) map, suggesting the presence of common segregation distortion factors in Vigna species on this LG. One major and six minor QTLs were identified for pod length variation between yardlong bean and wild cowpea. Using flanking markers, six of the seven QTLs were confirmed in an F(2) population of JP81610 × TVnu457. The molecular linkage map developed and markers linked to pod length QTLs would be potentially useful for yardlong bean and cowpea breeding.

  2. Construction of an interspecific genetic map based on InDel and SSR for mapping the QTLs affecting the initiation of flower primordia in pepper (Capsicum spp.).

    Science.gov (United States)

    Tan, Shu; Cheng, Jiao-Wen; Zhang, Li; Qin, Cheng; Nong, Ding-Guo; Li, Wei-Peng; Tang, Xin; Wu, Zhi-Ming; Hu, Kai-Lin

    2015-01-01

    Re-sequencing permits the mining of genome-wide variations on a large scale and provides excellent resources for the research community. To accelerate the development and application of molecular markers and identify the QTLs affecting the flowering time-related trait in pepper, a total of 1,038 pairs of InDel and 674 SSR primers from different sources were used for genetic mapping using the F2 population (n = 154) derived from a cross between BA3 (C. annuum) and YNXML (C. frutescens). Of these, a total of 224 simple PCR-based markers, including 129 InDels and 95 SSRs, were validated and integrated into a map, which was designated as the BY map. The BY map consisted of 13 linkage groups (LGs) and spanned a total genetic distance of 1,249.77 cM with an average marker distance of 5.60 cM. Comparative analysis of the genetic and physical map based on the anchored markers showed that the BY map covered nearly the whole pepper genome. Based on the BY map, one major and five minor QTLs affecting the number of leaves on the primary axis (Nle) were detected on chromosomes P2, P7, P10 and P11 in 2012. The major QTL on P2 was confirmed based on another subset of the same F2 population (n = 147) in 2014 with selective genotyping of markers from the BY map. With the accomplishment of pepper whole genome sequencing and annotations (release 2.0), 153 candidate genes were predicted to embed in the Nle2.2 region, of which 12 important flowering related genes were obtained. The InDel/SSR-based interspecific genetic map, QTLs and candidate genes obtained by the present study will be useful for the downstream isolation of flowering time-related gene and other genetic applications for pepper.

  3. 基于松科树种EST序列的落叶松SSR引物开发%Development of Larix leptolepis SSR Primers from EST Sequence of Pinaceae Family

    Institute of Scientific and Technical Information of China (English)

    贯春雨; 张含国; 张磊; 朱航勇; 邓继峰

    2011-01-01

    登陆NCBI的dbEST数据库搜索松科树种EST序列,应用SSRIT软件在线搜索EST-SSR,用Primer3设计EST-SSR引物.选用日本落叶松(L.leptolepis)×兴安落叶松(L.gmelinii)及其145个F1为检测植株,对所开发EST-SSR引物进行扩增,并以丙烯酰胺凝胶检测扩增产物,以获得适合落叶松的SSR引物,以期用于该家系的图谱构建及QTL定位的研究.NCBI数据库搜索松科EST序列40608条,使用SSRIT检测得到SSR位点1011个,频率为2.49%.使用primer 3设计EST-SSR引物132对.SSRs以二核苷酸重复最为常见,重复基元11种,重复数量5598个,占全部重复基元比例达到83.79%;其次为三核苷酸,重复基元40种,重复数量1067,占全部重复单元的比例为15.97%;四核苷酸为3种重复基元,重复数量16,所占比例为1.95%.经扩增检测125对EST-SSR引物在日×兴亲本及F1中获得扩增产物,占94.7%.%A search for EST sequence of Pinaceae species were made hy dhEST datahase of NCBI. SSRIT software was used to search EST-SSR online and primer3 to design EST-SSR primers. Larix leptolepis , L. gmelinii and their 145 full-sib F1 individuals were amplified by the EST-SSR primers, and then the amplified products were detected by acrylamide gel. Suitable SSR primers were selected for larch to construct genetic map and QTL mapping for the family. Through the sequence analysis of 40608 ESTs in Pinaceae deposited in NCBI. a total of 1011 SSR loci were obtained using the SSRIT software.and the frequency was 2. 49% . One hundred and thirty-two pairs of EST-SSR primers were designed by primer3. The dinucleotide repeats were most c:ommon in SSRs. and the repeated primitives were 11, accounting for 83. 79% of the total repeated primitives. and the repeat number was 5 598. The trinucleotide repeats were more common, and the repeated primitives and repeat numher were 40 and 1 067. respectively, accounting for 15. 97% of the total repeated primitives.Tetranucleotide repeats included three

  4. Detection of genome donor species of neglected tetraploid crop Vigna reflexo-pilosa (créole bean), and genetic structure of diploid species based on newly developed EST-SSR markers from azuki bean (Vigna angularis).

    Science.gov (United States)

    Chankaew, Sompong; Isemura, Takehisa; Isobe, Sachiko; Kaga, Akito; Tomooka, Norihiko; Somta, Prakit; Hirakawa, Hideki; Shirasawa, Kenta; Vaughan, Duncan A; Srinives, Peerasak

    2014-01-01

    Vigna reflexo-pilosa, which includes a neglected crop, is the only one tetraploid species in genus Vigna. The ancestral species that make up this allotetraploid species have not conclusively been identified, although previous studies suggested that a donor genome of V. reflexo-pilosa is V. trinervia. In this study, 1,429 azuki bean EST-SSR markers were developed of which 38 EST-SSR primer pairs that amplified one product in diploid species and two discrete products in tetraploid species were selected to analyze 268 accessions from eight taxa of seven Asian Vigna species including V. reflexo-pilosa var. glabra, V. reflexo-pilosa var. reflexo-pilosa, V. exilis, V. hirtella, V. minima, V. radiata var. sublobata, V. tenuicaulis and V. trinervia to identify genome donor of V. reflexo-pilosa. Since both diploid and tetraploid species were analyzed and each SSR primer pair detected two loci in the tetraploid species, we separated genomes of the tetraploid species into two different diploid types, viz. A and B. In total, 445 alleles were detected by 38 EST-SSR markers. The highest gene diversity was observed in V. hirtella. By assigning the discrete PCR products of V. reflexo-pilosa into two distinguished genomes, we were able to identify the two genome donor parents of créole bean. Phylogenetic and principal coordinate analyses suggested that V. hirtella is a species complex and may be composed of at least three distinct taxa. Both analyses also clearly demonstrated that V. trinervia and one taxon of V. hirtella are the genome donors of V. reflexo-pilosa. Gene diversity indicates that the evolution rate of EST-SSRs on genome B of créole bean might be faster than that on genome A. Species relationship among the Vigna species in relation to genetic data, morphology and geographical distribution are presented.

  5. Historical landmarks and second cruises researches AS UkSSR (NAS UKRAINE) in the tropical Atlantic and its implications for further development the oceans and seas geology in Ukraine

    OpenAIRE

    Polovka S.N.

    2014-01-01

    The article is devoted to the I-th Ukrainian SSR researchers (NAS) sea expedition (XII flight VAT «Mikhail Lomonosov») in the tropical Atlantic. Briefly describe the development of marine geology at different periods of its existence: in the days of the USSR and Ukraine. Made a historic section of the development of scientific areas and schools, geological dynasties, the development of hardware and methods, improving the methods of research in the sea, providing swimming facilities maritime e...

  6. Detection of genome donor species of neglected tetraploid crop Vigna reflexo-pilosa (creole bean, and genetic structure of diploid species based on newly developed EST-SSR markers from azuki bean (Vigna angularis.

    Directory of Open Access Journals (Sweden)

    Sompong Chankaew

    Full Text Available Vigna reflexo-pilosa, which includes a neglected crop, is the only one tetraploid species in genus Vigna. The ancestral species that make up this allotetraploid species have not conclusively been identified, although previous studies suggested that a donor genome of V. reflexo-pilosa is V. trinervia. In this study, 1,429 azuki bean EST-SSR markers were developed of which 38 EST-SSR primer pairs that amplified one product in diploid species and two discrete products in tetraploid species were selected to analyze 268 accessions from eight taxa of seven Asian Vigna species including V. reflexo-pilosa var. glabra, V. reflexo-pilosa var. reflexo-pilosa, V. exilis, V. hirtella, V. minima, V. radiata var. sublobata, V. tenuicaulis and V. trinervia to identify genome donor of V. reflexo-pilosa. Since both diploid and tetraploid species were analyzed and each SSR primer pair detected two loci in the tetraploid species, we separated genomes of the tetraploid species into two different diploid types, viz. A and B. In total, 445 alleles were detected by 38 EST-SSR markers. The highest gene diversity was observed in V. hirtella. By assigning the discrete PCR products of V. reflexo-pilosa into two distinguished genomes, we were able to identify the two genome donor parents of créole bean. Phylogenetic and principal coordinate analyses suggested that V. hirtella is a species complex and may be composed of at least three distinct taxa. Both analyses also clearly demonstrated that V. trinervia and one taxon of V. hirtella are the genome donors of V. reflexo-pilosa. Gene diversity indicates that the evolution rate of EST-SSRs on genome B of créole bean might be faster than that on genome A. Species relationship among the Vigna species in relation to genetic data, morphology and geographical distribution are presented.

  7. De novo assembly and characterization of bark transcriptome using Illumina sequencing and development of EST-SSR markers in rubber tree (Hevea brasiliensis Muell. Arg.

    Directory of Open Access Journals (Sweden)

    Li Dejun

    2012-05-01

    Full Text Available Abstract Background In rubber tree, bark is one of important agricultural and biological organs. However, the molecular mechanism involved in the bark formation and development in rubber tree remains largely unknown, which is at least partially due to lack of bark transcriptomic and genomic information. Therefore, it is necessary to carried out high-throughput transcriptome sequencing of rubber tree bark to generate enormous transcript sequences for the functional characterization and molecular marker development. Results In this study, more than 30 million sequencing reads were generated using Illumina paired-end sequencing technology. In total, 22,756 unigenes with an average length of 485 bp were obtained with de novo assembly. The similarity search indicated that 16,520 and 12,558 unigenes showed significant similarities to known proteins from NCBI non-redundant and Swissprot protein databases, respectively. Among these annotated unigenes, 6,867 and 5,559 unigenes were separately assigned to Gene Ontology (GO and Clusters of Orthologous Group (COG. When 22,756 unigenes searched against the Kyoto Encyclopedia of Genes and Genomes Pathway (KEGG database, 12,097 unigenes were assigned to 5 main categories including 123 KEGG pathways. Among the main KEGG categories, metabolism was the biggest category (9,043, 74.75%, suggesting the active metabolic processes in rubber tree bark. In addition, a total of 39,257 EST-SSRs were identified from 22,756 unigenes, and the characterizations of EST-SSRs were further analyzed in rubber tree. 110 potential marker sites were randomly selected to validate the assembly quality and develop EST-SSR markers. Among 13 Hevea germplasms, PCR success rate and polymorphism rate of 110 markers were separately 96.36% and 55.45% in this study. Conclusion By assembling and analyzing de novo transcriptome sequencing data, we reported the comprehensive functional characterization of rubber tree bark. This research

  8. Genetic relationship analysis of apple cultivars with SSR and SRAP markers%基于SSR和SRAP标记的苹果品种亲缘关系分析

    Institute of Scientific and Technical Information of China (English)

    巴巧瑞; 赵政阳; 高华; 王艳丽; 孙彪

    2011-01-01

    【目的】用SSR和SRAP分子标记技术,分析苹果(Malus domestica Borkh.)重要栽培品种的亲缘关系,为苹果杂交育种亲本及组合的选配提供参考。【方法】用亲缘关系较近的金冠和秦冠筛选SSR和SRAP多态性引物,利用SSR和SRAP分子标记技术对37个苹果栽培品种进行遗传多样性和亲缘关系分析。【结果】筛选出了用于37个苹果主栽品种亲缘关系分析的10对SSR和10对SRAP引物,其分别产生56和64条扩增带,平均多态性比率分别为61.09%和70.8%。根据SSR+SRAP分析结果,37个苹果品种被聚为6大类。【结论】所选取的引物能够有效地揭示供试苹果品种的遗传多样性,并且苹果品种分类与传统系谱基本一致。%【Objective】 The study was done in order to select the proper parents in apple breeding.【Method】 The genetic diversity and genetic relationship of 37 apple cultivars were studied with the SSR and SRAP markers.【Result】 The results showed that 56 and 64 bands were obtained by SSR and SRAP markers amplified through 10 selected primers respectively.Polymorphic percentage was 61.09% and 70.8%.【Conclusion】 Based on the SSR+SRAP results,the selected primers were effective in revealing genetic diversity of the tested varieties,and the apple cultivars could be classified into the six groups,which were similar to the traditional classification.

