WorldWideScience

Sample records for byelorussian ssr

  1. Disability Prevention and Vocational Rehabilitation of the Disabled in the Byelorussian SSR.

    Science.gov (United States)

    Kriulin, G. A.

    1986-01-01

    Discusses measures taken by the Soviets immediately following World War II to provide medical, social, and vocational rehabilitation for disabled individuals in Byelorussia, which had a large number of deaths and serious injuries. (CH)

  2. Social representations of Russian and Byelorussians about man's roles depending on communication with psychological measurements of culture

    OpenAIRE

    Brazhnik Julia Vladimirovna; Gritsenko Valentina Vasilevna

    2012-01-01

    Given article is devoted the analysis of social representations of young men about man's roles. On sample of Russian and Byelorussians (334 persons) by means of a scale of cultural values (G.Hofstede) and the modified variant of a technique «Semantic differential» directed on studying of representations of young men about traditional man's roles (the getter, the defender, the professional figure, the head of the family, the husband, the father), social representations about man's roles depend...

  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. Analysis of SSR Using Artificial Neural Networks

    OpenAIRE

    Nagabhushana, BS; Chandrasekharaiah, HS

    1996-01-01

    Artificial neural networks (ANNs) are being advantageously applied to power system analysis problems. They possess the ability to establish complicated input-output mappings through a learning process, without any explicit programming. In this paper, an ANN based method for subsynchronous resonance (SSR) analysis is presented. The designed ANN outputs a measure of the possibility of the occurrence of SSR and is fully trained to accommodate the variations of power system parameters over the en...

  6. Clarification of SSR mitigation mechanism of TCSC; TCSC ni yoru SSR kaihi kiko no kaimei

    Energy Technology Data Exchange (ETDEWEB)

    Kakimoto, N.; Iida, A.; Seki, M.; Minoyama, K.; Takuma, T. [Kyoto University, Kyoto (Japan)

    1997-01-20

    Thyristor controlled series capacitor (TCSC) is considered to be effective not only for flow control and stabilization of power systems, but also for mitigation of subsynchronous resonance (SSR). This paper clarifies SSR mitigation mechanism of TCSC. First, we show by time simulations that SSR appears and disappears depending on the firing angle of TCSC. Next, we show that its frequency characteristics varies much with the firing angle. Further, we show that SSR occurs in TCSC-compensated systems as well as in conventional series-capacitor compensated systems when 60 Hz minus an electrical resonance frequency of a transmission system coincides with a tortional oscillation frequency of a generator-turbine shaft. TCSC can avert SSR by changing its firing angle and by shifting the electrical resonance frequency. Next, we propose an equivalent circuit of TCSC which consists of a series capacitor in parallel with a resistor and a reactor. We adjust its parameters so that it shows frequency characteristics same as TCSC. We apply it to time simulations to see if it work equivalently as TCSC. Finally, we do eigenvalue analysis with the equivalent circuit. We can get results corresponding to the time simulations. 11 refs., 10 figs., 5 tabs.

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

    Science.gov (United States)

    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. Segregation analysis of microsatellite (SSR) markers in sugarcane polyploids.

    Science.gov (United States)

    Lu, X; Zhou, H; Pan, Y-B; Chen, C Y; Zhu, J R; Chen, P H; Li, Y-R; Cai, Q; Chen, R K

    2015-01-01

    No information is available on segregation analysis of DNA markers involving both pollen and self-progeny. Therefore, we used capillary electrophoresis- and fluorescence-based DNA fingerprinting together with single pollen collection and polymerase chain reaction (PCR) to investigate simple sequence repeat (SSR) marker segregation among 964 single pollens and 288 self-progenies (S1) of sugarcane cultivar LCP 85-384. Twenty SSR DNA fragments (alleles) were amplified by five polymorphic SSR markers. Only one non-parental SSR allele was observed in 2392 PCRs. SSR allele inheritance was in accordance with Mendelian laws of segregation and independent assortment. Highly significant correlation coefficients were found between frequencies of observed and expected genotypes in pollen and S1 populations. Within the S1 population, the most frequent genotype of each SSR marker was the parental genotype of the same marker. The number of genotypes was higher in pollen than S1 population. PIC values of the five SSR markers were greater in pollen than S1 populations. Eleven of 20 SSR alleles (55%) were segregated in accordance with Mendelian segregation ratios expected from pollen and S1 populations of a 2n = 10x polyploid. Six of 20 SSR alleles were segregated in a 3:1 (presence:absence) ratio and were simplex markers. Four and one alleles were segregated in 77:4 and 143:1 ratios and considered duplex and triplex markers, respectively. Segregation ratios of remaining alleles were unexplainable. The results provide information about selection of crossing parents, estimation of seedling population optimal size, and promotion of efficient selection, which may be valuable for sugarcane breeders. PMID:26782486

  9. 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.

  10. On possibility of SSR in longitudinal power systems; Chokyori kushigata keito ni okeru SSR no kanosei ni tsuite

    Energy Technology Data Exchange (ETDEWEB)

    Kakimoto, N.; Takuma, M. [Kyoto University, Kyoto (Japan); Sugihara, H. [Chugoku Electric Power Co. Inc., Hiroshima (Japan)

    1998-04-10

    In this paper, theoretical consideration is made on possibility of subsynchronous resonance (SSR) in longitudinal power systems. Shunt capacitors are used for reactive power compensation in our country, but series capacitors are not used in general. Possibility of SSR is therefore small. However, if power transmission increases, and accordingly, if shunt compensation increases in amount, there is no guarantee that SSR never occur. First, we investigate network impedance viewed from a generator. Its resonant frequencies get lower with increase in transmission power. One of them gets subsynchronous if the power exceeds a value. In this area, there is some possibility of SSR, which is confirmed with the damping property of the generator. The admittance matrix of the load buses are singular at the resonant frequencies. The number of them is equal to the dimension of the matrix. The frequencies are common to all generators but not limited to one particular generator. One of them gets equal to 60 Hz as we increase transmission power. We regard this power as a limit for SSR. However, steady state stability limit is lower than this limit, and steady operation is not possible at the limit. Therefore, it is impossible to enter the area of SSR. Thus we obtain a conclusion that SSR does not occur in shunt compensated systems. However, this property is easily lost if some series compensation is introduced. 13 refs., 7 figs., 2 tabs.

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

    Science.gov (United States)

    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.

  12. Genetic diversity analysis of Brassica oleracea L.by SSR

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    SSR analysis on genetic diversity of 30 samples was carried out. Five primers selected from 36 primers were used to amplify 30 samples in this experiment, PCR products were separated by 6% polyacrylamide gel electrophoresis, silver staining and photographed. The results of SSR were analyzed by UPGMA clustering. The results showed that a total of 21 gene alleles were detected by 5 SSR primers. The number of alleles ranged from 2 to 5 with an average of 4.2.PIC range was 0.257-0.921, with an average of 0.543. The average coefficient of genetic similarity of SSR markers among materials was 0.432. Some of cabbage cultivars in the experiment were divided into four groups except cultivars which come from Japan.

  13. SSR mitigation with SSSC thanks to fuzzy control

    OpenAIRE

    HOSSEINI, Seyed Mohammad Hassan; SAMADZADEH, Hadi; OLAMAEI, Javad; FARSADI, Murtaza

    2012-01-01

    This paper deals with the capability of a static synchronous series compensator (SSSC) to attenuate the subsynchronous resonance (SSR). Two well-known controllers are designed, namely a conventional damping controller (CDC) and fuzzy logic damping controller (FLDC). These 2 damping controllers are added to a main control loop of a SSSC operating as a SSR damping controller. It should be noted that, to optimize the parameters of the CDC, a versatile optimization technique is implemented,...

  14. Generation and application of SSR markers in avocado

    International Nuclear Information System (INIS)

    Simple Sequence Repeat (SSR) DNA markers were generated and applied to avocado. An SSR marker is based on a pair of primers which are synthesized on the basis of DNA sequences flanking a micro satellite. These markers are PCR based, quite polymorphic and abundant in several species. These are the markers, of choice in the human genome. The number of SSR markers in the avocado genome was calculated to be about 45,000, with the A/T micro satellite being the most frequent (1 in 40 kb). SSR markers are quite expensive to generate due to the required multi-step procedure; Screening a genomic library, about 66% of the positive clones turned out after sequencing to be SSR containing clones. In only about 55% of these, was it possible to synthesize primers and, of this group, only about 50% of the markers were useful for typing a specific family. Typing of five avocado cultivars using 59 SSR markers results in one to eight alleles per locus, mean heterozygosity ranging between 0.51 and 0.66 and gene diversity ranging between 0.42 and 0.66. The SSR markers were used to estimate the genetic relationships between various Persea species. The number of alleles in these species ranged between five and twelve with heterozygosity levels between 0.11-0.78 and gene diversity between 0.69-0.89. A preliminary genetic map, based on these SSR markers together with some DNA fingerprints (DFP) and randomly amplified polymorphic DNA (RAPD) markers, was drawn. The map consists of 12 linkage group having two to five markers each. Linkage analysis with several quantitative trait loci (QTLs) was performed by genetic typing and phenotypic assessment of the progeny of a controlled cross. The results of the interval mapping suggest that the gene(s) coding for the existence of fibers in the flesh, are probably linked to linkage group 3. (author)

  15. 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

  16. FullSSR: Microsatellite Finder and Primer Designer

    Directory of Open Access Journals (Sweden)

    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. 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.

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

    OpenAIRE

    Meryem Ipek; Nihan Sahin; Ahmet Ipek; Asuman Cansev; Simon, Philipp W

    2015-01-01

    Only a limited number of simple sequence repeat (SSR) markers is available for the genome of garlic (Allium sativum L.) despite the fact that SSR markers have become one of the most preferred DNA marker systems. To develop new SSR markers for the garlic genome, garlic expressed sequence tags (ESTs) at the publicly available GarlicEST database were screened for SSR motifs and a total of 132 SSR motifs were identified. Primer pairs were designed for 50 SSR motifs and 24 of these primer pairs we...

  19. 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

    2016-01-01

    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

  20. 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

    2016-01-01

    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

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

    Directory of Open Access Journals (Sweden)

    Meryem Ipek

    2015-02-01

    Full Text Available Only a limited number of simple sequence repeat (SSR markers is available for the genome of garlic (Allium sativum L. despite the fact that SSR markers have become one of the most preferred DNA marker systems. To develop new SSR markers for the garlic genome, garlic expressed sequence tags (ESTs at the publicly available GarlicEST database were screened for SSR motifs and a total of 132 SSR motifs were identified. Primer pairs were designed for 50 SSR motifs and 24 of these primer pairs were selected as SSR markers based on their consistent amplification patterns and polymorphisms. In addition, two SSR markers were developed from the sequences of garlic cDNA-AFLP fragments. The use of 26 EST-SSR markers for the assessment of genetic relationship was tested using 31 garlic genotypes. Twenty six EST-SSR markers amplified 130 polymorphic DNA fragments and the number of polymorphic alleles per SSR marker ranged from 2 to 13 with an average of 5 alleles. Observed heterozygosity and polymorphism information content (PIC of the SSR markers were between 0.23 and 0.88, and 0.20 and 0.87, respectively. Twenty one out of the 31 garlic genotypes were analyzed in a previous study using AFLP markers and the garlic genotypes clustered together with AFLP markers were also grouped together with EST-SSR markers demonstrating high concordance between AFLP and EST-SSR marker systems and possible immediate application of EST-SSR markers for fingerprinting of garlic clones. EST-SSR markers could be used in genetic studies such as genetic mapping, association mapping, genetic diversity and comparison of the genomes of Allium species.

  2. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

  4. OXYGENATED ORGANIC COMPOUND CONCENTRATIONS NEAR A ROADWAY IN LITHUANIA, SSR

    Science.gov (United States)

    During the period June 1 to June 9, 1989, aldehyde and other oxygenated organic compound concentrations were examined at sites 3, 10, and 80 meters northeast of the Vilnius-Kaunas highway in Lithuania, SSR by collecting 120 liter (1 L/min for 120 min) samples on 2,4-dinitrophenyl...

  5. Segregation analysis of microsatellite (SSR) markers in sugarcane polyploids

    Science.gov (United States)

    Although the microsatellite (SSR) DNA markers have been extensively used in sugarcane breeding research, little is known about its inheritance mechanism. To address this problem, a high throughput molecular genotyping experiment was conducted on 964 single pollen grains and a 288-self progeny S1 map...

  6. 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...

  7. 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.

  8. 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.

  9. 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.

  10. Assessment of genetic diversity in Saccharum using SSR markers and capillary electrophoresis

    Science.gov (United States)

    This study was conducted to assess the genetic diversity amongst 12 Saccharum clones from 3 species using SSR markers and CE (capillary electrophoresis). Genomic DNA of 12 sugarcane cultivars was amplified with 19 SSR primer pairs. A total of 229 bands generated with a size range between 100 and 26...

  11. 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.

  12. 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 ...

  13. Genetic relation in Capcicum annum [L.] cultivars through microsatellite markers: SSR and ISSR

    Directory of Open Access Journals (Sweden)

    Avni S Patel, Sasidharan N., Ashish G Vala and Vinay kumar

    2011-03-01

    Full Text Available Capsicum annum [L.] is one of the most economically important vegetable crops in India. In order to assess the genetic relation,DNA from thirteen capsicum cultivars were screened using inter simple sequence repeat (ISSR and microsatellite (SSRmarkers. Five ISSR primers amplified 204 reproducible bands of which 139 were polymorphic. The percentage of polymorphicbands detected by ISSR was 100%. The highest polymorphic bands obtained by the use of primers UBC-809 (34 and UBC-66(53. A total of 1-5 alleles were detected by six SSR primers, with an average of two alleles per primer. The number of alleles perlocus ranged one (ssrCAMS-811 to five (ssrCAMS-142. The polymorphism information content (PIC values ranged from 0.27(ssrCAMS-405 to 0.67 (ssrCAMS - 142. This study reveals the great importance of guaranteeing the differentiation of chillicultivars and the application for certification purposes

  14. Development, chromosome location and genetic mapping of EST-SSR markers in wheat

    Institute of Scientific and Technical Information of China (English)

    CHEN Haimei; LI Linzhi; WEI Xianyun; LI Sishen; LEI Tiandong; HU Haizhou; WANG Honggang; ZHANG Xiansheng

    2005-01-01

    A number of 151695 wheat expression sequence tags (ESTs) that originated from GenBank/dbEST from July 14, 2003 to August 24, 2004 were used to search for simple sequence repeats (SSRs) with motif 2―5 bp, and 2038 simple sequence repeats (EST-SSRs), which accounted for 1.34% of EST database, were identified. Based on these SSR sequences, 249 EST-SSR primer pairs and 166 amplified clear bands in various wheat cultivars were designed. These EST-SSR markers can be used as new molecular markers in wheat and related species. Using Chinese Spring nulli-tetrasomic lines, 93 EST-SSR primer pairs and 193 EST-SSR loci were located on 19 wheat chromosomes except for 4A and 4B. Forty-three loci were mapped on 11 chromosomes of the genetic framework map previously constructed using recombinant inbred lines.

  15. Development and characterization of polymorphic EST-SSR and genomic SSR markers for Tibetan annual wild barley.

    Science.gov (United States)

    Zhang, Mian; Mao, Weihua; Zhang, Guoping; Wu, Feibo

    2014-01-01

    Tibetan annual wild barley is rich in genetic variation. This study was aimed at the exploitation of new SSRs for the genetic diversity and phylogenetic analysis of wild barley by data mining. We developed 49 novel EST-SSRs and confirmed 20 genomic SSRs for 80 Tibetan annual wild barley and 16 cultivated barley accessions. A total of 213 alleles were generated from 69 loci with an average of 3.14 alleles per locus. The trimeric repeats were the most abundant motifs (40.82%) among the EST-SSRs, while the majority of the genomic SSRs were di-nuleotide repeats. The polymorphic information content (PIC) ranged from 0.08 to 0.75 with a mean of 0.46. Besides this, the expected heterozygosity (He) ranged from 0.0854 to 0.7842 with an average of 0.5279. Overall, the polymorphism of genomic SSRs was higher than that of EST-SSRs. Furthermore, the number of alleles and the PIC of wild barley were both higher than that of cultivated barley, being 3.12 vs 2.59 and 0.44 vs 0.37. Indicating more polymorphism existed in the Tibetan wild barley than in cultivated barley. The 96 accessions were divided into eight subpopulations based on 69 SSR markers, and the cultivated genotypes can be clearly separated from wild barleys. A total of 47 SSR-containing EST unigenes showed significant similarities to the known genes. These EST-SSR markers have potential for application in germplasm appraisal, genetic diversity and population structure analysis, facilitating marker-assisted breeding and crop improvement in barley. PMID:24736399

  16. Development and characterization of polymorphic EST-SSR and genomic SSR markers for Tibetan annual wild barley.

    Directory of Open Access Journals (Sweden)

    Mian Zhang

    Full Text Available Tibetan annual wild barley is rich in genetic variation. This study was aimed at the exploitation of new SSRs for the genetic diversity and phylogenetic analysis of wild barley by data mining. We developed 49 novel EST-SSRs and confirmed 20 genomic SSRs for 80 Tibetan annual wild barley and 16 cultivated barley accessions. A total of 213 alleles were generated from 69 loci with an average of 3.14 alleles per locus. The trimeric repeats were the most abundant motifs (40.82% among the EST-SSRs, while the majority of the genomic SSRs were di-nuleotide repeats. The polymorphic information content (PIC ranged from 0.08 to 0.75 with a mean of 0.46. Besides this, the expected heterozygosity (He ranged from 0.0854 to 0.7842 with an average of 0.5279. Overall, the polymorphism of genomic SSRs was higher than that of EST-SSRs. Furthermore, the number of alleles and the PIC of wild barley were both higher than that of cultivated barley, being 3.12 vs 2.59 and 0.44 vs 0.37. Indicating more polymorphism existed in the Tibetan wild barley than in cultivated barley. The 96 accessions were divided into eight subpopulations based on 69 SSR markers, and the cultivated genotypes can be clearly separated from wild barleys. A total of 47 SSR-containing EST unigenes showed significant similarities to the known genes. These EST-SSR markers have potential for application in germplasm appraisal, genetic diversity and population structure analysis, facilitating marker-assisted breeding and crop improvement in barley.

  17. 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.

  18. Development of SSR Markers and Assessment of Genetic Diversity in Medicinal Chrysanthemum morifolium Cultivars

    Science.gov (United States)

    Feng, Shangguo; He, Renfeng; Lu, Jiangjie; Jiang, Mengying; Shen, Xiaoxia; Jiang, Yan; Wang, Zhi'an; Wang, Huizhong

    2016-01-01

    Chrysanthemum morifolium, is a well-known flowering plant worldwide, and has a high commercial, floricultural, and medicinal value. In this study, simple-sequence repeat (SSR) markers were generated from EST datasets and were applied to assess the genetic diversity among 32 cultivars. A total of 218 in silico SSR loci were identified from 7300 C. morifolium ESTs retrieved from GenBank. Of all SSR loci, 61.47% of them (134) were hexa-nucleotide repeats, followed by tri-nucleotide repeats (17.89%), di-nucleotide repeats (12.39%), tetra-nucleotide repeats (4.13%), and penta-nucleotide repeats (4.13%). In this study, 17 novel EST-SSR markers were verified. Along with 38 SSR markers reported previously, 55 C. morifolium SSR markers were selected for further genetic diversity analysis. PCR amplification of these EST-SSRs produced 1319 fragments, 1306 of which showed polymorphism. The average polymorphism information content of the SSR primer pairs was 0.972 (0.938–0.993), which showed high genetic diversity among C. morifolium cultivars. Based on SSR markers, 32 C. morifolium cultivars were separated into two main groups by partitioning of the clusters using the unweighted pair group method with arithmetic mean dendrogram, which was further supported by a principal coordinate analysis plot. Phylogenetic relationship among C. morifolium cultivars as revealed by SSR markers was highly consistent with the classification of medicinal C. morifolium populations according to their origin and ecological distribution. Our results demonstrated that SSR markers were highly reproducible and informative, and could be used to evaluate genetic diversity and relationships among medicinal C. morifolium cultivars. PMID:27379163

  19. 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. PMID:27504250

  20. 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..

  1. 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

  2. Development and annotation of perennial Triticeae ESTs and SSR markers.

    Science.gov (United States)

    Bushman, B Shaun; Larson, Steve R; Mott, Ivan W; Cliften, Paul F; Wang, Richard R-C; Chatterton, N Jerry; Hernandez, Alvaro G; Ali, Shahjahan; Kim, Ryan W; Thimmapuram, Jyothi; Gong, George; Liu, Lei; Mikel, Mark A

    2008-10-01

    Triticeae contains hundreds of species of both annual and perennial types. Although substantial genomic tools are available for annual Triticeae cereals such as wheat and barley, the perennial Triticeae lack sufficient genomic resources for genetic mapping or diversity research. To increase the amount of sequence information available in the perennial Triticeae, three expressed sequence tag (EST) libraries were developed and annotated for Pseudoroegneria spicata, a mixture of both Elymus wawawaiensis and E. lanceolatus, and a Leymus cinereus x L. triticoides interspecific hybrid. The ESTs were combined into unigene sets of 8 780 unigenes for P. spicata, 11 281 unigenes for Leymus, and 7 212 unigenes for Elymus. Unigenes were annotated based on putative orthology to genes from rice, wheat, barley, other Poaceae, Arabidopsis, and the non-redundant database of the NCBI. Simple sequence repeat (SSR) markers were developed, tested for amplification and polymorphism, and aligned to the rice genome. Leymus EST markers homologous to rice chromosome 2 genes were syntenous on Leymus homeologous groups 6a and 6b (previously 1b), demonstrating promise for in silico comparative mapping. All ESTs and SSR markers are available on an EST information management and annotation database (http://titan.biotec.uiuc.edu/triticeae/). PMID:18923529

  3. Outlook on radioisotope production at TRIGA SSR 14 MW reactor

    International Nuclear Information System (INIS)

    INR Pitesti, endowed with a research nuclear reactor of TRIGA SSR 14 MW type, has developed activities of radioisotope production, being at present licensed for production and selling Ir-192 sources for industrial gamma radiography and Co-60 sources (2,000 Ci) for medical uses (cobalto therapy). A collaboration was initiated with the CPR Department of IFIN-HH Bucharest, particularly after the WWR-S reactor shutdown on December 21, 1997. In the frame of this program the INR Pitesti offers services of raw material irradiations followed by the radioisotope production performed subsequently at the Radioisotope Production Department (CPR) of IFIN-HH Bucharest which also deals with selling the product on internal market . The experimental facilities with the two TRIGA reactors (TRIGA SSR 14 MW and TRIGA ACPR) of INR Pitesti are described. The maximum neutron flux is 2.9 · 1014 n/cm2s. The irradiation channels are of two neutron spectra types. Also the neutron flux is characterized by radial and axial distribution which are taken into account when a given raw material is to be irradiated, to avoid perturbing non-homogeneities in the raw material activation. Five irradiation devices are presented. Preparations are currently under way for production of fission radioisotopes Mo-99, I-131 and Xe-133 and activation radioisotope I-125 for medical application

  4. Sequence-tagged microsatellite profiling (STMP): a rapid technique for developing SSR markers

    Science.gov (United States)

    Hayden, M. J.; Sharp, P. J.

    2001-01-01

    We describe a technique, sequence-tagged microsatellite profiling (STMP), to rapidly generate large numbers of simple sequence repeat (SSR) markers from genomic or cDNA. This technique eliminates the need for library screening to identify SSR-containing clones and provides an ∼25-fold increase in sequencing throughput compared to traditional methods. STMP generates short but characteristic nucleotide sequence tags for fragments that are present within a pool of SSR amplicons. These tags are then ligated together to form concatemers for cloning and sequencing. The analysis of thousands of tags gives rise to a representational profile of the abundance and frequency of SSRs within the DNA pool, from which low copy sequences can be identified. As each tag contains sufficient nucleotide sequence for primer design, their conversion into PCR primers allows the amplification of corresponding full-length fragments from the pool of SSR amplicons. These fragments permit the full characterisation of a SSR locus and provide flanking sequence for the development of a microsatellite marker. Alternatively, sequence tag primers can be used to directly amplify corresponding SSR loci from genomic DNA, thereby reducing the cost of developing a microsatellite marker to the synthesis of just one sequence-specific primer. We demonstrate the utility of STMP by the development of SSR markers in bread wheat. PMID:11292857

  5. Sequence-tagged microsatellite profiling (STMP): a rapid technique for developing SSR markers.

    Science.gov (United States)

    Hayden, M J; Sharp, P J

    2001-04-15

    We describe a technique, sequence-tagged microsatellite profiling (STMP), to rapidly generate large numbers of simple sequence repeat (SSR) markers from genomic or cDNA. This technique eliminates the need for library screening to identify SSR-containing clones and provides an approximately 25-fold increase in sequencing throughput compared to traditional methods. STMP generates short but characteristic nucleotide sequence tags for fragments that are present within a pool of SSR amplicons. These tags are then ligated together to form concatemers for cloning and sequencing. The analysis of thousands of tags gives rise to a representational profile of the abundance and frequency of SSRs within the DNA pool, from which low copy sequences can be identified. As each tag contains sufficient nucleotide sequence for primer design, their conversion into PCR primers allows the amplification of corresponding full-length fragments from the pool of SSR amplicons. These fragments permit the full characterisation of a SSR locus and provide flanking sequence for the development of a microsatellite marker. Alternatively, sequence tag primers can be used to directly amplify corresponding SSR loci from genomic DNA, thereby reducing the cost of developing a microsatellite marker to the synthesis of just one sequence-specific primer. We demonstrate the utility of STMP by the development of SSR markers in bread wheat. PMID:11292857

  6. 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.

  7. 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.

  8. Construction of an electronic physical map of Magnaporthe oryzae using genomic position-ready SSR markers

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Magnaporthe oryzae is a model for plant pathogenic filamentous fungi. We have assembled a simple sequence repeat (SSR)-based physical map of the species, using in silico sequence data. A set of 120 SSR markers was developed from the genomic sequence of the reference isolate 70-15. These markers were readily amplified from the genomic DNA of other isolates, and high levels of allelic variation characterised the parental isolates of the two crosses tested. All the markers were locatable to one of the seven M. oryzae chromosomes. An SSR-based physical in silico map was constructed, and pre-existing SSR and RFLP loci were integrated into the map, along with 23 Avr (avirulence) genes and two other genes of importance to the plant/pathogen interaction. This map provides a platform for population genetics and functional genomics studies in the model pathogen, and even in other evolutionally related pathogens.

  9. 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.

  10. Regulation of Transcription from Two ssrS Promoters in 6S RNA Biogenesis

    Science.gov (United States)

    Lee, Ji Young; Park, Hongmarn; Bak, Geunu; Kim, Kwang-sun; Lee, Younghoon

    2013-01-01

    ssrS-encoded 6S RNA is an abundant noncoding RNA that binds σ70-RNA polymerase and regulates expression at a subset of promoters in Escherichia coli. It is transcribed from two tandem promoters, ssrS P1 and ssrS P2. Regulation of transcription from two ssrS promoters in 6S RNA biogenesis was examined. Both P1 and P2 were growth phase-dependently regulated. Depletion of 6S RNA had no effect on growth-phase-dependent transcription from either promoter, whereas overexpression of 6S RNA increased P1 transcription and decreased P2 transcription, suggesting that transcription from P1 and P2 is subject to feedback activation and feedback inhibition, respectively. This feedback regulation disappeared in Δfis strains, supporting involvement of Fis in this process. The differential feedback regulation may provide a means for maintaining appropriate cellular concentrations of 6S RNA. PMID:23864284

  11. 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.

  12. Comparison of RAMP and SSR markers for the study of wild barley genetic diversity.

    Science.gov (United States)

    Dávila, J A; Loarce, Y; Ramsay, L; Waugh, R; Ferrer, E

    1999-01-01

    Two molecular marker technologies, random amplified microsatellite polymorphism (RAMP) and simple sequence repeats (SSR), were used to determine genetic diversity of 27 accessions of the wild barley Hordeum vulgare ssp. spontaneum. 19 primer combinations were used to generate RAMP fragments and 16 SSR loci were analysed. A high level of polymorphism was found with both kind of markers as revealed by the mean polymorphism information content (PIC) values obtained: 0.838 and 0.855 for RAMP and SSR, respectively. Genetic dissimilarities between genotypes were estimated from RAMP and SSR data. A lack of correlation was found between both sets of data. This was reflected in the two dendrograms obtained which presented accessions clustered differently. The results suggest that both sets of markers reveal genetic variation induced by different mechanisms. The dendrogram produced from the RAMP dissimilarity estimates showed most of the groups related to the geographic origin of the accessions. PMID:10628292

  13. Analysis of the apple fruit acid/low-acid trait by SSR markers

    Institute of Scientific and Technical Information of China (English)

    Yuxin YAO; Heng ZHAI; Lingling ZHAO; Kai YI; Zhi LIU; Ye SONG

    2008-01-01

    It is necessary to find out the genetic character-istics of malic acid in the course of apple genomic research and breeding. In this study, the SSR marker linked to the acid/low-acid trait in apple fruit was identified from 140 SSR primer pairs, using 91 F1 population hybrids from the intra-specific cross between apple cultivar 'Dongguang' and 'Fuji' as the experimental materials. Of 140 SSR primer pairs, only primer SDY085 produced a polymorphic band linked to acid trait, and the linkage distance was 8.89 cM. Also, the titrated acid and malic acid in different developmental stages were determined. The SSR marker analysis, coupled with the change of the total acid and malic acid contents, revealed that the acid/low-acid trait was governed by a major gene and acid trait was completely dominant.

  14. 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.

  15. 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.

  16. Investigation of SSR Characteristics of Hybrid Series Compensated Power System with SSSC

    OpenAIRE

    Thirumalaivasan, R.; M. Janaki; Nagesh Prabhu

    2011-01-01

    The advent of series FACTS controllers, thyristor controlled series capacitor (TCSC) and static synchronous Series Compensator (SSSC) has made it possible not only for the fast control of power flow in a transmission line, but also for the mitigation of subsynchronous resonance (SSR) in the presence of fixed series capacitors. SSSC is an emerging controller and this paper presents SSR characteristics of a series compensated system with SSSC. The study system is adapted from IEEE first benchma...

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

    OpenAIRE

    Minqiang Hu; Chanxia Zhu; Zaijun Wu

    2012-01-01

    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 supplemen...

  18. Development and characterization of SSR markers for pomegranate (Punica granatum L.) using an enriched library

    OpenAIRE

    Hasnaoui, Nejib; Buonamici, Anna; Sebastiani, Federico; Mars, Messaoud; Trifi, Mokhtar; Vendramin, Giovanni

    2010-01-01

    In the present work, we report the development of 11 microstallite markers (SSR) for Punica granatum. Evaluated on a set of 27 pomegranate accessions sampled in Tunisia, they displayed 25 alleles, with number of alleles per locus ranging between 1 and 4, and an observed heterozygosity from 0.037 and 0.592. This set of SSR markers can be very useful for studies dealing with genetic diversity assessment of germplasm, with cultivars/varieties fingerprinting and pedigree analysis of this economic...

  19. Heat treatments effect on the EN AC-46500 alloy produced by SSR

    OpenAIRE

    Campillo Betbese, Manel; Baile Puig, Maria Teresa; Martín Fuentes, Enrique; Forn Alonso, Antonio

    2008-01-01

    This work demonstrates the possibility to apply T5 and T6 heat treatments to EN AC-46500 aluminium components conformed by Semi-Solid Rheocasting (SSR). The study of temperature and time effect in annealing, tempering and artificial aging conditions has permitted to optimize the component mechanical properties. The experimentation has been accomplished by means of hardness Brinell tests, tensile tests, optic and electronic microscopy. The mechanical properties obtained in SSR comp...

  20. Genetic diversity analysis of Valencia and Navel group sweet orange cultivars by SSR markers

    Directory of Open Access Journals (Sweden)

    İlknur POLAT

    2015-06-01

    Full Text Available Sweet orange [Citrus sinensis (L. Osbeck] fruit is one of the main citrus fruits, Navel and Valencia group sweet orange being the most representative and recognizable species of this species. The aims of this study were to determine genetic relationships and diversity of 84 Navel and 36 Valencia groups of sweet orange using SSR (simple sequence repeat molecular markers. Twenty-six SSR primers were tested on these accessions. Seven SSR primers produced thirteen polymorphic fragments, eight SSR primers produced monomorphic fragments, and eleven SSR primers produced no scorable fragments. Thirteen SSR primers produced a total of 29 fragments and 13 of them were polymorphic. The number of average polymorphic fragments per primer was 1.93. The mean polymorphism information content (PIC and marker index (MI are 0.16 and 11.74, respectively. The Dice’s similarity coefficient among Navel and Valencia group sweet oranges ranged from 0.42 to 1.00 and matrix correlation (r was 0.79. In the cluster analysis, Navel group sweet oranges were indicated as a separate group from Valencia group sweet oranges. ‘Antalya (40’ was most distinct accessions from the others.

  1. Analysis of the genetic diversity of super sweet corn inbred lines using SSR and SSAP markers.

    Science.gov (United States)

    Ko, W R; Sa, K J; Roy, N S; Choi, H-J; Lee, J K

    2016-01-01

    In this study, we compared the efficiency of simple sequence repeat (SSR) and sequence specific amplified polymorphism (SSAP) markers for analyzing genetic diversity, genetic relationships, and population structure of 87 super sweet corn inbred lines from different origins. SSR markers showed higher average gene diversity and Shannon's information index than SSAP markers. To assess genetic relationships and characterize inbred lines using SSR and SSAP markers, genetic similarity (GS) matrices were constructed. The dendrogram using SSR marker data showed a complex pattern with nine clusters and a GS of 53.0%. For SSAP markers, three clusters were observed with a GS of 50.8%. Results of combined marker data showed six clusters with 53.5% GS. To analyze the genetic population structure of SSR and SSAP marker data, the 87 inbred lines were divided into groups I, II, and admixed based on the membership probability threshold of 0.8. Using combined marker data, the population structure was K = 3 and was divided into groups I, II, III, and admixed. This study represents a comparative analysis of SSR and SSAP marker data for the study of genetic diversity and genetic relationships in super sweet corn inbred lines. Our results would be useful for maize-breeding programs in Korea. PMID:26909914

  2. Fingerprints for two grain amaranthus varieties KBGA1 and Suvarna using RAPD and legume based SSR markers

    OpenAIRE

    Meera N., Lohithaswa HC, Niranjana Murthy and Shailaja Hittalmani

    2014-01-01

    Genotype specific fingerprints were detected in two grain amaranthus varieties KBGA1 and Suvarna using SSR and RAPD markers. In this study 41 Pigeon Pea SSR markers and 6 RAPD markers were used to generate DNA fingerprints for the two varieties of grain amaranthus. Analysis of polymorphic fragments generated from SSR and RAPD markers revealed the genetic variation between grain amaranthus varieties KBGA1 and Suvarna. The results indicate that DNA markers are appropriate tools for assessing ge...