  9. SSR Analysis on Genetic Relationships of Xinjiang Malus Germplasm Resources%新疆苹果种质资源亲缘关系的SSR分析

    Institute of Scientific and Technical Information of China (English)

    秦伟; 刘立强; 廖康; 耿文娟; 唐芳

    2011-01-01

    [ Objective] The aim of this thesis is to analyze the genetci relationships of 21 portions of apple germplasm resources in Xinjiang to provide the important key basis for inference of source of Xinjiang Malus. [Method] SSR techniques of molecular biology were used to provide the important basis for the diduction based on which Xinjiang Malus varieties were directly domesticated from Xinjiang Wild apple varieties, through DNA extraction, purity and concentration detection, SSR amplification procedures and composition of the system, primers selection, PCR amplification and data analysis to explore the genetic relationships between Xinjiang Malus germplasm resources. [ Result] The twenty - one portions of materials were divided three groups when the genetic similarity coefficient was 0.63 . The results of clustenng germplasm resources showed the cultivars in Xinjiang M. sieversii cross - distribution, the cultivar in Xinjiang M. sieversii had the same genetic background, the high genetic similarity and closer ggnetic relationship. [ Cociclusion] Local apple varieties in Xinjiang may be domesticated directly from Malus sieversii Roem for the long - term breeding of domesticated or cultivated hybrid genetic variation .%[目的]以21份新疆苹果种质资源为实验材料,研究新疆苹果种质资源的亲缘关系,以期为新疆地方苹果品种可能是由新疆野苹果直接驯化而来的推论提供重要证据.[方法]利用分子生物学SSR技术,通过DNA的提取、纯度与浓度检测,SSR扩增反应的程序和体系组成、引物选择、PCR扩增及数据分析等,探讨新疆苹果资源间亲缘关系.[结果]若以遗传相似系数0.63为阈值,可将新疆苹果21份地方资源聚类成3组,新疆野苹果和新疆地方苹果品种交叉分布,说明新疆地方苹果品种与新疆野苹果具有相同的遗传背景,遗传相似度高,亲缘关系很近.[结论]新疆地方苹果品种可能是由新疆野苹果直接驯化而来,或是

  10. Evaluation of a novel real-time PCR test based on the ssrA gene for the identification of group B streptococci in vaginal swabs.

    LENUS (Irish Health Repository)

    Wernecke, Martina

    2009-01-01

    BACKGROUND: Despite the implementation of prevention guidelines, early-onset group B streptococci (GBS) disease remains a cause of neonatal morbidity and mortality worldwide. Strategies to identify women who are at risk of transmitting GBS to their infant and the administration of intrapartum antibiotics have greatly reduced the incidence of neonatal GBS disease. However, there is a requirement for a rapid diagnostic test for GBS that can be carried out in a labour ward setting especially for women whose GBS colonisation status is unknown at the time of delivery. We report the design and evaluation of a real-time PCR test (RiboSEQ GBS test) for the identification of GBS in vaginal swabs from pregnant women. METHODS: The qualitative real-time PCR RiboSEQ GBS test was designed based on the bacterial ssrA gene and incorporates a competitive internal standard control. The analytical sensitivity of the test was established using crude lysate extracted from serial dilutions of overnight GBS culture using the IDI Lysis kit. Specificity studies were performed using DNA prepared from a panel of GBS strains, related streptococci and other species found in the genital tract environment. The RiboSEQ GBS test was evaluated on 159 vaginal swabs from pregnant women and compared with the GeneOhm StrepB Assay and culture for the identification of GBS. RESULTS: The RiboSEQ GBS test is specific and has an analytical sensitivity of 1-10 cell equivalents. The RiboSEQ GBS test was 96.4% sensitive and 95.8% specific compared to "gold standard" culture for the identification of GBS in vaginal swabs from pregnant women. In this study, the RiboSEQ GBS test performed slightly better than the commercial BD GeneOhm StrepB Assay which gave a sensitivity of 94.6% and a specificity of 89.6% compared to culture. CONCLUSION: The RiboSEQ GBS test is a valuable method for the rapid, sensitive and specific detection of GBS in pregnant women. This study also validates the ssrA gene as a suitable and

  11. Evaluation of a novel real-time PCR test based on the ssrA gene for the identification of group B streptococci in vaginal swabs

    Directory of Open Access Journals (Sweden)

    Barry Thomas

    2009-09-01

    Full Text Available Abstract Background Despite the implementation of prevention guidelines, early-onset group B streptococci (GBS disease remains a cause of neonatal morbidity and mortality worldwide. Strategies to identify women who are at risk of transmitting GBS to their infant and the administration of intrapartum antibiotics have greatly reduced the incidence of neonatal GBS disease. However, there is a requirement for a rapid diagnostic test for GBS that can be carried out in a labour ward setting especially for women whose GBS colonisation status is unknown at the time of delivery. We report the design and evaluation of a real-time PCR test (RiboSEQ GBS test for the identification of GBS in vaginal swabs from pregnant women. Methods The qualitative real-time PCR RiboSEQ GBS test was designed based on the bacterial ssrA gene and incorporates a competitive internal standard control. The analytical sensitivity of the test was established using crude lysate extracted from serial dilutions of overnight GBS culture using the IDI Lysis kit. Specificity studies were performed using DNA prepared from a panel of GBS strains, related streptococci and other species found in the genital tract environment. The RiboSEQ GBS test was evaluated on 159 vaginal swabs from pregnant women and compared with the GeneOhm™ StrepB Assay and culture for the identification of GBS. Results The RiboSEQ GBS test is specific and has an analytical sensitivity of 1-10 cell equivalents. The RiboSEQ GBS test was 96.4% sensitive and 95.8% specific compared to "gold standard" culture for the identification of GBS in vaginal swabs from pregnant women. In this study, the RiboSEQ GBS test performed slightly better than the commercial BD GeneOhm™ StrepB Assay which gave a sensitivity of 94.6% and a specificity of 89.6% compared to culture. Conclusion The RiboSEQ GBS test is a valuable method for the rapid, sensitive and specific detection of GBS in pregnant women. This study also validates the

  12. Development of a SSR Molecular Marker for Puccinia graminis f.sp.tritici%小麦秆锈菌特异性SSR分子标记的开发

    Institute of Scientific and Technical Information of China (English)

    王曦; 刘太国; 向文胜; 陈万权

    2011-01-01

    [目的]研发简单、快速、准确的分子检测技术用于小麦秆锈菌的准确诊断和秆锈病的早期预警.[方法]采用FIASCO法构建秆锈菌基因组微卫星富集文库,分离微卫星DNA序列,设计合成小麦秆锈菌的特异性引物.[结果]根据小麦秆锈菌基因组微卫星富集文库,设计1对小麦秆锈菌特异性微卫星引物Pgtfssr1(f/r),可在来自中国不同麦区的20份小麦秆锈菌分离物基因组DNA中扩增出395 bp的特异性片段,而在小麦条锈菌、小麦叶锈菌和其它麦类病原真菌中未扩增出该特异性片段.病菌侵入寄主30 h后便可检测到特异性DNA片段的存在,灵敏度达到1 ng·μL-1模板DNA浓度水平.[结论]成功研发出小麦秆锈菌的特异性SSR分子标记,为小麦秆锈病早期诊断在生产上的应用奠定了基础.%[Objective] The objective of this study is to build a simple, quick and accurate molecular technique to detect Puccinia graminis f. Sp. Tritici and forecast this destructive disease. [Method] A microsatellite-enriched genomic library of Pgt was constructed by using the method of FIASCO. Based on the sequence of Pgt microsatellite, pairs of specific SSR primers were developed and screened. [Result] The primer Pgtfssrl (fir) generated a polymorphic pattern displaying a 395 bp DNA fragment specific for Pgt, whereas no DNA fragment was obtained in other 24 non-target wheat fungal pathogens. The existence of specific DNA fragment was detected in the infected wheat tissues at 30 h post-inoculation, and the sensitivity of this molecular marker was Pgt DNA template of 1 ng-uL'1. [Conclusion] A specific SSR marker for the detection of wheat stem rust has been successfully developed, which could be used for the early diagnosis and forecast of wheat stem rust.

  13. Genetic variation in Whitmania pigra, Hirudo nipponica and Poecilobdella manillensis, three endemic and endangered species in China using SSR and TRAP markers.

    Science.gov (United States)

    Liu, Fei; Guo, Qiao-Sheng; Shi, Hong-Zhuan; Cheng, Bo-Xing; Lu, Yu-Xi; Gou, Ling; Wang, Jia; Shen, Wen-Biao; Yan, Shi-Meng; Wu, Man-Jun

    2016-04-01

    Leeches are not only important medicinal animals worldwide but also are endangered. We aimed to (i) explore the level of genetic diversity within/among populations of three leeches, (ii) assess genetic differentiation among these three leeches, and (iii) discuss an appropriate strategy for conserving leech germplasm. A total of 315 individuals of Whitmania pigra, Hirudo nipponica and Poecilobdella manillensis from 21 populations were collected in China and Vietnam. The genetic structure and genetic diversity among and within the 21 populations were evaluated using target region amplified polymorphism (TRAP) and simple sequence repeat (SSR) markers. Sixteen pairs of TRAP primers generated a total of 398 fragments, of which 396 (99.50%) were polymorphic; fourteen pairs of SSR primers generated a total of 60 fragments, of which 59 (98.33%) were polymorphic. Shannon's index (I) and Nei's gene diversity index (H) for the three leeches were high at the species level (I=0.4980 and H=0.3323 for TRAPs, I=0.4487 and H=0.2969 for SSRs in W. pigra; I=0.4147/0.3769, H=0.2788/0.2566 for H. nipponica; and I=0.4616/0.4717, H=0.3099/0.3203 for P. manillensis). However, low genetic diversity was determined at the population level; the average genetic diversity measures within populations were H=0.1767/0.1376, I=0.2589/0.2043 for W. pigra, H=0.2149/0.2021, I=0.3184/0.3000 for H. nipponica and H=0.2850/0.2724, I=0.4152/0.3967 for P. manillensis. We conclude that there was limited gene exchange within/among populations and species, as the gene flow number (Nm) was 0.5493/0.5807. However, for all three species, the genetic diversity was different at the population level. Gene differentiation (Gst) and Nm were 0.4682 /0.5364 and 0.5678/0.4321 for W. pigra, 0.2294/0.2127 and 1.6797/1.8512 for H. nipponica and 0.1214/0.1496 and 3.6202/2.8412 for P. manillensis. STRUCTURE analysis, Unweighted Pair-Group Method with Arithmetic means (UPGMA) cluster analysis and Principal Coordinates Analysis

  14. A high-density consensus map of barley linking DArT markers to SSR, RFLP and STS loci and agricultural traits

    Directory of Open Access Journals (Sweden)

    Wang Junping

    2006-08-01

    Full Text Available Abstract Background Molecular marker technologies are undergoing a transition from largely serial assays measuring DNA fragment sizes to hybridization-based technologies with high multiplexing levels. Diversity Arrays Technology (DArT is a hybridization-based technology that is increasingly being adopted by barley researchers. There is a need to integrate the information generated by DArT with previous data produced with gel-based marker technologies. The goal of this study was to build a high-density consensus linkage map from the combined datasets of ten populations, most of which were simultaneously typed with DArT and Simple Sequence Repeat (SSR, Restriction Enzyme Fragment Polymorphism (RFLP and/or Sequence Tagged Site (STS markers. Results The consensus map, built using a combination of JoinMap 3.0 software and several purpose-built perl scripts, comprised 2,935 loci (2,085 DArT, 850 other loci and spanned 1,161 cM. It contained a total of 1,629 'bins' (unique loci, with an average inter-bin distance of 0.7 ± 1.0 cM (median = 0.3 cM. More than 98% of the map could be covered with a single DArT assay. The arrangement of loci was very similar to, and almost as optimal as, the arrangement of loci in component maps built for individual populations. The locus order of a synthetic map derived from merging the component maps without considering the segregation data was only slightly inferior. The distribution of loci along chromosomes indicated centromeric suppression of recombination in all chromosomes except 5H. DArT markers appeared to have a moderate tendency toward hypomethylated, gene-rich regions in distal chromosome areas. On the average, 14 ± 9 DArT loci were identified within 5 cM on either side of SSR, RFLP or STS loci previously identified as linked to agricultural traits. Conclusion Our barley consensus map provides a framework for transferring genetic information between different marker systems and for deploying DArT markers in

  15. Genetic analysis and molecular characterization of Chinese sesame (Sesamum indicum L.) cultivars using insertion-deletion (InDel) and simple sequence repeat (SSR) markers.

    Science.gov (United States)

    Wu, Kun; Yang, Minmin; Liu, Hongyan; Tao, Ye; Mei, Ju; Zhao, Yingzhong

    2014-03-19

    Sesame is an important and ancient oil crop in tropical and subtropical areas. China is one of the most important sesame producing countries with many germplasm accessions and excellent cultivars. Domestication and modern plant breeding have presumably narrowed the genetic basis of cultivated sesame. Several modern sesame cultivars were bred with a limited number of landrace cultivars in their pedigree. The genetic variation was subsequently reduced by genetic drift and selection. Characterization of genetic diversity of these cultivars by molecular markers is of great value to assist parental line selection and breeding strategy design. Three hundred and forty nine simple sequence repeat (SSR) and 79 insertion-deletion (InDel) markers were developed from cDNA library and reduced-representation sequencing of a sesame cultivar Zhongzhi 14, respectively. Combined with previously published SSR markers, 88 polymorphic markers were used to assess the genetic diversity, phylogenetic relationships, population structure, and allele distribution among 130 Chinese sesame accessions including 82 cultivars, 44 landraces and 4 wild germplasm accessions. A total of 325 alleles were detected, with the average gene diversity of 0.432. Model-based structure analysis revealed the presence of five subgroups belonging to two main groups, which were consistent with the results from principal coordinate analysis (PCA), phylogenetic clustering and analysis of molecular variance (AMOVA). Several missing or unique alleles were identified from particular types, subgroups or families, even though they share one or both parental/progenitor lines. This report presented a by far most comprehensive characterization of the molecular and genetic diversity of sesame cultivars in China. InDels are more polymorphic than SSRs, but their ability for deciphering genetic diversity compared to the later. Improved sesame cultivars have narrower genetic basis than landraces, reflecting the effect of genetic

  16. Tumor vasculature is regulated by FGF/FGFR signaling-mediated angiogenesis and bone marrow-derived cell recruitment: this mechanism is inhibited by SSR128129E, the first allosteric antagonist of FGFRs.

    Science.gov (United States)

    Fons, Pierre; Gueguen-Dorbes, Geneviève; Herault, Jean-Pascal; Geronimi, Fabien; Tuyaret, Joël; Frédérique, Dol; Schaeffer, Paul; Volle-Challier, Cécile; Herbert, Jean-Marc; Bono, Françoise

    2015-01-01

    Tumor angiogenesis is accompanied by vasculogenesis, which is involved in the differentiation and mobilization of human bone marrow cells. In order to further characterize the role of vasculogenesis in the tumor growth process, the effects of FGF2 on the differentiation of human bone marrow AC133(+) cells (BM-AC133(+)) into vascular precursors were studied in vitro. FGF2, like VEGFA, induced progenitor cell differentiation into cell types with endothelial cell characteristics. SSR128129E, a newly discovered specific FGFR antagonist acting by allosteric interaction with FGFR, abrogated FGF2-induced endothelial cell differentiation, showing that FGFR signaling is essential during this process. To assess the involvement of the FGF/FRGR signaling in vivo, the pre-clinical model of Lewis lung carcinoma (LL2) in mice was used. Subcutaneous injection of LL2 cells into mice induced an increase of circulating EPCs from peripheral blood associated with tumor growth and an increase of intra-tumoral vascular index. Treatment with the FGFR antagonist SSR128129E strongly decreased LL2 tumor growth as well as the intra-tumoral vascular index (41% and 50% decrease vs. vehicle-treated mice respectively, P FGFR pathway by SSR128129E reduces EPC recruitment during angiogenesis-dependent tumor growth. In this context, circulating EPCs could be a reliable surrogate marker for tumor growth and angiogenic activity.

  17. Transcriptome analysis of colored calla lily (Zantedeschia rehmannii Engl.) by Illumina sequencing: de novo assembly, annotation and EST-SSR marker development.

    Science.gov (United States)

    Wei, Zunzheng; Sun, Zhenzhen; Cui, Binbin; Zhang, Qixiang; Xiong, Min; Wang, Xian; Zhou, Di

    2016-01-01

    Colored calla lily is the short name for the species or hybrids in section Aestivae of genus Zantedeschia. It is currently one of the most popular flower plants in the world due to its beautiful flower spathe and long postharvest life. However, little genomic information and few molecular markers are available for its genetic improvement. Here, de novo transcriptome sequencing was performed to produce large transcript sequences for Z. rehmannii cv. 'Rehmannii' using an Illumina HiSeq 2000 instrument. More than 59.9 million cDNA sequence reads were obtained and assembled into 39,298 unigenes with an average length of 1,038 bp. Among these, 21,077 unigenes showed significant similarity to protein sequences in the non-redundant protein database (Nr) and in the Swiss-Prot, Gene Ontology (GO), Cluster of Orthologous Group (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Moreover, a total of 117 unique transcripts were then defined that might regulate the flower spathe development of colored calla lily. Additionally, 9,933 simple sequence repeats (SSRs) and 7,162 single nucleotide polymorphisms (SNPs) were identified as putative molecular markers. High-quality primers for 200 SSR loci were designed and selected, of which 58 amplified reproducible amplicons were polymorphic among 21 accessions of colored calla lily. The sequence information and molecular markers in the present study will provide valuable resources for genetic diversity analysis, germplasm characterization and marker-assisted selection in the genus Zantedeschia.

  18. SSR_pipeline--computer software for the identification of microsatellite sequences from paired-end Illumina high-throughput DNA sequence data

    Science.gov (United States)

    Miller, Mark P.; Knaus, Brian J.; Mullins, Thomas D.; Haig, Susan M.

    2013-01-01

    SSR_pipeline is a flexible set of programs designed to efficiently identify simple sequence repeats (SSRs; for example, microsatellites) from paired-end high-throughput Illumina DNA sequencing data. The program suite contains three analysis modules along with a fourth control module that can be used to automate analyses of large volumes of data. The modules are used to (1) identify the subset of paired-end sequences that pass quality standards, (2) align paired-end reads into a single composite DNA sequence, and (3) identify sequences that possess microsatellites conforming to user specified parameters. Each of the three separate analysis modules also can be used independently to provide greater flexibility or to work with FASTQ or FASTA files generated from other sequencing platforms (Roche 454, Ion Torrent, etc). All modules are implemented in the Python programming language and can therefore be used from nearly any computer operating system (Linux, Macintosh, Windows). The program suite relies on a compiled Python extension module to perform paired-end alignments. Instructions for compiling the extension from source code are provided in the documentation. Users who do not have Python installed on their computers or who do not have the ability to compile software also may choose to download packaged executable files. These files include all Python scripts, a copy of the compiled extension module, and a minimal installation of Python in a single binary executable. See program documentation for more information.

  19. QTL Analysis of Spike Morphological Traits and Plant Height in Winter Wheat (Triticum aestivum L. Using a High-Density SNP and SSR-Based Linkage Map

    Directory of Open Access Journals (Sweden)

    Huijie Zhai

    2016-11-01

    Full Text Available Wheat yield can be enhanced by modifying the spike morphology and the plant height. In this study, a population of 191 F9 recombinant inbred lines (RILs was developed from a cross between two winter cultivars Yumai 8679 and Jing 411. A dense genetic linkage map with 10,816 markers was constructed by incorporating single nucleotide polymorphism (SNP and simple sequence repeat (SSR marker information. Five spike morphological traits and plant height were evaluated under nine environments for the RILs and parental lines, and the number of detected environmentally stable QTLs were 18 and 3, respectively. The 1RS/1BL (rye translocation increased both spike length and spikelet number with constant spikelet compactness. The QPht.cau-2D.1 was identical to gene Rht8, which decreased spike length without modifying spikelet number. Notably, four novel QTLs locating on chromosomes 1AS (QSc.cau-1A.1, 2DS (QSc.cau-2D.1 and 7BS (QSl.cau-7B.1 and QSl.cau-7B.2 were firstly identified in this study, which provide further insights into the genetic factors that shaped the spike morphology in wheat. Moreover, SNP markers tightly linked to previously reported QTLs will eventually facilitate future studies including their positional cloning or marker-assisted selection.

  20. Development of SSR markers in oil palm (Elaeis guineensis)based on information from transcriptome sequencing%油棕转录组SSR标记开发研究

    Institute of Scientific and Technical Information of China (English)

    周丽霞; 肖勇; 杨耀东

    2014-01-01

    从NCBI网站下载40 728条油棕EST,结合文献报道的油棕果肉转录组序列信息,通过聚类拼接和处理,得到全长为32 637.947 kb的无冗余序列20 054条.在这些序列中共检索出4 538个SSR,检出率为22.6%.其中以单核苷酸重复基序为主导类型,出现频率为51.2%,二核苷酸、三核苷酸重复基序的出现频率分别为20.4%和17.9%.随机挑选了400对SSR引物进行PCR多态性检测,获得29对PCR多态性引物,并随机选取11对引物进行验证,在4种不同来源的油棕样本中表现出多态性.

  1. Detection of Distorted Segregation in Genotype of Pollen Calli Derived from Hybrid F1 of Cultivated Rice (Oryza sativa L.) Using SSR Markers

    Institute of Scientific and Technical Information of China (English)

    YAO Yan; LU Yong-gen; LIU Xiang-dong; FENG Jiu-huan; ZHANG Gui-quan

    2006-01-01

    S-a, S-b and S-c are three loci for F1 pollen sterility in cultivated rice (Oryza sativa L.). Taichung 65 (T65) is all Sj/Sj at these three loci, while its F1 pollen sterile near-isogenic lines, TISL2 (S-b), TISL4 (S-a) and TISL5 (S-c) is Si/Si according to their respective sterility locus. Using SSR molecular marker to detect the segregation of the allele Si and Sj in pollen calli population induced from different hybrid F1, which have different pollen sterility locus, showed that the segregation of allele Si and Sj was distorted. The distorted direction of pollen calli population in vitro was not the same as F2 population in vivo. The quantities of pollen callus carrying Sj were much more than that of carrying Si at S-a and S-c locus, the ratio of Si and Sj were 1:4.81 and 1:1.96 respectively. But the opposite tendency was observed at S-b locus, the ratio of Si and Sj being 1:0.35. At the same time, all these results were undisturbed by either culture medium or culture period.