  3. An LQG based PSS design for controlling the SSR in power systems with series-compensated lines

    Energy Technology Data Exchange (ETDEWEB)

    Seo, J.C.; Kim, T.H.; Park, J.K. [Seoul National Univ. (Korea, Republic of); Moon, S.I. [Chonbuk National Univ., Chonju (Korea, Republic of)

    1996-06-01

    This paper presents a linear quadratic Gaussian (LQG) based power system stabilizer (PSS) to control the subsynchronous resonance (SSR) that may occur in a series capacitor compensated power system. This paper investigates the dominant parameters on the SSR using the critical compensation level (CCL), and selects the design parameters to confirm the stability robustness. The complete SSR simulation system based on the IEEE first benchmark is employed in this study. Eigenvalue analysis and time domain simulations using a nonlinear system model show that the proposed PSS can control the SSR efficiently.

  4. An intelligently optimized SEDC for multimodal SSR mitigation

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Donghui; Xie, Xiaorong; Liu, Shiyu; Zhang, Shuqing [State Key Laboratory of Security Control and Simulation of Power Systems and Large-scale Generation Equipments, Department of Electrical Engineering, Tsinghua University, Beijing 100084 (China)

    2009-07-15

    This paper presents an intelligently optimized multimodal supplementary excitation damping control (OMSEDC) to depress subsynchronous resonance (SSR) that may occur in series-compensated power systems. In the proposed OMSEDC, each torsional mode is controlled through an independent feedback path in order to achieve better and multimodal damping. To make OMSEDC feasible and robust, the control parameters are optimized on a number of linearized system models over a set of carefully selected operating conditions. During system modeling, the time-delay of the firing control in the thyristor-based excitation system is taken into consideration for the first time, making OMSEDC practicable in real systems. The task of simultaneously tuning for stable control parameters considering multiple torsional modes and under different system conditions is formulated into a constrained nonlinear optimization problem, which is generally difficult for traditional methods. In this paper, the genetic and simulated annealing algorithm (GASA) is adapted and implemented to obtain the optimal parameters with high efficiency. A practical series-compensated system is employed to evaluate the effectiveness of OMSEDC. Both eigenvalue analysis and nonlinear electromagnetic simulations have demonstrated a satisfactory damping performance of the controller on multiple torsional modes and in different system conditions. (author)

  5. Genetic diversity analysis of Tibetan wild barley using SSR markers.

    Science.gov (United States)

    Feng, Zong-Yun; Liu, Xian-Jun; Zhang, Yi-Zheng; Ling, Hong-Qing

    2006-10-01

    One hundred and six accessions of wild barley collected from Tibet, China, including 50 entries of the two-rowed wild barley Hordeum vulgare ssp. spontaneum (HS), 29 entries of the six-rowed wild barley Hordeum vulgare ssp. agriocrithon (HA), and 27 entries of the six-rowed wild barley Hordeum vulgare ssp. agriocrithon var. lagunculiforme (HL), were analyzed using 30 SSR markers selected from the seven barley linkage groups for studying genetic diversity and evolutionary relationship of the three subspecies of Tibetan wild barley to cultivated barley in China. Over the 30 genetic loci that were studied, 229 alleles were identified among the 106 accessions, of which 70 were common alleles. H. vulgare ssp. spontaneum possesses about thrice more private alleles (2.83 alleles/locus) than HS (0.93 alleles/locus), whereas almost no private alleles were detected in HL. The genetic diversity among-subspecies is much higher than that within-subspecies. Generally, the genetic diversity among the three subspecies is of the order HS > HL > HA. Phylogenetic analysis of the 106 accessions showed that all the accessions of HS and HA was clustered in their own groups, whereas the 27 accessions of HL were separated into two groups (14 entries with group HS and the rest with group HA). This indicated that HL was an intermediate form between HS and HA. Based on this study and previous works, we suggested that Chinese cultivated barley might evolve from HS via HL to HA. PMID:17046592

  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. 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.

  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. 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.

  10. 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.

  11. 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.

  12. Investigation of SSR Characteristics of Hybrid Series Compensated Power System with SSSC

    Directory of Open Access Journals (Sweden)

    R. Thirumalaivasan

    2011-01-01

    Full Text Available The advent of series FACTS controllers, thyristor controlled series capacitor (TCSC and static synchronous Series Compensator (SSSC has made it possible not only for the fast control of power flow in a transmission line, but also for the mitigation of subsynchronous resonance (SSR in the presence of fixed series capacitors. SSSC is an emerging controller and this paper presents SSR characteristics of a series compensated system with SSSC. The study system is adapted from IEEE first benchmark model (FBM. The active series compensation is provided by a three-level twenty four-pulse SSSC. The modeling and control details of a three level voltage source converter-(VSC-based SSSC are discussed. The SSR characteristics of the combined system with constant reactive voltage control mode in SSSC has been investigated. It is shown that the constant reactive voltage control of SSSC has the effect of reducing the electrical resonance frequency, which detunes the SSR. The analysis of SSR with SSSC is carried out based on frequency domain method, eigenvalue analysis and transient simulation. While the eigenvalue and damping torque analysis are based on linearizing the D-Q model of SSSC, the transient simulation considers both D-Q and detailed three phase nonlinear system model using switching functions.

  13. 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.

  14. 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.

  15. 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.

  16. 不同来源 SSR 和 EST-SSR 在披碱草属和鹅观草属物种中的通用性分析%The transferability of SSR and EST-SSR markers of different origins in Elymus and Roegneria in the Triticeae (Poaceae)

    Institute of Scientific and Technical Information of China (English)

    陈仕勇; 马啸; 张新全; 陈智华; 周凯

    2016-01-01

    披碱草属和鹅观草属是禾本科小麦族两个重要的多年生属,其种属界限及系统关系一直存在争议,是其种质资源利用的难点。本研究基于小麦族中不同来源的已开发的 SSR 标记,筛选出在披碱草属和鹅观草属中高通用性的 SSR 标记,为其生物系统关系研究提供重要参考。试验选用了来自小麦族小麦、大麦、披碱草属、拟鹅观草属及赖草属5个属的230个 SSR 和 EST-SSR 标记对小麦族 St、H、Y 基因组的23个物种进行了 SSR 扩增及通用性分析。结果表明,1)在筛选的230个标记中,163个(70.87%)SSR 和 EST-SSR 标记能在所有的供试物种中扩增出清晰的条带,在披碱草属和鹅观草属等物种中表现出了较高的通用性;2)在扩增出的163个 标 记 中,EST-SSR (87.60%)比基因组 SSR(49.50%)标记在种属间表现出了较高的通用性,而基因组 SSR 标记(85.98%)则比EST-SSR(79.37%)标记表现出更高的多态性;3)163个标记在供试物种中共扩增出579个清晰条带,其中多态性条带为533个,多态性比率为92.05%;每个标记扩增的条带数变化为1~11条,平均扩增条带数为3.55条;4)基于 UPGMA 聚类结果与供试物种的基因组之间表现出了较高的相关性,相同或相似基因组物种间表现出较近的亲缘关系,其中 H 基因组与 St 基因组的亲缘关系较远,H 基因组二倍体物种与其他物种也表现出了较远的亲缘关系。本研究选用的5个属的 SSR 和 EST-SSR 标记均能在披碱草属和鹅观草属物种中扩增,最后共筛选出了163个高通用性的 SSR 和 EST-SSR 分子标记,揭示了供试物种及不同基因组间的亲缘关系,为下一步披碱草属和鹅观草属的种属关系及系统学研究提供了重要参考。%Elymus and Roegneria,two important genera in the tribe Triticeae,include many

  17. 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.

  18. Mitigation of SSR and LFO with a TCSC based-conventional damping controller optimized by the PSO algorithm and a fuzzy logic controller

    OpenAIRE

    GHAHRAMANI, Hasan; LAK, Akbar; FARSADI, Murtaza; Hosseini, Hossein

    2013-01-01

    The subsynchronous resonance (SSR) phenomenon may occur when a steam turbine-generator is connected to a long transmission line with series compensation. Flexible AC transmission systems (FACTS) devices are widely applied to damp the SSR and low-frequency oscillation (LFO). A thyristor-controlled series capacitor (TCSC) is a commercially available FACTS device that was developed for damping the SSR and LFO. In this paper, 2 control methods for damping the SSR and LFO are added to ...

  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

    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

  2. Phylogenetic Relationships in Genus Arachis Based on SSR and AFLP Markers

    Institute of Scientific and Technical Information of China (English)

    TANG Rong-hua; ZHUANG Wei-jian; GAO Guo-qing; HE Liang-qiong; HAN Zhu-qiang; SHAN Shi-hua; JIANG Jing; LI Yang-rui

    2008-01-01

    Fourteen wild species of different sections in the genus Arachis and 24 accessions of the AABB allotetraploid A. hypogaea (cultivated peanut) from several countries which belong to different botanical varieties, were analyzed by SSR and AFLP marker systems. The assay-units per system needed to distinguish among all the tested accessions were at least five for SSR or two for AFLP. The genetic distance detected by the SSR markers ranged from 0.09 to 0.95, and the mean was 0.73; and the genetic distance detected by the AFLP markers ranged from 0.01 to 0.79 with an average of 0.42. All the tested peanut SSR primer pairs were multilocus ones, and the amplified fragments per SSR marker in each peanut genome ranged from 2 to 15 with the mean of 4.77. The peanut cultivars were closely related to each other, and shared a large numbers of SSR and AFLP fragments. In contrast, the species in the genus Arachis shared few fragments. The results indicated that the cultivated peanut (A. hypogaea L.) varieties could be partitioned into two main groups and four subgroups at the molecular level, and that A. duranensis is one of the wild ancestors of A. hypogaea. The lowest genetic variation was detected between A. cardenasii and A. batizocoi, and the highest was detected between A. pintoi and the species in the section Arachis. The relationships among the botanical varieties in the cultivated peanut (A. hypogaea L.) and among wild species accessions in section Arachis and those in other sections in the genus Arachis were discussed.

  3. 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. PMID:24301792

  4. 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.

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

    OpenAIRE

    Abdul Majid Ansari,* and Y. V. Singh

    2014-01-01

    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% [betw...

  6. Establishment and Optimization of SSR-PCR Reaction System of Potato%马铃薯SSR-PCR体系的优化与建立

    Institute of Scientific and Technical Information of China (English)

    李建武; 李高峰; 胡新元; 国宏; 魏子杰

    2013-01-01

    The main component which affects SSR-PCR reaction system on potato, including template DNA, dNTPs concentration, primer concentration, buffer concentration, Taq enzyme concentration and annealing temperature, were optimized in a single factor experiment, and the optimized SSR amplification reaction system was established. The results indicated that 20 µL volume SSR-PCR system containing 60 ng template DNA, 0.3125 mmol/L dNTPs, 2.4 pmol primer, 1.5 mmol/L Mg2+, and 0.5 U Taq polymerase, combined with optimal annealing temperature for each primer, performed wel , and the optimized system of SSR-PCR, which was steady and reproducible, could be applied to the study of genetic diversity of potato after PCR results were run by 2.0%agarose gel.%以马铃薯叶片DNA为模板,采用单因素试验的方法,对影响马铃薯SSR-PCR反应体系的主要成分模板DNA、dNTP浓度、引物浓度、Mg2+浓度、Taq酶浓度及退火温度进行了优化,并建立最优化的马铃薯SSR扩增反应体系。结果表明:在20μL反应体系中,模板DNA用量为60 ng,dNTP为0.3125 mmol/L,引物浓度为2.4 pmol,Mg2+为1.5 mmol/L,Taq酶为0.5 U,筛选各引物最适宜的退火温度,经2.0%琼脂糖凝胶电泳检测,扩增条带清晰,优化后的SSR反应体系稳定性好,可用于马铃薯遗传多样性分析。

  7. 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 wer

  8. 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.

  9. 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,

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

    Directory of Open Access Journals (Sweden)

    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.

  11. Development of simple sequence repeat (SSR) markers for discrimination among isolates of Fusarium proliferatum.

    Science.gov (United States)

    Moncrief, I; Garzon, C; Marek, S; Stack, J; Gamliel, A; Garrido, P; Proaño, F; Gard, M; Dehne, H; Fletcher, J

    2016-07-01

    The plant pathogen Fusarium proliferatum has a wide host range and occurs worldwide. Many isolates of the fungus produce mycotoxins in plant tissues, which, if ingested, can cause harm to animals and humans. In 2008, an outbreak of salmon blotch of onions, caused by F. proliferatum, was detected in southern Israel. The source and distribution of the fungus in Israel were unknown. Inter-simple sequence repeats (ISSR) were used to identify repetitive motifs present in seven isolates of F. proliferatum from Israel, Germany and Austria. ISSR repeat motifs were, used to develop 17 simple sequence repeat (SSR) loci. Six of these SSR markers were polymorphic in and consistently amplified from ten isolates collected in Israel, Germany, Austria and North America, from cucumber, onion, garlic, maize, and asparagus. These six polymorphic SSR alleles included 5 to 12 copies of di-, tri, and pentanucleotide motifs and yielded six to 9 alleles each. Sixteen of the SSR loci were amplified at least one of the seven Fusarium species, F. verticillioides, F. thapsinum, F. subglutinans, F. andiyazi, F. globosum, F. fujikoroi and F. oxysporum. The data demonstrate that these SSRs can be used for characterization of F. proliferatum isolates from diverse hosts and geographic locations and that they are transferable to other species of Fusarium. PMID:27021663

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

    Directory of Open Access Journals (Sweden)

    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.

  13. Genetic diversity of carrot (Daucus carota L.) cultivars revealed by analysis of SSR loci

    Science.gov (United States)

    In this work we evaluate a collection of 88 carrot cultivars and landraces for polymorphisms at SSR loci and use the obtained markers to assess the genetic diversity, and we show molecular evidence for divergence between Asiatic and Western carrot genetic pools. The use of primer pairs flanking repe...

  14. 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...

  15. A high density barley microsatellite consensus map with 775 SSR loci

    NARCIS (Netherlands)

    Varshney, R.K.; Marcel, T.C.; Ramsay, L.; Russell, J.; Roder, M.S.; Stein, N.; Waugh, R.; Langridge, P.; Niks, R.E.; Graner, A.

    2007-01-01

    A microsatellite or simple sequence repeat (SSR) consensus map of barley was constructed by joining six independent genetic maps based on the mapping populations 'Igri x Franka', 'Steptoe x Morex', 'OWBRec x OWBDom', 'Lina x Canada Park', 'L94 x Vada' and 'SusPtrit x Vada'. Segregation data for micr

  16. Mining and gene ontology based annotation of SSR markers from expressed sequence tags of Humulus lupulus.

    Science.gov (United States)

    Singh, Swati; Gupta, Sanchita; Mani, Ashutosh; Chaturvedi, Anoop

    2012-01-01

    Humulus lupulus is commonly known as hops, a member of the family moraceae. Currently many projects are underway leading to the accumulation of voluminous genomic and expressed sequence tag sequences in public databases. The genetically characterized domains in these databases are limited due to non-availability of reliable molecular markers. The large data of EST sequences are available in hops. The simple sequence repeat markers extracted from EST data are used as molecular markers for genetic characterization, in the present study. 25,495 EST sequences were examined and assembled to get full-length sequences. Maximum frequency distribution was shown by mononucleotide SSR motifs i.e. 60.44% in contig and 62.16% in singleton where as minimum frequency are observed for hexanucleotide SSR in contig (0.09%) and pentanucleotide SSR in singletons (0.12%). Maximum trinucleotide motifs code for Glutamic acid (GAA) while AT/TA were the most frequent repeat of dinucleotide SSRs. Flanking primer pairs were designed in-silico for the SSR containing sequences. Functional categorization of SSRs containing sequences was done through gene ontology terms like biological process, cellular component and molecular function.

  17. 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.

  18. Transferability and polymorphism of barley EST-SSR markers used for phylogenetic analysis in Hordeum chilense

    Directory of Open Access Journals (Sweden)

    Dorado Gabriel

    2008-09-01

    Full Text Available Abstract Background Hordeum chilense, a native South American diploid wild barley, is a potential source of useful genes for cereal breeding. The use of this wild species to increase genetic variation in cereals will be greatly facilitated by marker-assisted selection. Different economically feasible approaches have been undertaken for this wild species with limited direct agricultural use in a search for suitable and cost-effective markers. The availability of Expressed Sequence Tags (EST derived microsatellites or simple sequence repeat (SSR markers, commonly called as EST-SSRs, for barley (Hordeum vulgare represents a promising source to increase the number of genetic markers available for the H. chilense genome. Results All of the 82 barley EST-derived SSR primer pairs tested for transferability to H. chilense amplified products of correct size from this species. Of these 82 barley EST-SSRs, 21 (26% showed polymorphism among H. chilense lines. Identified polymorphic markers were used to test the transferability and polymorphism in other Poaceae family species with the aim of establishing H. chilense phylogenetic relationships. Triticum aestivum-H. chilense addition lines allowed us to determine the chromosomal localizations of EST-SSR markers and confirm conservation of the linkage group. Conclusion From the present study a set of 21 polymorphic EST-SSR markers have been identified to be useful for diversity analysis of H. chilense, related wild barleys like H. murinum, and for wheat marker-assisted introgression breeding. Across-genera transferability of the barley EST-SSR markers has allowed phylogenetic inference within the Triticeae complex.

  19. A high density barley microsatellite consensus map with 775 SSR loci.

    Science.gov (United States)

    Varshney, R K; Marcel, T C; Ramsay, L; Russell, J; Röder, M S; Stein, N; Waugh, R; Langridge, P; Niks, R E; Graner, A

    2007-04-01

    A microsatellite or simple sequence repeat (SSR) consensus map of barley was constructed by joining six independent genetic maps based on the mapping populations 'Igri x Franka', 'Steptoe x Morex', 'OWB(Rec) x OWB(Dom)', 'Lina x Canada Park', 'L94 x Vada' and 'SusPtrit x Vada'. Segregation data for microsatellite markers from different research groups including SCRI (Bmac, Bmag, EBmac, EBmag, HVGeneName, scsssr), IPK (GBM, GBMS), WUR (GBM), Virginia Polytechnic Institute (HVM), and MPI for Plant Breeding (HVGeneName), generated in above mapping populations, were used in the computer program RECORD to order the markers of the individual linkage data sets. Subsequently, a framework map was constructed for each chromosome by integrating the 496 "bridge markers" common to two or more individual maps with the help of the computer programme JoinMap 3.0. The final map was calculated by following a "neighbours" map approach. The integrated map contained 775 unique microsatellite loci, from 688 primer pairs, ranging from 93 (6H) to 132 (2H) and with an average of 111 markers per linkage group. The genomic DNA-derived SSR marker loci had a higher polymorphism information content value (average 0.61) as compared to the EST/gene-derived SSR loci (average 0.48). The consensus map spans 1,068 cM providing an average density of one SSR marker every 1.38 cM. Such a high-density consensus SSR map provides barley molecular breeding programmes with a better choice regarding the quality of markers and a higher probability of polymorphic markers in an important chromosomal interval. This map also offers the possibilities of thorough alignment for the (future) physical map and implementation in haplotype diversity studies of barley. PMID:17345060

  20. 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.

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

    Directory of Open Access Journals (Sweden)

    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

  2. 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.

  3. 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.

  4. 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. PMID:26398819

  5. 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.

  6. 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.

  7. SSR results obtained with a dynamic phasor model of SVC using modal analysis

    Energy Technology Data Exchange (ETDEWEB)

    Jusan, Fernando Cattan [Furnas Centrais Eletricas S.A, Av. Real Grandeza, 219, Sala B-605, Rio de Janeiro, RJ (Brazil); Gomes, Sergio Jr. [CEPEL, Av. Horacio Macedo, 354, 21941-911, Rio de Janeiro, RJ (Brazil); Taranto, Glauco Nery [Federal University of Rio de Janeiro/COPPE, Centro de Tecnologia, Sala H-343, Ilha do Fundao, P.O. Box 68504, Rio de Janeiro, RJ (Brazil)

    2010-07-15

    This paper presents the application of an improved dynamic phasor model of Static Var Compensator (SVC) in small-signal subsynchronous resonance (SSR) studies. The model is suitable for high frequency analysis (above 5 Hz) and takes into account the influence of Phase Locked Loop (PLL) circuit dynamics. A supplementary controller is designed for damping torsional modes due to SSR. The controller is designed using modal control theory to damp out critical modes in a wide range of series compensation and loading conditions. The study is conducted on the system-2 of the IEEE Second Benchmark Model. Excitation systems and power system stabilizers (PSS) are properly represented and incorporated into the system. Thus, the dynamic interactions among the several power system controllers and the network are considered in the supplementary controller design. The program PSCAD/EMTDC is used for the validation of the results obtained in the time domain simulations. (author)

  8. Clone identification in Japanese flowering cherry (Prunus subgenus Cerasus) cultivars using nuclear SSR markers.

    Science.gov (United States)

    Kato, Shuri; Matsumoto, Asako; Yoshimura, Kensuke; Katsuki, Toshio; Iwamoto, Kojiro; Tsuda, Yoshiaki; Ishio, Shogo; Nakamura, Kentaro; Moriwaki, Kazuo; Shiroishi, Toshihiko; Gojobori, Takashi; Yoshimaru, Hiroshi

    2012-09-01

    Numerous cultivars of Japanese flowering cherry (Prunus subgenus Cerasus) are recognized, but in many cases they are difficult to distinguish morphologically. Therefore, we evaluated the clonal status of 215 designated cultivars using 17 SSR markers. More than half the cultivars were morphologically distinct and had unique genotypes. However, 22 cultivars were found to consist of multiple clones, which probably originate from the chance seedlings, suggesting that their unique characteristics have not been maintained through propagation by grafting alone. We also identified 23 groups consisting of two or more cultivars with identical genotypes. Most members of these groups were putatively synonymously related and morphologically identical. However, some of them were probably derived from bud sport mutants and had distinct morphologies. SSR marker analysis provided useful insights into the clonal status of the examined Japanese flowering cherry cultivars and proved to be a useful tool for cultivar characterization. PMID:23226085

  9. 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.

  10. 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

  11. School education in Lithuania and the Lithuanian SSR (1920s—1950s

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    Kretinin G.

    2010-01-01

    Full Text Available The author considers the problems of schooling in the bourgeois Lithuania and later, in the Lithuanian SSR. On the basis of archival documents and statistical data that were unavailable in the Soviet period, the author analyses historiographical materials and studies the peculiarities of the education system, as well as evaluates the attitude of the state, the national authorities and the republic's population towards this issue.

  12. 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.

  13. Mutual Coupling Between IFF/SSR Microstrip Antennas with Reduced Transversal Size - Experimental Study

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    L. Sorokosz

    2011-04-01

    Full Text Available Mutual coupling between IFF/SSR microstrip antennas is investigated experimentally in this paper. At the begining configuration and performance of isolated microstrip antenna fed by H-shaped coupling slot is presented. Next, the vertical and horizontal arrangement of the microstrip antennas array were investigated. The measurements of return loss and coupling coefficients at two operating frequencies for the two orthogonal planes are presented and compared with the results of numerical calculations, showing satisfactory agreement.

  14. Novel and Stress Relevant EST Derived SSR Markers Developed and Validated in Peanut.

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    Tejas C Bosamia

    Full Text Available With the aim to increase the number of functional markers in resource poor crop like cultivated peanut (Arachis hypogaea, large numbers of available expressed sequence tags (ESTs in the public databases, were employed for the development of novel EST derived simple sequence repeat (SSR markers. From 16424 unigenes, 2784 (16.95% SSRs containing unigenes having 3373 SSR motifs were identified. Of these, 2027 (72.81% sequences were annotated and 4124 gene ontology terms were assigned. Among different SSR motif-classes, tri-nucleotide repeats (33.86% were the most abundant followed by di-nucleotide repeats (27.51% while AG/CT (20.7% and AAG/CTT (13.25% were the most abundant repeat-motifs. A total of 2456 EST-SSR novel primer pairs were designed, of which 366 unigenes having relevance to various stresses and other functions, were PCR validated using a set of 11 diverse peanut genotypes. Of these, 340 (92.62% primer pairs yielded clear and scorable PCR products and 39 (10.66% primer pairs exhibited polymorphisms. Overall, the number of alleles per marker ranged from 1-12 with an average of 3.77 and the PIC ranged from 0.028 to 0.375 with an average of 0.325. The identified EST-SSRs not only enriched the existing molecular markers kitty, but would also facilitate the targeted research in marker-trait association for various stresses, inter-specific studies and genetic diversity analysis in peanut.

  15. 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.

  16. 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.

  17. 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.

  18. Nuclear SSR Markers for Miscanthus, Saccharum, and Related Grasses (Saccharinae, Poaceae

    Directory of Open Access Journals (Sweden)

    Trevor R. Hodkinson

    2013-11-01

    Full Text Available 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.

  19. Simple sequence repeat (SSR) vs. sequence-related amplified polymorphism (SRAP) markers for Cynara cardunculus characterization

    Energy Technology Data Exchange (ETDEWEB)

    Casadevall, R.; Martin, E.; Cravero, V.

    2011-07-01

    A little is known about the genetic variability present in globe artichoke, cultivated and wild cardoons. This knowledge is very important for efficient genetic resources utilization, and to gain a better understanding of genetic structure of this botanical varieties. With the aims to determine genetic distances between Cynara cardunculus accessions and to compare two molecular markers systems for their efficiency to differ between botanical varieties, a molecular characterization of sixteen accessions from different geographical origins was performed. Seven SSR and seven SRAP markers were used for varieties characterization and to calculate genetic distances between them. Both distance matrices were subjected to cluster analysis. Exclusive SSR alleles were found for globe artichoke and for wild cardoon, but non exclusive alleles were found for cultivated cardoon. For both markers systems two major groups were identified, one of them included mostly globe artichoke accessions and the other one grouped mainly cardoons. The differences observed in the sub-cluster conformation with each marker systems may be due to intrinsic characteristics of the markers. Concluding, both kind of molecular markers are valuable tools for studying genetic distances between C. cardunculus accessions although they give different information. Nevertheless, SSR electrophoretic profiles are simpler to score than SRAP markers because they consist of just a few bands. As well, bands are highly informative because of the great number of alleles existing in population and they are codominant markers. In addition, SSRs use would reduce time and costs. (Author) 31 refs.

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

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    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.

  1. 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℃.

  2. 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.

  3. 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.

  4. Comparative analysis of genetic diversity among the maize inbred lines (Zea mays L. obtained by RAPD and SSR markers

    Directory of Open Access Journals (Sweden)

    Silvia Graciele Hülse de Souza

    2008-02-01

    Full Text Available The RAPD and SSR markers were used to compare the genetic diversity among the 16 maize inbred lines. Twenty-two primers were used in the RAPD reactions, resulting in the amplification of 265 fragments, while 16 pairs of SSR primers resulted in 75 fragments. The similarity based on Dice coefficient for the RAPD ranged from 53 to 84% and for the SSR from 11 to 82%. The dendrogram obtained by the RAPD showed five groups, while dendrogram obtained by the SSR showed three groups and one isolated line. The association constructed from the markers and the principal coordinate’s analysis separated lines into two groups according to endosperm color, either orange or yellow. The RAPD were effective to validate pedigree data, while the SSR were effective to recognize the differences between the quantitative characters. Because they assess the distinct regions of the genome, the selection of one or other marker would depend on the characteristics of the material used and the objectives of the project.RAPD e SSR foram utlizados para comparar a diversidade genética entre 16 linhagens de milho. Nas reações de RAPD foram utlizados 22 primers que resultaram na amplificação de 265 fragmentos, enquanto que 16 pares de primes de SSR resultaram em 75 fragmentos. A similaridade baseada no coeficiente de Dice variou de 53% a 84% para o RAPD; para o SSR variou de 11% a 82%. O dendrograma obtido a partir do RAPD mostrou 5 grupos enquanto que o dendrograma obtido a partir do SSR mostrou 3 grupos e uma linhagem isolada. A associação construída a partir dos marcadores e a análise de coordenadas principais separaram as linhagens em dois grupos de acordo coloração de endosperma alaranjado ou amarelo, os marcadores RAPD foram eficientes para a validação dos dados de pedigree enquanto os de microssatélites para reconhecerem diferenças entre caracteres quantitativos. Por acessarem regiões distintas do genoma a escolha de um ou outro marcador vai depender das

  5. 与黄瓜有毛基因紧密连锁的 SSR 标记%SSR Marker Linked to Cucumber Trichomes Characteristic Related Gene

    Institute of Scientific and Technical Information of China (English)

    王惠哲; 李淑菊; 杨瑞环; 管炜

    2013-01-01

    以有毛亲本F80为母本,无毛突变体F80WM为父本杂交,配制F1、F2、BC1群体,通过对6世代群体有无刚毛特征的观察和统计分析,研究有刚毛性状的遗传规律,并利用BSA法、SSR技术筛选与刚毛性状基因紧密连锁的分子标记。结果表明,黄瓜无毛性状是由1对核基因控制的稳定遗传的隐性性状,有刚毛相对于无毛为完全显性。通过BSA法和SSR分子标记,应用1193对引物组合对无毛、有毛亲本进行筛选,筛选到了1个与黄瓜有毛性状相关的显性标记SSR01647。测序结果表明,片段长度为164 bp,在有毛个体中扩增出了164 bp的特异片段,具有13个TC重复序列,无毛个体中未扩增出条带。经组外其他F2单株验证发现鉴定结果符合率高达100%。该性状可以作为苗期遗传标记性状,在杂交育种和品种纯度鉴定上有极大的利用价值。%The glabrous mutant F80WM was found in the inbred line F80 and can be inherited stably .F2 and BC1 population derived from F1 of F80(trichomes female)and F80WM(glabrous male)was used as materials to study the inheritance and molecular marker associated to the trichomes and glabrous trait .The results indicated that the glabrous trait was controlled by a pair of recessive gene ,and the character of trichomes was dominant to that of glabrous .The polymorphism between trichomes and glabrous parents of cucumber were studied using BSA method and SSR technology.1 193 SSR markers were screened,and a dominant marker SSR01647 was obtained.Sequen-cing of the fragment indicated that the lengths were 164 bp.The trichomes F2 plants possessed the 164 bp frag-ments,and the glabrous F2plants were no fragments.The marker was closely linked to the cucumber trichomes trait-related gene ,and the marker was confirmed to be 100%accurate by F 2 individuals .The trait was a useful marker for hybridization and purity identification of F 1 hybrids .

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. Floral transcriptome sequencing for SSR marker development and linkage map construction in the tea plant (Camellia sinensis.

    Directory of Open Access Journals (Sweden)

    Li-Qiang Tan

    Full Text Available Despite the worldwide consumption and high economic importance of tea, the plant (Camellia sinensis is not well studied in molecular biology. Under the few circumstances in which the plant is studied, C. sinensis flowers, which are important for reproduction and cross-breeding, receive less emphasis than investigation of its leaves or roots. Using high-throughput Illumina RNA sequencing, we analyzed a C. sinensis floral transcriptome, and 26.9 million clean reads were assembled into 75,531 unigenes averaging 402 bp. Among them, 50,792 (67.2% unigenes were annotated with a BLAST search against the NCBI Non-Redundant (NR database and 10,290 (16.67% were detected that contained one or more simple sequence repeats (SSRs. From these SSR-containing sequences, 2,439 candidate SSR markers were developed and 720 were experimentally tested, validating 431 (59.9% novel polymorphic SSR markers for C. sinensis. Then, a consensus SSR-based linkage map was constructed that covered 1,156.9 cM with 237 SSR markers distributed in 15 linkage groups. Both transcriptome information and the genetic map of C. sinensis presented here offer a valuable foundation for molecular biology investigations such as functional gene isolation, quantitative trait loci mapping, and marker-assisted selection breeding in this important species.

  11. 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.

  12. An application of kernel methods to variety identification based on SSR markers genetic fingerprinting

    Directory of Open Access Journals (Sweden)

    Martin Florian

    2011-05-01

    Full Text Available Abstract Background In crop production systems, genetic markers are increasingly used to distinguish individuals within a larger population based on their genetic make-up. Supervised approaches cannot be applied directly to genotyping data due to the specific nature of those data which are neither continuous, nor nominal, nor ordinal but only partially ordered. Therefore, a strategy is needed to encode the polymorphism between samples such that known supervised approaches can be applied. Moreover, finding a minimal set of molecular markers that have optimal ability to discriminate, for example, between given groups of varieties, is important as the genotyping process can be costly in terms of laboratory consumables, labor, and time. This feature selection problem also needs special care due to the specific nature of the data used. Results An approach encoding SSR polymorphisms in a positive definite kernel is presented, which then allows the usage of any kernel supervised method. The polymorphism between the samples is encoded through the Nei-Li genetic distance, which is shown to define a positive definite kernel between the genotyped samples. Additionally, a greedy feature selection algorithm for selecting SSR marker kits is presented to build economical and efficient prediction models for discrimination. The algorithm is a filter method and outperforms other filter methods adapted to this setting. When combined with kernel linear discriminant analysis or kernel principal component analysis followed by linear discriminant analysis, the approach leads to very satisfactory prediction models. Conclusions The main advantage of the approach is to benefit from a flexible way to encode polymorphisms in a kernel and when combined with a feature selection algorithm resulting in a few specific markers, it leads to accurate and economical identification models based on SSR genotyping.

  13. New simulation method for the study of subsynchronous resonance (SSR) in variable speed wind turbines

    Energy Technology Data Exchange (ETDEWEB)

    Fadaeinedjad, R.; Moschopoulos, G.; Moallem, M. [Western Ontario Univ., London, ON (Canada). Dept. of Electrical and Computer Engineering

    2006-07-01

    A model using TurbSim, FAST and Simulink to simulate mechanical and electrical parts of a wind turbine was presented. The model was used to investigate the effects of compensation level, mechanical damping and wind distribution on the dynamic response of the study system when a power system disturbance occurred. Previous studies investigating sub-synchronous resonance (SSR) in wind power systems have only considered fixed speed wind turbines, and pitch control effect has been neglected. Time domain models for the induction machine, the bidirectional PWM converter and the power system were used to link a doubly fed induction generator (DFIG) model to FAST in a Simulink environment. The electrical variables and parameters were referred to the stator. The relation between the 3 phase quantities and d-q components was defined by Park's transformation. Case studies comparing torque amplifications for 2 different compensation levels were presented. Tower oscillations and pitch action were shown for 2 different tower dampings, and the effect of different wind speed distributions was investigated. Results of the studies showed that network resonance frequencies related to the series compensation level impacted the torsional torque amplitudes subsequent to an electrical disturbance. Results suggested that in order to study SSR in variable speed wind turbines, pitch controller action should be considered as well as generator control action. Results also indicated that the possibility of SSR during turbulent and high speed wind is greater than during smooth and low speed wind, as turbulent wind creates higher mechanical forces. 13 refs., 5 figs.

  14. 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. PMID:26808306

  15. 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.

  16. 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.

  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. Development of Polymorphic Genic SSR Markers by Transcriptome Sequencing in the Welsh Onion (Allium fistulosum L.)

    OpenAIRE

    Liuyi Yang; Changlong Wen; Hong Zhao; Qianchun Liu; Jingjing Yang; Lecheng Liu; Yongqin Wang

    2015-01-01

    Transcriptome analysis is an efficient way to explore molecular markers in plant species, for which genome sequences have not been published. To address the limited number of markers published for the Welsh onion, this study found 6486 loci of genic simple sequence repeats (SSR), which consisted of 1–5 bp repeat motifs, based on next-generation sequencing (NGS) technology and the RNA-Seq approach. The most abundant motif was mononucleotide (52.33%), followed by trinucleotide (31.96%), and din...