  2. Assessment of Functional EST-SSR Markers (Sugarcane in Cross-Species Transferability, Genetic Diversity among Poaceae Plants, and Bulk Segregation Analysis

    Directory of Open Access Journals (Sweden)

    Shamshad Ul Haq

    2016-01-01

    Full Text Available Expressed sequence tags (ESTs are important resource for gene discovery, gene expression and its regulation, molecular marker development, and comparative genomics. We procured 10000 ESTs and analyzed 267 EST-SSRs markers through computational approach. The average density was one SSR/10.45 kb or 6.4% frequency, wherein trinucleotide repeats (66.74% were the most abundant followed by di- (26.10%, tetra- (4.67%, penta- (1.5%, and hexanucleotide (1.2% repeats. Functional annotations were done and after-effect newly developed 63 EST-SSRs were used for cross transferability, genetic diversity, and bulk segregation analysis (BSA. Out of 63 EST-SSRs, 42 markers were identified owing to their expansion genetics across 20 different plants which amplified 519 alleles at 180 loci with an average of 2.88 alleles/locus and the polymorphic information content (PIC ranged from 0.51 to 0.93 with an average of 0.83. The cross transferability ranged from 25% for wheat to 97.22% for Schlerostachya, with an average of 55.86%, and genetic relationships were established based on diversification among them. Moreover, 10 EST-SSRs were recognized as important markers between bulks of pooled DNA of sugarcane cultivars through BSA. This study highlights the employability of the markers in transferability, genetic diversity in grass species, and distinguished sugarcane bulks.

  3. Mapping of the rice (Oryza sativa L.) thermo-sensitive genic male sterile gene tms5 with EST and SSR markers

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    With the cDNA suppression subtraction hybridization method, a spikelet-specific cDNA library was constructed that expressed at meiosis stage in rice. A total of 121 cDNA fragments were selected from the library and used as EST (expressed sequence tags) markers to detect the polymorphism between Annong N, a normal fertile Indica rice line and Annong S-1, its spontaneous mutant with thermo-sensitive genic male sterility, using the RFLP (restriction fragment length polymorphism) technique. HN57, one of the EST probes, could detect polymorphism between them. The results of segregation analysis with the F2 population developed from Annong S-1 and Annong N indicate that HN57 co-seg- regates with the thermo-sensitive genic male-sterility controlled by tms5, the recessive gene in Annong S-1. This marker is located on the 31.2-cM region of the chromosome 2 of RGP (rice genome research program) genetic map. To further determine the location of tms5, 80 SSR (simple sequence repeat) markers around this region were developed, and 12 of them were polymorphic. And finally, the tms5 was mapped within region of 181 kb by using these new markers.

  4. Genetic diversity and population structure of castor (Ricinus communis L.) germplasm within the US collection assessed with EST-SSR markers.

    Science.gov (United States)

    Wang, M L; Dzievit, M; Chen, Z; Morris, J B; Norris, J E; Barkley, N A; Tonnis, B; Pederson, G A; Yu, J

    2017-03-01

    Castor is an important oilseed crop and although its oil is inedible, it has multiple industrial and pharmaceutical applications. The entire US castor germplasm collection was previously screened for oil content and fatty acid composition, but its genetic diversity and population structure has not been determined. Based on the screening results of oil content, fatty acid composition, and country origins, 574 accessions were selected and genotyped with 22 polymorphic EST-SSR markers. The results from cluster analysis, population structure, and principal component analysis were consistent, and partitioned accessions into four subpopulations. Although there were certain levels of admixtures among groups, these clusters and subpopulations aligned with geographic origins. Both divergent and redundant accessions were identified in this study. The US castor germplasm collection encompasses a moderately high level of genetic diversity (pairwise dissimilarity coefficient = 0.53). The results obtained here will be useful for choosing accessions as parents to make crosses in breeding programs and prioritizing accessions for regeneration to improve germplasm management. A subset of 230 accessions was selected and will be planted in the field for establishing a core collection of the US castor germplasm. Further evaluation of the US castor germplasm collection is also discussed.

  5. Indication of Genetic Linkage Map for Sunflower by SSR Markers%SSR分子标记丰富向日葵(Helianthus annuus L.)遗传图谱的研究

    Institute of Scientific and Technical Information of China (English)

    黄先群; Genzbitelle L.; Fabre F.; Saraffi A.

    2012-01-01

    为了提高向日葵遗传图谱的密度和实用性,以125个来源于PAC-2和RHA-266杂交的F(8)代重组自交系(RIIs)群体为材料,利用筒单序列重复(Simple sequence repeat,SSR)标记,采用MAPMARKER软件对向日英遗传图谱进行标注,并从300对SSR引物中筛选出51对多态性引物对群体进行标记.结果表明:①51对多态性引物中有19对引物无多态性或条带不清晰,32对引物表现多态性;②共检测到35个多态性位点,分布在图谱的15条连锁群上.③标记后的图谱总长度为2914.5 Cm,比原来的图谱增长7.5 Cm.④标记间平均距离由9.0 Cm缩短为8.1 Cm.%This study aimed to improve density and practicality of the genetic map of sunflower baaed on a 125 Fs RILa population derived from a cross between PAC-2 and RHA-266 by adding some SSR markers. A total of 300 pairs of SSR primers were used to screen polymorphic markers between the parents and some of their RILs, of which 51 pain of the primers showed polymorphism. The results of screening the RILs population revealed that 19 SSR primer without polymorphism or non-reading, 32 SSR pairs showed polymorphism with 35 alleles added into the map. They were distributed in the 15 linkage groups of the maps. The new map covered a total length of 2914.5 cM, 7.5 cM longer than the original map. The average distance between adjacent markers was 8.1 cM instead of original 9.0 cM.

  6. JPRS Report, Science & Technology, USSR: Life Sciences.

    Science.gov (United States)

    1987-11-12

    NAUK KAZAKHSKOY SSR: SERIYA BIOLOGICHESKAYA, No 2, Mar-Apr 87) 30 MARINE MAMMALS Duration of EEG Stages in Dolphin Cerebral Hemispheres (L.M... MARINE MAMMALS UDC 591.186+599.537 DURATION OF EEG STAGES IN DOLPHIN CEREBRAL HEMISPHERES Moscow DOKLADY AKADEMII NAUK SSSR in Russian Vol 294...cyclohexyl)-2-propyne (III), were tested for inhibitory activity against phytopathogenic bacteria and actinomycetes . The three compounds were found

  7. 应用SSR分子标记分析小麦品种(系)的遗传重组%Genetic Recombination in Wheat Using SSR Markers

    Institute of Scientific and Technical Information of China (English)

    李小军; 冯素伟; 李淦; 董娜; 陈向东; 宋杰; 茹振钢

    2013-01-01

    To understand the characteristics of inheritance and recombination of parental chromosome fragments in wheat proge-nies, we screened the genomes of 23 genotypes derived from Zhoumai 18 and Bainong AK58 with 340 SSR markers covering the whole wheat genome, together with the parents. The average recombination frequency in cultivars from single-cross was 12.3, which was smaller than that in cultivars from single backcross (13.9). Recombination mostly occurred on chromosomes 4A, 5A, 7A, 1B, 3B, 4B, 7B, 1D, 2D, 3D, 5D, 6D, and 7D. The distal and central chromosomal regions had similar frequencies of recom-bination which were 6.1, and 6.0, respectively. Some chromosomal regions were hot in recombination, such as marker intervals gwm358–wmc357 on chromosome 5D, cfd49–barc196 on chromosome 6D, wmc158–barc23 on chromosome 7A, and gwm274–gwm146 on chromosome 7B, with 35, 19, 15, and 14 recombination events, respectively. The analysis for inheritance of large linkage blocks indicated that large chromosome fragments inherited from one parent varied from 14 to 29 in each derivative, with 2–8 consecutive and informative SSR loci in a fragment. These large fragments were mainly distributed on chromosomes 4A, 5A, 5B, 5D, and 7D, which might harbor genes controlling important agronomic traits.%  为了解小麦品种形成中亲本基因组的遗传重组和遗传保留区段的分布特点,对周麦18和百农AK58及其衍生品系共23个材料进行了全基因组SSR扫描分析.遗传重组分析表明,单交组合的平均重组数(12.3)低于回交组合(13.9);染色体4A、5A、7A、1B、3B、4B、7B、1D、2D、3D、5D、6D和7D重组发生较多,其余染色体重组相对较少,染色体的中间区段与远端区段重组数相当,分别为6.1和6.0.子代间基因组比较发现,一些染色体区段成为重组的多发区,如5D的gwm358–wmc357、6D的cfd49–barc196、7A的wmc158–barc23和7B的gwm274–gwm146区段,分别有35、19

  8. 花生表型及SSR遗传多样性的研究%Phenotype and SSR-Based Genetic Diversity Assessment in Peanut

    Institute of Scientific and Technical Information of China (English)

    康红梅; 李保云; 孙毅

    2012-01-01

    The study had analyzed the Shannon-Weaver and Simpson indexes of phenotypic traits including plant type,presence or absence of hair,grain color,grain shape,leaf shape,habit of growth,flowering habit,particle size, particle color on 75 peanut cultivars(28 identified cultivars and 47 local cultivars) from Institute of Industrial Crops,Shanxi Academy of Agricultral Science. The results showed that genetic diversity index of 75 peanut cultivars were SWI =0. 924,SI =0.500 respectively,flowering habit was the lowest(SWI = 0. 139,SI =0. 014) .while Shannon-Weaver index of grain color was the highest with value of 1.841 ,and Simpson index was 0. 712. 48 pairs SSR markers of peanut were used to analyse genetic diversity of the tested materials, the results were as follows: (1) 35 pairs SSR markers(72. 9% )were polymorphic,and 215 polymorphic bands had been detected,6 polymorphic bands could be detected by each marker averagely. (2) On the basis of the results, the genetic similarity(GS) among 75 peanut cultivars were in a range from 0. 25 to 0. 85, with the mean of 0. 55 , and the average genetic similarity among the 28 identified cultivars were 0. 6 at a range of 0. 39 -0. 85.%对山西省农业科学院经济作物研究所保存的75份花生材料(包括28个已审定的花生品种和47个地方品种)进行了包括株型、茸毛的有无、叶色、粒形、叶形、生长习性、开花习性、粒大小、粒色等表型性状的Shannon-Weaver遗传多样性指数(简称SWI)和Simpson遗传多样性指数(简称SI)分析.结果表明:参试的75份花生品种遗传多样性指数分别为SWI=0.924,SI=0.500,其中以开花习性最低(SWI=0.139,SI =0.014),而Shannon-Weaver指数以粒色最高为1.841,Simpson指数为0.712.利用48对SSR引物对这些材料进行了遗传多样性分析,结果如下:(1)在48对花生的SSR引物中,有35对(占所用引物总数的72.9%)具有多态性,共检测到215条多态性条带,平均每对引物可扩增6

  9. Identification of seeds of Pinus species by Microsatellite Markers%利用微卫星标记(SSR)鉴定松属近缘种

    Institute of Scientific and Technical Information of China (English)

    洑香香; 施季森

    2005-01-01

    用从松科7个树种中开发出来的276对SSR引物,利用分群法(bulked segregate analysis, BSA)对引物在黑松组的10个近缘种进行了筛选和鉴定.结果表明:276对引物中有23对在10个松树种中获得了扩增产物,其中有5对引物在种间具有多态性,而在种内具有保守性;用单个引物、2个或多个引物组合可以把10个松树种的8个完全区分开来,但目前还没有有效的SSR引物把高山松和思茅松区分开来. 图2表1参21.%The 276 pair-primers (nuclear and chloroplast microsatellite) developed from seven species of Pinaceae were selected and identified for cross-species transferability to ten Pinus species (P. Massoniana, P. Kesiya, P. Tabulaeformis, P. Densiflora, P. Thunbergii, P. Caribaea, P. Taeda, P. Yunnanensis, P. Densata, P. Sylvestris) belonging to Sect. Pinus by BSA (bulked segregate analysis) method. The results showed that 23 of 276 (8.0%) markers were successful to have amplification product in ten species, and 5 of 23 (21.7%) were polymorphic cross species and lack of polymorphic within species. Eight of 10 Pinus species were identified by using single primer, two and more combination of primers, but there were still no effective SSR primers for identifying other 2 species (P. Kesiya and P. Densata).