  19. Synapse成功开发出SSR162PCB高速AOI系统

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    执力于为新电子产品开发及方案提供高增值业务的香港科技园Synapse(思宏)微电子有限公司,正逐步将业务集中于自动光学辨识及检测系统的开发和销售,并成功开发出SSR162PCB高速自动光学检测(AOI)系统。

  20. 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.

  1. 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.

  2. 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.

  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. Development of SSR markers for Psychotria homalosperma (Rubiaceae) and cross-amplification in four other species1

    Science.gov (United States)

    Sugai, Kyoko; Watanabe, Kenta; Kato, Hidetoshi; Sugawara, Takashi

    2016-01-01

    Premise of the study: Twenty-six microsatellite (simple sequence repeat [SSR]) markers were characterized in Psychotria homalosperma (Rubiaceae), an endemic evergreen tree in the Bonin Islands, Japan, to investigate the genetic structure and gene flow of the species. Methods and Results: Using next-generation sequencing, we developed 26 SSR markers for P. homalosperma with perfect motifs from di- to pentanucleotide repeats. Of these, the Chichijima and Hahajima island populations of P. homalosperma had mean allele numbers of 6.50 and 6.81, respectively. The mean expected heterozygosities were 0.578 and 0.606, respectively. In addition, 10 and eight of these markers were successfully amplified for P. boninensis and P. serpens, respectively, occurring in the same or adjacent areas. Conclusions: The SSR markers developed in this study will be useful for future studies concerning the population genetics of P. homalosperma and will facilitate the development of a conservation strategy. PMID:27213122

  5. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.).

    Science.gov (United States)

    Thiel, T; Michalek, W; Varshney, R K; Graner, A

    2003-02-01

    A software tool was developed for the identification of simple sequence repeats (SSRs) in a barley ( Hordeum vulgare L.) EST (expressed sequence tag) database comprising 24,595 sequences. In total, 1,856 SSR-containing sequences were identified. Trimeric SSR repeat motifs appeared to be the most abundant type. A subset of 311 primer pairs flanking SSR loci have been used for screening polymorphisms among six barley cultivars, being parents of three mapping populations. As a result, 76 EST-derived SSR-markers were integrated into a barley genetic consensus map. A correlation between polymorphism and the number of repeats was observed for SSRs built of dimeric up to tetrameric units. 3'-ESTs yielded a higher portion of polymorphic SSRs (64%) than 5'-ESTs did. The estimated PIC (polymorphic information content) value was 0.45 +/- 0.03. Approximately 80% of the SSR-markers amplified DNA fragments in Hordeum bulbosum, followed by rye, wheat (both about 60%) and rice (40%). A subset of 38 EST-derived SSR-markers comprising 114 alleles were used to investigate genetic diversity among 54 barley cultivars. In accordance with a previous, RFLP-based, study, spring and winter cultivars, as well as two- and six-rowed barleys, formed separate clades upon PCoA analysis. The results show that: (1) with the software tool developed, EST databases can be efficiently exploited for the development of cDNA-SSRs, (2) EST-derived SSRs are significantly less polymorphic than those derived from genomic regions, (3) a considerable portion of the developed SSRs can be transferred to related species, and (4) compared to RFLP-markers, cDNA-SSRs yield similar patterns of genetic diversity. PMID:12589540

  6. 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.

  7. Dataset of SSR markers for ISSR-Suppression-PCR to detect genetic variation in Garcinia mangostana L. in Peninsular Malaysia.

    Science.gov (United States)

    Samsir, Sri A'jilah; Bunawan, Hamidun; Yen, Choong Chee; Noor, Normah Mohd

    2016-09-01

    In this dataset, we present 15 Simple Sequence Repeat (SSR) markers with the motifs (AC)n, (GA)n, and (AC)n(AG)n using a ISSR-Suppression-PCR technique in order to discriminate Garcinia mangostana from diverse geographical origins in Peninsular Malaysia. A few loci showed differences between 3 and 6 bp in allele size, indicating that there are some polymorphisms between individuals correlating to the number of SSR repeats that may be useful for differentiate of genotypes. Collectively, these data show that the ISSR-Suppression-PCR is a valuable method to illustrate genetic variation of selected G. mangostana in Malaysia. PMID:27617279

  8. 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

  9. Design of a Robust STATCOM Supplementary Controller to Suppress the SSR in the Series-compensated System

    Energy Technology Data Exchange (ETDEWEB)

    Seo, Jang Cheol; Moon, Seung-II; Park, Jong Keun [Seoul National University (Korea)

    2000-03-01

    This paper presents the design of an H{infinity} based robust Static Synchronous Compensator (STATCOM) supplementary controller to suppress the subsynchronous resonance (SSR) in the series-compensated system. The IEEE second benchmark, System-1 model is employed for this study. In order to design the effective controller, the modal controllability and observability indices to the oscillation modes are considered. Comprehensive time domain simulations using a nonlinear system model show that the proposed STATCOM supplementary controller can suppress the SSR efficiently in spite of the variations of power system operating conditions. (author). 11 refs., 13 figs., 4 tabs.

  10. Destructive Examination of Experimental Candu Fuel Elements Irradiated in TRIGA-SSR Reactor

    International Nuclear Information System (INIS)

    The object of this work is the behaviour of CANDU fuel elements under power cycling conditions. The tests were run in the 14 MW(th) TRIGA-SSR (Steady State Reactor) reactor from Institute for Nuclear Research (INR) Pitesti. zircaloy-4 is the material used for CANDU fuel sheath. The importance of studying its behaviour results from the fact that the mechanical properties of the CANDU fuel sheath suffer modifications during normal and abnormal operation. In the nuclear reactor the fuel elements endure dimensional and structural changes as well as cladding oxidation, hydriding and corrosion. These changes can lead to defects and even to the loss of integrity of the cladding. This paper presents the results of examinations performed in the Post- irradiation Examination Laboratory (PIEL) from INR Pitesti, on samples from a fuel element irradiated in TRIGA-SSR reactor: (i) Dimensional and macrostructural characterization; (ii) Microstructural characterization by metallographic analyses; (iii) Determination of mechanical properties; (iv) Fracture surface analysis by scanning electron microscopy (SEM). The obtained data could be used to evaluate the security, reliability and nuclear fuel performance, and for CANDU fuel improvement. (author)

  11. Post Irradiation Examination of Experomental CANDU Fuel Elements Irradiated in TRIGA-SSR Reactor

    International Nuclear Information System (INIS)

    The object of this work is the behaviour of CANDU fuel elements under power cycling conditions. The tests were run in the 14 MW (th) TRIGA-SSR (Steady State Reactor) reactor from Institute for Nuclear Research (INR) Pitesti. Zircaloy-4 is the material used for CANDU fuel sheath. The importance of studying its behaviour results from the fact that the mechanical properties of the CANDU fuel sheath suffer modifications during normal and abnormal operation. In the nuclear reactor the fuel elements endure dimensional and structural changes as well as cladding oxidation, hydriding and corrosion. These changes can lead to defects and even to the loss of integrity of the cladding. This paper presents the results of examinations performed in the Post Irradiation Examination Laboratory (PIEL) from INR Pitesti, on samples from a fuel element irradiated in TRIGA-SSR reactor: (i) Dimensional and macrostructural characterization; (ii) Gamma scanning and tomography; (iii) Measurement of pressure, volume and isotopic composition of fission gas; (iv) Microstructural characterization by metallographic analyses; (v) Determination of mechanical properties; amd (vi) Fracture surface analysis by scanning electron microscopy (SEM). The obtained data could be used to evaluate the security, reliability and nuclear fuel performance, and for CANDU fuel improvement. (author)

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.  

  17. 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. PMID:27156082

  18. 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.

  19. Analysis of genetic stability at SSR loci during somatic embryogenesis in maritime pine (Pinus pinaster).

    Science.gov (United States)

    Marum, Liliana; Rocheta, Margarida; Maroco, João; Oliveira, M Margarida; Miguel, Célia

    2009-04-01

    Somatic embryogenesis (SE) is a propagation tool of particular interest for accelerating the deployment of new high-performance planting stock in multivarietal forestry. However, genetic conformity in in vitro propagated plants should be assessed as early as possible, especially in long-living trees such as conifers. The main objective of this work was to study such conformity based on genetic stability at simple sequence repeat (SSR) loci during somatic embryogenesis in maritime pine (Pinus pinaster Ait.). Embryogenic cell lines (ECLs) subjected to tissue proliferation during 6, 14 or 22 months, as well as emblings regenerated from several ECLs, were analyzed. Genetic variation at seven SSR loci was detected in ECLs under proliferation conditions for all time points, and in 5 out of 52 emblings recovered from somatic embryos. Three of these five emblings showed an abnormal phenotype consisting mainly of plagiotropism and loss of apical dominance. Despite the variation found in somatic embryogenesis-derived plant material, no correlation was established between genetic stability at the analyzed loci and abnormal embling phenotype, present in 64% of the emblings. The use of microsatellites in this work was efficient for monitoring mutation events during the somatic embryogenesis in P. pinaster. These molecular markers should be useful in the implementation of new breeding and deployment strategies for improved trees using SE. PMID:19153739

  20. 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.

  1. 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.

  2. Development and Characterization of EST-SSR Markers in Ostryopsis (Betulaceae

    Directory of Open Access Journals (Sweden)

    Bing-Bing Liu

    2014-02-01

    Full Text Available Premise of the study: A set of expressed sequence tag (EST microsatellite markers were developed and characterized using next-generation sequencing technology for the Chinese genus Ostryopsis (Betulaceae. Methods and Results: A total of 38 high-quality simple sequence repeat (SSR primers were identified, of which 15 could be successfully amplified. Subsequently, we selected 80 individuals to represent the three species of the genus to evaluate the efficacy of these markers for examining genetic diversity of each species in the future. We found that the number of alleles per locus ranged from one to nine, with an average of 3.8. The expected heterozygosity and observed heterozygosity per locus varied from 0 to 0.829 and from 0 to 1, respectively, with their respective mean values as 0.483 and 0.416. Conclusions: These EST-SSR markers will be useful for evaluating the range-wide genetic diversity of each species and examining genetic divergence and gene flow between the three species.

  3. Assessment of genetic diversity in broomcorn millet (Panicum miliaceum L.) using SSR markers.

    Science.gov (United States)

    Hu, Xingyu; Wang, Jianfei; Lu, Ping; Zhang, Hongsheng

    2009-08-01

    The genetic diversity of 118 accessions of broomcorn millet (Panicum miliaceum L.), collected from various ecological areas, was analyzed. Using 46 SSR (Simple Sequence Repeat) polymorphic markers from rice, wheat, oat and barley, a total of 226 alleles were found, which exhibited moderate level of diversity. The number of alleles per primer ranged from two to nine, with an average of 4.91. The range of polymorphism information content (PIC) was 0.284-0.980 (average, 0.793). The expected heterozygosity (He) varied from 0.346 to 0.989, with an average of 0.834. The average coefficient of the genetic similarity of SSR markers among the 118 accessions was 0.609, and it ranged from 0.461 to 0.851. The UPGMA (Unweight Pair Group Method with Arithmetic Mean) clustering analysis at the genetic similarity value of 0.609 grouped the 118 accessions into five groups. Mantel test meant that geographical origin and genetic distance presented positive correlation. The clustering results were consistent with known information on ecological growing areas. The genetic similarity coefficient of the accessions in the Loess Plateau ecotype was significantly lower than those in the other ecotypes. It indicates that the highest level of genetic diversity occurred in the Loess Plateau, which is probably the original site of Panicum miliaceum. PMID:19683672

  4. 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

  5. 77 FR 58604 - Social Security Ruling (SSR), 12-1p; Title II: Determining Whether Work Performed in Self...

    Science.gov (United States)

    2012-09-21

    ... From the Federal Register Online via the Government Publishing Office SOCIAL SECURITY 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...

  6. 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%.

  7. Identification of QTLs Associated with Callogenesis and Embryogenesis in Oil Palm Using Genetic Linkage Maps Improved with SSR Markers.

    NARCIS (Netherlands)

    Ting, N.C.; Jansen, J.; Nagappan, J.; Ishak, Z.; Chin, C.W.; Tan, S.G.; Cheah, S.C.; Singh, R.

    2013-01-01

    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) marke

  8. Language Policy, Tacit Knowledge, and Institutional Learning: The Case of the Swiss Public Service Broadcaster SRG SSR

    Science.gov (United States)

    Perrin, Daniel

    2011-01-01

    "Promoting public understanding" is what the programming mandate asks the Swiss public broadcasting company SRG SSR to do. From a sociolinguistic perspective, this means linking speech communities with other speech communities, both between and within the German-, French-, Italian-, and Romansh-speaking parts of Switzerland. In the Ideesuisse…

  9. 78 FR 12130 - Social Security Ruling, SSR 13-3p; Appeal of an Initial Medical Disability Cessation...

    Science.gov (United States)

    2013-02-21

    ... Social Security--Disability Insurance; 96.004 Social Security--Survivors Insurance; 96.006 Supplemental... From the Federal Register Online via the Government Publishing Office SOCIAL SECURITY ADMINISTRATION Social Security Ruling, SSR 13-3p; Appeal of an Initial Medical Disability Cessation...

  10. 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 ...

  11. 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

    ... 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 Social Security Ruling; Correction. SUMMARY: The Social Security Administration published a document in...

  12. 78 FR 11939 - Social Security Ruling, SSR 13-2p.; Titles II and XVI: Evaluating Cases Involving Drug Addiction...

    Science.gov (United States)

    2013-02-20

    ...'' to ``addiction'' in the forthcoming DSM-V. For this SSR, there is no substantive difference between... as defined in the latest edition of the Diagnostic and Statistical Manual of Mental Disorders (DSM) published by the American Psychiatric Association.\\3\\ See Question 4. In general, the DSM defines...

  13. SSR based linkage and mapping analysis of C, a yellow cocoon gene in the silkworm, Bombyx mori

    Institute of Scientific and Technical Information of China (English)

    Yun-Po Zhao; Mu-Wang Li; An-Ying Xu; Cheng-Xiang Hou; Ming-Hui Li; Qiu-Hong Guo; Yong-Ping Huang; Xi-Jie Guo

    2008-01-01

    The yellow color of the cocoon of the silkworm Bombyx mori is controlled by three genes, Y ( Yellow haemolymph ), I (Yellow inhibitor) and C (Outer-layer yellow cocoon),which are located on linkage groups 2, 9 and 12, respectively. Taking advantage of a lack of crossing over in females, reciprocal backcrossed F1 (BC1) progeny were used for linkage analysis and mapping of the C gene using silkworm strains C108 and KY, which spin white and yellow cocoons, respectively. DNA was extracted from individual pupae and analyzed for simple sequence repeat (SSR) markers. The C gene was found to be linked to seven SSR markers. All the yellow cocoon individuals from a female heterozygous backcross (BC1F) showed a heterozygous profile for SSR markers on linkage group 12,whereas individuals with light yellow cocoons showed the homozygous profile of the strain C 108. Using a reciprocal heterozygous male backcross (BC1M), we constructed a linkage map of 36.4 cM with the C gene located at the distal end, and the closest SSR marker at a distance of 13.9 cM.

  14. 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)

  15. 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.

  16. 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

  17. 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

  18. Transferable EST-SSR markers for the study of polymorphism and genetic diversity in bread wheat.

    Science.gov (United States)

    Gupta, P K; Rustgi, S; Sharma, S; Singh, R; Kumar, N; Balyan, H S

    2003-12-01

    Nearly 900 SSRs (simple sequence repeats) were identified among 15,000 ESTs (expressed sequence tags) belonging to bread wheat ( Triticum aestivumL.). The SSRs were defined by their minimum length, which ranged from 14 to 21 bp. The maximum length ranged from 24 to 87 bp depending upon the length of the repeat unit itself (1-7 bp). The average density of SSRs was one SSR per 9.2 kb of EST sequence screened. The trinucleotide repeats were the most abundant SSRs detected. As a representative sample, 78 primer pairs were designed, which were also used to screen the dbEST entries for Hordeum vulgare and Triticum tauschii (donor of the D-genome of cultivated wheat) using a cut-off E (expectation) value of 0.01. On the basis of in silico analysis, up to 55.12% of the primer pairs exhibited transferability from Triticum to Hordeum, indicating that the sequences flanking the SSRs are not only conserved within a single genus but also between related genera in Poaceae. Primer pairs for the 78 SSRs were synthesized and used successfully for the study of (1) their transferability to 18 related wild species and five cereal species (barley, oat, rye, rice and maize); and (2) polymorphism between the parents of four mapping populations available with us. A subset of 20 EST-SSR primers was also used to assess genetic diversity in a collection of 52 elite exotic wheat genotypes. This was done with a view to compare their utility relative to other molecular markers (gSSRs, AFLPs, and SAMPL) previously used by us for the same purpose with the same set of 52 bread wheat genotypes. Although only a low level of polymorphism was detected, relative to that observed with genomic SSRs, the study suggested that EST-SSRs can be successfully used for a variety of purposes, and may actually prove superior to SSR markers extracted from genomic libraries for diversity estimation and transferability. PMID:14508680

  19. New analysis of EST-SSR distribution and development Of EST-SSR markers in Salvia miltiorrhiza%丹参新的EST-SSR分布规律及分子标记的建立

    Institute of Scientific and Technical Information of China (English)

    王学勇; 周晓丽; 高伟; 崔光红; 黄璐琦; 刘春生

    2011-01-01

    Objective: To establish the new EST-SSR markers for analyzing the genetic variation of different population of Salvia miltiorrhiza. Method: It was dealt with ESTs newly downloaded from Cenbank and that of acquired from HMPL lab EGassembler software,and then carried out SSR loci search and SSR type analysis by SSRIT software. After that, it was designed the EST-SSR primer pairs for PCR amplification condition optimization. Result: Abundant and high coverage of SSR loci distribution were found in S. miltiorrhiza with having one SSR per 5.8 kb ESTs. Among them, the occurrences of different repeat units were mainly the di(63.0%) and tri-(35.5% ). The CT/AG was the most frequent motif in dinucleotide motif type and the GAA/TCC was the most frequent motif in trinucleotide repeats. Out off 36 primer pairs, 29 primer pairs ( 80.5% ) were successfully amplified in all samples of S.miltiorrhiza while the rest failed to give PCR products at various annealing temperature and Mg2+ concentrations. The selected primer pairs also showed the polymorphism in samples from different S. miltiorrhiza populations. Conclusion: The newly establishment of EST-SSR markers showed high SSR loci coverage and genetic polymorphisms in S. miltiorrhiza population. It could be used for genetic variation analysis.%目的:建立新近较高覆盖度丹参KST-SSR分子标记,为不同产地来源丹参居群的遗传变异分析奠定基础.方法:对截止2010年11月Genbank下载的丹参EST序列结合HMPL实验室获取的共计1 408条EST序列,进行处理,获取高质量EST序列;经SSRIT软件搜索、分析EST序列中SSR位点的分布规律及类型;在此基础上,运用Websat软件设计EST-SSR引物,经对不同产地丹参样本DNA模板的PCR筛选和条件优化,建立最新EST-SSR分子标记.结果:丹参的EST-SSR种类丰富、覆盖度较大,平均每5.8 kb就检出1条SSR.各种类型出现的频率相差很大,主要重复类型为二核苷酸、三核

  20. 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

  1. 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.

  2. Chaos and bifurcation control of SSR in the IEEE second benchmark model

    Energy Technology Data Exchange (ETDEWEB)

    Harb, A.M. E-mail: aharb@just.edu.jo; Widyan, M.S

    2004-07-01

    Linear and nonlinear state feedback controllers are proposed to control the bifurcation of a phenomenon in power system, this phenomenon of electro-mechanical interaction between the series resonant circuits and torsional mechanical frequencies of the turbine-generator sections, which known as subsynchronous resonance (SSR). The first system of the IEEE second benchmark model is considered. The dynamics of the two axes damper windings, automatic voltage regulator and power system stabilizer are included. The linear controller gives better initial disturbance response than that of the nonlinear, but in a small narrow region of compensation factors. The nonlinear controller not only can be easily implemented, but also it stabilizes the operating point for all values of the bifurcation parameter.

  3. Analytical modeling of thyristor-controlled series capacitors for SSR studies

    Energy Technology Data Exchange (ETDEWEB)

    Othman, H.A. [ABB Power T and D Co. Inc., Raleigh, NC (United States). Transmission Technology Inst.; Aengquist, L. [ABB Power Systems AB, Vaesteraas (Sweden). Reactive Power Compensation Div.

    1996-02-01

    Thyristor-controlled series capacitors (TCSC) have dynamic characteristics that differ drastically from conventional series capacitors especially at frequencies outside the operating frequency range. Therefore suitable models are needed to properly study the applications of TCSC on a utility system. An accurate analytical model of the TCSC which is valid in the frequency range from 0 Hz to twice the operating frequency is presented. The model incorporates the thyristor triggering logic, the synchronization system, and higher level control loops such as power oscillation damping loop. This model is suited for linearized analyses of a power system using frequency domain methods such as eigenvalues. It is particularly valuable in studying subsynchronous resonance (SSR) and enables the utility industry to better evaluate the interactions between TCSC and other devices.

  4. 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.

  5. 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.

  6. 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 cM and including 208 simple sequence repeat (SSR) markers. The minimum distance between adjacent markers was 0.01 cM and the average was 9.95 cM. Each linkage group contained 2–22 markers. The largest linkage group covered 174.40 cM and the shortest one covered 36.80 cM, with an average of 94.11 cM. 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.

  7. 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

  8. 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.

  9. 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.

  10. 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.

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

    Science.gov (United States)

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

    2012-01-01

    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 F(2) 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. PMID:23271013

  12. SSR allelic variation of rice variety Hangxiangnuo bred by space mutation

    International Nuclear Information System (INIS)

    Hangxiangnuo, an indica fragrant glutinous rice mutant, was induced by space environment. Comparing with its wild type Nanfengnuo, the yield and blast resistance of Hangxiangnuo are improved significantly and the grain shape became slender and with fragrance. To understand the mechanisms of space mutation and identify the changes at molecular level associated with phenotypic variations, SSR allelic variation analysis were performed on Hangxiangnuo and Nanfengnuo in this study. The results showed that 45 loci were polymorphic among the 156 SSR loci tested throughout the genome, the frequency of variation was 28.85%. Among the polymorphic loci, 42 loci only showed variations in the molecular weight of the amplified bands, only on locus increased the number of amplification bands in Hangxiangnuo and two loci were differed by heterozygous loci (with two amplification bands at one locus) detected in Nanfengnuo and homozygous loci in Hangxiangnuo. It suggests that the change of some loci in mutants was due to the normal segregation and recombination of heterozygous loci of the wild type. The variation frequencies among different chromosomes were quite different, with the highest one at 50.00% detected on chromosomes 7, 8 and 12, and the lowest at 6.25% on chromosome 6. The polymorphic loci were clustered on chromosomes throughout the genome indicating that large DNA segments mutation is one of the major variation patterns induced by space environment. Some of reported QTLs involved in grain shape, yield, fragrance and blast resistance were found to be located exactly in the mutated regions. Therefore, further study is needed to confirm that these QTLs are responsible for the trait variations. (authors)

  13. 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.

  14. 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.

  15. Transcriptome sequencing of mung bean (Vigna radiate L. genes and the identification of EST-SSR markers.

    Directory of Open Access Journals (Sweden)

    Honglin Chen

    Full Text Available Mung bean (Vigna radiate (L. Wilczek is an important traditional food legume crop, with high economic and nutritional value. It is widely grown in China and other Asian countries. Despite its importance, genomic information is currently unavailable for this crop plant species or some of its close relatives in the Vigna genus. In this study, more than 103 million high quality cDNA sequence reads were obtained from mung bean using Illumina paired-end sequencing technology. The processed reads were assembled into 48,693 unigenes with an average length of 874 bp. Of these unigenes, 25,820 (53.0% and 23,235 (47.7% showed significant similarity to proteins in the NCBI non-redundant protein and nucleotide sequence databases, respectively. Furthermore, 19,242 (39.5% could be classified into gene ontology categories, 18,316 (37.6% into Swiss-Prot categories and 10,918 (22.4% into KOG database categories (E-value < 1.0E-5. A total of 6,585 (8.3% were mapped onto 244 pathways using the Kyoto Encyclopedia of Genes and Genome (KEGG pathway database. Among the unigenes, 10,053 sequences contained a unique simple sequence repeat (SSR, and 2,303 sequences contained more than one SSR together in the same expressed sequence tag (EST. A total of 13,134 EST-SSRs were identified as potential molecular markers, with mono-nucleotide A/T repeats being the most abundant motif class and G/C repeats being rare. In this SSR analysis, we found five main repeat motifs: AG/CT (30.8%, GAA/TTC (12.6%, AAAT/ATTT (6.8%, AAAAT/ATTTT (6.2% and AAAAAT/ATTTTT (1.9%. A total of 200 SSR loci were randomly selected for validation by PCR amplification as EST-SSR markers. Of these, 66 marker primer pairs produced reproducible amplicons that were polymorphic among 31 mung bean accessions selected from diverse geographical locations. The large number of SSR-containing sequences found in this study will be valuable for the construction of a high-resolution genetic linkage maps, association

  16. SSR Identification and Pedigree Analysis of PVP Application Cultivars in Tea Plant%茶树 PVP 申请品种的 SSR 分子标记鉴定和系谱关系分析

    Institute of Scientific and Technical Information of China (English)

    黄丹娟; 马建强; 陈亮

    2016-01-01

    利用30对 SSR 引物,对26个植物新品种保护(PVP)申请茶树品种及其13个近似品种与亲本进行了分子鉴定和系谱关系分析,探讨 SSR 分子标记在茶树新品种保护工作和 DUS 测试中的应用。研究结果显示,30对 SSR 引物共检测到131个等位基因,每对引物检测的等位基因数为3~7个,平均4.4个。平均 Shannon信息指数(I)和多态信息含量(PIC)分别为1.04和0.51。39个参试品种的遗传距离在0.03~0.70之间。在遗传距离为0.15时,可将39个品种划分为7类,其中地理来源一致或遗传背景相似的材料基本上聚为一类。30对引物的品种鉴定能力差异较大,每对引物能鉴定的品种数为3~16个。通过4对核心引物的组合可以鉴定全部39个参试品种,并依此构建了 SSR 指纹图谱。%Thirty SSR markers were used in this study for molecular identification and pedigree analysis of 26 PVP application tea cultivars, and 13 similar cultivars and parents, for probing the possible application of PVP and DUS testing using SSR markers in tea plant. A total of 131 alleles were detected, the number of alleles detected by each SSR marker ranged from 3 to 7, with a mean of 4.4. The average values of Shannon index and polymorphism information content were 1.04 and 0.51, respectively. The genetic distance ranged from 0.03 to 0.70 between 39 cultivars. When the genetic distance was 0.15, they could be classified into 7 groups. Tea cultivars from the same province and genetic background were clustered into one group to some extent. The identification ability of the 30 SSR markers was quite different, each marker could identify 3-16 cultivars. The 39 tea cultivars could be clearly distinguished by 4 core primers which were used to construct the molecular fingerprinting of all cultivars.

  17. 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.

  18. Estimation of outcrossing rates in interspecific backcross plants of Jatropha curcas (L.) using AFLP and SSR markers.

    Science.gov (United States)

    Sinha, Pratima; Islam, Md Aminul; Negi, Madan Singh; Tripathi, Shashi Bhushan

    2015-10-01

    In this paper, we report the estimates of outcrossing rates using open-pollinated progeny arrays of 40 BC1 individuals of Jatropha developed as a result of interspecific hybridization between J. curcas and J. integerrima. For analysis PCR-based dominant AFLP and codominant SSR markers were used. The multilocus outcrossing rate (tm) estimated from AFLP markers (0.892 ± 0.112) are almost in the same range with SSR (0.884 ± 0.293) markers which indicate a high level of heterozygosity. A low value of inbreeding coefficient (F) also points out to the fact that outcrossing was the prevalent mode of reproduction in Jatropha and suggests maintenance of adequate genetic variability within families. PMID:26600687

  19. 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.

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

    OpenAIRE

    Honglin Chen; Xin Chen; Jing Tian; Yong Yang; Zhenxing Liu; Xiyu Hao; Lixia Wang; Suhua Wang; Jie Liang; Liya Zhang; Fengxiang Yin; Xuzhen Cheng

    2016-01-01

    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 o...

  1. 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。

  2. 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.

  3. 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.

  4. 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. PMID:23657599

  5. Genetic diversity analysis of wild close relatives of barley from Tibet and the Middle East by ISSR and SSR markers.

    Science.gov (United States)

    Wang, Aihua; Yu, Zhiyong; Ding, Yi

    2009-04-01

    The genetic diversity analysis of 90 barley samples, including 45 wild close relatives of barley from the Tibet region of China and 45 wild accessions from different countries throughout the Middle East, were carried out using ISSR and SSR markers. The results showed that Tibetan wild close relatives of barley had a higher genetic diversity than those from the Middle East. Ten ISSR primers amplified 91 allelic variants, of which 79 were polymorphic (86.81%), in the Tibetan genotypes and 82 allelic variants, of which 66 were polymorphic (80.49%), in the Middle East genotypes. Eleven primer pairs of SSR markers amplified 100 allelic variants among the Tibetan genotypes with 100 polymorphic bands (100%). Among the Middle East genotypes, 78 allelic variants were produced containing 77 polymorphic bands (98.72%). Moreover, the total gene diversity analysis (HT) values of Tibetan barley (0.227 for ISSRs and 0.126 for SSRs) were higher than those of Middle East (0.212 for ISSRs and 0.102 for SSRs). Cluster analysis of the ISSR and SSR results by the UPGMA method revealed two distinct groups correlated with the geographic origin of sampling. These results offer a new evidence for the theory of the origin of Hordeum vulgare L. PMID:19304270

  6. Identification of SNP and SSR Markers in Finger Millet Using Next Generation Sequencing Technologies

    Science.gov (United States)

    Gimode, Davis; Odeny, Damaris A.; de Villiers, Etienne P.; Wanyonyi, Solomon; Dida, Mathews M.; Mneney, Emmarold E.; Muchugi, Alice; Machuka, Jesse; de Villiers, Santie M.

    2016-01-01

    Finger millet is an important cereal crop in eastern Africa and southern India with excellent grain storage quality and unique ability to thrive in extreme environmental conditions. Since negligible attention has been paid to improving this crop to date, the current study used Next Generation Sequencing (NGS) technologies to develop both Simple Sequence Repeat (SSR) and Single Nucleotide Polymorphism (SNP) markers. Genomic DNA from cultivated finger millet genotypes KNE755 and KNE796 was sequenced using both Roche 454 and Illumina technologies. Non-organelle sequencing reads were assembled into 207 Mbp representing approximately 13% of the finger millet genome. We identified 10,327 SSRs and 23,285 non-homeologous SNPs and tested 101 of each for polymorphism across a diverse set of wild and cultivated finger millet germplasm. For the 49 polymorphic SSRs, the mean polymorphism information content (PIC) was 0.42, ranging from 0.16 to 0.77. We also validated 92 SNP markers, 80 of which were polymorphic with a mean PIC of 0.29 across 30 wild and 59 cultivated accessions. Seventy-six of the 80 SNPs were polymorphic across 30 wild germplasm with a mean PIC of 0.30 while only 22 of the SNP markers showed polymorphism among the 59 cultivated accessions with an average PIC value of 0.15. Genetic diversity analysis using the polymorphic SNP markers revealed two major clusters; one of wild and another of cultivated accessions. Detailed STRUCTURE analysis confirmed this grouping pattern and further revealed 2 sub-populations within wild E. coracana subsp. africana. Both STRUCTURE and genetic diversity analysis assisted with the correct identification of the new germplasm collections. These polymorphic SSR and SNP markers are a significant addition to the existing 82 published SSRs, especially with regard to the previously reported low polymorphism levels in finger millet. Our results also reveal an unexploited finger millet genetic resource that can be included in the regional

  7. A second generation framework for the analysis of microsatellites in expressed sequence tags and the development of EST-SSR markers for a conifer, Cryptomeria japonica

    Directory of Open Access Journals (Sweden)

    Ueno Saneyoshi

    2012-04-01

    Full Text Available Abstract Background Microsatellites or simple sequence repeats (SSRs in expressed sequence tags (ESTs are useful resources for genome analysis because of their abundance, functionality and polymorphism. The advent of commercial second generation sequencing machines has lead to new strategies for developing EST-SSR markers, necessitating the development of bioinformatic framework that can keep pace with the increasing quality and quantity of sequence data produced. We describe an open scheme for analyzing ESTs and developing EST-SSR markers from reads collected by Sanger sequencing and pyrosequencing of sugi (Cryptomeria japonica. Results We collected 141,097 sequence reads by Sanger sequencing and 1,333,444 by pyrosequencing. After trimming contaminant and low quality sequences, 118,319 Sanger and 1,201,150 pyrosequencing reads were passed to the MIRA assembler, generating 81,284 contigs that were analysed for SSRs. 4,059 SSRs were found in 3,694 (4.54% contigs, giving an SSR frequency lower than that in seven other plant species with gene indices (5.4–21.9%. The average GC content of the SSR-containing contigs was 41.55%, compared to 40.23% for all contigs. Tri-SSRs were the most common SSRs; the most common motif was AT, which was found in 655 (46.3% di-SSRs, followed by the AAG motif, found in 342 (25.9% tri-SSRs. Most (72.8% tri-SSRs were in coding regions, but 55.6% of the di-SSRs were in non-coding regions; the AT motif was most abundant in 3′ untranslated regions. Gene ontology (GO annotations showed that six GO terms were significantly overrepresented within SSR-containing contigs. Forty–four EST-SSR markers were developed from 192 primer pairs using two pipelines: read2Marker and the newly-developed CMiB, which combines several open tools. Markers resulting from both pipelines showed no differences in PCR success rate and polymorphisms, but PCR success and polymorphism were significantly affected by the expected PCR product size

  8. 菊花EST-SSR分析及标记开发%EST-SSR Analysis and Marker Development for Chrysanthemum morifolium

    Institute of Scientific and Technical Information of China (English)

    万志兵; 陈燕; 闫莹莹; 陈黎

    2013-01-01

    为了开发菊花的分子标记,对7 087条菊花EST进行拼接,得到275个contigs,发现50个SSR位点;在拼接的contigs中SSR平均密度为每2 854.3 bp含有1个SSR.三核苷酸重复基元的SSR类型最多,占总数的50.00%;在二碱基重复中,最主要的优势重复基元是AC和AG;三碱基中CAT和CCA为优势重复基元;四碱基、五碱基重复类型中,(TTTN)n和(ATTTN)n重复基元为对应优势基元;这些优势重复基元中富含碱基A和T,菊花EST序列中高度变异的微卫星(长度>20 bp)约占2.00%.根据得到的菊花EST-SSR,共设计出428对引物,并选取了28对SSR引物对黄山贡菊基因组DNA进行PCR扩增,其中有27对引物扩增成功.%7087 EST of Chrysanthemum morifolium were assembled in order to provide molecular markers, and 275 contigs were obtained. There were 50 microsatellites (SSRs) were detected and averagely there was one SSR locus detected from 2 854. 3 bp of contigs. Trinucleotide repeats were the most abundant repeats (50. 00% ) a-mong these SSR types. As for the composition of microsatellites, AC, AG repeats were the richest motif in dinucle-otide repeats, and CAT, CCA repeats were the most frequent motifs in trinucleotide repeats, whereas (TTTN) n and (ATTTN ) n repeats were dominant in tetra- and penta-nucleotide repeats, respectively. All the dominant repeat motifs for different type of SSRs were rich in A and T alkali bases. In EST of C. morifolium, microsatellites longer than 20 bp accounted for about 00% of the detected SSRs. 428 pairs of primers were designed using Primer 5. 0 and Oligo 6. 0 according to these EST sequences containing SSR. 28 pairs of primers were randomly selected for PCR test with genomic DNA of Huangshan variety of Chrysanthemum morifolium, and 27 primer pairs succeeded in amplification, with successful ratio of 96. 4%.

  9. 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.

  10. Genetics of Fusarium Wilt Resistance in Pigeonpea (Cajanus cajan) and Efficacy of Associated SSR Markers.

    Science.gov (United States)

    Singh, Deepu; Sinha, B; Rai, V P; Singh, M N; Singh, D K; Kumar, R; Singh, A K

    2016-04-01

    Inheritance of resistance to Fusarium wilt (FW) disease caused by Fusarium udum was investigated in pigeonpea using four different long duration FW resistant genotypes viz., BDN-2004-1, BDN-2001-9, BWR-133 and IPA-234. Based on the F2 segregation pattern, FW resistance has been reported to be governed by one dominant gene in BDN-2004-1 and BDN-2001-9, two duplicate dominant genes in BWR-133 and two dominant complimentary genes in resistance source IPA-234. Further, the efficacy of six simple sequence repeat (SSR) markers namely, ASSR-1, ASSR-23, ASSR-148, ASSR-229, ASSR-363 and ASSR-366 reported to be associated with FW resistance were also tested and concluded that markers ASSR-1, ASSR-23, ASSR-148 will be used for screening of parental genotypes in pigeonpea FW resistance breeding programs. The information on genetics of FW resistance generated from this study would be used, to introgress FW resistance into susceptible but highly adopted cultivars through marker-assisted backcross breeding and in conventional breeding programs. PMID:27147929

  11. 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.

  12. 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.

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

    Science.gov (United States)

    Liu, Yang; Zhou, Tengxia; Ge, Haiyan; Pang, Wen; Gao, Lijie; Ren, Li; Chen, Huoying

    2016-01-01

    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. PMID:27517040

  14. Genetic diversity of Chinese summer soybean germplasm revealed by SSR markers

    Institute of Scientific and Technical Information of China (English)

    XIE Hua; GUAN Rongxia; CHANG Ruzhen; QIU Lijuan

    2005-01-01

    There are abundant soybean germplasm in China. In order to assess genetic diversity of Chinese summer soybean germplasm, 158 Chinese summer soybean accessions from the primary core collection of G. max were used to analyze genetic variation at 67 SSR loci. A total of 460 alleles were detected, in which 414 and 419 alleles occurred in the 80 Huanghuai and the 78 Southern summer accessions, respectively. The average number of alleles per locus was 6.9 for all the summer accessions, and 6.2 for both Huanghuai and Southern summer accessions. Marker diversity (D) per locus ranged from 0.414 to 0.905 with an average of 0.735 for all the summer accessions, from 0.387 to 0.886 with an average of 0.708 for the Huanghuai summer accessions, and from 0.189 to 0.884 with an average of 0.687 for the Southern summer accessions. The Huanghuai and Southern summer germplasm were different in the specific alleles, allelic-frequencies and pairwise genetic similarities. UPGMA cluster analysis based on the similarity data clearly separated the Huanghuai from Southern summer soybean accessions, suggesting that they were different gene pools. The results indicate that Chinese Huanghuai and Southern summer soybean germplasm can be used to enlarge genetic basis for developing elite summer soybean cultivars by exchanging their germplasm.

  15. GENETIC RELATEDNESS OF LENTIL (Lens culinaris L. GERMPLASM BY USING SSR MARKERS

    Directory of Open Access Journals (Sweden)

    U. K. S. Kushwaha

    2013-09-01

    Full Text Available Ninety six lentil accessions from different origins were collected from National Grain Legume Research Program, Rampur; Regional Agriculture Research Station, Nepalgunj and National Agriculture Genetic Resource Center, Khumaltar, Lalitpur. Among them; four lines were Nepal Local, forty two lines were Nepal Cross; forty seven lines were ICARDA Line and finally three lines were Indian Line. All ninety six accessions were analysed by DNA fingerprinting using thirty three selected polymorphic SSR markers. The characterization was performed in Biotechnology Unit, Nepal Agricultural Research Council, Khumaltar, Lalitpur by using standard protocols. Molecular variance analysis showed that 14 % genetic variation was found between population and 86 % genetic variation was found within population with estimated variance 0.23 between population and 1.35 within population. Highest genetic distance (9 was found between landrace ILL-7979 and RL-20. In the same way, highest Nei genetic distance (0.03 between population was shown by population 1 and population 4; and lowest genetic distance were observed within the same population accessions. The heterozygosity was probably due to the introgression of genes or duplication of microsatellite motif during the breeding and or the course of lentil line evolution. All the accessions included in this study displayed significant amount of genetic variability and genetic relatedness due to different center of origin and different genetic constitutions. The diversity detected in this study may constitute the new materials for future systematic lentil breeding programs.

  16. Research on genetic difference of maize mutants by irradiation based on phenotypic and SSR

    International Nuclear Information System (INIS)

    The genetic difference between mutants and corresponding basic materials was studied based on phenotypic characters and SSR markers, in which maize inbred lines R08 and its nine mutants, 48-2 and its thirteen mutants were selected as materials. The results showed that different degree variation of days to silking, plant height, plant type, seed color, yield per plant, etc. as the molecular level was detected in mutants. Among them, phenotypic variation of R08 mutants 12, 17 and 48-2 mutants 23, 27, 28, 29 and 31 were larger, oppositely, R08 mutants 16 and 48-2 mutants 22, 26, 33 were relatively smaller. The amplitude of polymorphism information content (PIC) between R08, 48-2 and their corresponding mutants were 0.18-0.70 and 0.34-0.83, and the average values of them were 0.46 and 0.61 respectively. The genetic similarity coefficient between R08 and its mutants ranged from 0.474 to 0.842 with an average of 0.712, 48-2 and its mutants varied from 0.463 to 0.782 with an average of 0.645. Experiments proved that genetic difference between mutants and basic material was true

  17. Identification of QTLs for Yield Related Traits in Indica Type Rice Using SSR and AFLP Markers

    Directory of Open Access Journals (Sweden)

    Babak Rabiei

    2015-11-01

    Full Text Available This research was carried out to identify quantitative trait loci (QTLs controlling yield and yield components in rice using 196 F2:4 lines derived from a cross between two rice varieties of indica, Sepidrood and Gharib. Quantitative trait loci analysis using composite interval mapping was carried out by 105 SSR and 111 AFLP markers. Results showed that 8 chromosomes contain 28 regions (QTLs controlling 11 studied traits. One QTL was mapped for the number of spikelet per panicle on chromosome 12, three QTLs for number of filled grains per panicle on chromosomes 1, 6 and 11, three QTLs for empty spikelets per panicle on chromosomes 2, 3 and 12, five QTLs for plant height on chromosomes 1, 7 (2 QTLs, eight and 11, four QTLs for days to 50% flowering on chromosomes 2, 3 (2 QTLs and 6, one QTL for panicle length on chromosome 1, two QTLs for 1000 grain weight on chromosomes 1 and 2, three QTLs for number of panicles per plant on chromosomes 1, 3 and 6, one QTL for grain yield on chromosome 3, four QTLs for days to maturity on chromosomes 2, 3 (2 QTLs and 6 and one QTL for fertility percentage on chromosome 11. The identified QTLs on specific chromosome regions explaining high phenotypic variance can be considered for use in marker-assisted selection (MAS programs.

  18. 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.

  19. 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.

  20. 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.)

  1. 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.

  2. 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.

  3. 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

  4. 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.

  5. 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.

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

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    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

  7. The assessment of genetic diversity between and within brassica species and their wild relative (eruca sativa) using ssr markers

    International Nuclear Information System (INIS)

    Microsatellites markers were tested for their ability to distinguish genomic distribution of the Brassica species of the U Triangle and E. sativa. The objectives of the present study were to investigate the genetic diversity of six Brassica species from U-Triangle (representing three genomes, A, B, C) and one from genus Eruca and to identify promising sources of genetic variation for breeding purposes. A total of 54 SSR markers were analyzed in order to detect variation between and within the selected genomes. Three primer pairs depicted the greatest genetic diversity showing 97% polymorphism between Brassica and Eruca genomes (2.55 alleles per locus). Polymorphic Information Content (PIC) values ranged from 0.40 (SSR primer Na14-DO7) to 0.79 (NA10-G09). For comparison within Brassica genomes and Eruca, all the genomes were grouped in three modules i.e., ABE, ACE and BCE (Fig. 1). The tetraploid originating from their parental diploids along-with Eruca was considered in the same module. For the estimation of relatedness within and among genomes, dice coefficients were computed as a measure of genetic similarity matrix. On the basis of genetic distances, dendrogram was constructed through cluster analysis. Two major clusters at coefficient of similarity level (0.47) were observed. One cluster comprised of all Brassica genomes and their accessions, while another consisting of all accessions of Eruca genome. The cluster containing Brassica genomes was further subdivided into four sub-groups that contained diploid and tetraploid species in a way that tetraploid species were grouped in between their diploid parental species with varying genetic distances. Present findings confirmed the validity of SSR markers in genomic studies. (author)

  8. 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.

  9. 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.

  10. 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.

  11. Tagging and mapping of SSR marker for rust resistance gene in lentil (Lens culinaris Medikus subsp. culinaris).

    Science.gov (United States)

    Dikshit, H K; Singh, Akanksha; Singh, D; Aski, M; Jain, Neelu; Hegde, V S; Basandrai, A K; Basandrai, D; Sharma, T R

    2016-06-01

    Lentil, as an economical source of protein, minerals and vitamins, plays important role in nutritional security of the common man. Grown mainly in West Asia, North Africa (WANA) region and South Asia, it suffers from several biotic stresses such as wilt, rust, blight and broomrape. Lentil rust caused by autoecious fungus Uromyces viciae fabae (Pers.) Schroet is a serious lentil disease in Algeria, Bangladesh, Ethiopia, India, Italy, Morocco, Pakistan and Nepal. The disease symptoms are observed during flowering and early podding stages. Rust causes severe yield losses in lentil. It can only be effectively controlled by identifying the resistant source, understanding its inheritance and breeding for host resistance. The obligate parasitic nature of pathogen makes it difficult to maintain the pathogen in culture and to apply it to screen segregating progenies under controlled growth conditions. Hence, the use of molecular markers will compliment in identification of resistant types in different breeding programs. Here, we studied the inheritance of resistance to rust in lentil using F₁, F₂ and F₂:₃ from cross PL 8 (susceptible) x L 4149 (resistant) varieties. The phenotyping of lentil population was carried out at Sirmour, India. The result of genetic analysis revealed that a single dominant gene controls rust resistance in lentil genotype L 4149. The F2 population from this cross was used to tag and map the rust resistance gene using SSR and SRAP markers. Markers such as 270 SRAP and 162 SSR were studied for polymorphism and 101 SRAP and 33 SSRs were found to be polymorphic between the parents. Two SRAP and two SSR markers differentiated the resistant and susceptible bulks. SSR marker Gllc 527 was estimated to be linked to rust resistant locus at a distance of 5.9 cM. The Gllc 527 marker can be used for marker assisted selection for rust resistance; however, additional markers closer to rust resistant locus are required. The markers linked to the rust

  12. 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...... subsynchronous damping control loop for the STATCOM based on a novel design procedure of nonlinear optimization are developed to meet the damping torque in the range of critical torsional frequencies. The Intelligent Shaft Monitor (ISM) scheme with Synthesized Special Indicator Signals are developed and examined...

  13. Effectiveness of thyristor controlled series capacitors in damping SSR on Mohave generators and its comparison with the NGH device

    Energy Technology Data Exchange (ETDEWEB)

    Bhargava, B. [Southern California Edison Co., Rosemead, CA (United States)

    1995-12-31

    The Thyristor Controlled Series Capacitors offer a very promising solution to the problem of dynamic system instability and subsynchronous resonance. Their application on a system can increase the power transfer capability significantly. Some subsynchronous resonance studies have been conducted to examine the application of TCSC on the Mohave system to determine the likely impacts the TCSC could have on the Mohave generating machines. This paper presents the results of these studies and discusses the benefits of TCSC in damping SSR on Mohave machines and the possible undamping that could also result from their application. 14 refs, 12 figs, 3 tabs

  14. 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.

  15. 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.

  16. 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 levels...... the magnitude of the SSR180711-evoked increase by 65%. These results demonstrate that pharmacological stimulation of α7 nAChRs within the prefrontal cortex is sufficient to evoke rapid yet transient increases in glutamate levels. Such increases may underlie the cognition-enhancing effects of the drug in animals......; further justifying studies on the use of α7 nAChR-positive modulators in treating cognition-impairing disorders in humans....

  17. 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

  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. 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.

  20. 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.

  1. Next-generation sequencing of the Chrysanthemum nankingense (Asteraceae transcriptome permits large-scale unigene assembly and SSR marker discovery.

    Directory of Open Access Journals (Sweden)

    Haibin Wang

    Full Text Available BACKGROUND: Simple sequence repeats (SSRs are ubiquitous in eukaryotic genomes. Chrysanthemum is one of the largest genera in the Asteraceae family. Only few Chrysanthemum expressed sequence tag (EST sequences have been acquired to date, so the number of available EST-SSR markers is very low. METHODOLOGY/PRINCIPAL FINDINGS: Illumina paired-end sequencing technology produced over 53 million sequencing reads from C. nankingense mRNA. The subsequent de novo assembly yielded 70,895 unigenes, of which 45,789 (64.59% unigenes showed similarity to the sequences in NCBI database. Out of 45,789 sequences, 107 have hits to the Chrysanthemum Nr protein database; 679 and 277 sequences have hits to the database of Helianthus and Lactuca species, respectively. MISA software identified a large number of putative EST-SSRs, allowing 1,788 primer pairs to be designed from the de novo transcriptome sequence and a further 363 from archival EST sequence. Among 100 primer pairs randomly chosen, 81 markers have amplicons and 20 are polymorphic for genotypes analysis in Chrysanthemum. The results showed that most (but not all of the assays were transferable across species and that they exposed a significant amount of allelic diversity. CONCLUSIONS/SIGNIFICANCE: SSR markers acquired by transcriptome sequencing are potentially useful for marker-assisted breeding and genetic analysis in the genus Chrysanthemum and its related genera.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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).

  7. Exploiting EST databases for the mining and characterization of short sequence repeat (SSR) markers in Catharanthus roseus L.

    Science.gov (United States)

    Joshi, Raj Kumar; Kar, Basudeba; Nayak, Sanghamitra

    2011-01-01

    Periwinkle (Catharanthus roseus L.) (Family: Apocyanaceae) is a ornamental plants with great medicinal properties. Although it is represented by seven species, little work has been carried out on its genetic characterization due to non-availability of reliable molecular markers. Simple sequence repeats (SSRs) have been widely applied as molecular markers in genetic studies. With the rapid increase in the deposition of nucleotide sequences in the public databases and advent of bioinformatics tools, it has become a cost effective and fast approach to scan for microsatellite repeats and exploit the possibility of converting it into potential genetic markers. Expressed sequence tags (EST's) from Catharanthus roseus were used for the screening of Class I (hyper variable) simple sequence repeats (SSR's). A total of 502 microsatellite repeats were detected from 21730 EST sequences of turmeric after redundancy elimination. The average density of Class I SSRs account to 1 SSR per 10.21 kb of EST. Mononucleotides was the most abundant class of microsatellite motifs. It accounted for 44.02% of the total, followed by the trinucleotide (26.09%) and dinucleotide repeats (14.34%). Among all the repeat motifs, (A/T)n accounted for the highest Proportion (36.25%) followed by (AAG)n. These detected SSRs can be used to design primers that have functional importance and should also facilitate the analysis of genetic diversity, variability, linkage mapping and evolutionary relationships in plants especially medicinal plants. PMID:21383904

  8. Genetic diversity of the progeny of cotton (Gossypium hirsutum L.) irradiated by γ ray with SSR markers

    International Nuclear Information System (INIS)

    The objective of this study is to understand the effect of γ-ray irradiation on cotton. The genetic diversity of 74 mutagenic progenies M5 in 3 cotton varieties, Arcot-1, Su9108 and J11, irradiated by γ-ray were analyzed with 39 polymorphism SSR primer pairs. The variance range of mutagenic progeny’s (M5) pair similarity coefficient of 3 cotton varieties were 0.61290.9848, 0.62121.000, 0.48570.9905 respectively. The pair similarity coefficient that was higher or equal to 8.000 was more than 60.0% for the mutagenic progenies M5 of two varieties (Arcot-1 and Su9108). The pair similarity coefficient less than 7.000 was 62.5% for the mutagenic progenies M5 of J11. The variance ranges of genetic similarity coefficient of mutagenic progeny M5 SSR markers of 3 cotton varieties and their original CK were 0.65150.9697, 0.69701.000, 0.552408095 respectively. The analysis of molecular markers indicated that abundant genetic variations can result and genetic bases in original varieties can be broadened from the γ-ray radiation. The study also clarified that the radiation of different cotton varieties resulted in the different variation

  9. Comparative analysis of genetic diversity in Canadian barley assessed by SSR, DarT, and pedigree data.

    Science.gov (United States)

    Lamara, Mebarek; Zhang, Li Yi; Marchand, Suzanne; Tinker, Nicholas A; Belzile, François

    2013-06-01

    The aim of this study was to measure genetic diversity and population structure among 92 Canadian barley cultivars using two types of molecular markers (SSRs and DArTs) and pedigree data. A total of 368 alleles were identified at 50 SSR loci. The number of alleles per locus ranged between 2 and 13 ([Formula: see text] = 7.36) and PIC values ranged from 0.34 to 0.86 ([Formula: see text] = 0.69). For the biallelic DArT markers, the genetic distance matrix was based on 971 markers whose PIC values ranged between 0.06 and 0.50 ([Formula: see text] = 0.39). A third distance matrix was computed based on the kinship coefficient. Clustering of genotypes was performed based on the genetic distance matrix and the three dendrograms obtained showed the genetic relationships among barley cultivars. The topological similarity of the three dendrograms was estimated using a congruence index and showed the three dendrograms to be in very good agreement. Statistical analysis also showed a highly significant correlation between the SSR and DArT matrices (r = 0.80, p 0.5 was 3.8 cM. Information obtained from comparing results of different genetic diversity estimation methods should be useful for the improvement and conservation of barley genetic resources. PMID:23957675

  10. Using SSR Markers For Assessment Genetic Diversity And Detection Drought Escape Candidate Genes In Barley Lines (Hordeum Vulgare L.

    Directory of Open Access Journals (Sweden)

    Gougerdchi Vahideh

    2014-12-01

    Full Text Available Assessment of genetic diversity using molecular markers is one of the primary and important steps in breeding programs. In this study, genetic diversity of 52 barley lines evaluated using 68 SSR primer pairs and 47 primer pairs produced clear and polymorphic banding pattern. In general, 153 polymorphic alleles detected. The number of observed polymorphic alleles varied from 2 to 9, with an average of 3.26 alleles per locus. Polymorphic Information Content (PIC ranged from 0.07 to 0.81, with an average of 0.45. In this research, SSR markers differentiated the studied lines efficiently. Using cluster analysis, studied barley lines divided into two groups. Genetic diversity was relatively corresponding with geographical origins, because the lines related to a country somewhat diverged from each other. Two-rowed Iranian and Chinese barleys classified in one subgroup. Also, most six-rowed barleys classified in one subgroup. Association mapping analysis was used to identify candidate genes for drought escape in barley lines and 16 informative markers were identified after which confirmation in other tests could be suitable for marker assisted breeding drought escape.

  11. Effects of space mutation on P(T) GMS-line Pei'ai 64S of rice and SSR analysis of mutants

    International Nuclear Information System (INIS)

    Some traits of the progenies SP1, SP2 and SP3 derived from Pei'ai 64S treated by space flight of recoverable satellite were studied, and polymorphism analysis of SSR for the mutants were carried out. The results showed that no difference between the treated Pei'ai 64S and the original one in germination rate, survival seedling rate, plant height, heading data and plant type in SP1 was observed, but there was significant difference in fertility, plant height and grain shape in generation of SP2. Some mutants with much bigger stigma than that of the original Pei'ai 64S were obtained in SP3, and it would be useful in improving the out-crossing rate and enhancing the seed production of Pei'ai 64S. In addition, SSR marker analysis for ten mutants indicated that the average mutant frequency of SSR loci for the mutants was 23.33% and the mutant loci randomly distributed along the chromosomes. Among the mutant SSR loci about 55.21% showed changes in band number and 44.78% in molecular weight. DNA deficiency and duplication might be the main reason of mutation caused by space flight. (authors)

  12. The nicotinic alpha7 acetylcholine receptor agonist ssr180711 is unable to activate limbic neurons in mice overexpressing human amyloid-beta1-42

    DEFF Research Database (Denmark)

    Søderman, Andreas; Thomsen, Morten Skøtt; Hansen, Henrik H;

    2008-01-01

    systemic administration of the alpha7 nAChR agonist SSR180711 (10 mg/kg) result in a significant increase in Fos protein levels in the shell of nucleus accumbens in wild-type mice, but has no effect in the transgene mice. There were fewer cell bodies expressing Fos in the prefrontal cortex of transgene...

  13. Genomic rearrangements and signatures of breeding in the allo-octoploid strawberry as revealed through an allele dose based SSR linkage map

    NARCIS (Netherlands)

    Dijk, van T.; Pagliarani, G.; Pikunova, A.; Noordijk, Y.; Yilmaz-Temel, H.; Meulenbroek, B.; Visser, R.G.F.; Weg, van de W.E.

    2014-01-01

    Background Breeders in the allo-octoploid strawberry currently make little use of molecular marker tools. As a first step of a QTL discovery project on fruit quality traits and resistance to soil-borne pathogens such as Phytophthora cactorum and Verticillium we built a genome-wide SSR linkage map fo

  14. Development and Characterization of Novel SSR Markers in Carrot (Daucus Carota L.) and Their Application for Mapping and Diversity Analysis in Apiaceae

    Science.gov (United States)

    Genomic resources in carrot and other Apiaceae are relatively underdeveloped. The availability of a large set of pcr-based codominant markers, such as simple sequence repeats (SSR), would allow integration of the different carrot genetic maps constructed to date (mainly using anonymous dominant mark...

  15. 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.

  16. Population structure revealed by different marker types (SSR or DArT) has an impact on the results of genome-wide association mapping in European barley cultivars

    NARCIS (Netherlands)

    Matthies, I.E.; Hintum, van T.J.L.; Weise, S.; Röder, M.S.

    2012-01-01

    Diversity arrays technology (DArT) and simple sequence repeat (SSR) markers were applied to investigate population structure, extent of linkage disequilibrium and genetic diversity (kinship) on a genome-wide level in European barley (Hordeum vulgare L.) cultivars. A set of 183 varieties could be cle

  17. 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.

  18. Long-term strategy of rehabilitation of Byelorussian territories contaminated by radionuclides

    International Nuclear Information System (INIS)

    Thus, by applying a combination of countermeasures on various technological stages of agricultural production, one can control the process of production and the use of agricultural products, ensuring the production of major foodstuffs in contaminated regions in quantities sufficient for the population living there and in accordance with the consumption standards, and also corresponding to the standards of ecological and radiation safety. The following works in agriculture will require investment by the state: selection of new varieties of agricultural crops and creation of new technologies; development of seed production in a way allowing to reduce the contamination of the final product with radionuclides; refinement of the maps showing contamination of arable land with 137Cs and 90Sr based on the constant monitoring; improvement of pastures and hay fields for the private livestock. The following works are needed to stabilize livestock production and ensure production of clean livestock products in contaminated areas: increase the volume of production for major products made of livestock; equip livestock farms with machinery; improve production of forage at the farms by enhancing the structure of fields sown with forage crops, achieving higher yields, introducing progressive methods of harvesting and storing of forage, introduction of mineral additives and biologically active substances. The realistic assessment of the radioactive situation and its forecast lead to the conclusion that the contaminated territory can be rehabilitated with the help of the combined application of the above mentioned organisational and special measures leading to the reduction of the individual dose to 1 mSv per year. (authors)

  19. Automation of controller's management by train work on the byelorussian ferrous road

    Directory of Open Access Journals (Sweden)

    A.A. Erofeev

    2012-04-01

    Full Text Available The description of the automated system of working out of the look-ahead train schedule is resulted. Appointment, structure and system structure are considered. Requirements to the entrance information are established. Procedures of automatic construction and dispatching updatings of the look-ahead train schedule are regulated

  20. 番茄果实EST资源SSR信息分析%Analysis of SSR Information in EST Resource of Tomato (Solanum lycopersicum ) Fruit

    Institute of Scientific and Technical Information of China (English)

    韩明利; 崔娜; 于志海; 李天来; 侯丽霞

    2011-01-01

    表达序列标签( Expressed sequence tags,EST)中存在广泛的微卫星或简单重复序列(Simple sequence repeats,SSR),为SSR标记的开发提供了宝贵的资源.以NCBI中与番茄(Solanum lycopersicum)果实性状相关EST序列为材料,对EST序列进行聚类去冗余、拼接等前期处理后,再进行EST-SSR搜寻及分析.结果表明:NCBI中与番茄果实性状相关的83 613条EST序列经CAP3拼接后获得18 878个UniGene,其中9 650个Contigs,9 228个Singlets.对UniGene利用MISA软件进行SSR位点搜寻,获得2 039条含有EST-SSR的序列,拼接后的UniGene的检出率为12.62%,包括97种重复基元.其中单核苷酸、二核苷酸、三核苷酸重复占主导地位,三者占总SSR位点数的98.91%.SSR在番茄果实EST上的分布密度为每5 451.6 mer出现1个SSR.%Expressed sequence tags ( ESTs ) are important resources for development of new SSR markers. 83 613 ESTs of the tomato fruit in the database of NCB1 were downloaded and early treatmented, such as being clusterd to redundancy and spliced,and so on. It is concluted that there were 18 878 UniGene after being spliced by CAP3 tool, in which of 9 650 Contigs and 9 228 Singlets. 2 039 EST-SSRs were gotten by using MISA tool searched SSR, accounting for 12.62% of the UniGene and including 97 repeat motifs. Mononucleotide, Dinucle-otide and Trinuclotide were the dominant repeat motifs and occupied 98. 91% in all the number of SSR. Every 5 451. 6 mer appeared a SSR in the ESTs of the tomato fruit of containing SSR.

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

    Science.gov (United States)

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

    2013-01-01

    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. PMID:23970083

  2. 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.

  3. Development of EST-SSR markers in Barringtonia racemosa (Lecythidaceae) and cross-amplification in related species1

    Science.gov (United States)

    Xie, Hongxian; Yuan, Yang; Fang, Xiaoting; Liu, Ying; Yang, Chao; Jin, Jianhua; Tan, Fengxiao; Huang, Yelin

    2015-01-01

    Premise of the study: Microsatellite markers were identified and characterized to study the genetic diversity and structure of Barringtonia racemosa (Lecythidaceae). Methods and Results: Based on the transcriptome data of B. racemosa, 30 primer pairs were initially designed and tested, of which 15 were successfully amplified and displayed clear polymorphisms across the 43 individuals from three distant populations tested in the study. The results showed that the number of alleles per locus ranged from two to seven and the expected heterozygosity and observed heterozygosity per locus varied from 0 to 0.772 and from 0 to 0.933, respectively. Conclusions: The expressed sequence tag–simple sequence repeat (EST-SSR) markers described here will be useful for studying genetic diversity and structure of B. racemosa. Furthermore, all loci were successfully cross-amplified in B. asiatica and B. acutangula and will be of great value for genetic studies across this genus. PMID:26697277

  4. Analysis of SSR information in EST resource of asparagus%芦笋EST资源的SSR信息分析

    Institute of Scientific and Technical Information of China (English)

    吴建霞; 李亚玲; 张智俊; 管雨

    2012-01-01

    To develop asparagus EST -SSRs function of molecular marker, Simple sequence repeats!(SSRs) were investigated in 8590 qualified ESTs downloaded from Nucleotide ESTs database of Lentinula edodes in NCBI . After eliminated redundancy, we got 8377 sequence of nonredundancy, in which there were 469 EST - SSRs, the mean distance was 14.80 kb in non - redundant ESTs. Of the total EST - SSRs, 40.51% (190/469 ) were dinucleotides repeats(DNRs) ,34.79% (164/469) were trinucleotide repeats (TNRs) and 21.11% (99/469) were hexanucle-otide repeats (HNRs). In which the repeat motifs CT/AG were the most abundant up to 13. 22% (62/469). Random filter out 30 EST - SSR sequences, then using primer5 software designed its primers for PCR amplification. 27 of primers showed amplifications, in which 21 pairs could amplify distinct bands ,accounted for 80% (24/30). Al-leles in asparagus were abundant , average 4. 93 each pair. These EST - SSR markers will be useful in studies of population genetics, linkage mapping, molecular mapping, gene tagging, and pedigree analysis and other aspects for this species.%为了在芦笋中开发EST - SSR功能性标记,对来源于NCBI公共数据库的8 590条芦笋(Asparagus officinalis L.)EST序列进行简单重复序列SSR搜索.剔除冗余序列,得到非冗余序列8 377条.在非冗余序列中共挖掘出469个EST - SSR,平均相隔14.80 kb出现1个SSR.在所有的重复基序中,二核苷酸重复基序的SSR所占比例最高40.51% (190/469),其次是三核苷酸34.97% (164/469),六核苷酸21.11%(99/469).在所有基序里,CT/AG出现的频率最高有62次,占全部重复基序的13.22% (62/469).选取含SSR的EST序列30条,并利用primer5软件设计引物,进行SSR位点的扩增,其中27对引物扩增产物,24对有较清晰可靠的目标扩增条带,占引物数的80%,且所检测出的芦笋等位基因数量较丰富,平均4.93个/对.这些EST - SSR标记的开发将有助于芦笋群体遗传多样性、遗传图谱

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. Functional molecular markers (EST-SSR) in the full-sib reciprocal recurrent selection program of maize (Zea mays L.).

    Science.gov (United States)

    Galvão, K S C; Ramos, H C C; Santos, P H A D; Entringer, G C; Vettorazzi, J C F; Pereira, M G

    2015-01-01

    This study aimed to improve grain yield in the full-sib reciprocal recurrent selection program of maize from the North Fluminense State University. In the current phase of the program, the goal is to maintain, or even increase, the genetic variability within and among populations, in order to increase heterosis of the 13th cycle of reciprocal recurrent selection. Microsatellite expressed sequence tags (EST-SSRs) were used as a tool to assist the maximization step of genetic variability, targeting the functional genome. Eighty S1 progenies of the 13th recur-rent selection cycle, 40 from each population (CIMMYT and Piranão), were analyzed using 20 EST-SSR loci. Genetic diversity, observed heterozygosity, information content of polymorphism, and inbreeding co-efficient were estimated. Subsequently, analysis of genetic dissimilarity, molecular variance, and a graphical dispersion of genotypes were conducted. The number of alleles in the CIMMYT population ranged from 1 to 6, while in the Piranão population the range was from 2 to 8, with a mean of 3.65 and 4.35, respectively. As evidenced by the number of alleles, the Shannon index showed greater diversity for the Piranão population (1.04) in relation to the CIMMYT population (0.89). The genic SSR markers were effective in clustering genotypes into their respective populations before selection and an increase in the variation between populations after selection was observed. The results indicate that the study populations have expressive genetic diversity, which cor-responds to the functional genome, indicating that this strategy may contribute to genetic gain, especially in association with the grain yield of future hybrids. PMID:26214413

  11. 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. PMID:26858551

  12. 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

  13. 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

  14. 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

  15. Study on Establishment of cpSSR Marker Technology and Optimization of Its Reaction System in Jatropha curcas Linn%麻疯树cpSSR标记技术的建立与体系优化

    Institute of Scientific and Technical Information of China (English)

    向倩; 周兰英; 万静; 张旭; 雷宝盛; 金银春; 冯毅; 于绪任; 赵晓英

    2009-01-01

    [Objective] The aim of this study was to establish the optimum cpSSR-PCR system for Jatropha curcas Linn. [Method] cpSSR-PCR amplification system for Jatropha curcas Linn influenced by five factors including Taq DNA polymerase, Mg2+, DNA template, dNTP and primer were optimized from several levels. [Result] The optimum concentration of 20 μl reaction system was 10×Buffer, 2.00 mmol/L Mg2+, 2 U/μl Taq DNA polymerase, 0.2 mmol/L dNTP, 0.2 μmol/L primer and 35 ng/μl DNA template. [Conclusion] The optimum annealing temperature for cpSSR-PCR reaction system is 52 ℃, and the cpSSR reaction system is steady and reproducible.

  16. SSR-based Genetic Diversity of Jatropha curcas Germplasm in China%中国麻风树种质资源SSR遗传多样性的研究初报

    Institute of Scientific and Technical Information of China (English)

    蔡郁; 赵华; 陈晓东; 吴国江; 彭俊华

    2011-01-01

    Jatropha curcas is an oil-bearing plant with multiple uses and great potential for energy application. In the present study, we preliminarily investigated genetic diversity of Chinese J. curcas germplasm by using SSR markers. A set of 219 J. curcas samples from all adaptation areas in China was adopted. Twenty pairs of SSR primers and four pairs of eSSR primers were designed based on the public database for nucleotide sequences of J. curcas. These SSR or eSSR well amplified all DNA samples. Among the 24 SSR or eSSR markers, eight ( 33.3% ) detected polymorphism in the J. curcas population. The 24 SSR or eSSR markers amplified 36 loci in total,of which 12 (33.33%) showed polymorphism. The average number of loci amplified by the SSR markers was 1.5. Therefore,there is a modest level of genetic diversity in Chinese J. curcas germplasm.%麻风树(Jatropha curcas)是世界上最有潜力的能源植物之一.本研究针对来自全国6省区的219份麻风树种质资源,应用SSR分子标记对其进行了初步的遗传多样性分析.根据公共数据库中的所有序列设计出了20对SSR及4对eSSR引物,这些引物均能很好地扩增麻风树DNA片段.在上述24个SSR标记中,有8个(33.33%)探测到麻风树群体的DNA多态性.这24个SSR标记共扩增出36个位点,平均每个标记扩增1.5个位点,其中12个(33.33%)位点显现出多态性.这表明中国麻风树是一个具有中等SSR多态性水平的物种,其多态百分率为33.3%.

  17. 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.