  10. 豇豆产量性状与SSR分子标记的关联分析%Association Analysis between Yield Trait in Cowpea and SSR Molecular Markers

    Institute of Scientific and Technical Information of China (English)

    潘磊; 李依; 余晓露; 郭瑞; 陈禅友

    2015-01-01

    利用156对多态性豇豆[Vigna unguiculata(L.)Walp.]简单重复序列(Simple sequence repeat,SSR)引物检测83份豇豆种质材料基因组,分析群体遗传结构,并对14个豇豆产量性状与SSR标记进行全基因组关联分析.结果表明,群体遗传结构分析将83份豇豆样品划分为2个亚群.关联分析则有10个SSR标记位点与8个性状关联,主要分布在LG2、LG3、LG4、LG7、LG11连锁群上.这些关联位点在豇豆基因组上分布不均,对关联性状的表型变异解释率为9% (CLM0022)~33%(CLM0347);有1个标记(CLM0251)与多个性状关联;另外也有同一个性状与多个SSR标记关联,包括叶宽(CLM0251、CLM0850),单荚重(CLM0347、CLM0251、CLM0614).这些与豇豆性状关联的SSR标记将为豇豆分子育种和遗传改良提供依据.

  11. Analysis of Tomato Germplasm Phylogenetic Relationship Using SSR Markers%番茄种质资源亲缘关系的SSR分析

    Institute of Scientific and Technical Information of China (English)

    丘漫宇; 张素平; 郭爽; 李伯寿; 刘玉平

    2012-01-01

    25 SSR primers were used to study the genetic diversities among 20 accesions of tomato (Lycopersicon esculentum Mill.) germplasm resources detected from 66 bands. There were 52 bands which had polymorphism, and the polymorphism rate was 78.8%. The results of genetic distance analysis showed that the genetic distance of 20 tomato materials were 1.489 2-9.180 6. There were 18 tomato materials which the genetic distance was more than 7, No.1 and No.15 had the largest genetic distance. That was 9.180 6. The result of cluster analysis showed that 20 tomato germplasm resources could be classified into 4 groups.%采用25对SSR特异引物对20份番茄材料进行分析,其中21对引物扩增出条带,18对引物具有多态性,扩增出的66条谱带中有52条具有多态性,多态率为78.8%.遗传距离分析结果表明:20份番茄材料两两间的遗传距离(GD)在1.489 2 ~ 9.180 6之间,遗传距离大于7的育种材料共有18份,其中No.1与No.15之间的遗传距离最大,为9.180 6.以遗传相似系数0.67为标准可将20份番茄育种材料划分为4大类.

  12. Population Structure, Diversity and Trait Association Analysis in Rice (Oryza sativa L.) Germplasm for Early Seedling Vigor (ESV) Using Trait Linked SSR Markers.

    Science.gov (United States)

    Anandan, Annamalai; Anumalla, Mahender; Pradhan, Sharat Kumar; Ali, Jauhar

    2016-01-01

    Early seedling vigor (ESV) is the essential trait for direct seeded rice to dominate and smother the weed growth. In this regard, 629 rice genotypes were studied for their morphological and physiological responses in the field under direct seeded aerobic situation on 14th, 28th and 56th days after sowing (DAS). It was determined that the early observations taken on 14th and 28th DAS were reliable estimators to study ESV as compared to 56th DAS. Further, 96 were selected from 629 genotypes by principal component (PCA) and discriminate function analyses. The selected genotypes were subjected to decipher the pattern of genetic diversity in terms of both phenotypic and genotypic by using ESV QTL linked simple sequence repeat (SSR) markers. To assess the genetic structure, model and distance based approaches were used. Genotyping of 96 rice lines using 39 polymorphic SSRs produced a total of 128 alleles with the phenotypic information content (PIC) value of 0.24. The model based population structure approach grouped the accession into two distinct populations, whereas unrooted tree grouped the genotypes into three clusters. Both model based and structure based approach had clearly distinguished the early vigor genotypes from non-early vigor genotypes. Association analysis revealed that 16 and 10 SSRs showed significant association with ESV traits by general linear model (GLM) and mixed linear model (MLM) approaches respectively. Marker alleles on chromosome 2 were associated with shoot dry weight on 28 DAS, vigor index on 14 and 28 DAS. Improvement in the rate of seedling growth will be useful for identifying rice genotypes acquiescent to direct seeded conditions through marker-assisted selection.

  13. Gains in QTL detection using an ultra-high density SNP map based on population sequencing relative to traditional RFLP/SSR markers.

    Directory of Open Access Journals (Sweden)

    Huihui Yu

    Full Text Available Huge efforts have been invested in the last two decades to dissect the genetic bases of complex traits including yields of many crop plants, through quantitative trait locus (QTL analyses. However, almost all the studies were based on linkage maps constructed using low-throughput molecular markers, e.g. restriction fragment length polymorphisms (RFLPs and simple sequence repeats (SSRs, thus are mostly of low density and not able to provide precise and complete information about the numbers and locations of the genes or QTLs controlling the traits. In this study, we constructed an ultra-high density genetic map based on high quality single nucleotide polymorphisms (SNPs from low-coverage sequences of a recombinant inbred line (RIL population of rice, generated using new sequencing technology. The quality of the map was assessed by validating the positions of several cloned genes including GS3 and GW5/qSW5, two major QTLs for grain length and grain width respectively, and OsC1, a qualitative trait locus for pigmentation. In all the cases the loci could be precisely resolved to the bins where the genes are located, indicating high quality and accuracy of the map. The SNP map was used to perform QTL analysis for yield and three yield-component traits, number of tillers per plant, number of grains per panicle and grain weight, using data from field trials conducted over years, in comparison to QTL mapping based on RFLPs/SSRs. The SNP map detected more QTLs especially for grain weight, with precise map locations, demonstrating advantages in detecting power and resolution relative to the RFLP/SSR map. Thus this study provided an example for ultra-high density map construction using sequencing technology. Moreover, the results obtained are helpful for understanding the genetic bases of the yield traits and for fine mapping and cloning of QTLs.

  14. Analysis of the Salmonella regulatory network suggests involvement of SsrB and H-NS in σ(E)-regulated SPI-2 gene expression.

    Science.gov (United States)

    Li, Jie; Overall, Christopher C; Nakayasu, Ernesto S; Kidwai, Afshan S; Jones, Marcus B; Johnson, Rudd C; Nguyen, Nhu T; McDermott, Jason E; Ansong, Charles; Heffron, Fred; Cambronne, Eric D; Adkins, Joshua N

    2015-01-01

    The extracytoplasmic functioning sigma factor σ(E) is known to play an essential role for Salmonella enterica serovar Typhimurium to survive and proliferate in macrophages and mice. However, its regulatory network is not well-characterized, especially during infection. Here we used microarray to identify genes regulated by σ(E) in Salmonella grown in three conditions: a nutrient-rich condition and two others that mimic early and late intracellular infection. We found that in each condition σ(E) regulated different sets of genes, and notably, several global regulators. When comparing nutrient-rich and infection-like conditions, large changes were observed in the expression of genes involved in Salmonella pathogenesis island (SPI)-1 type-three secretion system (TTSS), SPI-2 TTSS, protein synthesis, and stress responses. In total, the expression of 58% of Salmonella genes was affected by σ(E) in at least one of the three conditions. An important finding is that σ(E) up-regulates SPI-2 genes, which are essential for Salmonella intracellular survival, by up-regulating SPI-2 activator ssrB expression at the early stage of infection and down-regulating SPI-2 repressor hns expression at a later stage. Moreover, σ(E) is capable of countering the silencing of H-NS, releasing the expression of SPI-2 genes. This connection between σ(E) and SPI-2 genes, combined with the global regulatory effect of σ(E), may account for the lethality of rpoE-deficient Salmonella in murine infection.

  15. Population Structure, Diversity and Trait Association Analysis in Rice (Oryza sativa L. Germplasm for Early Seedling Vigor (ESV Using Trait Linked SSR Markers.

    Directory of Open Access Journals (Sweden)

    Annamalai Anandan

    Full Text Available Early seedling vigor (ESV is the essential trait for direct seeded rice to dominate and smother the weed growth. In this regard, 629 rice genotypes were studied for their morphological and physiological responses in the field under direct seeded aerobic situation on 14th, 28th and 56th days after sowing (DAS. It was determined that the early observations taken on 14th and 28th DAS were reliable estimators to study ESV as compared to 56th DAS. Further, 96 were selected from 629 genotypes by principal component (PCA and discriminate function analyses. The selected genotypes were subjected to decipher the pattern of genetic diversity in terms of both phenotypic and genotypic by using ESV QTL linked simple sequence repeat (SSR markers. To assess the genetic structure, model and distance based approaches were used. Genotyping of 96 rice lines using 39 polymorphic SSRs produced a total of 128 alleles with the phenotypic information content (PIC value of 0.24. The model based population structure approach grouped the accession into two distinct populations, whereas unrooted tree grouped the genotypes into three clusters. Both model based and structure based approach had clearly distinguished the early vigor genotypes from non-early vigor genotypes. Association analysis revealed that 16 and 10 SSRs showed significant association with ESV traits by general linear model (GLM and mixed linear model (MLM approaches respectively. Marker alleles on chromosome 2 were associated with shoot dry weight on 28 DAS, vigor index on 14 and 28 DAS. Improvement in the rate of seedling growth will be useful for identifying rice genotypes acquiescent to direct seeded conditions through marker-assisted selection.

  16. La implementación de la política pública de salud sexual y reproductiva (SSR) en el Eje Cafetero colombiano: el caso del embarazo adolescente

    OpenAIRE

    2008-01-01

    La política nacional de salud sexual y reproductiva (SSR) definida en Colombia en 2002 por el Ministerio de la Protección Social para los años 2002 a 2006 señala los temas prioritarios en este campo: maternidad segura, planificación familiar, salud sexual y reproductiva de las y los adolescentes, cáncer de cuello uterino, infecciones de transmisión sexual y reproductiva, VIH/SIDA, y violencia doméstica y sexual. La investigación que se reporta se ha focalizado en el análisis...

  17. La implementación de la política pública de salud sexual y reproductiva (SSR) en el Eje Cafetero colombiano: el caso del embarazo adolescente

    OpenAIRE

    Sara E. del Castillo Matamoros; André Noël Roth Deubel; Clara Inés Wartski Patiño; Ricardo Rojas Higuera; Orlando Arnulfo Chacón Barliza

    2008-01-01

    La política nacional de salud sexual y reproductiva (SSR) definida en Colombia en 2002 por el Ministerio de la Protección Social para los años 2002 a 2006 señala los temas prioritarios en este campo: maternidad segura, planificación familiar, salud sexual y reproductiva de las y los adolescentes, cáncer de cuello uterino, infecciones de transmisión sexual y reproductiva, VIH/SIDA, y violencia doméstica y sexual. La investigación que se reporta se ha focalizado en el análisis...