  18. 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. PMID:19158670

  19. 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.

  20. EST-derived SSR markers used as anchor loci for the construction of a consensus linkage map in ryegrass (Lolium spp.

    Directory of Open Access Journals (Sweden)

    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.

  1. 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.

  2. Analysis of Genetic Diversity Using Simple Sequence Repeat (SSR) Markers and Growth Regulator Response in Biofield Treated Cotton (Gossypium hirsutum L.)

    OpenAIRE

    Trivedi, Mahendra Kumar

    2015-01-01

    Cotton is the most important crop for the production of fiber that plays a key role in economic and social affairs. The aim of the study was to evaluate the impact of biofield energy treatment on cotton seeds regarding its growth, germination of seedling, glutathione (GSH) concentration, indole acetic acid (IAA) content and DNA fingerprinting using simple sequence repeat (SSR) markers for polymorphism analysis. The seeds of cotton cv. Stoneville-2 (Gossypium hirsutum L.) was obtained from DNA...

  3. 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。

  4. 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

  5. Identification of SSR and RAPD markers linked to a resistance allele for angular leaf spot in the common bean (Phaseolus vulgaris line ESAL 550

    Directory of Open Access Journals (Sweden)

    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.

  6. Development of a gene-centered ssr atlas as a resource for papaya (Carica papaya marker-assisted selection and population genetic studies.

    Directory of Open Access Journals (Sweden)

    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.

  7. Cellular localisation of the kinin B1R in the pancreas of streptozotocin-treated rat and the anti-diabetic effect of the antagonist SSR240612.

    Science.gov (United States)

    Tidjane, Nejla; Gaboury, Louis; Couture, Réjean

    2016-04-01

    The mechanism by which kinin B1 receptor (B1R) contributes to type 1 diabetes is addressed by determining the impact of its inhibition on diabetes and on its pancreatic expression and cellular localisation on immunocompetent cells and primary sensory C-fibres. Rats were made diabetic with streptozotocin (STZ). On day 4, they were treated daily for 7 days with a B1R antagonist (SSR240612, 10 mg/kg) or its vehicle. The surviving β-cells were measured by immunostaining. The expression of B1R, iNOS, TNF-α, macrophages, TCD4+, CGRP and TRPV1 was measured by Western blotting, qRT-PCR and immunofluorescence. Macrophages and TCD4+ lymphocytes were absent in control, but distributed abundantly in the pancreas of STZ-diabetic rats. B1R was upregulated on these immune cells infiltrating the diabetic rat pancreas while it was not expressed on primary sensory C-fibres even if the expression of TRPV1 and CGRP was enhanced. SSR240612 prevented the infiltration of macrophages and TCD4+ lymphocytes and the upregulation of B1R, iNOS, TNF-α and TRPV1. SSR240612 corrected hyperglycaemia and hypoinsulinaemia by improving the Langerhans islets survival or regeneration. It is concluded that kinin B1R antagonism exerts anti-diabetic action by preventing the infiltration of immune cells in the pancreas and by preserving the integrity of Langerhans islets β-cells. PMID:26841446

  8. 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.

  9. DArT markers: diversity analyses, genomes comparison, mapping and integration with SSR markers in Triticum monococcum

    Directory of Open Access Journals (Sweden)

    Huttner Eric

    2009-09-01

    Full Text Available Abstract Background Triticum monococcum (2n = 2x = 14 is an ancient diploid wheat with many useful traits and is used as a model for wheat gene discovery. DArT (Diversity Arrays Technology employs a hybridisation-based approach to type thousands of genomic loci in parallel. DArT markers were developed for T. monococcum to assess genetic diversity, compare relationships with hexaploid genomes, and construct a genetic linkage map integrating DArT and microsatellite markers. Results A DArT array, consisting of 2304 hexaploid wheat, 1536 tetraploid wheat, 1536 T. monococcum as well as 1536 T. boeoticum representative genomic clones, was used to fingerprint 16 T. monococcum accessions of diverse geographical origins. In total, 846 polymorphic DArT markers were identified, of which 317 were of T. monococcum origin, 246 of hexaploid, 157 of tetraploid, and 126 of T. boeoticum genomes. The fingerprinting data indicated that the geographic origin of T. monococcum accessions was partially correlated with their genetic variation. DArT markers could also well distinguish the genetic differences amongst a panel of 23 hexaploid wheat and nine T. monococcum genomes. For the first time, 274 DArT markers were integrated with 82 simple sequence repeat (SSR and two morphological trait loci in a genetic map spanning 1062.72 cM in T. monococcum. Six chromosomes were represented by single linkage groups, and chromosome 4Am was formed by three linkage groups. The DArT and SSR genetic loci tended to form independent clusters along the chromosomes. Segregation distortion was observed for one third of the DArT loci. The Ba (black awn locus was refined to a 23.2 cM region between the DArT marker locus wPt-2584 and the microsatellite locus Xgwmd33 on 1Am; and the Hl (hairy leaf locus to a 4.0 cM region between DArT loci 376589 and 469591 on 5Am. Conclusion DArT is a rapid and efficient approach to develop many new molecular markers for genetic studies in T. monococcum. The

  10. 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

  11. SSR Analysis of Maize Regenerated Haploid Plants%玉米单倍体再生植株的SSR分析

    Institute of Scientific and Technical Information of China (English)

    黄敏; 杜何为

    2011-01-01

    10 haploid regenerated maize (Zea mays L.) plants were analyzed using 47 pairs of SSR markers. Results showed that no somaclonal variation was found in the haploid plants as their banding patterns were all from their parents'. Among the 47 SSR markers, 29 were polymorphic between maize inbred line Zheng58 and B73; while 16 were polymorphic between Xi502 and Chang72. According to the analysis on genetic similarity coefficient, the 6 haploid plants derived coming from Zheng58/B73 were genetic segregated toward B73 as their genetic similarity coefficients with Zheng58 (51.06%~61.70%) were all smaller than that with B73 (76.60%~87.23%); While no segregation distortion was detected in the 4 haploid plants with genetic background of Xi502/Chang72.%使用47个SSR标记,对10株玉米(Zea mays L.)单倍体再生植株进行了遗传分析,结果表明,单倍体植株的带型均来源于其亲本,未发现无性系变异.分别筛选出29对在郑58与B73间有多态性、16对在西502与昌72间有多态性的引物,对单倍体植株与其亲本间的遗传相似性系数进行分析,发现来源于郑58/B73的6株单倍体植株与郑58的遗传相似性系数(51.06% ~61.70%)均小于其与B73的遗传相似性系数(76.60%~87.23%),发生了偏向于B73的遗传分离;具有西502/昌72遗传背景的4株单倍体植株未见偏分离现象.

  12. 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

  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. A genetic linkage map of marine shrimp Penaeus ( Fenneropenaeus) chinensis based on AFLP, SSR, and RAPD markers

    Science.gov (United States)

    Liu, Bo; Wang, Qingyin; Li, Jian; Liu, Ping; He, Yuying

    2010-07-01

    The Chinese shrimp Penaeus ( Fenneropaeneus) chinensis is an important species in marine fishery and aquaculture in China. A female Chinese shrimp Penaeus ( Fenneropaeneus) chinensis was captured from west coast of the Korean peninsula and mated with a “Yellow Sea No. 1” male to produce the first filial generation (F1) 100 F2 full-sib progeny from brother-sister crosses between F1 families was used for the mapping study. A genetic linkage map of the Chinese shrimp was constructed, based on 354 markers, including 300 amplified fragment length polymorphism (AFLP) markers, 42 microsatellite (SSR) markers, and 12 randomly amplified polymorphism (RAPD) markers. Forty-seven linkage groups (LGs) were identified. The total map length was 4 580.5 cM, with an average spacing of 11.3 cM, covering 75.8% of the estimated genome size. The construction of this genetic linkage map was part of a genetic breeding program. This linkage map will contribute to the discovery of genes and quantitative trait loci (QTLs) in Chinese shrimp.

  16. 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.

  17. 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

  18. Detection of Allelic Variation in Chinese Wheat (Triticum aestivum L.) Germplasm with Drought Tolerance Using SSR Markers

    Institute of Scientific and Technical Information of China (English)

    JING Rui-lian; CHANG Xiao-ping; Marcello Broggio; JIA Ji-zeng

    2002-01-01

    Allelic variation in two domestic wheat landraces, Pingyaobaimai and Mazhamai, two cornerstone breeding materials and their derived cultivars with drought tolerance was detected by SSR (simple sequence repeat) markers. The clustering of 25 accessions showed that the similarity between Pingyaobaimai and Yanda1817, the latter was developed from the former, was 0.71, the highest one of all accessions, but the similarities were very low between these two accessions and other accessions including their derived cultivars. A similar situation was revealed between Mazhamai and its derived cultivars. Pingyaobaimai and its three derived cultivars shared three alleles at loci Xgwm526, Xgwm538 and Xgwm126 on chromosome arms 2BL, 4BL and 5AL, respectively. There were six shared alleles in Mazhamai and its derived cultivars, in order of Xgwm157,Xgwm126, Xgwm212, Xgwm626, Xgwm471 and Xgwm44 on chromosome arms 2DL, 5AL, 5DL, 6BL, 7AS and 7DC, respectively. Only one shared allele was detected between the pedigrees of Pingyaobaimai and Mazhamai. The difference of shared alleles in two cornerstone breeding materials and their derived cultivars revealed the diversity in Chinese wheat germplasm with drought tolerance and the complication in genetic basis of drought tolerance in wheat.

  19. 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

    2016-01-01

    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. PMID:26853908

  20. 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.

  1. 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.

  2. 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.

  3. 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

    2016-01-01

    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.

  4. Isolation and Characterization of Novel Genomic and EST-SSR Markers in Coreoperca whiteheadi Boulenger and Cross-Species Amplification

    Directory of Open Access Journals (Sweden)

    YaQi Dou

    2012-10-01

    Full Text Available We described and characterized 11 expressed sequence tag (EST-derived simple sequence repeats (SSR and seven genomic (G-derived SSRs in Coreoperca whiteheadi Boulenger. The EST-SSRs comprised 62.2% di-nucleotide repeats, 32.2% tri-nucleotide repeats and 5.5% tetra-nucleotide repeats, whereas the majority of the G-SSRs were tri-nuleotide repeats (81.4%. The number of alleles for the 18 loci ranged from 3 to 6, with a mean of 3.8 alleles per locus. The observed (Ho and expected heterozygosities (He values ranged from 0.375 to 1.000, and 0.477 to 0.757, respectively. The polymorphic information content (PIC values ranged from 0.466 to 0.706. The mean values number of alleles, Ho, He, and PIC of EST-SSRs were higher than those of the G-SSRs. Four microsatellite loci deviated significantly from Hardy-Weinberg equilibrium (HWE after Bonferroni correction and no significant deviations in linkage disequilibrium (LD were observed. These loci are the first to be characterized in C. whiteheadi and should be useful in the investigation of a genetic evaluation for conservation. Compared with 11 loci in C. whiteheadi, 37 potential polymorphic EST-SSRs were found in Siniperca chuatsi (Basilewsky, which will provide a valuable tool for mapping studies and molecular breeding programs in S. chuatsi.

  5. 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.

  6. 虫草属EST-SSR标记系统的建立研究%Study of EST-SSR marker system of Cordyceps

    Institute of Scientific and Technical Information of China (English)

    管俊娇; 虞泓; 解云峰; 左世梅; 马荣锋; 曾文波

    2011-01-01

    Objective: To establish the EST-SSR marker system for Cordyceps by using ESTs of C. Bassiana and C. mUitaris. Method; The ESTs of Cordyceps were downloaded from the public database of NCBI, and the redundant ESTs with low quality were removed. The EST-SSR primers were designed by Sequece Seiner 1.2. And the primers were screened through PAGE-Electrophoresis. Result; The 4 556 non-redundant ESTs which from C. Bassiana with total length of 2 953 173 bp were selected. 718 EST-SSRs distributed in 616 ESTs were totally screened out, accounting for 15. 8%of the non-redundant ESTs. It was discovered that the average distance of EST-SSSR was 1/4 0% bp in EST-SSRs distribution of C. Bassiana. Trinucleotide repeats were the most abundant types with 419 repeated sequences. Regarding to C. Militaris, totally 1 363 non-redundant ESTs were acquired, from which 1 117 EST-SSRs were screened, and rate of SSR sites in ESTs was 81. 95%. The leading motif of SSR was nucleotide A. The 50 pairs of EST-SSR primers were designed according to the ESTs of C. Bassiana,and preliminary test showed the 34 pairs of primers amplified clear fragments,accounting for 68% of all primers. Furthermore, the 39 of the 40 pairs of primers from the ESTs of C. Militaris were found to be amplified as the clear fragments, accounting for 97. 5%. The phylogenetic analysis revealed that different anamorph of Cordyceps spieces were divided into four branches. Conclusion: The EST-SSR of Cordyceps had comparably higher utility value. The EST-SSR markers developed from ESTs of C. Bassiana and C. Militaris had well transferability in Cordyceps. And it was suggested that the EST-SSR markers should be an easy and effective way to assay molecular genetic structure of Cordyceps.%目的:通过球孢虫草、蛹虫草EST设计EST-SSR引物,建立虫草属EST-SSR标记系统.方法:从NCBI公共数据库下载获得虫草EST,利用Sequece Seiners 1.2软件去除冗余序列并设计引物,进行PAGE电泳.结果:通过去

  7. 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

  8. 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

  9. In vivo imaging of neuro-inflammation in the rodent brain with [11C]SSR180575, a novel indoleacetamide radioligand of the translocator protein (18 kDa)

    International Nuclear Information System (INIS)

    Purpose Neuro-inflammation is involved in neurological disorders through the activation of micro-glial cells. Imaging of neuro-inflammation with radioligands for the translocator protein (18 kDa) (TSPO) could prove to be an attractive bio-marker 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 neuro-protective effects. Methods Here we report the radiolabelling of SSR180575 with 11C and in vitro and in vivo imaging in an acute model of neuro-inflammation in rats. Results The image contrast and the binding of [11C] SSR180575 are higher than that obtained with the isoquinoline- based TSPO radioligand, [11C]PK11195. Competition studies demonstrate that [11C]SSR180575 has high specific binding for the TSPO. Conclusion [11C]SSR180575 is the first PET radioligand for the TSPO based on an indoleacetamide scaffold designed for imaging neuro-inflammation in animal models and in the clinic. (authors)

  10. 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.

  11. Black Locust (Robinia pseudoacacia L. Root Cuttings: Diversity and Identity Revealed by SSR Genotyping: A Case Study

    Directory of Open Access Journals (Sweden)

    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.

  12. Development of SSR and gene-targeted markers for construction of a framework linkage map of Catharanthus roseus

    Science.gov (United States)

    Shokeen, Bhumika; Choudhary, Shalu; Sethy, Niroj Kumar; Bhatia, Sabhyata

    2011-01-01

    Background and Aims Catharanthus roseus is a plant of great medicinal importance, yet inadequate knowledge of its genome structure and the unavailability of genomic resources have been major impediments in the development of improved varieties. The aims of this study were to develop co-dominant sequence-tagged microsatellite sites (STMS) and gene-targeted markers (GTMs) and utilize them for the construction of a framework intraspecific linkage map of C. roseus. Methods For simple sequence repeat (SSR) isolation, a genomic library enriched for (GA)n repeats was constructed from C. roseus ‘Nirmal’ (CrN1). In addition, GTMs were also designed from 12 genes of the TIA (terpenoid indole alkaloid) pathway – the medicinally most significant pathway in C. roseus. An F2 mapping population was also generated by crossing two diverse accessions of C. roseus CrN1 (Nirmal)×CrN82 (Kew). Key Results A new set of 314 STMS markers and 64 GTMs were developed in this study. A segregating F2 mapping population consisting of 111 F2 individuals was generated. For generating the linkage map, a set of 423 co-dominant markers (378 newly developed and 45 published earlier) were screened for polymorphism between the parental genotypes, of which 134 were identified to be polymorphic. A total of 114 markers were mapped on eight linkage groups that spanned a 632·7 cM region of the genome with an average marker distance of 5·55 cM. Further, the mechanism of hypervariability at the gene-targeted loci was investigated at the sequence level. Conclusions For the first time, a large array of STMS markers and GTMs was generated in the model medicinal plant C. roseus. Moreover, the first microsatellite marker-based linkage map was described in this study. Together, these will serve as a foundation for future genomics studies related to quantitative trait loci analysis and molecular breeding in C. roseus. PMID:21788377

  13. 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

  14. A genetic linkage map with 178 SSR and 1 901 SNP markers constructed using a RIL population in wheat (Triticum aestivum L.)

    Institute of Scientific and Technical Information of China (English)

    ZHAI Hui-jie; FENG Zhi-yu; LIU Xin-ye; CHENG Xue-jiao; PENG Hui-ru; YAO Ying-yin; SUN Qi-xin; NI Zhong-fu

    2015-01-01

    The construction of high density genetic linkage map provides a powerful tool to detect and map quantitative trait loci (QTLs) control ing agronomical y important traits. In this study, simple sequence repeat (SSR) markers and Il umina 9K iSelect single nucleotide polymorphism (SNP) genechip were employed to construct one genetic linkage map of common wheat (Triticum aestivum L.) using 191 recombinant inbred lines (RILs) derived from cross Yu 8679×Jing 411. This map included 1 901 SNP loci and 178 SSR loci, covering 1 659.9 cM and 1 000 marker bins, with an average interval distance of 1.66 cM. A, B and D genomes covered 719.1, 703.5 and 237.3 cM, with an average interval distance of 1.66, 1.45 and 2.9 cM, respectively. Notably, the genetic linkage map covered 20 chromosomes, with the exception of chromosome 5D. Bioinformatics analysis revealed that 1 754 (92.27%) of 1 901 mapped SNP loci could be aligned to 1 215 distinct wheat unigenes, among which 1 184 (97.4%) were located on one single chromosome, and the rest 31 (2.6%) were located on 2 to 3 chromosomes. By performing in silico comparison, 214 chromosome deletion bin-mapped expressed sequence tags (ESTs), 1 043 Brachypodium genes and 1 033 rice genes were further added onto the genetic linkage map. This map not only integrated genetic and physical maps, SSR and SNP loci, respectively, but also provided the information of Brachypodium and rice genes corresponding to 1 754 SNP loci. Therefore, it wil be a useful tool for comparative genomics analysis, ifne mapping of QTL/gene control ing agronomical y important traits and marker-assisted selection breeding in wheat.

  15. Analysis of Gene Expression Profiles in Leaf Tissues of Cultivated Peanuts and Development of EST-SSR Markers and Gene Discovery.

    Science.gov (United States)

    Guo, Baozhu; Chen, Xiaoping; Hong, Yanbin; Liang, Xuanqiang; Dang, Phat; Brenneman, Tim; Holbrook, Corley; Culbreath, Albert

    2009-01-01

    Peanut is vulnerable to a range of foliar diseases such as spotted wilt caused by Tomato spotted wilt virus (TSWV), early (Cercospora arachidicola) and late (Cercosporidium personatum) leaf spots, southern stem rot (Sclerotium rolfsii), and sclerotinia blight (Sclerotinia minor). In this study, we report the generation of 17,376 peanut expressed sequence tags (ESTs) from leaf tissues of a peanut cultivar (Tifrunner, resistant to TSWV and leaf spots) and a breeding line (GT-C20, susceptible to TSWV and leaf spots). After trimming vector and discarding low quality sequences, a total of 14,432 high-quality ESTs were selected for further analysis and deposition to GenBank. Sequence clustering resulted in 6,888 unique ESTs composed of 1,703 tentative consensus (TCs) sequences and 5185 singletons. A large number of ESTs (5717) representing genes of unknown functions were also identified. Among the unique sequences, there were 856 EST-SSRs identified. A total of 290 new EST-based SSR markers were developed and examined for amplification and polymorphism in cultivated peanut and wild species. Resequencing information of selected amplified alleles revealed that allelic diversity could be attributed mainly to differences in repeat type and length in the SSR regions. In addition, a few additional INDEL mutations and substitutions were observed in the regions flanking the microsatellite regions. In addition, some defense-related transcripts were also identified, such as putative oxalate oxidase (EU024476) and NBS-LRR domains. EST data in this study have provided a new source of information for gene discovery and development of SSR markers in cultivated peanut. A total of 16931 ESTs have been deposited to the NCBI GenBank database with accession numbers ES751523 to ES768453. PMID:19584933

  16. Genetic diversity and geographical differentiation of cultivated six-rowed naked barley landraces from the Qinghai-Tibet plateau of China detected by SSR analysis

    Directory of Open Access Journals (Sweden)

    Zong-Yun Feng

    2006-01-01

    Full Text Available Cultivated six-rowed naked barley (Hordeum vulgare ssp. hexastichon var. nudum Hsü is the oldest cultivated barley in China. We used 35 simple sequence repeat (SSR markers selected from seven barley linkage groups to study the genetic diversity, geographical differentiation and evolutionary relationships among 65 H. vulgare ssp. hexastichon landrace accessions collected from the Qinghai-Tibet plateau of China, 25 accessions from Tibet (TB, 20 from Qinghai (QH and 20 from Ganzi (GZ prefecture in Sichuan province. At the 35 SSR loci we identified 248 alleles among the 65 accessions, 119 (47.98% of the alleles being common alleles. We also found that the TB accessions possessed 47 private alleles, about 1.5 times more than the 31 private alleles found in the QH accessions and about 5 times more than 9 private alleles found in the GZ accessions. Generally, the TB accessions showed significantly higher genetic diversity than either the QH or GZ accessions whereas no significant difference in genetic diversity was found between the QH and GZ accessions. Partitioning analysis of genetic diversity showed that about 81% of the total variation was due to within-subgroup diversity and about 19% was clearly accounted for by geographical differentiation among the three subgroups. The distributions of alleles for most loci (71.4% were significantly different among the three subgroups and geographical differentiation could be found according to the distribution of SSR alleles. Cluster analysis indicated that most of the accessions could be clustered into groups which basically coincided with their geographical distribution. These results suggest that Tibet might be a center of genetic diversity for cultivated barley, the cultivated six-rowed naked barley on the Qinghai-Tibet plateau of China may have evolved in Tibet and spread to Qinghai and then to Ganzi prefecture of Sichuan province.

  17. 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.

  18. Novel SSR markers from BAC-end sequences, DArT arrays and a comprehensive genetic map with 1,291 marker loci for chickpea (Cicer arietinum L..

    Directory of Open Access Journals (Sweden)

    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.

  19. Komparativní studie vybraných parametrů hráčů fotbalových reprezentačních týmů ČSSR a ČR v sezonách, kdy získal Josef Masopust a Pavel Nedvěd cenu "Zlatý míč"\\\\

    OpenAIRE

    Dvořák, Jan

    2008-01-01

    In my thesis I deal with exclude switches. The thesis is specialized on fourteen football representatives of ČSSR team and fourteen football representatives of ČR team with most implications in representative matches. The work is specialized on period by 1962 for ČSSR team and by 2003 for ČR team.

  20. Construction of full-length cDNA library and development of EST-derived simple sequence repeat (EST-SSR) markers in Senecio scandens.

    Science.gov (United States)

    Qian, Gang; Ping, Junjiao; Lu, Jian; Zhang, Zhen; Wang, Lei; Xu, Delin

    2014-12-01

    Senecio scandens Buch.-Ham. ex D. Don (Compositae) is a crucial source of Chinese traditional medicine with antibacterial properties. We constructed a cDNA library and obtained expressed sequence tags (ESTs) to show the distribution of gene ontology annotations for mRNAs, using an individual plant with superior antibacterial characteristics. Analysis of comparative genomics indicates that the putative uncharacterized proteins (21.07%) might be derived from "molecular function unknown" clones or rare transcripts. Furthermore, the Compositae had high cross-species transferability of EST-derived simple sequence repeats (EST-SSR), based on valid amplifications of 206 primer pairs developed from the newly assembled expressed sequence tag sequences in Artemisia annua L. Among those EST-SSR markers, 52 primers showed polymorphic amplifications between individuals with contrasting diverse antibacterial traits. Our sequence data and molecular markers will be cost-effective tools for further studies such as genome annotation, molecular breeding, and novel transcript profiles within Compositae species. PMID:25007751

  1. Changes of genetic diversity of maize inbred lines over four decades of hybrid breeding in the Bc institute revealed by SSR markers

    Directory of Open Access Journals (Sweden)

    Buhiniček Ivica

    2015-01-01

    Full Text Available In this paper, changes of genetic diversity of the most important maize inbred lines used for hybrid production within the Bc Institute in the 1970s, 1980s, 1990s and 2000s were examined using the SSR markers. The average number of alleles per SSR locus was 3.14, 3.43, 3.07 and 3.25 for lines from 1970s, 1980s, 1990s and 2000s, whereas the number of private alleles for the same four decades was 8, 4, 0 and 6, respectively. Mean genetic distance among inbreds within decades steadily decreased over time from 0.64 in 1970s to 0.57 in 2000s, but the observed differences were not statistically significant. The clustering of the studied inbred lines indicates the exploitation of a known BSSS x LSC heterotic pattern within the Bc Institute maize breeding program. The overall results show that recycled inbred lines within these pools do not decline in genetic variation over the past 40 years.

  2. 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.

  3. 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.

  4. 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

  5. 基于cpSSR分子标记的香蕉种质资源分类%The classification of Musa species using chloroplast SSR primers

    Institute of Scientific and Technical Information of China (English)

    李博; 冯慧敏; 王静毅; 童和林; 陈友; 武耀廷

    2011-01-01

    Choroplast genome was involved in the development of cpSSR primer pairs in Musa and the transferability of cpSSR markers from other plants across Musa wild species was observed. A set of 16 polymorphic cpSSR primers were selected to classify 42 related species/subspecies. A total of 86 polymorphic bands with an average of 5.5 bands (range 2 to 8) were identified. The PIC values ranged from 0.188 9 to 0.780 5. The UPGMA dendrogram divided the banana accessions into three main groups based on the similarity coefficient 0.76. Group Ⅰ included all the subspecies of M. acuminata and all the cultivated banana varieties. All the materials of M. balbisiana formed Group Ⅱ. Group m included all the wild materials except the species/subspecies of M. acuminata and M. balbisiana. The results showed that cpSSR marker was useful to distinguish the related species of Musa. The cluster analysis of cpSSR in present study revealed that the wild species/subspecies could be well grouped according to the geographical origin and but not to the morphological characters.%应用cpSSR分子标记来研究香蕉种质资源分类,用筛选到的16对多态性引物对42份香蕉材料进行扩增.共检测出86个多态性条带,每对引物产生的多态性条带为2~8,平均为5.5,多态信息含量为0.1889~0.7805。在相似系数为0.76时,供试的42份香蕉材料分成3大类群:类群Ⅰ为M.acuminata的全部亚种和供试的所有栽培蕉品种;类群Ⅱ为供试的全部M.balbisiana材料;类群Ⅲ为除了M.acuminata和M.balbisiana外其他全部供试的野生蕉材料。结果表明基于cpSSR分子标记的香蕉种质资源的分类在种间具有较好的区分能力,但是cpSSR分类表现出较大的地理分布的相关性,而与形态特征关系不密切。

  6. 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.

  7. 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.

  8. A Comparative Study of SSR Diversity in Chinese Major Rice Varieties Planted in 1950s and in the Recent Ten Years (1995-2004)

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Forty pairs of SSR markers were used to compare the genetic diversity changes in 151 Chinese major rice varieties planted in 1950s and in the recent ten years. Of 40 SSR loci, 39 were found to be polymorphic while one locus(RM479) monomorphic. A total of 213 alleles were identified from the 39 polymorphic loci. The average number of alleles per locus (Na) was of 5.5, ranging from 2 to 11. Nei's gene diversity index (He) varied drastically among loci from 0.309 at RM174to 0.869 at RM418, with an average value of 0.649. There existed significant difference in SSR allelic diversity between indica and japonica subspecies, and indica had more variation than japonica both in Na and He. By comparison with the genetic changes in Na and He, it was revealed that the varieties planted in 1950s had more alleles and higher He than those in the recent ten years both for indica and japonica rices. The difference between two subspecies for Na was significant in a tendency over.time (indica: z = 2.677, P = 0.007; japonica: z = 3.441, P = 0.001), but not significant for He (indica: z = 1.471,P = 0.141; japonica: z = 1.932, P = 0.053). Analysis of molecular variance (AMOVA) indicated that there existed significant difference (P < 0.05) in genetic variation between the two periods, of which more genetic variation was contributed by indica(Fst = 0.050) and japonica (Fst = 0.082) subsets. Using locus-by-locus AMOVA procedure, significant genetic differentiations were observed in 13 loci (RM21, RM128, RM147, RM169, RM190, RM221, RM231, RM251, RM253, RM317, RM341,RM418, and RM478) for indica varieties and 11 loci (RM101, RM135, RM152, RM159, RM169, RM190, RM251, RM253,RM311, RM418, and RM478) for japonica ones between the two periods. It was found some alleles had been lost in current major rice varieties as comparing with those in 1950s. Therefore, it should be necessary to exploit more alien elite genetic resources for extension of genetic background in current rice breeding program.

  9. Development and Application of EST-SSR Markers in Pepper%辣椒EST-SSR标记的开发与应用

    Institute of Scientific and Technical Information of China (English)

    吴智明; 刘伟强; 唐鑫; 崔竣杰; 程蛟文; 胡开林

    2012-01-01

    通过对数据库中32 295条非冗余的辣椒EST序列进行搜索,发现3 396个SSR分布于3 277条EST序列中,EST-SSR频率为10.52%,平均分布距离为4.46 kb.在辣椒EST-SSR中,二核苷酸和三核苷酸重复基元占主导地位,分别占总SSR的43.02%和37.84%.优势重复基元为GA/TC、AG/CT和AT,分别占15.99%、11.98%和11.37%.用Primer Premier 5.0软件设计了420对引物,对辣椒抗疫病自交系‘B072’和感疫病自交系‘B088’进行PCR扩增,403对引物有扩增产物,引物有效扩增率为95.96%,其中76对引物有多态性,多态性引物占可扩增引物的18.86%.试验证明,利用辣椒EST序列开发SSR标记是可行的.%A total of 32 295 non-redundant expressed sequence tags (ESTs) in pepper were screened by using bioinformatics software to search for SSR motifs, 3 396 SSRs were sought out, distributing in 3 277 ESTs, corresponding to one SSR in every 4. 46 kb of the ESTs. Dinucleotide and trinucleotide repeats were major types among the obtained unigenes, accounting for 43. 02% and 37. 84% , respectively. GA/ TC (15. 99% ) , AG/CT( 11. 98% ) and AT( 11. 37% ) were the most abundant motifs. Based on the flanking sequences of these 3 396 SSRs, 420 primer pairs were designed by using Primer Premier 5. 0 software. 403 SSRs (95. 96% ) were successfully amplified and 76 of them (18. 86% ) showed polymorphism between ' B072' (the resistance inbred line) and ' B088' (the susceptible inbred line). These results proved that it is an effective and feasible approach to developing SSR markers based on ESTs in Capsicum annuum L.

  10. 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

  11. 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.

  12. 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.

  13. Progress in the way to develop SSR molecular marker%SSR分子标记的开发技术研究进展

    Institute of Scientific and Technical Information of China (English)

    唐荣华; 张君诚; 吴为人

    2002-01-01

    综述简单重复序列标记(SSR)的特点及在作物遗传图谱构建、品种鉴定及分子标记辅助育种等方面的应用价值.重点描述开发SSR标记的两种方法的基本原理和主要步骤,一种是通过克隆酶切片段和大量测序寻找SSR标记的传统方法,一种是应用SAGE原理不需要克隆的STMP技术.介绍这两种方法在创建小麦或大豆SSR标记中的应用.它们都能有效地开发可扩增出特定位点SSR的PCR引物.

  14. The alpha7 nicotinic receptor agonist SSR180711 increases activity regulated cytoskeleton protein (Arc) gene expression in the prefrontal cortex of the rat

    DEFF Research Database (Denmark)

    Kristensen, Søren; Thomsen, Morten Skøtt; Hansen, Henrik H;

    2007-01-01

    Nicotinic alpha7 acetylcholine receptors (alpha7 nAChR) have been shown to enhance attentional function and aspects of memory function in experimental models and in man. The protein Arc encoded by the effector immediate early gene arc or arg3.1 has been shown to be strongly implicated in long......-term memory function. We have sought to determine if alpha7 nAChR mediate the stimulation of arc gene expression, and if so, where in the brain such activation may occur using semi-quantitative in situ hybridisation. Administration of the novel and selective alpha7 nAChR agonist, SSR180711 (1, 3 and 10 mg...

  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. 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.

  17. Genetic Diversity Analysis of Hulless Barley Germplasm by SSR Markers%青稞种质资源的SSR标记遗传多样性分析

    Institute of Scientific and Technical Information of China (English)

    吴昆仑

    2011-01-01

    Hulless barley is the typical crop in Tibetan Plateau.The genetic diversity of 55 hulless barley materials from Tibetan Plateau was studied by SSR markers.A total of 48 alleles were identified at 13 polymorphic SSR loci.The number of alleles per locus ranged from 2 to 10 with an average of 3.7,1 to 21 genotypes could be detected by the polymorphic loci,and Nei's gene diversity index ranged from 0 to 0.4998 with an average of 0.2921.Shannon information index ranged from 0 to 0.6930 with an average of 0.4461.All of the results indicated that the genetic diversity of hulless barley from Tibetan Plateau was abundant.There was a great difference among the hulless barley cultivars from different ecological regions.The alleles of 15 materials from Yunnan were more than Tibet,Sichuan and Qinghai,with the highest of Nei's gene diversity index,and the lowest Shannon information index.The genetic diversity of Yunnan was the most abundant,while Sichuan was the less.The materials were divided into five groups by cluster analysis,and some materials were not distinguished clearly by cluster analysis based on ecological types,indicating that growth habits of these materials were independent with related behaviors of SSR primer loci,but clustering based on SSR polymorphism was related to ecological areas generally.Obtaining the affinity of hulless barley materials by cluster analysis would provide references for genetic study and breeding.%为了明确青藏高原青稞种质资源的遗传多样性,并为青稞育种提供依据,利用分布于青稞14条染色体长、短臂上的14对SSR引物对来自青藏高原区域内西藏、青海、四川和云南的55份青稞材料的遗传多样性进行了分析。结果表明,每个位点检测出的等位基因数为2~10个,共检测出总位点数48个,平均3.7个,各多态位点检测出基因型为1~21种,Nei’s基因多样性指数为0~0.4998,平均为0.2921,Shannon信息指数为0~0.6930,平均为0.4461,表明

  18. The principle of laughter in Byelorussian vocal culture as a form of reflection on images of the world

    Directory of Open Access Journals (Sweden)

    Tawlai Galina V.

    2014-01-01

    Full Text Available This paper considers particular ways of organizing musical material in songs connected with the culture of laughter, as well as the coordination and interaction of different artistic spheres in this group of traditional Belarus song forms. Our long standing, complex ethno-musicological research, constant documentations of our own field work, comparison of ritual songs’ stylistics with their respective cognitive methods, together with observations and generalizations made by the real exponents of traditional Belarus song have given us the possibility to hear and recognize this strict, logically-adjusted selection of forms of musical expressiveness among folk melodies.

  19. Organization of nuclear education at the Faculty of Chemistry of the Byelorussian state university: progress and problems

    International Nuclear Information System (INIS)

    The strategy of the nuclear education in the Republic of Belarus is discussed. Nuclear knowledge management course is introduced into the curricular according to the IAEA recommendations. Podcasting lectures, advanced handbooks, interdisciplinary courses, cooperative learning is the main components of the nuclear education processes. The aspects of the interaction between the university and employers are considered

  20. 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.

  1. A genetic linkage map with 178 SSR and 1 901 SNP markers constructed using a RIL population in wheat (Triticum aestivum L.)

    Institute of Scientific and Technical Information of China (English)

    ZHAI Hui-jie; FENG Zhi-yu; LIU Xin-ye; CHENG Xue-jiao; PENG Hui-ru; YAO Ying-yin; SUN Qi-xin; NI Zhong-fu

    2015-01-01

    The construction of high density genetic linkage map provides a powerful tool to detect and map quantitative trait loci (QTLs) controlling agronomically important traits. In this study, simple sequence repeat (SSR) markers and Illumina 9K iSelect single nucleotide polymorphism (SNP) genechip were employed to construct one genetic linkage map of common wheat (Triticum aestivum L.) using 191 recombinant inbred lines (RILs) derived from cross Yu 8679xJing 411. This map included 1 901 SNP loci and 178 SSR loci, covering 1 659.9 cM and 1 000 marker bins, with an average interval distance of 1.66 cM. A, B and D genomes covered 719.1,703.5 and 237.3 cM, with an average interval distance of 1.66, 1.45 and 2.9 cM, respectively. Notably, the genetic linkage map covered 20 chromosomes, with the exception of chromosome 5D. Bioinformatics analysis revealed that 1 754 (92.27%) of 1 901 mapped SNP loci could be aligned to 1 215 distinct wheat unigenes, among which 1 184 (97.4%) were located on one single chromosome, and the rest 31 (2.6%) were located on 2 to 3 chromosomes. By performing in silico comparison, 214 chromosome deletion bin-mapped expressed sequence tags (ESTs), 1 043 Brachypodium genes and 1 033 rice genes were further added onto the genetic linkage map. This map not only integrated genetic and physical maps, SSR and SNP loci, respectively, but also provided the information of Brachypodium and rice genes corresponding to 1 754 SNP loci. Therefore, it will be a useful tool for comparative genomics analysis, fine mapping of QTL/gene controlling agronomically important traits and marker-assisted selection breeding in wheat.

  2. 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.

  3. 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.

  4. Development and Utilization of EST-SSR Marker in Sugarbeet (Beta vulgaris L.)%甜菜EST-SSR引物的开发与应用

    Institute of Scientific and Technical Information of China (English)

    史树德; 魏磊; 张子义; 邵金旺; 田自华

    2011-01-01

    利用NCBI公共数据库现有的甜菜(Beta vulgaris L.)表达序列标签(expressed sequence tags,EST)数据信息,开发了甜菜EST-SSR标记.在所有的29830条甜菜EST序列中共确认得到20109条非冗余EST序列,总长为11287.6kb.在含有微卫星重复的6951条EST序列中按照SSR引物设计要求,最终获得了2845个EST-SSR,平均每3.96 kb含有1个SSR.EST-SSR的分布频率和特征分析表明,A/T单碱基重复最多,其次是AAG/CTT三核苷酸重复,AG/CT二核苷酸重复,ACCTCC/AGGTGG等六核苷酸重复最少.随机合成了100对SSR引物,并分别选用6个甜菜品种进行多态性检验,将其按遗传相似性分为两组,多态信息含量(polymorphism information content,PIC)平均值为0.47.本研究证实这种全新的开发甜菜SSR标记的方法具有高效、多态性较高的特点,在甜菜遗传多样性分析、功能基因定位、遗传图谱构建以及比较基因组等研究方面有广阔的利用前景.

  5. 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. PMID:26341802

  6. Comparative use of InDel and SSR markers in deciphering the interspecific structure of cultivated citrus genetic diversity: a perspective for genetic association studies.

    Science.gov (United States)

    García-Lor, Andrés; Luro, François; Navarro, Luis; Ollitrault, Patrick

    2012-01-01

    Genetic stratification associated with domestication history is a key parameter for estimating the pertinence of genetic association study within a gene pool. Previous molecular and phenotypic studies have shown that most of the diversity of cultivated citrus results from recombination between three main species: C. medica (citron), C. reticulata (mandarin) and C. maxima (pummelo). However, the precise contribution of each of these basic species to the genomes of secondary cultivated species, such as C. sinensis (sweet orange), C. limon (lemon), C. aurantium (sour orange), C. paradisi (grapefruit) and recent hybrids is unknown. Our study focused on: (1) the development of insertion-deletion (InDel) markers and their comparison with SSR markers for use in genetic diversity and phylogenetic studies; (2) the analysis of the contributions of basic taxa to the genomes of secondary species and modern cultivars and (3) the description of the organisation of the Citrus gene pool, to evaluate how genetic association studies should be done at the cultivated Citrus gene pool level. InDel markers appear to be better phylogenetic markers for tracing the contributions of the three ancestral species, whereas SSR markers are more useful for intraspecific diversity analysis. Most of the genetic organisation of the Citrus gene pool is related to the differentiation between C. reticulata, C. maxima and C. medica. High and generalised LD was observed, probably due to the initial differentiation between the basic species and a limited number of interspecific recombinations. This structure precludes association genetic studies at the genus level without developing additional recombinant populations from interspecific hybrids. Association genetic studies should also be affordable at intraspecific level in a less structured pool such as C. reticulata. PMID:22160318

  7. Development of Simple Sequence Repeat (SSR) and Insertion/Deletion (InDel) Markers in Chinese Cabbage (Brassica rapa ssp.pekinesis) and Analysis of Their Transferability%大白菜简单序列重复(SSR)和插入/缺失(InDel)标记的开发及通用性分析

    Institute of Scientific and Technical Information of China (English)

    仪泽会; 卢有飞; 郭晓芹; 惠麦侠; 张鲁刚; 张明科

    2012-01-01

    为探讨大白菜基因组序列中SSR位点的分布规律并开发SSR引物,利用SSRHunter软件对大白菜A10(16899818~17299817)的DNA序列进行简单序列重复(SSR)位点查找,共得到394个SSRs,平均每1.02 kb出现1个SSR.二核苷酸和三核苷酸重复是最主要的SSR类型,分别占79.44%和18.78%.为了提高SSR标记开发的准确性和通用性,对检索得到的含SSR位点的序列进行了同源比对,选取符合条件的15条SSR序列并设计引物;依据Blast过程中发现的在SSR位点不存在差异而在其侧翼序列中存在插入/缺失(InDel)差异的序列,设计了19条InDel引物.用34对SSR及InDel引物在6个大白菜(Brassica rapa ssp.pekinesis)材料中进行多态性研究,发现28对引物能扩增出理想的PCR产物,有效扩增率为82.35%,其中27对引物具有多态性,多态性比率为79.41%.为验证SSR引物的真实性,随机对4对SSR引物的部分白菜扩增片段进行了测序,发现100%的片段具有相应的SSR位点.28对SSR和InDel引物在甘蓝(B.oleracea)、油菜(B.napus)和萝卜(Raphanus sativus)品种的有效扩增率分别为85.71%、100%和77.78%,说明新开发的SSR和InDel标记具有较好的多态性和通用性.利用6对引物分析了48份十字花科种质的遗传多样性,结果表明48份材料被明显地区分成白菜和甘蓝组、萝卜组、油菜组3大类群,与传统分类一致.大白菜SSR和InDel标记的开发对于十字花科种质亲缘关系及遗传多样性分析具有重要的应用价值.%In order to analyze the SSR distribution in genomic sequence of Brassica rapa and develop new SSR markers, the DNA sequences of Chinese cabbage A10 (16899818~17299817) were screened using SSRHunter software and 394 Simple sequence repeats (SSRs) were mined with an average distance of 1.02 kb. Dinucleotide and trin ucleotide repeat SSRs were the dominant types, accounting for 79.44% and 18.78%, respectively, of the SSR obtained. In order to

  8. 基于苹果基因组开发梨的多态性SSR引物%Development of Polymorphic SSR Primers for Pear Based on Apple Genome

    Institute of Scientific and Technical Information of China (English)

    关玲; 黄金凤; 刘金义; 高志红; 章镇; 乔玉山

    2012-01-01

    从NCBI网站获取‘金冠,苹果基因组数据,在每条染色体上随机设计4对共68对引物.利用梨品种‘黄冠,和‘莱阳茌梨'及其F1代杂交群体(共94个单株)对这些引物的应用性进行验证,同时分析了该群体遗传多样性.(1)引物扩增结果显示,有40对引物可以扩增出预期目的条带,占设计引物数量的58.82%,其中16对引物能够扩增出多态性条带.(2)群体遗传多样性分析结果显示,有16对多态性引物扩增产物的等位基因数平均为2.312 5,有效等位基因数平均为2.001 4,平均杂合度观测值、期望杂合度和香农指数分别为0.548 3、0.490 5和0.746 2,表明可以在梨上运用.研究证明,SSR位点在苹果与梨之间可以转移应用.%The genome data of Malus×domestica Borkh. 'Golden Delicious' were downloaded from NCBI website,and 68 SSR primers I. E. Four pairs from every chromosome were designed according to the SSR loci of genome and these primers were detected using 94 F1 progenies of Pyrus 'Huangguan' (from Pyrus bretschneideri ' Xuehuali'×X Pyrus pyri folia 'Shinseiki') × Pyrus bretschneideri ' Laiyang Chili', and the genetic diversity of this progeny was analyzed. The results were shown that; (l)the amounts of primer which could produce the expected product is 40 (58. 82% of total primers), and 16 primers were shown polymorphic by PCR reaction. (2)Based on the results of amplification using the 16 polymorphic primers in the above progeny, the average number of alleles (Na) and the effective number of alleles (Ne) were 2.312 5 and 2.001 4, respectively. The mean observed heterozygosity (Ho), the mean expected heterozy-gosity (He) and the mean Shannon's information index (I) were 0. 548 3,0. 490 5 and 0. 746 2 respectively. 16 polymorphic primers used for Pyrus L. Were developed based on apple genome. The transferability of the SSR locus from genus Malus to Pyrus was also demonstrated in this paper.

  9. DNA Extraction and SSR-PCR of Single Leaves of Wheat%小麦单片叶片DNA 提取及SSR-PCR

    Institute of Scientific and Technical Information of China (English)

    丁晨

    2016-01-01

    [目的]使用PCR扩增鉴定哪些微卫星引物可用于鉴定小麦遗传背景下的黑麦遗传成分。[方法]以小麦单片叶片为材料,采用CTAB法提取DNA,以获得的DNA为模板进行SSR-PCR扩增,再进行普通小麦与黑麦之间多态性引物筛选,筛选出可用于鉴定小麦遗传背景下的黑麦遗传成分的引物。[结果]在所研究的20对SSR引物中,有18对在普通小麦与黑麦之间扩增出的产物有差异,引物发生变化的比例为90%。这些产生差异带的多态性引物大体可划分为两大类:一类是在黑麦与普通小麦之间均出现一种或者多种具有差异的产物带,如SCM2、SCM109、SCM180、SCM304,另一类是在黑麦上能扩增但在普通小麦上却未能扩增或者扩增的条带不清晰,如SCM101、SCM120、SCM138、SCM268。[结论]以上这2种情况下的引物均可用于鉴定小麦遗传条件下的黑麦遗传成分。%Objective] To find the micro-satellite primers obtained by PCR amplification, which was suitable for the identification of rye genetic component under wheat genetic background.[Method] With wheat single leaf as the test material, DNA was extracted by CTAB method.SSR-PCR amplification was carried out with the obtained DNA as the template .Screening of pleomorphic primer was carried out between common wheat and rye, so as to find the primer of rye genetic component suitable for the identification of wheat genetic background.[Result] From 20 pairs SSR primers, 18 pairs of SSR primers could amplify the different sites between common wheat and rye .The percentage of primer change was 90%.These polymorphic primers could be divided into two types .There were one or more product bands with differences between common wheat and rye, such as SCM2, SCM109, SCM180 and SCM304.The other type could amplify in rye but could not amplify in common wheat or the band was unclear, including SCM 101, SCM120, SCM138 and SCM268.[Conclusion] Under the

  10. Phylogenetic Relationships Among Fragaria Germplasm by SSR Markers%草莓属种质资源亲缘关系的SSR标记分析

    Institute of Scientific and Technical Information of China (English)

    韩柏明; 赵密珍; 王静; 于红梅

    2012-01-01

    Twenty SSR primer pairs were used to amplify SSR fragments for 83 Fragaria materials which belonging to 14 species, natural pentaploid strawberry and the unknown species. The 20 SSR primers generated a total 363 alleles. The number of alleles per locus ranged from 8 to 34, and averaged 18.2. The value of allelic polymorphism information content (PIC) ranged from 0.6691 to 0.9431, and averaged 0.8598. The dendrogram result showed that the samples clustered clearly among the same species. Among the species, the three octoploid species F. chiloensis, F. virginiana and F. x ananassa were clustered together, which showed the closest relationship. The three octoploid species had the distant relationship from other species. F. corymbosa, F. pentaphylla, F. nipponica, F. yezoensis, F. tibetica, F. nilgerrensis and F. viridis were clustered together and have closest relationship. And F. vesca, F. mandschurica, F. oriebtalis, F. moschata and the natural pentaploid strawberry were clustered together and have closest relationship. The origin of natural pentaploid strawberry may come from the cross of F. oriebtalis, F. moschata and E vesca, E mandschurica.%用20对SSR引物对草莓属83份资源包括14个种和自然五倍体以及未鉴定的材料进行PCR扩增。在20个SSR位点共获得363个等位基因。每个位点扩增等位基因8~34个,平均18.2个,各位点多态性信息含量(PIC)在0.6691~0.9431,平均为O.8598。聚类分析表明,同属一个种的草莓资源被紧密地聚在一起。以种为单位,3个八倍体种智利草莓、弗州草莓和栽培种凤梨草莓亲缘关系很近,而八倍体种与其他低倍性野生种亲缘关系较远;在低倍性草莓种中,伞房草莓、五叶草莓、日本草莓、嘏夷草莓、高原草莓、黄毛草莓和绿色草莓聚在一组,具有较近的亲缘关系,而森林草莓、东北草莓、东方草莓、麝香草莓和自然五倍体草莓聚在一组,具有较

  11. 刺叶苏铁EST序列中SSR信息分析%Analysis of SSR Information in EST Resource of Cycas rumphii Miq.

    Institute of Scientific and Technical Information of China (English)

    李加敏; 肖龙骞; 李青青

    2012-01-01

    This study analyzed the distribution pattern and compared the characters of EST-SSR,which were derived from a total of 21 997 ESTs of Cycas rumphii Miq.downloaded from the NCBI database.After removing redundant and poor quality sequences,13 640 non-redundant ESTs with 7 926 783 bp length were obtained,and 875 EST sequences,which accounted for 8.6% the total number of non-redundant ESTs,were detected to contain 1 176 SSRs.In these SSRs,the major repeat motifs included A/T,C/G,AC/GT,AG/CT,AT/AT,CG/CG,AAC/GTT,AAG/CTT,AAT/ATT,ACC/GGT,ACG/CGT,AGC/CTG,AGG/CCT,ATC/ATG,AAAT/ATTT,AAGG/CCTT,AATT/AATT,ACAT/ATGT and AAACCC/GGGTTT,and the major repeat types were mononucleotide,dinucleotide and trinucleotide,which were accounted for 99.1% of the total number of acquired SSRs.Among these repeats,A/T、AT/AT、AG/CT、AAG/CTT and AAT/ATT were the most frequent motifs,accounting for 41.7%,11.5%,11.9%,2.6% and 2.5%,respectively.The present study laid the foundation for the development and further use of EST-SSR markers in Cycas rumphii Miq..%基于NCBI数据库中刺叶苏铁的21 997条EST序列,统计分析了其EST-SSR的组成与分布特点。经过剔除冗余和低质量序列后,得到长度为7 926 783 bp的无冗余EST序列13 640条。在这些序列中共搜索出了875条EST序列含有1 176个SSR,出现频率为8.6%。这些SSR的主要重复基序有A/T,C/G,AC/GT,AG/CT,AT/AT,CG/CG,AAC/GTT,AAG/CTT,AAT/ATT,ACC/GGT,ACG/CGT,AGC/CTG,AGG/CCT,ATC/ATG,AAAT/ATTT,AAGG/CCTT,AATT/AATT,ACAT/ATGT和AAACCC/GGGTTT。一、二、三核苷酸重复类型是主体,三者共占总数的99.1%。A/T、AT/AT、AG/CT、AAG/CTT和AAT/ATT分别是其优势重复基元,分别占总数的41.7%、11.5%、11.9%、2.6%和2.5%。该研究为刺叶苏铁EST-SSR标记的开发与应用奠定了基础。

  12. Gene-based SSR markers for common bean (Phaseolus vulgaris L. derived from root and leaf tissue ESTs: an integration of the BMc series

    Directory of Open Access Journals (Sweden)

    Giraldo Martha C

    2011-03-01

    Full Text Available Abstract Background Sequencing of cDNA libraries for the development of expressed sequence tags (ESTs as well as for the discovery of simple sequence repeats (SSRs has been a common method of developing microsatellites or SSR-based markers. In this research, our objective was to further sequence and develop common bean microsatellites from leaf and root cDNA libraries derived from the Andean gene pool accession G19833 and the Mesoamerican gene pool accession DOR364, mapping parents of a commonly used reference map. The root libraries were made from high and low phosphorus treated plants. Results A total of 3,123 EST sequences from leaf and root cDNA libraries were screened and used for direct simple sequence repeat discovery. From these EST sequences we found 184 microsatellites; the majority containing tri-nucleotide motifs, many of which were GC rich (ACC, AGC and AGG in particular. Di-nucleotide motif microsatellites were about half as common as the tri-nucleotide motif microsatellites but most of these were AGn microsatellites with a moderate number of ATn microsatellites in root ESTs followed by few ACn and no GCn microsatellites. Out of the 184 new SSR loci, 120 new microsatellite markers were developed in the BMc (Bean Microsatellites from cDNAs series and these were evaluated for their capacity to distinguish bean diversity in a germplasm panel of 18 genotypes. We developed a database with images of the microsatellites and their polymorphism information content (PIC, which averaged 0.310 for polymorphic markers. Conclusions The present study produced information about microsatellite frequency in root and leaf tissues of two important genotypes for common bean genomics: namely G19833, the Andean genotype selected for whole genome shotgun sequencing from race Peru, and DOR364 a race Mesoamerica subgroup 2 genotype that is a small-red seeded, released variety in Central America. Both race Peru and Mesoamerica subgroup 2 (small red beans

  13. 大麦种质资源的SSR遗传多样性分析%Genetic Diversity Analysis of Barley Varieties by SSR

    Institute of Scientific and Technical Information of China (English)

    刘志敏; 金能; 吕超; 黄祖六; 许如根

    2011-01-01

    为研究不同来源大麦品种资源的亲缘关系,利用107对多态性好的SSR引物对不同来源的96份大麦品种资源的遗传多样性进行了分析。结果表明,107对SSR引物共检测出470个位点,每个引物可检测出2~10个位点,平均每个引物4.4个位点,剔除部分等位性位点,共有319个多态性位点,占总检测位点的67.8%。引物的多态性信息含量PIC最高为0.75,最低为0.04,平均为0.42。聚类结果表明,参试品种的遗传相似系数(GS)分布在0.5480~0.9195之间。在GS值为0.674水平时,可将参试品种聚为4大类,其中42份来自我国不同地区及日本引进的冬大麦品种(系)和另外2份美国引进品种(系)被聚为同一亚类;45份美国引进品种(系)和2份国内品种(系)被聚为同一亚类,即本研究材料的SSR遗传差异主要与材料的来源有关,但也出现了少量材料的交叉分类,说明国内外大麦育种均存在遗传基础较狭窄的问题,需加强外来种质的引进与利用。%The genetic diversity among 96 barley varieties(lines) from Different sources were analyzed by 107 pairs of SSR markers of good Polymorphism to provide genetic information in barley varieties.107 pairs of SSR primers with polymorphism were detected and 470 loci were measured in total.Each primer ccould detect 2~10 loci with 4.4 loci in average.Among those,319 loci have polymorphism which accounted 67.8 %.The polymorphism information content among the primers got the highest PIC of 0.75 and the lowest of 0.04,with the average of 0.42 among the 107 pairs.Clustering analysis showed that the genetic similarity coefficient(GS) ranged between 0.5480~0.9195.At the genetic similarity coefficient level of 0.674,these varieties could be clustered into 4 groups.Among them,42 of the winter barley varieties(lines) from different areas in China and introduced from Japan,and another 2 varieties(lines) introduced from USA were clustered

  14. Research of SSR Resolution of Series Compensation Transmission System of Guohua Jinjie Power Plant%国华锦界电厂串补输电次同步谐振解决方案的研究

    Institute of Scientific and Technical Information of China (English)

    顾强; 林惊涛

    2012-01-01

    国华锦界电厂串补输电系统是典型的点对网远距离大容量输电模式,由于串联补偿度较高,次同步谐振(SSR)成为威胁电网稳定和机组安全的现实问题。本文以锦界电厂串补输电系统为对象,在深入分析其SSR阻尼特性和故障风险的基础上,重点研究了基于静止无功补偿器(SVC)的次同步谐振抑制方案,采用特征值分析和电磁暂态时域仿真方法详细验算了方案的有效性。%The series compensation transmission system of GUOHUA JINJIE POWER PLANT is a typical station to grid,long distance and large capacity transmission mode. Because of higher series compensation level,SSR has been practical problem which becomes threat to the power system stability and operation safety. Based on the series compensation transmission system of JINJIE POWER PLANT, this paper deeply analyses SSR damping characteristic and risk of failure, focuses on SSR suppression scheme based on SVC and checks its effectiveness with the eigenvalue analysis and the electromagnetic transient time-domain simulation.

  15. 二次雷达S模式应答信号与ADS-B信号的甄别研究%Research on the discrimination between SSR mode S transponder signal and ADS-B signal

    Institute of Scientific and Technical Information of China (English)

    李明洋; 时宏伟; 颜可壹

    2015-01-01

    阐述了 SSR 的 S 模式应答信号与1090ES ADS-B 系统的信号格式与特点,并对其进行了对比分析;针对这两种同频信号,提出了一种结合民航空管实际应用的区分方法。理论分析及仿真实验证明,该方法可较好地解决二次雷达 S 模式应答信号与 ADS-B 信号的甄别问题。%This paper describes the signal formats and characteristics between mode S transponder signal of SSR and 1090ES ADS-B signal, on which comparative and analytic studies are also conducted. To distinguish these two signals of the same frequency, this paper proposes a method considering the practical application of civil aviation. By theoretical analysis and doing simulation experiment, this method proposeed in this paper can better solve the problem of distinguishing SSR mode S transponder signal and ADS-B signal.

  16. 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

  17. 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

  18. 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

  19. The characterization of a new set of EST-derived simple sequence repeat (SSR markers as a resource for the genetic analysis of Phaseolus vulgaris

    Directory of Open Access Journals (Sweden)

    Borba Tereza CO

    2011-05-01

    Full Text Available Abstract Background Over recent years, a growing effort has been made to develop microsatellite markers for the genomic analysis of the common bean (Phaseolus vulgaris to broaden the knowledge of the molecular genetic basis of this species. The availability of large sets of expressed sequence tags (ESTs in public databases has given rise to an expedient approach for the identification of SSRs (Simple Sequence Repeats, specifically EST-derived SSRs. In the present work, a battery of new microsatellite markers was obtained from a search of the Phaseolus vulgaris EST database. The diversity, degree of transferability and polymorphism of these markers were tested. Results From 9,583 valid ESTs, 4,764 had microsatellite motifs, from which 377 were used to design primers, and 302 (80.11% showed good amplification quality. To analyze transferability, a group of 167 SSRs were tested, and the results showed that they were 82% transferable across at least one species. The highest amplification rates were observed between the species from the Phaseolus (63.7%, Vigna (25.9%, Glycine (19.8%, Medicago (10.2%, Dipterix (6% and Arachis (1.8% genera. The average PIC (Polymorphism Information Content varied from 0.53 for genomic SSRs to 0.47 for EST-SSRs, and the average number of alleles per locus was 4 and 3, respectively. Among the 315 newly tested SSRs in the BJ (BAT93 X Jalo EEP558 population, 24% (76 were polymorphic. The integration of these segregant loci into a framework map composed of 123 previously obtained SSR markers yielded a total of 199 segregant loci, of which 182 (91.5% were mapped to 14 linkage groups, resulting in a map length of 1,157 cM. Conclusions A total of 302 newly developed EST-SSR markers, showing good amplification quality, are available for the genetic analysis of Phaseolus vulgaris. These markers showed satisfactory rates of transferability, especially between species that have great economic and genomic values. Their diversity

  20. 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.

  1. 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. PMID:27635342

  2. Assessment of Functional EST-SSR Markers (Sugarcane) in Cross-Species Transferability, Genetic Diversity among Poaceae Plants, and Bulk Segregation Analysis

    Science.gov (United States)

    Ul Haq, Shamshad; Kumar, Pradeep; Singh, R. K.; Verma, Kumar Sambhav; Bhatt, Ritika; Sharma, Meenakshi; Kachhwaha, Sumita; Kothari, S. L.

    2016-01-01

    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. PMID:27340568

  3. 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.

  4. Assessment of Functional EST-SSR Markers (Sugarcane) in Cross-Species Transferability, Genetic Diversity among Poaceae Plants, and Bulk Segregation Analysis.

    Science.gov (United States)

    Ul Haq, Shamshad; Kumar, Pradeep; Singh, R K; Verma, Kumar Sambhav; Bhatt, Ritika; Sharma, Meenakshi; Kachhwaha, Sumita; Kothari, S L

    2016-01-01

    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. PMID:27340568

  5. 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.

  6. SSR Information in Transcriptome of White Ginger (Zingiber officinale Roscoe)%白姜转录组中的SSR位点信息分析

    Institute of Scientific and Technical Information of China (English)

    邹勇; 黄科; 姜玉松; 刘奕清

    2016-01-01

    利用Trinity软件对白姜转录组进行de novo组装,CAP3软件对组装的contig拼接删选;MISA工具对unigene进行SSR检索.从153 724条unigene中共发现16 593个SSR,分布在14 436条unigene序列中,出现频率为9.39%,平均每9.26kb含有1个SSR位点.其中二核苷酸、三核苷酸所占比例最大,分别为37.59%和45.24%;二者分别以AG/CT和AGG/CCT重复基元为主,占22.47%和11.79%.基序长度主要分布于12~20bp,占总数的85.06%.研究结果表明,白姜SSR位点频率、密度较高,类型多样,在生姜分子标记辅助育种、遗传多样性研究中有较大应用潜能.

  7. Development of EST-SSR markers by data mining in three species of shrimp: Litopenaeus vannamei, Litopenaeus stylirostris, and Trachypenaeus birdy.

    Science.gov (United States)

    Pérez, Franklin; Ortiz, Juan; Zhinaula, Mariuxi; Gonzabay, Cesar; Calderón, Jorge; Volckaert, Filip A M J

    2005-01-01

    We report on the data mining of publicly available Litopenaeus vannamei expressed sequence tags (ESTs) to generate simple sequence repeat (SSRs) markers and on their transferability between related Penaeid shrimp species. Repeat motifs were found in 3.8% of the evaluated ESTs at a frequency of one repeat every 7.8 kb of sequence data. A total of 206 primer pairs were designed, and 112 loci were amplified with the highest success in L. vannamei. A high percentage (69%) of EST-SSRs were transferable within the genus Litopenaeus. More than half of the amplified products were polymorphic in a small testing panel of L. vannamei. Evaluation of those primers in a larger testing panel showed that 72% of the markers fit Hardy-Weinberg equilibrium, which shows their utility for population genetic analysis. Additionally, a set of 26 of the EST-SSRs were evaluated for Mendelian segregation. A high percentage of monomorphic markers (46%) proved to be polymorphic by singles-stranded conformational polymorphism analysis. Because of the high number of ESTs available in public databases, a data mining approach similar to the one outlined here might yield high numbers of SSR markers in many animal taxa. PMID:16027992

  8. Combined use of a new SNP-based assay and multilocus SSR markers to assess genetic diversity of Xylella fastidiosa subsp. pauca infecting citrus and coffee plants.

    Science.gov (United States)

    Montes-Borrego, Miguel; Lopes, Joao R S; Jiménez-Díaz, Rafael M; Landa, Blanca B

    2015-03-01

    Two haplotypes of Xylella fastidiosa subsp. pauca (Xfp) that correlated with their host of origin were identified in a collection of 90 isolates infecting citrus and coffee plants in Brazil, based on a single-nucleotide polymorphism in the gyrB sequence. A new single-nucleotide primer extension (SNuPE) protocol was designed for rapid identification of Xfp according to the host source. The protocol proved to be robust for the prediction of the Xfp host source in blind tests using DNA from cultures of the bacterium, infected plants, and insect vectors allowed to feed on Xfp-infected citrus plants. AMOVA and STRUCTURE analyses of microsatellite data separated most Xfp populations on the basis of their host source, indicating that they were genetically distinct. The combined use of the SNaPshot protocol and three previously developed multilocus SSR markers showed that two haplotypes and distinct isolates of Xfp infect citrus and coffee in Brazil and that multiple, genetically different isolates can be present in a single orchard or infect a single tree. This combined approach will be very useful in studies of the epidemiology of Xfp-induced diseases, host specificity of bacterial genotypes, the occurrence of Xfp host jumping, vector feeding habits, etc., in economically important cultivated plants or weed host reservoirs of Xfp in Brazil and elsewhere. PMID:26415663

  9. 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.

  10. 梨矮化基因pcDw的SSR标记定位%Location of a pear dwarf gene pcDw by SSR marker

    Institute of Scientific and Technical Information of China (English)

    田义轲; 王彩虹; 贾彦利; 王亮; 戴洪义

    2008-01-01

    以矮化梨(Pyrus communis L.)与茌梨(P. bretschneideri Rehd.)的F1杂交分离群体共110个单株(3 a生,矮化型和正常型各55株)为试材,对来自西洋梨的矮化型突变基因pcDw进行了SSR分子标记研究.用分离群体分组分析法(Bulked Segregant Analysis,BSA),通过对源自梨、苹果和桃基因组的共40对SSR(Simple Sequence Repeat)引物的筛选,获得了一个与pcDw基因连锁距离为9.3 cM的SSR标记KA14 210,由此将该基因定位到了梨品种Barlett遗传图谱的第16连锁群上.

  11. 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.

  12. 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.

  13. 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)

    Cui, Binbin; Zhang, Qixiang; Xiong, Min; Wang, Xian

    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.

  14. Breeding strains of Panax notoginseng by using EST-SSR markers%EST-SSR标记对三七选育品系的研究

    Institute of Scientific and Technical Information of China (English)

    张金渝; 杨维泽; 崔秀明; 虞泓; 金航; 陈中坚; 沈涛

    2011-01-01

    目的:通过对不同三七选育品系的遗传变异和遗传分化程度进行分析比较,为三七的品种选育提供理论依据.方法:利用自行设计和他人开发的17对EST-SSR引物,对来自4个不同区域的17份三七选育品系进行遗传多样性及遗传分化分析.结果:在17份三七选育品系中一共扩增出136个多态位点,平均多态信息量PIC值为0.78,Nei's基因多样性H0.139,Shannon多样性指数I0.208.选育品系间的遗传分化系数为0.382,遗传相似度和聚类分析的结果表明17份三七选育品系和屏边三七被划分为4个大类群,其中17份三七选育品系被分为3个类群,屏边三七单独在一个类群.结论:通过集团选择后,从相同栽培居群内筛选出的不同品系存在一定程度的遗传分化,可以用EST-SSR标记来检测集团选择的结果.%Objective: To comparatively determine the genetic variation and differentiation of different breeding strains of Panax notoginseng for providing the basic information for genetic breeding. Method: The genetic diversity and genetic structure of the 17 breeding strains of P. notoginseng were assayed by using EST-SSR molecular marker. Result: A total of 136 polymorphic loci of ESTSSR were detected in the 17 breeding strains of P. notoginseng, with the PIC ( polymorphism information content) being 0. 78, H ( the gene diversity within population) being 0. 139, the I ( the Shannon's information index) being 0.208. Gat ( coefficient of gene differentiation) was 0. 382 among the 17 strains. The cluster analysis of genetic similarity showed that the 17 strains of P. notoginseng and P. stipuleanatus were classified into 4 groups, while the 17 strains of P. notoginseng were classified into three subgroups. Conclusion: The genetic differentiation was detected among the 17 strains of P. notoginseng from the same cultivation population by bulk selecting. And it was feasible to detect the effect of bulk selection by EST-SSR markets.

  15. 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

  16. 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.

  17. 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.

  18. SSR marker analysis on genetic variation of M3 from maize inbred lines 48-2 and R08 after irradiation inducement

    International Nuclear Information System (INIS)

    Analyzing the biological effects and the genetic variations of maize mutagenic progenies is important to facilitate effective selections and utilization of the mutants. In this study, the genetic variation of 103 mutagenic progenies of M3 lines of inbred lines 48-2 and R08 with 60Co γ-rays inducement were evaluated with SSR molecular markers. The results indicated that, the amplitude of polymorphism information content (PIC) of the 48-2 and R08 M3 lines ranged 0.307 ∼ 0.948 and 0.108 ∼ 0.955, with an average of 0.762 and 0.701, respectively. The amplitude of genetic diversity indexes (H') ranged 0.552 ∼ 2.830 and 0.254 ∼ 3.309, with an average of 1.830 and 1.777, respectively. The average value of genetic similarity coefficient of the 49 M3 lines of 48-2 with its check (M673) was 0.8194. However, the average value of genetic similarity coefficient of the M3 lines of R08 with its check (M487) was 0.8373. Based on the genetic similarity coefficient, inbred lines 48-2, R08 and their 101 M3 lines were clustered in 7 and 5 populations respectively. This phenomenon indicated that massive genetic variation could appear in progenies due to irradiation. The strengthen of selection and utilization of mutants based on the breeding objectives and in accordance with the feature and regularity on genetic variations of main characteristics of mutant lines in various populations could be enhanced in breeding program, to some extent, which can increase the breeding efficiency of irradiation induced mutation in maize. (authors)

  19. 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.

  20. 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.

  1. Cytogenetic diversity of SSR motifs within and between Hordeum species carrying the H genome: H. vulgare L. and H. bulbosum L.