  18. Genetic Diversity of SSR Markers in Cultivated Hordeum vulgare L. in Qinghai Province%青海省栽培青稞SSR标记遗传多样性研究

    Institute of Scientific and Technical Information of China (English)

    田海宁; 杨菁; 何桂芳

    2011-01-01

    [ Objective] The aim was to analyze genetic diversity of SSR markers in Hordeum vulgare L. in Qinghai Province and lay a foundation for screening and protecting some excellent H. vulgare cultivars. [ Method] SSR markers were used to evaluate the genetic diversity of 42 cultivated H. vulgare from Qinghai Province. [ Result ] 42 H. vulgare showed polymorphism in 7 SSR markers locus. A total of 24 alleles were identified, and the number of alleles per locus ranged from 1 to 6, with an average of 3.0. According to SSR markers polymorphism, 42 H. vulgare could be divided into 4 groups, namely Ⅰ, Ⅱ, Ⅲ and IV. [ Result] The study indicated that cultivated H. vulgare from Qinghai Province is rich in genetic diversity, which will provide reference for selecting parent of H. vulgare breeding.%[目的]分析我国青海省青稞SSR标记遗传多样性,为具有某些优异特性的青稞品种或资源筛选及青稞资源的保护奠定基础.[方法]利用SSR标记评估42份青海省栽培青稞的遗传多样性.[结果]42份青稞材料在7个SSR标记位点处表现出多态性,各位点扩增的等位基因数为1~6个,共鉴定出24个等位基因,每位点平均3.0个;根据SSR标记多态性可将42份青稞材料分为4组,即Ⅰ、Ⅱ、Ⅲ和Ⅳ.[结论]该研究表明青海省栽培青稞具有丰富的遗传多样性,可为青稞育种亲本选择提供参考.

  19. Evolution of the bomolochiform superfamily complex (Copepoda: Cyclopoida): new insights from ssrDNA and morphology, and origin of Umazuracolids from polychaete-infesting ancestors rejected.

    Science.gov (United States)

    Huys, Rony; Fatih, Farrah; Ohtsuka, Susumu; Llewellyn-Hughes, Julia

    2012-01-01

    Poecilostome cyclopoids are among the most morphologically diverse copepods, having established symbiotic relationships with teleosts, elasmobranchs and invertebrate hosts belonging to no fewer than 14 marine phyla. Many parasitic lineages display radically divergent body plans and on that basis have traditionally been placed at higher taxonomic rank than they deserve. The most recent example is the monotypic family Umazuracolidae, established for a derived fish parasite with bomolochiform affinities. Phylogenetic analysis of complete ssrDNA (18S) sequences of 44 species belonging to 21 families of cyclopoid copepods shows that there is no support for the familial distinctiveness of the Umazuracolidae. Both maximum parsimony tree reconstruction and Bayesian inference, operating under the GTR+I+Γ model of nucleotide substitution, unambiguously placed Umazuracola elongatus in the Taeniacanthidae within the predominantly fish parasitic bomolochiform complex, refuting the original suggestion of a shared most recent common ancestry with polychaete symbionts. The phylogenies also revealed that the bomolochiform families and the Clausidiidae (and allies) form a monophyletic group, the clausidiiform complex, with high nodal support under both methods. Bayesian inference suggested a diphyletic origin of the "Poecilostomatoida" with the clausidiiform family-group holding a basal position while the traditional cyclopoid families form a monophyletic group in apposition to a second poecilostomatoid clade; however, maximum parsimony results were equivocal, depending on outgroup selection. Scrutiny of the morphological characters diagnosing the monotypic families Tegobomolochidae and Tuccidae demonstrated that they merely represent derived lineages within more inclusive taxa, the former being related to a group of nostril-inhabiting genera within the Bomolochidae, the latter forming the sistergroup of Taeniacanthodes within the Taeniacanthidae. The taeniacanthid genus

  20. Levels of benzo(a)pyrene in oil shale industry wastes, some bodies of water in the Estonian S.S.R. and in water organisms.

    Science.gov (United States)

    Veldre, I A; Itra, A R; Paalme, L P

    1979-06-01

    Data on the content of benzo(a)pyrene (BP) in oil shale industry wastewater, the effectiveness of various effluent treatment processes (evaporation, extraction with butyl acetate, trickling filters, aeration tanks) in reducing the level of BP in oil shale wastewater, the level of BP in various bodies of water of Estonia, and in fish and other water organisms are reviewed. The quantitative determination of BP in concentrated diethyl ether extracts of water samples was carried out by ultraviolet and spectroluminescence procedures by use of the quasi-linear spectra at -196 degrees C in solid paraffins. It has been found that oil shale industry wastewater contains large amounts of BP. The most efficient purification process for removing the BP in oil shale industry phenol water is extraction with butyl acetate. The level of BP in the rivers of the oil shale industry area is comparatively higher than in other bodies of water of the Republic. The concentration of BP in the lakes of the Estonian S.S.R. is on the whole insignificant. Even the maximum concentration found in our lakes is as a rule less than the safety limit for BP in bodies of water (0.005 microgram/l). During water is treated at the waterworks. The effectiveness of the water treatment in reducing the level of BP varies from 11 to 88%. Filtration was found to be the most effective treatment. About 20 samples of fish from nine bodies of water in Estonia have been analyzed for content of BP. The average content of BP in the muscular tissue of various species of fish is as a rule less than 1 microgram/kg. There is no significant difference in the concentration of BP in sea and freshwater fish. There is no important difference in the content of BP in the organs of various fish. Fat fish contain more BP than lean ones. The weight (age) of fish does not influence the content of BP in the muscular tissue of fish.

  1. SSR markers in transcripts of genes linked to post-transcriptional and transcriptional regulatory functions during vegetative and reproductive development of Elaeis guineensis.

    Science.gov (United States)

    Tranbarger, Timothy John; Kluabmongkol, Wanwisa; Sangsrakru, Duangjai; Morcillo, Fabienne; Tregear, James W; Tragoonrung, Somvong; Billotte, Norbert

    2012-01-03

    The oil palm (Elaeis guineensis Jacq.) is a perennial monocotyledonous tropical crop species that is now the world's number one source of edible vegetable oil, and the richest dietary source of provitamin A. While new elite genotypes from traditional breeding programs provide steady yield increases, the long selection cycle (10-12 years) and the large areas required to cultivate oil palm make genetic improvement slow and labor intensive. Molecular breeding programs have the potential to make significant impacts on the rate of genetic improvement but the limited molecular resources, in particular the lack of molecular markers for agronomic traits of interest, restrict the application of molecular breeding schemes for oil palm. In the current study, 6,103 non-redundant ESTs derived from cDNA libraries of developing vegetative and reproductive tissues were annotated and searched for simple sequence repeats (SSRs). Primer pairs from sequences flanking 289 EST-SSRs were tested to detect polymorphisms in elite breeding parents and their crosses. 230 of these amplified PCR products, 88 of which were polymorphic within the breeding material tested. A detailed analysis and annotation of the EST-SSRs revealed the locations of the polymorphisms within the transcripts, and that the main functional category was related to transcription and post-transcriptional regulation. Indeed, SSR polymorphisms were found in sequences encoding AP2-like, bZIP, zinc finger, MADS-box, and NAC-like transcription factors in addition to other transcriptional regulatory proteins and several RNA interacting proteins. The identification of new EST-SSRs that detect polymorphisms in elite breeding material provides tools for molecular breeding strategies. The identification of SSRs within transcripts, in particular those that encode proteins involved in transcriptional and post-transcriptional regulation, will allow insight into the functional roles of these proteins by studying the phenotypic traits

  2. Screening of IR50 x Rathu Heenati F7 RILs and identification of SSR markers linked to brown planthopper (Nilaparvata lugens Stål) resistance in rice (Oryza sativa L.).

    Science.gov (United States)

    Kumari, Sanju; M Sheba, Jennifer; Marappan, Maheshwaran; Ponnuswamy, Shanmugasunderam; Seetharaman, Suresh; Pothi, Nagarajan; Subbarayalu, Mohankumar; Muthurajan, Raveendran; Natesan, Senthil

    2010-09-01

    Brown planthopper (Nilaparvata lugens Stål) is one of the major insect pests of rice. A Sri Lankan indica rice cultivar Rathu Heenati was found to be resistant to all biotypes of the brown planthopper. In the present study, a total of 268 F(7) RILs of IR50 and Rathu Heenati were phenotyped for their level of resistance against BPH by the standard seedbox screening test (SSST) in the greenhouse. A total of 53 SSR primers mapped on the chromosome 3 were used to screen the polymorphism between the parents IR50 and Rathu Heenati, out of which eleven were found to be polymorphic between IR50 and Rathu Heenati. The eleven primers that have shown polymorphism between the IR50 and Rathu Heenati parents were genotyped in a set of five resistant RILs and five susceptible RILs along with the parents for co-segregation analysis. Among the eleven primers, two primers namely RM3180 (18.22 Mb) and RM2453 (20.19 Mb) showed complete co-segregation with resistance. The identification of SSR markers linked with BPH resistant could be used for the maker assisted selection (MAS) program in rice breeding and to map the resistant genes on rice chromosomes for further gene cloning.

  3. Dva doktora nauk v odnoi lodke semeinoi / Ingrid Rüütel ; intervjueerinud Tatjana Opekina

    Index Scriptorium Estoniae

    Rüütel, Ingrid, 1935-

    2001-01-01

    Intervjuu filosoofiateaduste doktori, Eesti presidendi Arnold Rüütli abikaasa Ingrid Rüütliga, teemadeks Arnold Rüütli presidendiks valimise järgne kommentaar Mihkel Mutilt, suhted endise presidendipaariga, Ingrid Rüütli elu evakuatsioonis Venemaal, kooliaastad, elukutsevalik, väikerahva kultuur ja globaliseerumine

  4. Sieciowe usługi informacyjne dla nauk technicznych : BazTech, BazTOL

    OpenAIRE

    2007-01-01

    The paper presents the current state and plans for development of the BazTech "Polish Technical Journals Contents" database. It is created by 22 academic libraries and centers for scientific information. The project is coordinated by the Cracow University of Technology. The Baz Tech database, situated at http://baztech.icm.edu.pl (ICM UW server), within the framework of the project "Virtual Scientific Library" lists over 400 journals. The paper also describes the assumptions for the creation ...

  5. ORAL ISSUE OF THE JOURNAL "USPEKHI FIZICHESKIKH NAUK": Intense shock waves and extreme states of matter

    Science.gov (United States)

    Fortov, Vladimir E.

    2007-04-01

    The physical properties of hot dense matter over a broad domain of the phase diagram are of immediate interest in astrophysics, planetary physics, power engineering, controlled thermonuclear fusion, impulse technologies, enginery, and several special applications. The use of intense shock waves in dynamic physics and high-pressure chemistry has made the exotic high-energy-density states of matter a subject of laboratory experiments and enabled advancing by many orders of magnitude along the pressure scale to range into the megabars and even gigabars. The present report reviews the latest experimental research involving shock waves in nonideal plasmas under conditions of strong collective interparticle interaction. The results of investigations into the thermodynamic, transport, and optical properties of strongly compressed hot matter, as well as into its composition and conductivity, are discussed. Experimental techniques for high energy density cumulation, the drivers of intense shock waves, and methods for the fast diagnostics of high-energy plasma are considered. Also discussed are compression-stimulated physical effects: pressure-induced ionization, plasma phase transitions, the deformation of bound states, plasma blooming ('transparentization' of plasma), etc. Suggestions for future research are put forward.

  6. ORAL ISSUE OF THE JOURNAL "USPEKHI FIZICHESKIKH NAUK": Modern radio-optical methods in quantum magnetometry

    Science.gov (United States)

    Aleksandrov, Evgenii B.; Vershovskii, Anton K.

    2009-06-01

    This paper is an extension of a part of the talk delivered under the more general title "Narrow spectral lines in fundamental metrology: state of the art, prospects, and problems"' at the session of the 90th anniversary of Physics-Uspekhi. The talk reviewed past developments and the current status of the metrology of length, frequency/time, and magnetic fields. The measurement of these quantities currently relies on the high stability of energies of standard transitions between metastable atomic states. Because of space restrictions in the journal, all metrology topics other than the title one were omitted in the present review.

  7. ORAL ISSUE OF THE JOURNAL "USPEKHI FIZICHESKIKH NAUK": Physics at the Large Hadron Collider

    Science.gov (United States)

    Dremin, Igor M.

    2009-06-01

    The goals of the physics to be studied at the Large Hadron Collider (LHC) are very impressive. Four major experimental installations are ready to compete in obtaining and analyzing the data from high-energy hadron collisions. The main hope is to answer the most intricate questions ever asked concerning the most fundamental problems of matter and its fundamental forces and space structure. The design of the LHC and its four detectors is briefly described. We then review the main facts revealed previously by experimentalists at other accelerators. The most pertinent topics and the stage-by-stage plans for LHC investigations are discussed. Further prospects for high-energy physics are outlined.

  8. ORAL ISSUE OF THE JOURNAL "USPEKHI FIZICHESKIKH NAUK": Theoretical investigations of the ferroelectric transition

    Science.gov (United States)

    Maksimov, Evgenii G.

    2009-06-01

    The paper presents a historical review of theoretical concepts regarding the nature of the ferroelectric transition in crystals with a perovskite structure. We discuss Ginzburg's phenomenological theory, including the idea of the soft phonon mode as a reason for the ferroelectric transition. The role played by the dipole-dipole interaction in softening the optical phonon mode is considered in the framework of the theory of lattice dynamics. The experimental data and theoretical results are presented that prove that the ferroelectric transition in perovskite crystals is due to the soft mode and is a displacement-type transition.

  9. ORAL ISSUE OF THE JOURNAL "USPEKHI FIZICHESKIKH NAUK": Nonlinear waves: some biomedical applications

    Science.gov (United States)

    Rudenko, Oleg V.

    2007-04-01

    The field of nonlinear physics, item No. 11 on Ginzburg's list of "the most important and interesting problems", is reviewed. An example at the intersection of applied physics, medicine, and instrument engineering is discussed to illustrate the range and scope of the field and how deep the ideas and approaches it involves are incorporated in modern natural science and engineering. Results of relevant research and development, which has attracted much recent interest and financial support, are briefly examined.

  10. ORAL ISSUE OF THE JOURNAL "USPEKHI FIZICHESKIKH NAUK": Modeling of gas discharge plasma

    Science.gov (United States)

    Smirnov, Boris M.

    2009-06-01

    The condition for the self-maintenance of a gas discharge plasma (GDP) is derived from its ionization balance expressed in the Townsend form and may be used as a definition of a gas discharge plasma in its simplest form. The simple example of a gas discharge plasma in the positive column of a cylindrical discharge tube allows demonstrating a wide variety of possible GDP regimes, revealing a contradiction between simple models used to explain gas discharge regimes and the large number of real processes responsible for the self-maintenance of GDP. The variety of GDP processes also results in a stepwise change of plasma parameters and developing some instabilities as the voltage or discharge current is varied. As a consequence, new forms and new applications of gas discharge arise as technology progresses.

  11. Phylogenetic Relationships Among Citrus and Its Relatives as Revealed by SSR Markers%用SSR标记研究柑橘属及其近缘属植物的亲缘关系

    Institute of Scientific and Technical Information of China (English)

    庞晓明; 胡春根; 邓秀新

    2003-01-01

    Phylogenetic relationships among 29 accessions belonging to Citrus,Poncirus,Fortunella,Microcitrus,Eremocitrus,Atlantia and Severinia were investigated using SSR markers.Seven SSR primers generated 114 polymorphic alleles,with an average of 16.3 alleles per primer.Cluster analysis via neighbour-joining method showed that Microcitrus was close to Citrus;Poncirus was distant from Citrus,which suggested that Poncirus could not be derived from Citrus.High frequency of the homozygous SSR locus supported the species status of Fumin trifoliate orange.Seperation of neither Papeda and Citrus nor Archicitrus and Metacitrus was well resolved.The present work confirmed citron,pummelo and mandarin as basic species of cultivated citrus since they could be placed into three distinct clusters.%用SSR标记分析了29份柑橘属及近缘属植物的亲缘关系.7对SSR引物在29个样品中扩增得到114个等位基因,平均每个位点有16.3个等位基因.计算匹配系数后用邻接法进行聚类,结果表明,澳洲指橘与柑橘属的亲缘关系很近;SSR位点的高纯合频率支持富民枳种的地位;枳与柑橘属的关系较远,枳不大可能是从柑橘属衍生而来;Swingle的亚属的划分以及田中的原生柑橘类和后生柑橘类的划分界线都不清晰;现代栽培柑橘的起源与大翼橙关系密切;柑橘属的枸橼、柚和宽皮橘都能很好地分离,支持其为现代栽培柑橘的3个基本种的观点.

  12. An expanded genetic linkage map of an intervarietal Agaricus bisporus var. bisporusxA. bisporus var. burnettii hybrid based on AFLP, SSR and CAPS markers sheds light on the recombination behaviour of the species.

    Science.gov (United States)

    Foulongne-Oriol, Marie; Spataro, Cathy; Cathalot, Vincent; Monllor, Sarah; Savoie, Jean-Michel

    2010-03-01

    A genetic linkage map for the edible basidiomycete Agaricus bisporus was constructed from 118 haploid homokaryons derived from an intervarietal A. bisporus var. bisporus x A. bisporus var. burnettii hybrid. Two hundred and thirty-one AFLP, 21 SSR, 68 CAPS markers together with the MAT, BSN, PPC1 loci and one allozyme locus (ADH) were evenly spread over 13 linkage groups corresponding to the chromosomes of A. bisporus. The map covers 1156cM, with an average marker spacing of 3.9cM and encompasses nearly the whole genome. The average number of crossovers per chromosome per individual is 0.86. Normal recombination over the entire genome occurs in the heterothallic variety, burnettii, contrary to the homothallic variety, bisporus, which showed adaptive genome-wide suppressed recombination. This first comprehensive genetic linkage map for A. bisporus provides foundations for quantitative trait analyses and breeding programme monitoring, as well as genome organisation studies.

  13. SSR marker, ISSR marker and their application to plant genetics and breeding%SSR和ISSR分子标记及其在植物遗传育种研究中的应用

    Institute of Scientific and Technical Information of China (English)

    张立荣; 徐大庆; 刘大群

    2002-01-01

    SSR(Simple Sequence Repeat)和ISSR(Inter-Simple Sequence Repeat)技术是在PCR基础上发展起来的两种DNA多态性检测技术,已开始应用于基因组研究的各个领域.概述了SSR、ISSR反应的原理、特点,总结了其在植物亲缘关系和遗传多态性研究、DNA指纹库的建立、遗传图谱的构建和基因定位及分子标记辅助育种等方面的应用,并肯定了SSR、ISSR在植物遗传育种领域的广阔应用前景.

  14. Mining and transferability analysis of EST-SSR primers in Kiwifruit (Actinidia spp.)%猕猴桃EST-SSR引物筛选及通用性分析

    Institute of Scientific and Technical Information of China (English)

    廖娇; 黄春辉; 辜青青; 曲雪艳; 徐小彪

    2011-01-01

    ESTs of Actinidia in the NCBI database were downloaded and screened by SSRHunter software, the EST-SSR primers were designed by Primer 5.0, and their transferabilities were analyzed in some Citrus plants. The 97 EST-SSR primers which were deigned were mined by using genomic DNA of Actinidia lijiangensis. The results indicated that the 77 pairs of primer showed amplification, accounting for 79.38%. Twenty pairs of primer selected were detected to PCR for DNAs from 10 A ctinidia varieties, the 17 primer pairs of the 20 showed amplification and polymorphism, accounting for 85%. The transferability of 20 pairs of EST-SSR primers which were randomly selected was explored in 9 Citrus germplasms (Okit-su, Kumquat, Trifoliate Orange, Ponkan, Sour Pummelo, Sweet Orange, Huyou, Owari, Miyagawa). The results showed that the 11 primer pairs of the 20 tested primers had the amplification, accounting for 55%. And the 8 primer pairs showed polymorphism, accounting for 72.7%. The results revealed that the EST-SSR markers in A ctinidia were transferable in some Citrus germplasms.%应用SSRHunter软件对NCBI公共数据库中的猕猴桃EST序列进行筛查,利用Primer5.0软件设计引物并进行筛选,同时对其在部分柑橘类植物的通用性进行分析。以漓江猕猴桃DNA为模板,对所设计的97对EST-SSR引物进行筛选,结果表明其中77对引物能扩增出清晰条带,有效扩增率为79-38%。随机选取20对引物对10份猕猴桃资源进行检测,结果发现有17对引物对所有材料都有扩增产物并呈现出多态性,多态性扩增率为85%。随机应用20对有效EST-SSR引物对兴津、金柑、枳壳、桠柑、酸柚、甜橙、胡柚、尾张、宫川等柑橘类植物基因组DNA进行扩增,结果表明,其中有11对引物在供试材料中有扩增产物,占引物总数的55%:有8对引物的扩增产物具有多态性,扩增率为72.7%。据此,基于猕猴桃EST序列而筛选的SSR

  15. Screening for SSR markers linked to wheat powdery mildew resistance gene Pm2%小麦抗白粉病基因Pm2的SSR标记筛选

    Institute of Scientific and Technical Information of China (English)

    王黎明; 朱玉丽; 李兴锋; 王洪刚

    2011-01-01

    为筛选与小麦抗白粉病基因Pm2紧密连锁的分子标记,将感病品种Chancellor与Pm2的近等基因系杂交,获得F1、F2分离群体,采用分离群体分组法对Pm2进行了微卫星(microsatellite,又称simple sequence repeats,SSR)标记分析.结果表明,定位于小麦5D染色体上的71对SSR引物中有12对引物能在Pm2的近等基因系、Chancellor间稳定地揭示出多态性差异,7对引物Xcfd189、Xcfd29、Xcfd8、Xcfd102、Xcfd7、Xcfd57和Xgwm190分别能在抗病、感病池间和F2分离群体的抗病、感病单株间稳定地扩增出特异性产物.7对引物所扩增的特异谱带分别为:Xcfd189360、Xcfd29190、Xcfd8160、Xcfd102250、Xcfd7200、Xcfd57245和Xgwm190210,它们与Pm2基因间的遗传距离分别为0、1.5、2.3、5.4、10.2、31.5和54.3 cM,其中标记Xcfd189360与Pm2共分离,标记Xcfd29190、Xcfd8160和Xcfd102250与Pm2紧密连锁,可用于Pm2的标记辅助选择.%To detect molecular markers linked to wheat powdery mildew resistance gene Pni2, microsatel-lite (simple sequence repeats, SSR) markers and bulked segregant analysis (BSA) method were used in the F2 segregation population derived from the F, of between common wheat susceptible cultivar Chancellor and Pm2 near-isogonics line ( NIL). The polymorphisms were revealed by 12 from 71 pairs SSR primers originally assigned to chromosome 5D of wheat between NIL of Pm2 and Chancellor. The polymorphic bands were found by 7 of these 12 SSR primers between the resistant and susceptible DNA pools, and the resistant and susceptible plants of the F2 population, respectively. These specific DNA bands were designated as Xcfd 189360, Xcfd29190, Xcfd8160, XcfdlO22JO, Xcfd, Xcfd57245 and Xgwml90210, respectively. The genetic distance between these marks and Pm2 was 0, 1.5, 2. 3, 5.4, 10. 2, 31.5 and 54. 3 cM, respectively. On the genetic linkage map of Pm2, Xcfdl89360 was shown to co-segregate with the Pm2 gene, and markers Xcfd29190, Xcfd8l60 and Xcfdl02j50

  16. 采用SSR和RAPD标记研究黄瓜属(葫芦科)的系统发育关系%Phylogenetic relationships in Cucumis (Cucurbitaceae) revealed by SSR and RAPD analyses

    Institute of Scientific and Technical Information of China (English)

    陈劲枫; 庄飞云; 逯明辉; 钱春桃; 任刚

    2003-01-01

    野黄瓜Cucumis hystrix (2n=24)是在亚洲发现的第一个染色体基数为12的黄瓜属物种.这一发现对现行的以染色体基数和地理分布为基础的黄瓜属分类系统提出了质疑.采用SSR和RAPD两种分子标记对黄瓜属22份不同类型材料的亲缘关系进行了研究.结果表明,野黄瓜C. hystrix与黄瓜C. sativus var. sativus(2n=14)间的遗传距离(SSR: 0.59, RAPD: 0.57)小于其与甜瓜C. melo var. melo(2n=24)间的距离(SSR: 0.87, RAPD: 0.70).SSR计算的各物种间遗传距离值高于RAPD的结果,线性方程为y=0.859x+0.141,但两者相关性较好,r=0.94.综合109个SSR位点和398个RAPD条带对22份材料进行聚类分析,共分为两群:CS群(黄瓜、西南野黄瓜C. sativus var. hardwickii、C. hytivus及野黄瓜C. hystrix)和CM群(甜瓜、菜瓜C. melo var. conomon、野生小甜瓜C. melo ssp. agrestis及非洲角黄瓜C. metuliferus).