    Science.gov (United States)

    Carmona, Alejandro; Friero, Eva; de Bustos, Alfredo; Jouve, Nicolás; Cuadrado, Angeles

    2013-04-01

    Non-denaturing FISH (ND-FISH) was used to compare the distribution of four simple sequence repeats (SSRs)-(AG) n , (AAG) n , (ACT) n and (ATC) n -in somatic root tip metaphase spreads of 12 barley (H. vulgare ssp. vulgare) cultivars, seven lines of their wild progenitor H. vulgare ssp. spontaneum, and four lines of their close relative H. bulbosum, to determine whether the range of molecular diversity shown by these highly polymorphic sequences is reflected at the chromosome level. In both, the cultivated and wild barleys, clusters of AG and ATC repeats were invariant. In contrast, clusters of AAG and ACT showed polymorphism. Karyotypes were prepared after the identification of their seven pairs of homologous chromosomes. Variation between these homologues was only observed in one wild accession that showed the segregation of a reciprocal translocation involving chromosomes 5H and 7H. The two subspecies of H. vulgare analysed were no different in terms of their SSRs. Only AAG repeats were found clustered strongly on the chromosomes of all lines of H. bulbosum examined. Wide variation was seen between homologous chromosomes within and across these lines. These results are the first to provide insight into the cytogenetic diversity of SSRs in barley and its closest relatives. Differences in the abundance and distribution of each SSR analysed, between H. vulgare and H. bulbosum, suggest that these species do not share the same H genome, and support the idea that these species are not very closely related. Southern blotting experiments revealed the complex organization of these SSRs, supporting the findings made with ND-FISH. PMID:23242107

  2. Resistance to the WhiteflyAleurotrachelus socialis(Hemiptera:Aleyrodidae) and SSR Marker Identifi cation in Advanced Populations of the HybridManihot esculentasubsp.Manihotfl abellifolia

    Institute of Scientific and Technical Information of China (English)

    Arturo Carabal; James Montoya-Lerma; Anthony C. Belloti; Martin Fregene; Gerardo Gallego

    2013-01-01

    Genes resistant toAleurotrachelus socialis were transferred to the F1from the interspecifi c hybrid wild species ofManihot fl abellifoliatoM. esculenta and two advanced generations of backcrosses (BC1 and BC2). We characterized the resistance ofA. socialis transferred to BC2parents (CW67-160, CW67-130, CW67-44), MTAI-8 (BC1), resistant (CMB9B-73) and susceptible (CMB9B-104) genotypes from contrasting pools, and resistant (MEcu-72) and susceptible (CMC-40) genotypes. Whitefl y demography and biology were evaluated. SSR molecular markers associated with a phenotypic response of plant resistance were detected in segregating populations (BC2). Results showed that although female survival time was similar on all hosts, the lowest averages of longevity, fecundity and oviposition rate were observed in the resistant control MEcu-72, only being signifi cantly similar to the parent CW67-130. When the BC1and BC2 populations were compared, it was found thatA. socialis fecundity was eight times lower on CMB9B-73 progeny than on CW67-130, expressing the highest levels of resistance to the whitefl y. Ten genotypes of CMB9A and CMB9B family had the best segregation. A total of 486 microsatellite primers were evaluated using bulked segregant analysis (BSA), 11 showed polymorphism between the contrasting pools and only one showed signifi cant differences between resistant and susceptible individuals. In conclusion, fecundity was the parameter that impacted most on the intrinsic rate ofA. socialis population growth.

  3. Mitigating Thermal Power' s SSR by Additional Damping Controller of DFIG%风火电组合外送系统中风电改善火电机组SSR的研究

    Institute of Scientific and Technical Information of China (English)

    雷虹云; 郑超; 岳兴华; 徐光年; 鲍建飞

    2013-01-01

    大型煤炭基地电力与风电基地电力的组合外送在中国具有现实需求.外送通道中一般需加装串联补偿装置,以提升风火电组合外送能力,但可能导致送端火电机组发生次同步谐振(sub-synchronous resonance,SSR).为此,基于加入风电系统的IEEE SSR第一标准测试模型,采用时域仿真及Prony阻尼比辨识法,定量分析风电场接人对其近端火电机组SSR特性的影响;并根据相位补偿原理设计风电机组附加阻尼控制器,通过动态调节风电机组的无功出力,在次频域内提供电气正阻尼,以消除SSR.此时,由于双馈风电机组采用有功、无功解耦控制,风电机组的有功出力基本不受影响.仿真结果表明,该方法能改善经串联补偿外送的大容量风火电组合系统动态特性,提高大规模风电跨区消纳能力.%Combined power delivery from thermal and wind power bases is the practical needs in China. Series compensators are usually installed in transmission channels to improve the capability of the delivery system, but may cause sub-synchronous resonance (SSR) on the thermal power units at the sending end. In order to solve the problem, the impact of wind power integration on the nearby thermal power units' SSR is analyzed quantitatively by time-domain simulation and Prony damping ratio identification, in which the IEEE SSR first benchmark modified model with a wind farm is used, and an additional damping controller of wind turbine is designed according to principles of phase compensation, which can provide positive damping in sub-frequency domain and eliminate SSR by adjusting its reactive power dynamically. In the meanwhile, the active power outputs of doubly-fed induction generators (DFIGs) are improbably affected due to their decoupling control functions. The simulation results show that this control strategy can improve dynamic characteristics of combined power delivery system of high capacity with series compensation and

  4. 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.

  5. Transferability analysis of EST-SSR markers of Castanea mollissima to Castanopsis fargesii%中国板栗EST-SSR分子标记在栲树中的通用性分析

    Institute of Scientific and Technical Information of China (English)

    李春; 孙晔

    2012-01-01

    Simple sequence repeats(SSR),also known as microsatellite molecular markers,have been cross-amplified successfully in closely related species of the same genus and even across genera within the same family. In the present study, 124 primer pairs of polymorphic EST-SSR originally developed from Castanea mollissima were cross-amplified in Castanopsis fargesii. Results indicated that 42. 7% of Castanea mollssima EST-SSR primers were successfully cross-amplified in Castanopsis far gesii and 56. 6% were polymorphic. The genetic diversity of 4 populations of C. fargesii were investigated with polymorphic EST-SSRs, preliminary results showed that C. fargesii possessed high levels of genetic diversity(Na=6.105,Ho=0. 563,He-0.621). These polymorphic EST-SSR primers would provide a powerful tool for further investigation on population genetics of C. fargesii.%简单重复序列也称为微卫星分子标记,不仅在同属近缘种间具有良好的通用性,甚至在近缘属间也具有一定的通用性.本研究利用壳斗科基因组信息数据库中公布的中国板栗124对多态的EST-SSR引物在栲树中进行跨属(栗属到栲属)通用性研究,结果显示中国板栗EST-SSR引物在栲树中通用性和多态性分别为42.7%和56.6%;使用19对多态的EST-SSR引物对4个栲树自然居群的遗传多样性进行初步分析,结果显示栲树自然居群具有较高的遗传多样性(Na=6.105,Ho=0.563,He=0.621).这些引物为栲树群体遗传学的深入研究提供了有力工具.

  6. SSR markers in transcripts of genes linked to post-transcriptional and transcriptional regulatory functions during vegetative and reproductive development of Elaeis guineensis

    Directory of Open Access Journals (Sweden)

    Tranbarger Timothy

    2012-01-01

    Full Text Available Abstract Background 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. Results 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. Conclusions 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

  7. Design of additional SSR damping controller for power system with DFIG wind turbine%含DFIG风机的电力系统次同步谐振附加阻尼控制器设计

    Institute of Scientific and Technical Information of China (English)

    张宋彬; 江全元; 陈跃辉; 张文磊; 宋军英

    2014-01-01

    为抑制双馈异步风机经串联补偿线路并网导致的次同步谐振(SSR),基于阻抗分析的奈奎斯特稳定判据设计了相应的次同步谐振阻尼控制器(SSRDC).该附加控制器以风机转速偏差作为反馈输入信号引入转子变流器控制的内环中,采用典型的超前-滞后校正模型.以附加SSRDC引入系统后带来好的稳定效果为目的建立优化模型,并且调用粒子群优化算法求解该优化模型,得到该控制器参数.MATLAB/Simulink下的仿真结果表明附加SSRDC能够有效地抑制SSR,并且在转子侧引入附加SSRDC抑制SSR的效果明显比在定子侧引入SSRDC好,同时验证了基于阻抗法设计的附加SSRDC抑制SSR的效果比基于状态空间法设计的SSRDC更好.

  8. Genetic Relationship Analysis of Thirty-eight Sun/Air-Cured Tobacco Germplasms Based on Simple Sequence Repeat (SSR) Markers%38份晾晒烟种质资源遗传关系的SSR分析

    Institute of Scientific and Technical Information of China (English)

    张雪廷; 童治军; 焦芳婵; 肖炳光; 曾千春

    2013-01-01

    从自主开发的近3000对烟草SSR引物中随机选出30对SSR引物,对38份晾晒烟种质资源的遗传关系进行了分析.在38份供试材料中共检测出173个等位基因,每对SSR引物可检测到的等位基因数为2~11个,平均为5.77个;遗传相似系数(GS)的变化范围为0.140 ~0.928,平均为0.534.表明38份晾晒烟的遗传多样性丰富,遗传差异较大,亲缘关系较远.聚类分析表明,在L1(GS =0.165)处可将38个品种分为2个类群,即晾晒烟类群和美国从烟草起源地收集的烟草(TI,tobacco instruction)类群;晾晒烟类群又可进一步分为4个亚类,其聚类结果与所期望的结果基本一致.表明SSR是一种有效、稳定和可靠的分子标记,能较好地从分子水平上揭示晾晒烟种质资源的遗传背景和亲缘关系.%The first phylogenesis of 38 sun/air-cured tobacco germplasms analyzed by simple sequence repeat (SSR) markers were reported in this study.30 primer pairs were randomly selected from a nearly total of 3000 self-developed tobacco SSR primers.A total of 173 polymorphic alleles were amplified in 38 varieties,and the number of alleles detected by each SSR primer ranged from 2 to 11,with an average of 5.77 alleles per markers.Genetic similarity coefficient (GS) among the 38 varieties ranged from 0.140 to 0.928,with an average of 0.534,which indicated the genetic variation of the 38 varieties was quite large and the genetic diversity was much abundant in sun/aircured tobacco varieties.The result of cluster analysis based on SSR markers showed that 38 varieties could be clustered into 2 groups including sun/air-cured and TI tobacco groups at a relative low level of GS =0.165.And the sun/air-cured group was further classified into 4 subgroups,which was basically according with expected case.The results showed that SSR was a stable,reliable,and valuable molecular marker system which was more efficient in generating accurate information on genetic background and

  9. 稻瘟病菌ABC转运蛋白基因中SSR的分布及其功能预测%SSR distribution and its potential effects on function of ABC transporter genes in rice blast fungus Magnaporthe grisea

    Institute of Scientific and Technical Information of China (English)

    刘林; 李成云; 杨静; 苏源; 吴晗; 徐玲; 胡燕玲

    2011-01-01

    ABC transporters play an important role in pathogenicity of fungi. In this study, 47 ABC transporter genes were retrieved from the genome of Magnaporthe grisea. The component and distribution of simple sequence repeats (SSR) within the extron, intron, 5'-UTR and 3'-UTR regions of these genes were analyzed respectively. Furthermore, effects of SSR expansion and contraction on protein structure in the gene coding regions was predicted. The results showed that component and distribution of the SSRs in these regions were different and the SSRs also distributed unevenly in regulation and function regions of these genes. Compared with other regions, the tri-nucleotide and hexa-nucleotide appeared more frequently in coding region. In addition, the G + C component was more abundant and the frequency of hydrophilic amino acids was relatively higher than that of hydrophobic amino acids in the SSRs. Depending on the variation among field isolates of M. Grisea, the expansion or contraction of amino acids encoding SSR sequence were potentially affected on protein secondary structure and gene function. These data implicated that the mutation of SSR might play an important role in variation of pathogenicity-related genes.%ABC转运蛋白在真菌的致病性方面起着重要的作用.本研究查找和分析了稻瘟病菌基因组中47个ABC转运蛋白基因的外显子区、内含子区、5′-UTR和3′-UTR区中的SSR,并对编码区中SSR的扩张或收缩对蛋白结构的影响进行了预测.结果表明,SSR在这些基因的调控区和编码区分布不均一,且在基因的外显子区、内含子区、5′-UTR和3′-UTR区中SSR的组成和分布均不相同;基因的编码区中三碱基和六碱基SSR相对较多,SSR的基序大都表现为GC含量较高,编码的亲水性氨基酸出现频率远远高于疏水性氨基酸.根据稻瘟病菌自然群体中SSR的变化幅度,预测了SSR的扩张或收缩对蛋白二级结构的影响,发现SSR的扩张或收

  10. Analysis of Genetic Diversity among Barleys Came from 19 Asian Countries Using Fluorescent SSR Markers%19个亚洲国家大麦种质材料的遗传多样性分析

    Institute of Scientific and Technical Information of China (English)

    白盼; 李荣华; 郭培国; 宁正祥; 夏岩石; 何其芳

    2012-01-01

    为了解大麦种质材料的遗传多样性,并为合理选择育种亲本及保护与利用大麦种质资源材料提供依据,采用21对SSR荧光标记引物对来自19个亚洲国家的175份大麦种质材料进行遗传多样性分析,筛选出的19对SSR引物共检测到134个等位变异,平均每对引物检测到7.05个等位变异,其中SSR17位点对亚洲大麦基因组DNA变异检测最有效,其多态性信息含量指数(PIC)和标记指数MI均最高,分别为0.9和10.77;基于SSR数据,对19个亚洲国家175份大麦材料进行UPGMA聚类分析,结果聚为三组:组群Ⅰ共包含19个国家的161个品种;组群Ⅱ共包含4个国家的12个品种;组群Ⅲ只包括来自土库曼斯坦的2个品种。根据按国家划分的19个群体的遗传一致度数据,聚类分析可以分为3组群(其中组群1可分为4个亚组),主坐标分析可分为3个组群和7个亚组。本研究表明,聚类法和主坐标分析法结果基本吻合,均表明亚洲大麦种质资源存在丰富的变异,但主坐标分析法更精细。%Understanding the genetic diversity of barley germplasm could be the basis for appropriate selection of parents in breeding program,and could enhance protection and utilization of barley germplasm.In this study,genetic diversity analysis of 175 barely accessions from 19 Asian countries was analyzed by 21 combinations of fluorescent SSR primers.The polymorphic information content(PIC) and marker index(MI) were calculated for each SSR primer.According to the genetic similarity,the polygenetic tree of the genetic relationship among the 175 barley accessions was drawn.According to the Genetic identity(GI),the polygenetic tree and the charts of principle coordinates analysis of the genetic relationship in barley accessions from the populations of 19 countries were classified by origins.The results showed nineteen pairs of SSR primers amplified 134 allelic loci with 7.05 per SSR primer pairs among the

  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. Genetic diversity analysis of varieties resistant to stripe rust based on SSR markers%小麦抗条锈品种遗传多样性的SSR分析

    Institute of Scientific and Technical Information of China (English)

    刘文涛; 程登发; 康晓慧; 孙京瑞; 张云慧; 罗宵凤; 张梅; 张利; 张娜

    2011-01-01

    [Objective] Genetic diversity of wheat varieties resistant to stripe rust in the main wheat production areas in China were analyzed by SSR markers to provide a reference for selection of parental materials resistant to wheat stripe rust. [Method] Several dominant wheat cultivars were assessed for resistance to stripe rust at adult stage by using the current races of the stripe rust. Genetic diversity was investigated by SSR markers. [Result] Totally 104 alleles were produced by 27 pairs of SSR primers. The average alleles per pair of primers were 3.85. The polymorphism information content (PIC) ranged from 0.210 to 0.712 with an average value of 0.455. Wheat cultivars resistant to stripe rust had a genetic similarity coefficient of 0.723 on average, which indicated that the genetic diversity of the resistant varieties was low. [Conclusion] Cluster analysis results showed that wheat cultivars resistant to stripe rust were divided into 4 groups,and genetic distance was related to geographical distance to some extent.%[目的]利用SSR标记分析我国几大小麦产区主栽品种中抗锈品种的遗传多样性,为小麦抗条锈育种亲本材料的选择提供参考.[方法]以当前条锈菌优势小种接种成株期小麦,从几大小麦产区主栽品种中筛选出抗条锈品种.然后利用SSR标记对筛选出的抗锈品种的遗传多样性进行分析.[结果]27对SSR引物在上述抗锈品种中共检测到104个等位变异,平均为3.85个;引物的多态信息含量(PIC)在0.210~0.712之间,平均为0.455;抗锈品种间遗传相似系数平均为0.723,表明筛选出的抗锈品种遗传多样性较低,亲缘较近.[结论]聚类分析的结果将抗锈品种分为了4个类群,类群的分布与亲缘的远近和品种的地域有一定的相关性.

  13. 不同居群野生狗牙根材料的SSR分析%SSR Analyses of Different Bermudagrass Populations

    Institute of Scientific and Technical Information of China (English)

    张延辉; 帕提古丽; 李江华; 于辉; 阿不来提

    2013-01-01

    In order to evaluate the diversity level of Xinjiang Bermudagrass,the genetic diversities of Bermudagrass from Xinjiang,Huanan and abroad were investigated using SSR marker.Results indicated that 142 allelic variations were amplified by 20 primers,of which 124 were polymorphism and each locus had 7 allelic variations.The percentage of polymorphic loci was 87.86%,the average of Nei's (H) was 0.4347.The genetic similarities (GS) of 106 materials ranged from 0.43 to 1.0,the average was 0.715.The genetic differentiation coefficient was 41.19% among the population and 58.81% inside the population.Data illustrated genetic variation within populations was larger than among populations according to genetic identity and differentiation.The general clustering consequences by UPGMA method indicated that 106 materials were classified into three groups when the similarity coefficient was 0.39.The genetic variance of Bermuda grass was not obviously related to the origin,but the materials from the same region were more classified into the same group.These clustering results were correlated with geographic origin in some extent.%为评价新疆狗牙根(Cynodon dactylon)资源的遗传多样性水平,以采自新疆不同地域的狗牙根与部分华南地区及国外的狗牙根为材料,用SSR标记开展遗传多样性研究.结果表明:20对引物共产生142个等位变异,平均每个位点7个,其中有124个等位变异显示多态性,多态位点百分率为87.86%,位点Nei's基因多样性(H)指数平均为0.4347;根据遗传一致性及遗传分化结果,106份狗牙根材料的遗传相似性系数值在0.43~1.0之间,平均0.715,居群间遗传分化系数为0.4119,表明有41.19%的变异存在于居群间,58.81%的变异存在于居群内,居群内的遗传分化大于居群间的遗传分化;根据UPGMA法聚类表明,106份供试材料相似系数为0.39时可聚为3类,材料间的遗传差异与其采集地的关系不很明显,但来自同一

  14. 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

  15. 基于SSR标记的江苏沿江地区糯玉米种质资源遗传多样性研究%Genetic diversity of waxy corn germplasm resources in Jiangsu coastal district by SSR markers

    Institute of Scientific and Technical Information of China (English)

    刘丽君; 张丹; 薛林; 李建; 徐辰武

    2011-01-01

    为研究江苏沿江地区糯玉米种质的遗传多样性以及江苏省糯玉米的遗传改良和杂种优势利用提供参考,利用93对SSR标记研究55份糯玉米自交系和30份糯玉米单交种的遗传多样性,并利用UPGMA方法对所有自交系材料进行系统聚类.结果表明在自交系中筛选出88对多态性较好的引物,共扩增出350个差异片断,每对引物检测出2-9个差异片段,平均为3.98个;SSR标记的多态性信息量值在0.137与0.832之间,平均为0.520.在单交种中筛选出87对多态性好的引物,扩增出311个差异片断,每对引物可检测出2~9个差异片断,平均3.57个,SSR标记的多态性信息量值在0.064与0.839之间,平均为0.4.75.利用UPGMA聚类分析方法将所有供试自交系分为4类,划分结果基本符合品系的来源情况,江苏沿江地区糯玉米种质资源主要由通系5群、衡白522群以及突变体材料组成,多样性较为丰富,可为糯玉米遗传改良提供一定的遗传基础.%Germplasm resources are vital for genetic improvement. A narrow germplasm base will restrict plant breeding, and reduces the potential for improving heterosis and the possibility of enhancing resistance to biological or non-biological pressure. The Jiangsu coastal district is one of the regions where waxy corn breeding has been earliestly developed. However, the genetic diversity of breeding resources was still unknown. In this study, a total of 85 waxy com resources (55 waxy corn inbreds and 30 hybrids) in this area were collected as a panel, and the genetic diversity was studied by 93 pairs of SSR primers distributed on 10 chromosomes of maize. 88 pairs of primers were polymophic in inbred lines, and each could stablyamplify 2-9 differential fragments with an average of 3. 98. The value of polymorphism information content (PIC) for each SSR locus in inbred lines varied from 0. 137 to 0.832 with an average of 0.520. In hybrids, 87 primers produced 311 polymorphic

  16. 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.

  17. 适用于玉米特定分离群体的高通量SSR检测技术研究%Mapping Population of Maize by High Throughput Measurement SSR Electrophoresis Technique

    Institute of Scientific and Technical Information of China (English)

    邹丽梅; 王凤格; 赵久然; 许理文; 易红梅; 宋伟

    2011-01-01

    In order to improve the efficiency of mapping population of maize and to reduce the cost, capillary electrophoresis was applied to multiple composite primers. This method was discussed in the maize targeted groups of SSR analysis, and provided a new way to improve the efficiency in maize molecular breeding.%为了提高利用玉米DH群体进行遗传连锁图谱构建的效率,降低其成本,提出利用毛细管荧光电泳技术进行多个引物复合电泳的策略,讨论此策略在玉米特定分离群体SSR分析中的应用,为提高玉米分子育种中的实验效率提供新思路.

  18. 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

  19. 欧洲与东亚小麦品种遗传多样性的比较分析%Comparison of Genetic Diversity Level between European and East-Asian Wheat Collections Using SSR Markers

    Institute of Scientific and Technical Information of China (English)

    王兰芬; BALFOURIER F; 郝晨阳; EXBRAYAT-VINSON F; 董玉琛; 盖红梅; 张学勇

    2007-01-01

    [目的]在分子水平上回答欧洲和东亚小麦品种的遗传关系和多样性差异;同时对Genomic-SSR(gSSR)和EST-SSR(eSSR)多态性水平进行比较分析.[方法]利用38个Genomic-SSR引物对和44对EST-SSR引物对分析371份欧洲小麦品种和363份东亚品种.[结果]共检测到865个等位变异,每个引物对的等位变异数为1~50,平均为10.42;多态性信息含量(PIC)为0~0.91, 平均为 0.53;欧洲和东亚品种分别检测到730、716个等位变异,特有等位变异分别为150、135,平均遗传丰富度分别为8.80和8.61,遗传多样性指数分别为 0.46 和0.52.欧洲和东亚小麦品种在聚类图上明显地划分为两大类群;每个国家或大区聚类结果与其地理分布基本一致,即相邻国家或地区的品种亲缘关系更近一些.近一半基因座的等位变异频率及其分布在欧洲与东亚材料间存在明显差异. 通过标记/性状关联分析,在4B、5A、6A、7B染色体上发现6个影响穗粒数、千粒重、株高、抽穗期、有效分蘖等重要农艺性状的基因座,其中个别基因座优势等位变异差异可能与东亚、欧洲品种的分化密切相关.中国20世纪50~80年代育成品种在大的聚类上明显靠近欧洲材料、而远离中国50年代以前的育成品种和地方品种,这与中国的育种实际相吻合.基于Genomic-SSR和基于EST-SSR的聚类图整体趋势是一致的,但由前者估算的遗传距离远高于后者,因此,一般的SSR较功能基因SSR更易发生变异,由育种选择所引起的分化更快.[结论]在中国今后的小麦育种中,需要通过杂交、回交,对欧洲品种的一些重要基因座等位变异(基因)进行置换,方有可能实现"洋为中用"的目的.

  20. 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.

  1. Fingerprinting Patterns of SSR Markers Constructed for 33 Loquat [Eriobotrya japonica (Thunb.) Lindl.] Germplasms%枇杷种质资源SSR标记指纹图谱的构建

    Institute of Scientific and Technical Information of China (English)

    岳娜; 胡倩倩; 方星; 邱学林; 储春荣; 祁红丽; 孟祥勋

    2012-01-01

    SSR sequences are the reproducible, stable, rich polymorphism DNA molecular markers. Fingerprint patterns of the SSR markers for 33 loquat varieties in national loquat germplasm resource garden were constructed by specifically amplifying polymorphism from 7 pairs of primers screened from 51 pairs of primers of the relatives Malus and Pyrus. The results showed that, the uses of seven primers, Hi01d05F, Hil2fO4F, CH02B10F, Hi03a03, Hi03e04, Hi04a05 and Hi02c07, could distinguish 33 loquat germplasm from one another, completely, providing an essential criterion for classification and identification of the loquat resources.%为构建枇杷种质资源指纹图谱,采用SSR标记技术对国家枇杷种质资源圃33份品种进行多态性分析,从近缘属苹果属和梨属的51对SSR引物中筛选出能够稳定扩增,多态性好的7对引物,Hi01d05F、Hi12f04F、CH02B10F、Hi03a03、Hi03e04、Hi04a05和Hi02c07来构建指纹图谱.结果表明,应用这7对引物可100%区别33个枇杷种质.这种SSR标记构建的枇杷种质资源指纹图谱对于品种分类及鉴定具有重要的应用价值.

  2. Development of a Wheat Variety Identification System Based on Fluorescently Labeled SSR Markers%基于荧光检测技术的小麦品种SSR鉴定体系的建立

    Institute of Scientific and Technical Information of China (English)

    郑永胜; 张晗; 王东建; 孙加梅; 王雪梅; 段丽丽; 李华; 王玮; 李汝玉

    2014-01-01

    【目的】建立基于 SSR 荧光标记的小麦品种 DNA 指纹鉴定体系,为中国小麦育成品种鉴定提供高通量技术手段。【方法】收集已定位到小麦21条染色体上的SSR标记引物,通过PCR扩增和变性聚丙烯酰胺凝胶电泳检测技术,筛选在中国小麦育成品种中多态性高的标记,对筛选出的引物5′末端利用6-FAM、HEX、ROX和TAMRA 4种荧光染料之一进行标记,利用DNA分析仪对扩增产物的峰型进行评价并检测不同等位变异的扩增片段大小,选择峰型简单易读、多态性高、较均匀分布到21条染色体上的标记,确定不同位点等位变异的大小及相应的参照品种,建立基于荧光SSR标记的高通量小麦品种鉴定体系。【结果】利用2438对SSR标记对8份植物学性状差异大的小麦育成品种进行初步筛选,共筛选出260对多态性较高、扩增稳定的SSR引物。利用上述260对引物对48份小麦品种继续进行复筛,选出130对扩增稳定、多态性高、带型好的SSR引物。对这些引物的正向5′末端分别标记6-FAM、HEX、ROX和TAMRA荧光后,利用DNA分析仪进行检测评价,最终选择了42个PCR扩增稳定、峰图简单、多态性高、连锁群分布均匀的SSR荧光标记。根据DNA分析仪检测到的每个标记的不同等位变异大小,为相应位点的不同等位变异进行了命名,并为每个等位变异选取了相应参照品种。根据每个引物标记的荧光和扩增的片段大小范围对42对引物进行合理搭配,在同一毛细管内对多个荧光标记进行检测,提高了DNA指纹数据采集效率,降低了检测成本。利用该体系对1625份小麦育成品种进行DNA指纹数据采集,在42个位点中共检测到434个等位变异,每个位点的等位变异个数在3-23,平均10.3个;每个位点的PIC值范围为0.240-0.829,平均0.610。利用1625份小麦育成品种DNA指纹数据,构建了中

  3. 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. PMID:27525909

  4. The SSR-based molecular profile of 1005 grapevine (Vitis vinifera L.) accessions uncovers new synonymy and parentages, and reveals a large admixture amongst varieties of different geographic origin.

    Science.gov (United States)

    Cipriani, Guido; Spadotto, Alessandro; Jurman, Irena; Di Gaspero, Gabriele; Crespan, Manna; Meneghetti, Stefano; Frare, Enrica; Vignani, Rita; Cresti, Mauro; Morgante, Michele; Pezzotti, Mario; Pe, Enrico; Policriti, Alberto; Testolin, Raffaele

    2010-11-01

    A collection of 1005 grapevine accessions was genotyped at 34 microsatellite loci (SSR) with the aim of analysing genetic diversity and exploring parentages. The comparison of molecular profiles revealed 200 groups of synonymy. The removal of perfect synonyms reduced the database to 745 unique genotypes, on which population genetic parameters were calculated. The analysis of kinship uncovered 74 complete pedigrees, with both parents identified. Many of these parentages were not previously known and are of considerable historical interest, e.g. Chenin blanc (Sauvignon × Traminer rot), Covè (Harslevelu selfed), Incrocio Manzoni 2-14 and 2-15 (Cabernet franc × Prosecco), Lagrein (Schiava gentile × Teroldego), Malvasia nera of Bolzano (Perera × Schiava gentile), Manzoni moscato (Raboso veronese × Moscato d'Amburgo), Moscato violetto (Moscato bianco × Duraguzza), Muscat of Alexandria (Muscat blanc à petit grain × Axina de tres bias) and others. Statistical robustness of unexpected pedigrees was reinforced with the analysis of an additional 7-30 SSRs. Grouping the accessions by profile resulted in a weak correlation with their geographical origin and/or current area of cultivation, revealing a large admixture of local varieties with those most widely cultivated, as a result of ancient commerce and population flow. The SSRs with tri- to penta-nucleotide repeats adopted for the present study showed a great capacity for discriminating amongst accessions, with probabilities of identity by chance as low as 1.45 × 10(-27) and 9.35 × 10(-12) for unrelated and full sib individuals, respectively. A database of allele frequencies and SSR profiles of 32 reference cultivars are provided. PMID:20689905

  5. A rapid and precise SSR-based procedure for bottle gourd seed quality survey%SSR分子标记技术在瓠瓜种子纯度快速鉴定中的应用

    Institute of Scientific and Technical Information of China (English)

    鲁忠富; 徐沛; 吴晓花; 汪宝根; 王莎; 刘永华; 李国景

    2012-01-01

    Current application of large number of commercial bottle gourd cultivars with very high genetic similarity has caused many disputes on seed quality. To provide a rapid, precise and reliable method for bottle gourd seed purity assay, we developed a set of SSR markers based on DNA sequences obtained from high-throughput sequencing. Eight of these markers were defined as diagnostic markers by genotyping a collection of 44 bottle gourd genotypes. Based on this, a rapid and precise SSR-based procedure as well as standard DNA fingerprints for bottle gourd seed quality survey was established, which will be beneficial for the industrialization of bottle gourd seeds.%当前生产上应用的瓠瓜品种众多,且商业品种间的遗传相似性愈来愈高,种子质量纠纷时有发生.为提供一种快速、准确、可靠的瓠瓜种子纯度检测方法,本研究以44份瓠瓜种质为试材,通过高通量测序自主设计开发适用于瓠瓜研究的SSR引物,从中筛选出8对诊断性引物,在此基础上建立基于SSR分子标记技术的瓠瓜种子纯度快速检测方法.根据本方法建立的瓠瓜主栽品种标准DNA指纹可高效鉴别瓠瓜种子真伪及纯度,满足瓠瓜种子产业化健康发展的需要.

  6. 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

  7. 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.