  17. 抗丝黑穗病玉米种质资源的SSR标记遗传多样性分析%Genetic Diversity Analysis of Maize Germplasm Resources against Sporosporium Reilianum with SSR Markers

    Institute of Scientific and Technical Information of China (English)

    王艳梅; 田歌; 王陆军; 王燕; 李欣; 赵明

    2011-01-01

    采用SSR标记方法研究了40份对丝黑穗病有不同抗性玉米自交系的遗传多样性.选用57对SSR扩增稳定的引物,将自交系划分为唐四平头,旅大红骨,Lancaster,Reid,PA,PB这6个类群,结果与系谱来源一致性很高.其中,33个抗病或中抗材料分布于6个类群中,根据杂种优势利用原理,均可用于改良类群内的感病自交系和选育抗病自交系.尤其是旅大红骨群、Lancaster群和PB群中抗病自交系较多,可以构建抗病种质群体.%Simple sequence repeats (SSR) markers were adopted in heterotic parts of 40 maize inbred lines of different resistance to head smut. By 57 SSR primers giving stable amplified profiles, 40 inbred lines are classified into 6 clusters, which are completely consistent with the heterotic groups determined by their pedigree information (I .e .Sipingtou, Luda Red Cob,PA,PB, Ried and Lancaster). Cluster analysis showed that 33 head smut-resistance com inbred lines could be classified into six distinct groups. According to the principle of heterosis utilization, resistant lines could be used to improve susceptible lines in the same group and to select new lines resistant to sporisorium reilianum. Especially in Luda Red Cob, Lancaster and PB, resistant lines were more, so resistant germplasm populations could be obtained.

  18. La implementación de la política pública de salud sexual y reproductiva (SSR en el Eje Cafetero colombiano: el caso del embarazo adolescente

    Directory of Open Access Journals (Sweden)

    Sara E. del Castillo Matamoros

    2008-05-01

    Full Text Available La política nacional de salud sexual y reproductiva (SSR definida en Colombia en 2002 por el Ministerio de la Protección Social para los años 2002 a 2006 señala los temas prioritarios en este campo: maternidad segura, planificación familiar, salud sexual y reproductiva de las y los adolescentes, cáncer de cuello uterino, infecciones de transmisión sexual y reproductiva, VIH/SIDA, y violencia doméstica y sexual. La investigación que se reporta se ha focalizado en el análisis cuantitativo y cualitativo del proceso de implementación de la política de salud sexual y reproductiva de los y las adolescentes en los tres departamentos y capitales que conforman el llamado “Eje Cafetero colombiano”. Los resultados del estudio mostraron que, si bien se mide una reducción en el número de nacimientos en adolescentes (10-19 años en la región vinculada al estudio entre 2003 y 2005, no se pudieron determinar estrategias y actividades explicativas de ello. La política ha permitido visibilizar y legitimar acciones específicas en este campo para la población adolescente. Sin embargo, se observó la existencia de importantes en las metodologías de recolección y sistematización de los datos relativos a la salud sexual y reproductiva de la población adolescente según las entidades estudiadas, así como la ausencia de retroalimentación cuantitativa utilizable para los actores de la política. En conclusión, se emiten unas recomendaciones para el ajuste de dicha política de SSR.

  19. Two-step identification of taro (Colocasia esculenta cv. Xinmaoyu) using specific psbE-petL and simple sequence repeat-sequence characterized amplified regions (SSR-SCAR) markers.

    Science.gov (United States)

    Dai, H J; Zhang, Y M; Sun, X Q; Xue, J Y; Li, M M; Cao, M X; Shen, X L; Hang, Y Y

    2016-01-01

    Colocasia esculenta cv. Xinmaoyu is an eddoe-type taro cultivar local to Taicang, Jiangsu Province, China; it is characterized by its pure flavor, glutinous texture, and high nutritional value. Due to its excellent qualities, the Trademark Office of the State Administration for Industry and Commerce of the People's Republic of China awarded Xinmaoyu, a geographical indication certification in 2014. Therefore, there is an urgent need to develop an efficient molecular marker for the specific identification of this cultivar, which would greatly facilitate the conservation and utilization of this unique germplasm resource. In the present study, amplifying the psbE-petL fragment from two dasheen-type and seven eddoe-type taro cultivars revealed three conserved insertions/deletions among sequences from the two taro types. Based on these sequence differences, a pair of site-specific primers was designed targeting the psbE-petL sequence from the dasheen-type taro, which specifically amplified a DNA band in all individuals from cultivars of this type, but not in those from the seven eddoe-type cultivars. To discriminate Xinmaoyu from the other eddoe-type taro cultivars, a pair of simple sequence repeat-sequence characterized amplified region (SSR-SCAR) primers was further developed to specifically amplify a DNA band from all Xinmaoyu individuals, but not from individuals of other eddoe-type taro cultivars. In conclusion, through a two-step-screening procedure using psbE-petL and SSR-SCAR markers, we developed a pair of primers that could specifically discriminate Xinmaoyu from nine taro cultivars commonly cultivated in Jiangsu Province and Fujian Province.

  20. Purity Identification of Jindan 999 Hybrid Maize Seed by SSR Marker%基于SSR标记的杂交玉米金单999种子的纯度检验

    Institute of Scientific and Technical Information of China (English)

    王安贵; 陈泽辉; 祝云芳; 郭向阳; 邬成; 李娟

    2011-01-01

    Two primers, Bnlg1496 and umc1222, which showed mutually supplementary bands of their parents and could identify the Jindan999's parents and hybrid clearly, stably and exactly, were screened out by SSR marker from 30 pairs of SSR primers to identify the purity of Jindan999 hybrid maize seed rapidly and exactly, effectively prevent the circulation of fake seeds on the market and enhance seed quality, and provide reference for purity identification of other hybrid maize seed. The results showed that Bnlg1496 and umc1222 could identify the purity of Jindan999 hybrid maize seed completely and its purity was 98. 12%.%为快速、准确地判断杂交玉米金单999种子的纯度,有效阻止伪劣种子在市场上的流通,提高种子市场的种子质量,同时为其他杂交玉米种子的纯度鉴定提供方法参考,利用SSR标记技术,从30对SSR引物中筛选出能够清楚、稳定、准确地鉴别出金单999的亲本及杂交种且呈现双亲互补带型的2个引物,对金单999玉米杂交种进行纯度检验.结果表明:Bnlg1496、umcl222这2对引物完全可以对杂交玉米金单999的种子进行纯度检验,并检验出金单999种子的纯度为98.12%.

  1. Cytoplasmic inheritance of somatic hybrids and development of primers for cpSSR in Citrus%柑橘体细胞胞质遗传及叶绿体SSR引物开发

    Institute of Scientific and Technical Information of China (English)

    程运江

    2011-01-01

    以38个组合的柑橘体细胞杂种(或胞质杂种)为试验材料,综合应用RFLP、CAPS和cpSSR分子标记技术,对这些杂种的线粒体和叶绿体遗传组成进行了分析;同时对试验技术体系进行了完善与拓展,开发了柑橘叶绿体SSR标记;并对柑橘愈伤组织长期继代保存过程中胞质基因组遗传变异进行了分析,主要结果如下.%In the present study,cytoplasmic inheritance of Citrus somatic hybrids and cybrids from 38 interge-neric and interspecific fusion combinations was analyzed with restriction fragment length polymorphisms (RFLPs), cleaved amplified polymorphic sequence (CAPS) and chloroplast simple sequence repeat (cpSSR) markers. The experimental procedures were modified and optimized. A novel marker, cpSSR, was developed in Citrus and other tropical fruit crops. Meanwhile,genetic variations of organelle from 23 Citrus calli were analyzed. The main results were as follows:1. A simple and efficient method for genomic DNA extraction from woody fruit crops containing high level of polysaccharides was developed. This method involves a modified CTAB or SDS procedure employing a purification step to remove polysaccharides by using water saturated ether at the presence of 1. 25-1. 30 mol/L NaCl. The quality of DNA samples extracted with this method was suitable for PCR and RFLPs analysis and for long-term storage. In addition, this procedure was successfully applied in DNA isolation from the freezed or withered or senile leaves of Citrus and more than 20 kinds of tropical and subtropical fruit crops.2. Five universal pairs of chloroplast DNA (cpDNA) primer and 3 universal pairs of mitochondrial DNA (mtDNA) primers amplified monomorphic fragments among 4 intergeneric hybrids and 3 inter-spefic fusion combinations. After digested by restriction endonuclease, polymorphic mitochondrial CAPS markers were displayed in the 4 intergeneric combinations, while polymorphic chloroplast CAPS markers were found in 3

  2. Development of SSR Markers from Citrus BAC End Sequences and Their Integration into Linkage Map%柑桔BES-SSR标记开发及连锁图延伸和加密

    Institute of Scientific and Technical Information of China (English)

    马喜军; 龚桂芝; 彭祝春; 韩学智; 洪棋斌

    2012-01-01

    Simple Sequence Repeats (SSR) were surveyed in citrus BAC-End sequence (BES) for the development of new SSR markers to extend and saturate existing genetic map. 22 403 SSRs with 1~6 bp motif were identified in 46 339 citrus BESs retrieved from NCBI. The estimated frequency of SSRs was approximately 1/1. 25 kb, nearly twice the frequency found in Citrus Expressed Sequence Tags. 323 primers were selected in the present mapping study,of which 40 were mono-nucleotide repeats, 184 di-nucleotide repeats, 99 tri-nucleotide or above repeats. Polymorphism tests showed that 316 primer-pairs (98%) could be amplified successfully and 173 pairs (55%) were polymorphic. Among the polymorphic primers, 15 pairs were of mono-nucleotide repeats, 100 pairs of di-nucleotide repeats,58 pairs of tri-nucleotide or above repeats. A new linkage map was produced by combining the segregating data of new markers and markers in the previous map. When compared with the published map, the new map integrated 334 SSR markers, 9 linkage groups and covered 844. 2 cM of citrus genome with an average genetic distance standing at 2. 53 cM. The results demonstrated that citrus BES was good for SSR marker development and the developed markers were useful in extending and saturating the citrus genetic maps. So this will provide a reference for development of other species SSR markers and lay a good foundation for citrus gene mapping,map-based cloning and marker-assisted breeding.%为了系统性地开发和拓展柑桔SSR标记,通过对公布的柑桔BAC文库末端序列(BAC-End sequence,BES)进行SSR分析,选择1500个SSR位点设计合成并检测323对引物.结果表明:(1)从总长度为28.1 Mb的46 339条序列中共检测出22403个SSR位点,约每2条序列就会出现一个SSR位点,发生频率为48%,相当于平均1.25 kb的序列中就会出现1个SSR,频率约为柑桔EST的2倍,且不同核心重复序列的SSR发生特点与EST也不同.(2)所合成的323对引物中,有效扩增316

  3. Population Structure of‘Candidatus Liberibacter asiaticus’ in China Revealed by SSR Markers%基于SSR标记的中国亚洲韧皮杆菌种群结构研究

    Institute of Scientific and Technical Information of China (English)

    黄爱军; 苏华楠; 王雪峰;