  8. 大蒜SSR体系的建立与优化大蒜SSR体系的建立与优化%Establishment and Optimization of SSR Reaction System in Garlic

    Institute of Scientific and Technical Information of China (English)

    周静; 陈书霞; 程智慧; 孟焕文

    2011-01-01

    为建立适宜大蒜(Allium sativum L.)的SSR反应体系和扩增程序,应用L16 (45 )正交设计对影响SSR-PCR的主要参数进行优化.结果表明,适宜大蒜的SSR反应体系总体积为20 μL,其中含Taq DNA聚合酶0.02 U/μL、引物为0.2 μmol/L、Mg2+ 2.0 mmol/L、dNTP 0.2 mmol/L、DNA 30 mg/L;PCR适宜扩增程序为:94 ℃预变性3 min,94 ℃变性30 s,55 ℃ 45 s,72 ℃延伸90 s,35次循环,94 ℃变性30 s,53 ℃ 45 s,72 ℃延伸1 min,10次循环的最后一个循环延伸增加为10 min.并优化引物最适合退火温度为53.5~58.5 ℃.利用此反应体系对40份大蒜品种进行SSR扩增并电泳检测,扩增谱带清晰且多态性较好,证明此体系稳定可靠.在此基础上,利用优化的SSR反应体系对100对大葱SSR引物进行筛选,从中筛选出1对扩增谱带清晰稳定性好的SSR引物,并对40份大蒜品种进行遗传多样性分析.这一对SSR引物共检测出3个多态性条带可将供试材料聚为2大类,大部分品种(系)都按照其地理来源和遗传背景进行聚类.%Orthogonal experiment with five factors including Taq polymerase, primer, Mg2 , dNTPs and template DNA concentration and several single factor experiments were designed and optimized in order to establish SSR reaction system in garlic. The results showed that 0. 02 U/μL Taq polymerase, 0. 2 μmol/L primer,2. 0 mmol/L Mg2 ,0. 2 mmol/L dNTP,30 mg/L template DNA were the optimal conditions in the reaction of 20 μL volume. PCR amplification was as follow: 94 °C (3 min) then 30 cycles each 94 °C(30 s) , 55 °C (45 s) , 72 °C (1 min), followed by 10 cycles of 94 °C (30 s) , 53 °C (45 s) , 72 °C (1 min) and aflnal extension at 72 °C for 10 min. The optimal annealing temperature ofprimer SSR003 ranged from 53. 5 °C to 58. 5 °C. Under optimal conditions, SSR reactions were carried out with 40 cultivars of garlic and tested with electrophoresis. The results revealed clear and high polymorphic bands which demonstrated that

  9. 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; 唐科志; 李中安; 周常勇

    2014-01-01

    of this research was to investigate the population structure of ‘Candidatus Liberibacter asiaticus’ in China by multi SSR (simple sequence repeat) loci. [Method] To identify the polymorphism of SSR loci in the genome of Ca. L. asiaticus, 25 reported SSR primer sets were tested using DNA samples obtained from HLB-affected plants from 8 provinces of China. The selected SSR loci were used to analyze 285 samples by PCR and PAGE electrophoresis. The software Quantity One 4.5.0 was applied to estimate the base pairs of the amplicons. The polymorphism of 285 samples in the selected loci were evaluated via the software PopGen version 1.31, and the clustering analysis was performed by software Powermarker 3.25 and structure 2.3.4.[Result]A total of 5 SSR loci were identified, with Nei’s gene diversity index ranging from 0.1542 to 0.9556. The locus LasA showed high diversity. Its effective number of allele (NE) and Nei’s gene diversity (H) were 22.5 and 0.9556, respectively. Analysis on population structure of Ca. L. asiaticus of China from different geographical samples revealed that the isolates from Yunnan province had high diversity, (NE=5.7, H=0.6580). The genetic distance of different geographical populations ranged from 0.0236 to 0.5786 and genetic identity ranged from 0.5607 to 0.9767. The longest genetic distance and lowest genetic identity were identified from the geographical population between Guangxi and Sichuan. The clustering analysis indicated all isolates from China were clustered into two groups. One is from Sichuan and Yunnan, the other is from Fujian, Zhejiang, Guizhou, Guangxi, Guangdong and Jiangxi. Structure analysis also showed the populations of Yunnan and Sichuan were constituted nearly by a single group and the rest of them were made up by mixed groups. [Conclusion]There are possible two kinds of different population structures of Ca. L. asiaticus in China by using the selected SSR markers and the results of this study will provide better

  10. 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

  11. 扁蓿豆24个居群遗传多样性的SSR研究%Genetic Diversity of 24 Medicago ruthenica Populations Using SSR Markers

    Institute of Scientific and Technical Information of China (English)

    赵敏; 戎郁萍

    2012-01-01

    The genetic diversity of twenty four populations of Medicago ruthenica distributed in Mongolian Plateau and Daxing'an mountain region was analyzed using simple sequence repeat (SSR) markers. This work aimed to know the genetic variation patterns within and among populations and the relationship between population distribution and environments. (1)10 primers were used and five of them showed polymorphism. The results indicated that 5 loci totally have 15 variation alleles,and the average polymorphic information content(PIC) was 0. 342 3. (2)The variation among populations was lower which showed by gene differentiation coefficient (Fst=0. 17) . There were 82. 8% of the variation in M. ruthenica within population,the gene flow (Nm) was 1. 2. (3)The cluster analysis indicated the 24 populations could be divided into three distinct groups. The population in northern of Daqinshan (hs) was the single population group. The populations in east,southeast and northeast of Inner Mongolia(kh,hb1,hb2,hb3,lq,lx,bl,zs, lh) were assembled as the second group and the others from northeast of Mongolia plateau transition to the Daxinganling region (dm, db, xs, eg, xb, eh, al, kj, aql, dw, hb4, ys, aq2, xl) were assembled as the third group. (4)The Mantel's test of the relationship between genetic distance and the environment factors showed that the genetic distance among M. ruthenica was affected by altitude, latitude and longitude. The impacts of geographical location (latitude and longitude) was greater than altitude and the single latitude or longitude(r=0. 402 7,P<0. 01). Between latitude and longitude,the impact of longitude was larger.%利用SSR技术研究分布于蒙古高原和大兴安岭地区24个扁蓿豆居群的遗传多样性,以明确扁蓿豆种群等位基因分布状况及在居群内和居群间的分异规律,揭示居群分布与环境的相关关系.结果显示:(1)利用紫花苜蓿的10个引物进行扩增,5个引物表现出多态性,共检测出15个等

  12. SSR标记的彩色马铃薯遗传多样性分析及指纹图谱构建%Genetic Diversity and Fingerprinting of 50 Pigmented Potato (Solanum tuberosum L.) Genetypes with SSR Markers

    Institute of Scientific and Technical Information of China (English)

    石景; 宋波涛; 金开建; 柳俊

    2012-01-01

    Pigments of potato tubers have been suggested the benefits for human beings health and have attracted interests in science which approach to their genetic improvement, and in fresh and industrial markets which have potentials of added-values. Little information is available for diversity of pigmented potato germplasms resulted in a bottle-neck of selection and enhancement of suitable parental materials for the potato breeding. In present research, SSR markers were employed to clarify the genetic diversity and to establish the fingerprinting of 50 pigmented potato (Solanum tuberosum L.) genotypes which were available in existed breeding programs. The results showed that 56 pairs of SSR primers having polymorphism were selected by screening over 200 SSR markers. A total of 236 alleles were identified, of which 230 were polymorphic and the ratio of polymorphism was as high as 97.46%, which indicated that the SSR markers selected were suitable for the genetic diversity clarification. The genetic similarity of the 50 tested materials ranged from 0.50 to 1.00, suggesting relative narrow genetic resources which they were derived from. The UPGMA cluster analysis indicated that all the materials could be assigned into three groups at genetic similarity' of 0.63. Cluster I contained 11 genotypes, 38 genotypes were assigned to ClusterⅡ while Cluster Ⅲ had only one genotype. Cluster Ⅰ was assigned into 2 subgroups at genetic similarity of 0.64, and cluster Ⅱ was assigned into 3 subgroups at genetic similarity of 0.67. Five pairs of SSR primer were successfully used to establish DNA fingerprints of the 50 tested materials by detecting 32 alleles. Marker StI005 alone could identify 32 genotypes, bi-marker combination of StI005/StI007 could detect 43 genotypes and tri-marker combination of StI005/StI007/S038 could distinguish 46 genotypes. The rest four cultivars, British Columbia and Congo as well as Macintosh Black and Black Beauty, could be further identified by S072

  13. 甲基磺酸甲酯处理毛泡桐丛枝病幼苗的形态变化及SSR分析%Morphological changes of the witches' broom seedlings of Paulownia tomentosa treated with methyl methanesulphonate and SSR analysis

    Institute of Scientific and Technical Information of China (English)

    曹喜兵; 范国强; 翟晓巧

    2012-01-01

    Witches' broom is one of the most serious diseases in Paulownia production. Morphological changes of the witches' broom seedlings of Paulownia tomentosa treated with methyl methanesulphonate and SSR analysis were investigated in order to further study the relation' between the disease and DNA changes. The results indicated that the diseased seedlings treated with optimal concentration of MMS might turn into the ones without symptom morphologically, but there still existed the phytoplasma in the seedlings treated with 20 mg · L-1 MMS. Not only might MMS of which the concentrations were more than 80 mg · L-1 eliminates the phytoplasma from the seedlings, but also inhibits the seedling growth. DNA base sequences of the healthy, diseased and the diseased-treated with 20 and 100 mg · L- MMS seedlings were the same at SSR level.

  14. 基于复合EST-SSR标记的大白菜种子纯度鉴定及SNP位点获取%Purity Identification and SNP Site Obtain of Chinese Cabbage Hybrids Using Multiplex EST-SSR Marker

    Institute of Scientific and Technical Information of China (English)

    赵新; 王永; 兰青阔; 贺长征; 陈锐; 李欧静; 刘娜; 朱珠; 郭永泽

    2013-01-01

      In this research,10 Chinese cabbage〔Brassica campestris L. ssp. pekinensis(Lour) Olsson〕hybrids and their parents were taken as study objects.Based on the EST sequences from NCBI genome data base,a SNP site and multiplex EST-SSR sites,which could be used to identify the purity of Chinese cabbage hybrids,were screened by SSR marker and high resolution melting(HRM) technology.According to the requirement of seed purity identification by high throughput molecular technology,the key techniques such as seedling culture condition of single seed,extraction status of single grain plant, rapid DNA extraction method and establishment of multiplex PCR system were groped and optimized.Results showed that the single germinating seed after 48 h could gain DNA with higher quality by the improved CTAB method in 3 h. Meanwhile,plant leaves reached seeding stage after 7 d,could complete DNA extraction by chexe-100 method within 40 min.The SNP site obtained by screening could be used to indentify the purity of 6 Chinese cabbage hybrids,and the multiplex EST-SSR locus could be used to indentify the purity of 10 Chinese cabbage hybrids.%  以10份大白菜杂交种及其亲本为研究对象,基于NCBI基因组数据库中EST序列信息,应用SSR标记及高分辨率溶解曲线技术筛选出用于大白菜杂交种纯度鉴定的SNP位点及复合SSR位点,并根据高通量分子检测技术种子纯度鉴定的需要,对单粒种子育苗条件、单株植株提取状态、快速DNA提取方法、复合PCR体系的建立等关键技术进行了摸索及优化。结果显示:经过48 h破壳状态的单粒种子,采用改良CTAB法可于3 h内得到较高质量的DNA;同时经7 d达到苗期状态的单株叶片,采用chexe-100法亦可于40 min内完成DNA提取;筛选得到的SNP位点可对6份大白菜杂交种进行纯度鉴定,复合SSR位点可对10份大白菜杂交种进行纯度鉴定。

  15. Rapidly Identifying Hybrids of Peanut (Arachis Hypogaea L.) Using SSR Molecular Markers%利用SSR快速鉴别花生杂交F1真伪

    Institute of Scientific and Technical Information of China (English)

    洪彦彬; 李少雄; 李杏瑜; 朱方何; 梁炫强

    2012-01-01

    In this research, we used six peanuts varieties as parents to make hybrid combinations for hybrid identification. Our practice showed that the authenticity of F1 hybrids would be easy validated by field agronomic investigation, if whose parents had visible and distinguishable phenotypic differences, otherwise it might be very difficult to identify the authenticity of F1 hybrids. Therefore, we established an SSR-PCR rapid detection system for peanut identification by modifying Thomson's one-step protocol to prepare DNA template, which was applied to identify the authenticity of peanut F, hybrids. The results showed that DNA templates extracted from Thomson's one-step protocol and modified Thomson's one-step protocol were able to generate sharp bands. Peanut DNA prepared by the modified protocol stored at 4℃ for almost a month was still fresh and working well, whereas peanut DNA prepared by Thomson's was completely degraded only staying a day at 4℃. The authenticity of F, hybrid combinations in this study were identified to be 38%~56%, the results further indicated that hybrid rates should be differences among different parents, even one pair parents for reciprocal cross. Therefore, we thought that using SSR markers to identify the authenticity of peanut hybrid might be great potential in future.%本研究,我们以6个花生品种为亲本配置杂交组合,田间调查发现亲本间形态表型差异大的杂交F1容易鉴别真伪,而形态表型差异小的则难于鉴别,甚至无法鉴别.为此,我们通过改良Thomson一步法制备DNA模板,建立了一套花生SSR-PCR快速检测体系,并在此基础上利用SSR鉴别花生杂交F1真伪.结果表明,采用Thomson一步法和改良后的一步法提取的DNA模版均能扩展出清晰条带,但改良后制备的DNA模板在4℃下可保存约1个月,未改良的仅能保存一天.利用SSR检测上述群体表明,F1真杂种率为38%~56%,不同亲本间杂交成功率存在差异,同一亲本

  16. Analysis of SSR Information in EST Resource of Ipomoea batatas (L.) Lam.and Ipomoea nil (L.) Roth%甘薯与牵牛EST资源的SSR信息分析

    Institute of Scientific and Technical Information of China (English)

    兰孟焦; 吴问胜; 王瑞珍; 赵朝森; 赵现伟

    2013-01-01

    为挖掘番薯(Ipomoea)属EST-SSR资源,从NCBI数据库下载23406条甘薯(Ipomoea batatas(L.)Lam.) EST和62282条牵牛(Ipomoea nil(L.)Roth) EST,利用生物信息学软件预处理、去冗余、拼接后得到12812条无冗余的甘薯EST(6.70Mb)和28422条牵牛唯一序列(17.19 Mb).对这些序列进行SSR搜索,在甘薯上获得328个SSR位点,出现频率为2.56%;牵牛上筛选到962个SSR位点,出现频率为3.38%.甘薯和牵牛EST-SSR具有多个共同特征:在SSR位点中,主要是二核苷酸重复类型,其次是三核苷酸重复;在二核苷酸重复中,出现最多的重复基序为AG/CT,其次是AT/AT;在三核苷酸重复中,主要基序是AAG/CCT; SSR位点的长度主要集中在20~22 bp.结果表明,搜索出的EST-SSR重复基序类型丰富、多态性潜能高,具有较高的开发和利用价值.%To excavate the EST-SSR resourses of lpomoea,12812 non-redundant ESTs with the total length about 6.70 Mb were obtained by assembling 23406 ESTs from Ipomoea batatas (L.) Lam.in NCBI.With the same way,28422 unique sequences covering 17.19 Mb were generated from Ipomoea nil (L.) Roth.A total of 328 SSR loci for Ipomoea batatas with the the frequency of 2.56% and 962 SSR loci for Ipomoea nil with the frequency of 3.38% were identified by MISA.The EST-SSRs from Ipomoea batatas and Ipomoea nil had many common features.Among all the identified SSRs,dinucleotide repeats were dominant motifs and then were trinucleotide repeats.For dinucleotide repeats,AG/CT was the major motif,followed by AT/AT.And AAG/CCT was the most frequent motif among the trinucleotide repeats.The length of EST-SSRs was mainly distributed among 20-22 bp.The results indicated that these EST-SSRs with abundant repeat motif types and high potential polymorphism had high value for exploitation and utilization.

  17. 利用SSR标记分析茄镰孢豌豆专化型的遗传多样性%Genetic diversity in Fusarium solani f.sp.pisi based on SSR markers

    Institute of Scientific and Technical Information of China (English)

    向妮; 肖炎农; 段灿星; 王晓鸣; 朱振东

    2012-01-01

    Pea root rot, caused by Fusarium solani f. sp. pisi (Fsp), is one of the most important diseases on pea (Pisum sativum). Assessing the genetic diversity of the pathogen isolates from different geographical regions is crucially important for understanding of the genetic background of this pathogen and intelligently deploying host resistance. We screened SSRs in complete genome sequence of Nectria haematococca MPVI, and 107 SSR loci were selected for designing markers, from which 24 polymorphic primer pairs were developed. The 24 primer pairs were used to assess genetic diversity of 96 Fsp isolates from different geographical regions. Among 24 SSR markers, a total of 132 alleles were detected among the 96 Fsp isolates, the number of alleles for each of the loci ranged from 3 to 15 with an average of 5.5. The genetic diversity was estimated to range from 0.4855 to 0.8264 with the average value of 0.738. Using these markers, 93 genotypes were detected. When the genetic similarity coefficient was 0.8, 96 Fsp isolates were clustered into 10 groups by phylogenetic analysis. There was no correlation between SSR profile and either geographic origin or pathogenicity. Analysis of AMOVA revealed that variation mainly presented within Fsp populations (86.14%), and genetic differentiation of Fsp was significantly affected by geographical conditions and ecological environment.%由茄镰孢豌豆专化型(Fusarium solani f.sp.pisi,Fsp)引起的根腐病是豌豆(Pisum sativum)最重要的病害之一.研究不同地理来源Fsp的遗传多样性,对了解该菌的遗传背景及防治病害具有重要意义.本研究从血红丛赤壳交配群Ⅵ(Nectria haematococca MPV)全基因组序列中筛选SSR位点,选取107个SSR位点设计引物,获得24对多态性引物.用24对多态性引物对不同地理来源的96个Fsp分离物进行遗传多样性分析,结果表明,24对引物共扩增出132个等位基因,变异范围为3-15,平均为5.5.基因多样性指数范围为0

  18. 玉米抗矮花叶病基因SSR分子标记定位研究%Location of maize dwarf mosaic virus-resistant genes with SSR makers

    Institute of Scientific and Technical Information of China (English)

    李晓玉; 赵靖; 文中仁; 周建; 朱苏文

    2013-01-01

    通过矮花叶病抗性鉴定筛选出玉米高抗自交系黄野四-3和高感自交系8112.遗传分析显示矮花叶病抗性表现为显性遗传.利用SSR分子标记,结合群体分离分析方法(BSA),对抗矮花叶病基因进行定位,筛选获得了与玉米抗矮花叶病基因位点连锁的SSR标记,并将该基因定位于第3连锁群,与两侧的Bnlg1035和Umc2266分子标记遗传距离分别为8.02 cM和3.04 cM.这一研究结果为快速筛选抗矮花叶病玉米新种质,培育抗性新品种提供了理论依据,为抗矮花叶病基因的分子标记辅助育种和抗病基因克隆奠定了基础.%In this study, we screened out highly resistant Huangyesi-3 and Susceptible 8112 maize inbred lines by identification of resistance to maize dwarf mosaic virus (MDMV). Genetic analysis showed that the resistance to MDMV was autosomal dominant. The resistant genes were located by BSA (bulked segregate analysis) method using SSR molecular markers. SSR molecular markers that linked tightly to the resistant gene were screened and located accurately on chromosome 3. The linkage distance between Bnlgl035 and Umc2266 are 8.02 cM and 3.04 cM, respectively. These results provide a theoretical basis for screening the resistant germplasm quickly and cultivating new varieties, and lay a foundation for molecular marker-assisted breeding and cloning of resistance gene to maize dwarf mosaic virus.

  19. 郑抗系列无籽西瓜品种SSR指纹图谱的构建%Fingerprinting of Zhengkang Triploid Seedless Watermelon Varieties Using SSR Markers

    Institute of Scientific and Technical Information of China (English)

    赵胜杰; 关立颖; 阎志红; 何楠; 路绪强; 刘文革

    2012-01-01

    为实现无籽西瓜品种的快速、准确鉴定,用23对西瓜核心SSR引物分析了15份无籽西瓜品种的DNA指纹.23对核心引物中有21对具多态性,共扩增出58个基因型,平均2.71个,平均多态性信息量(PlC)为0.36.10对引物在9个品种上具有特征谱带,组合PIC值>0.4的8对引物可以将参试的15个无籽西瓜品种一一区分开,并利用这8对引物构建了参试品种的数字指纹图谱.研究表明,西瓜核心SSR引物适合用于构建无籽西瓜品种的DNA指纹,将为无籽西瓜品种真实性鉴定和知识产权保护提供有效的技术依据.%Fifteen Zhengkang triploid seedless watermelon varieties were fingerprinted using the published 23 core SSR marker primer pairs for watermelon. Twenty one out of 23 primer pairs were polymorphic among tested triploids and produced 58 genotypes with an average of 2.71 per pair. The mean PIC was 0.36. Ten primer pairs produced unique bands for nine varieties. All 15 varieties were distinguished by 8 primer combinations,PIC > 0.4,and their digital fingerprinting code was also established. The results indicate that the published core SSR markers are suitable for the construction of DNA fingerprinting of triploid seedless watermelon varieties. The fingerprinting will provide reliable evidence for the variety identification and protection of intellectual property right for these varieties.

  20. Genetic relationships between Anhui and Heilongjiang populations of Phytophthora sojae assessed by SSR markers%安徽和黑龙江省大豆疫霉群体遗传结构的SSR分析

    Institute of Scientific and Technical Information of China (English)

    王子迎; 王朝霞; 沈洁; 鲁红侠

    2009-01-01

    The genetic diversity of two geographic populations of Phytophthora sojae Kauf. & Gerd. from Anhui and Heilongjiang Provinces was determined using the molecular marker of simple sequence repeats (SSRs). Genetic variation was analyzed for 83 isolates of P. sojae. By using 20 pairs of SSR primers, a total of 109 polymophic bands (alleles) were amplified at an average of 5.5 bands per pair of primers. Genetic similarity analysis showed that there were obvious differences between Helongjiang and Anhui populations. Cluster analysis with an unweighted pair group method revealed that the 83 isolates of P. sojae were clearly separated into seven clustering groups (genotypes) at a level of 80% similarity. We also found that isolates from Heilongjiang had lower genotypic diversity than those of Anhui. In addition, three particular P. sojae genotypes were only found in Anhui population and two particular genotypes were only found in Heilongjiang population. In conclusion, the results in this study do not support the hypothesis that P. sojae in Anhui has immigrated from Heilongjiang.%采用简单重复序列(SSR)的分析方法,对来自安徽和黑龙江省的大豆疫霉群体进行了遗传多样性分析.通过使用20对SSR引物对供试的83株大豆疫霉菌株进行PCR扩增,共得到109个SSR标记,全部为多态性标记,平均每对引物扩增出5.5条带.遗传变异与相似性分析表明,安徽群体具有更高的遗传变异度,安徽群体与黑龙江群体问遗传相似性较低:聚类分析显示,供试菌株在80%的相似性水平上可被区分为7个类群,且安徽群体分布于更多的聚类组中:Shannon-Wiener多样性指数也表明安徽群体的遗传多样性较黑龙江群体丰富.综合分析表明,本研究的结果不支持关于安徽的大豆疫霉可能来源于黑龙江的推测.

  1. On the Application of the SSR Model in Normal University Students's Educational Psychology Course%SSR模式在高师教育心理学课程中的运用研究

    Institute of Scientific and Technical Information of China (English)

    董江华; 赵晓燕

    2011-01-01

    Transmitting - accepting teaching model emphasizes the value of existing knowledge. However, SSR mode pursuing to cultivate the learner's independence, creativity and leadership. As normal college students" common learning, educational psychology is in dire need of turning the direction of rotation. This article explores ways of teaching model reforming.%“传递-接受”为主的教学模式重在肯定固化知识的价值,SSR模式则基于实践生成的知识观,着眼于培养具有自主性、创造力、领导力的学习者。作为师范专业的公共必修课,教育心理学课程教学急需实现教学模式的转向。结合实践,本研究对大班额情境下,SSR模式在高师教育心理学课程中的运用进行了探索。

  2. The proteolytic activation of the relNEs (ssr1114/slr0664) toxin-antitoxin system by both proteases Lons and ClpP2s/Xs of Synechocystis sp. PCC 6803.

    Science.gov (United States)

    Ning, Degang; Ye, Sen; Liu, Biao; Chang, Jianing

    2011-11-01

    The proteolytic regulation of toxin-antitoxin (TA) systems has been well studied in Escherichia coli but remains unclear in other bacteria. A chromosomal gene pair ssr1114/slr0664, named relNEs, of Synechocystis sp. PCC 6803 forms a TA system belonging to rel family. Here, we used E. coli strain BL21 (DE3) as a host to characterize the proteolytic regulation of relNEs. The proteases of this strain could not degrade the antitoxin RelN, and the ectopic production of the ATP-dependant protease Lons or ClpP2s/Xs of Synechocystis sp. PCC6803 did not affect E. coli growth. Either Lons or ClpP2s/Xs was able to degrade RelN resulting in growth arrest of E. coli due to the activation of RelEs's toxicity, and the presence of RelEs could protect RelN to a certain extent against Lons and ClpP2s/Xs. Our observations suggest that both Lons and ClpP2s/Xs are responsible for RelN proteolysis in the native host under certain conditions. RelN is the first protein substrate identified for cyanobacterial ATP-dependent proteases.

  3. 中国50个甘蓝代表品种EST-SSR指纹图谱的构建%EST-SSR Fingerprinting of Fifty Cabbage Representative Varieties from China

    Institute of Scientific and Technical Information of China (English)

    王庆彪; 张扬勇; 庄木; 杨丽梅; 刘玉梅; 吕红豪; 方智远

    2014-01-01

    [Objective]In this study, the method of cabbage DNA fingerprint was drawn, and fifty cabbage representative varieties from China were fingerprinted with EST-SSR primers to provide reference for variety distinctness, authenticity, and purity identification. [Method]First, EST-SSR primers were screened by using the technologies of 6% denaturing polyacrylamide gel electrophoresis and six cabbage varieties that come from different ecogeography. The length of amplified fragments was detected on DNA Analyzer platform using four fluorescent-labels (TAMRA, HEX, ROX and 6-FAM) in 5′end of forward primer, and then defined the reference variety for every alleles. Total twenty core primers were used to establish fifty cabbage varieties SSR fingerprinting, and for ‘Zhonggan 21’ variety identification. [Result] Six cabbage varieties of different resources were used to screen 978 EST-SSR primers, out of 128 polymorphic primers were obtained according to the PCR bands stability, high polymorphism information content (PIC), easy discrimination of different alleles and even distribution of molecular markers on each chromosome, and 20 pairs of primers were selected to detect a total of 58 alleles at 20 loci, with 2.22 loci per chromosome and 2.9 alleles per locus on average. The PIC values varied among the primers ranging from 0.34 to 0.76. The length of amplified fragment varied in the range of 143-296 bp. The maximum number of alleles for each primer pairs of BoE607 and BoE723 was five. Fingerprinting database of 50 cabbage representative varieties from China was established with 20 pairs of core primers. The authenticity of‘Zhonggan 21’ was identified by artificial simulated population and these results were identical with that made from field investigation.[Conclusion]Twenty pairs of core primers were selected and used to establish DNA fingerprint database of 50 cabbage representative varieties from China, and the authenticity of‘Zhonggan 21’ was identified by

  4. Analysis of SSR Information in ESTs Resource of Ipomoea trifida%甘薯近缘野生种三浅裂野牵牛EST资源的SSR信息分析

    Institute of Scientific and Technical Information of China (English)

    贾赵东; 马佩勇; 郭小丁; 谢一芝

    2012-01-01

    In the study ,1 458 ESTs of Ipomoea trifida in the database of NCBI were downloaded and analyzed by bioinformatics tools and method. The results showed that we got 868 non-redundant ESTs with total length about 334.368 kb after the preprocessed, some redundants and low qualities sequences were removed. Totally 35 SSRs (Simple sequence repeat) were screened and distributed in 35 ESTs, accounting for 4. 03% of the non-redundant ESTs,the average distribution distance of the EST-SSRs was about 9. 55 kb. In the different motifs ranging from 2 to 6 nucleotides, except to mononucleotide, di-nucleotide and tri-nucleotide repeats were dominant repeat types and accounted for 68.57% , ftri-nucleotide repeats types accounted for 45. 71%. In addition, Among all repeat motifs of SSRs, AT/AT was most high-frequent repeat motif and accounted for 14.29% followed by TCT/AGA accounted for 11.43% .thirdly TAA/TTA accounted for 8.57%. Among all SSRs,SSRs which repeated overstep 5 times accounted for 37.14% ,that of repeated 5 and 7 times accounted for 14.29%. The result in this paper indicated that the EST-SSR of Ipomoea trifida hadrevelance utility value in the study of sweetpotato genetic and breeding.%利用生物信息学方法对NCBI公共数据库的1 458条三浅裂野牵牛ESTs序列进行EST-SSRs信息特征分析.结果显示,剔除低质量的和冗余的序列后,得到总长度为334.368 kb无冗余序列868条.这些无冗余序列中有35个微卫星简单重复序列(Simple sequence repeat,SSR),分布于35条EST中,出现频率为4.03%,平均分布距离为9.55 kb.在2~6核苷酸的重复类型中,二、三核苷酸SSR之和占总EST-SSR的68.57%,其中三核苷酸SSR占总SSR数量的45.71%.在所有重复单元中,所占比例最高的是AT/AT(14.29%),其次是TCT/AGA为11.43%,TAA/TTA为8.57%列第3位.在所有的SSR中,EST-SSRs重复次数5次的有13个,占全部SSR的37.14%,其次是重复次数为4次和7次,各有5个,占全部SSR的14.29%.结

  5. EST-SSR Based Genetic Diversity Analysis on Salt Tolerant Plants from Six Species in Chenopodiaceae%藜科6种耐盐植物遗传多样性的EST-SSR分析

    Institute of Scientific and Technical Information of China (English)

    徐照龙; 易金鑫; 余桂红; 张大勇; 何晓兰; 王秀娥; 马鸿翔

    2011-01-01

    利用EST-SSR标记分析了藜科6种耐盐植物的遗传基础和遗传多样性,以期为藜科耐盐植物遗传育种提供快速、可靠的分子标记辅助选择工具.采用31对藜科海蓬子属和碱蓬属的EST-SSR引物对藜科6种植物进行PCR扩增,其中16对引物得到较好扩增,引物通用率为51.6%,共检测到18个多态性位点,每位点等位基因数2~4个,多态性丰富.进一步采用Nei's遗传距离聚类分析表明6种植物可以分为3组,主成分分析也支持上述分组,而且DY529957、DY529903和DY5298853个EST在分组中贡献率最高.经与GenBank中序列相似性比对,前两者分别编码生长素抑制蛋白(Auxin-repressed protein,ARP)和植物防御素(Defensins,Def),都参与植物逆境胁迫响应,但分属于不同代谢途径;后者则编码未知蛋白.总体而言,16对SSR引物在藜科6种植物间具有较好的通用性,能够揭示该6种植物间广泛的遗传多样性,及其存在不同耐盐机制提供分子证据.%This report focus on EST-SSR based evaluation of genetic diversity in salt tolerant plant from six species in Chenopodiaceae. Thirty-one pairs of EST-SSR primers were designed according to ESTs sequence collected from Salicornia and Suaeda genera. Only sixteen out of all primer pairs successfully amplified the DNA fragments by using PCR procedure across all samples, which demonstrated 51.6% over all primers was transferrable. Total 18 polymorphic loci were detected by the 16 primer pairs, and allele number at each locus ranged from 2 to 4, indicating a wide range of genetic diversity. Clusterring analysis based on Nei's genetic distance showed that the six plants could be grouped into three clades, and the division was confirmed by principal component analysis. Moreover, this grouping profile was mainly attributed to polymorphism of three ESTs, e. g. DY529957, DY529903 and DY529885.According to the sequence similarity, the three ESTs were assumed to encode an auxin

  6. 糯玉米种质 SSR 标记遗传及品质性状分析%Analysis of Genetic and Quality Traits of Waxy Corn Germplasms

    Institute of Scientific and Technical Information of China (English)

    孟强; 戴冬青; 杨利; 李娟; 齐望; 赵仁贵

    2014-01-01

    利用SSR标记研究50份糯玉米自交系的遗传变异,从40对核心引物中筛选出扩增条带清晰、稳定性和多态性好的18对引物,在50份糯玉米自交系中检测出87个等位基因变异,每对引物检测等位基因3~7个,平均4.83个;每对SSR引物的多态信息量(PIC )为0.211~0.759,平均0.584。利用UPGMA聚类分析方法把50份供试糯玉米自交系分为4个类群,其划分结果与系谱分析基本一致。分别测定了50份糯玉米自交系子粒中蛋白质、淀粉、水分、脂肪和游离氨基酸的含量,结果表明:糯玉米子粒营养成分含量各不相同,游离氨基酸变异系数最大,淀粉变异系数最小,具有丰富的遗传多样性。基于50份自交系的品质性状数据,利用SPSS分析软件中平方欧式距离聚类分析方法进行聚类,结果划分为2个大类,4个亚类,类群之间具有较大差异。%The SSR markers were used to study the genetic variation of 50 waxy maize inbred lines ,and 18 pairs of primers were selected from 40 pairs of primers .A total of 87 polymorphic bands ,variation of 3~7 alleles for each primer ,and an average of 4.83 alleles per primer were detected ;polymorphic infor-mation content of each pair of SSR primers ranged from 0.211 to 0.759 averaged 0.584 .Using clustering analysis in UPGMA ,the waxy corn inbred lines were classified into 4 groups ,which was basically the same as germplasmic genealogy .The contents of protein ,starch ,moisture ,fat and free amino acids in the grain of waxy maize inbred lines were determined .The results showed that grain nutrient content of each waxy maize was not identical ,free amino acid variation coefficient was the maximum and that of the starch was the minimum ,indicating that the inbred lines were of rich genetic diversity .Based on the data of the quality traits in the 50 inbred lines ,adopting the squared Euclidean distance cluster analysis ,the 50 waxy maize

  7. Development of polymorphic SSR markers for Phytophthora sojae and analysis of the genetic diversity%大豆疫霉多态性SSR标记开发及遗传多样性分析

    Institute of Scientific and Technical Information of China (English)

    徐静静; 王晓鸣; 武小菲; 朱振东

    2009-01-01

    Using FastPCR software, 1 234 perfect simple sequence repeats (SSRs) with 2 to 4 bp repeat motif were identified in complete genomic sequences of Phytophthora sojae. 260 SSRs were selected for primer design, and the validity of resulting primer pairs was detected by amplifying 5 isolates of P. Sojae. There were 212 (81.5%) primer pairs amplified characteristic SSR bands and 112 primer pairs (52.8%) amplified polymorphic bands among 5 different P. Sojae isolates. 18 primer pairs were selected to analyze the genetic diversity of 73 P. Sojae isolates came from USA, Heilongjiang Province and Fujian Province of China. On the 18 SSR loci, a total of 112 alleles were detected in 73 isolates. At each locus,4 to 9 alleles were detected with an average of 6.22. The results showed that the selected primer pairs were high polymorphic. There was the closest genetic distance between the P. Sojae populations from Heilongjiang and Fujian, while the populations from USA and Fujian had the farthest genetic distance. 73 P. Sojae isolates could be divided into 6 groups by UPGMA clustering, 8 USA isolates (72.73%) were clustered together with 53 Chinese isolates (85.48%), implicated that Chinese P. Sojae isolates and some USA isolates should have several common ancestors and Chinese isolates could be exotic species.%用FastPCR软件在大豆疫霉全基因组中搜索到1 234个含2~4个重复基元精确SSRs.选择260个SSRs设计引物,经对大豆疫霉5个分离物的基因组DNA检测,有212对(81.5%)有效扩增出SSR特征条带,112对(52.8%)扩增多态性.用18对多态性SSR引物分析了来自美国、中国黑龙江省和福建省大豆疫霉分离物的遗传多样性,在73个分离物中共扩增出112个等位变异,变异范围为4~9,平均为6.22个,表明选择的引物对具有高的多态性.在3个大豆疫霉群体中,黑龙江省和福建省分离物的遗传距离最近,美国和福建省分离物的遗传距离最远.UPGMA聚类将73个分离物划分为6

  8. DNA Fingerprint Construction of Different Generations of Saccharum spp. × Erianthus fulvus using SSR Marker%甘蔗与蔗茅杂交不同世代的SSR指纹图谱构建

    Institute of Scientific and Technical Information of China (English)

    姚春雪; 王先宏; 何丽莲; 李富生

    2011-01-01

    Twelve SSR primer pairs were used to analyse the polymorphism of different generation hybrids (F1, BC1 and BC2) that dervied from the cross between sugarcane (Saccharum spp.) and related wild species Erianthus fulvus. Totally 234 bands were amplified including 216 polymorphic bands and the polymorphic rate was 92.31%, the result showed that there were abundance genetic variation in these hybrids. The average genetic coefficient between these offsprings and their two original parents were 0.75 (Yacheng 89/9) and 0.47 (E. fulvus), respectively. The cluster result showed the hybrids and their original female parent Yacheng 89/9 were clustered in the same group, suggested the genetic material of original female parent Yacheng 89/9 was predominated in hybrids. The homology between YAU01/68 and YAU01/108 arrived to 94%, while the value was only 50% between Yacheng 89/9 and E. fulvus. The fingerprinting database of all the tested plant materials were constructed based on the 234 SSR fragments, which will be helpful for trace down the transmission of genetic material of E. fulvus in hybrids and the further utilization of these hybrids in sugarcane breeding program.%本研究采用12对引物对67份"崖城89/9×昆明蔗茅"杂种不同世代(F1,BC1,BC2)及其亲本材料进行SSR多态性分析,扩增的总条带数为234条,其中多态性带为216条,多态率为92.31%,表明崖城89/9与蔗茅野生种杂交后代材料间存在较大差异;各后代材料与原始亲本"崖城89/9"及"昆明蔗茅"间的平均遗传相似系数分别为0.75和0.47,且从聚类结果来看,各子代材料均与"崖城89/9"聚为一类,说明原始母本的遗传物质在后代材料中占绝对优势;供试材料的同源关系分析表明,YAU01/68和YAU01/108间的同源性高达94%,而其母本"崖城89/9"与父本"昆明蔗茅"间仅为50%;利用234个SSR标记片段组合构建供试材料的指纹图谱数据库,为追踪蔗茅野生种血缘在不同世代中的传递情

  9. Development of SSR Markers and Construction of Fingerprint for Cannabis (Cannabis sativa L.)%大麻SSR标记的开发及指纹图谱的构建

    Institute of Scientific and Technical Information of China (English)

    信朋飞; 臧巩固; 赵立宁; 高春生; 程超华; 唐蜻

    2014-01-01

    表达序列标签(expressed sequence tags,EST)是开发SSR标记的重要资源.本研究从NCBI中大麻EST数据库中检索到1114个SSR,分布于989条EST序列中,占EST总数的7.66%.其中三、六核苷酸重复基元类型居多,分别占EST-SSR总数的39.84%和34.56%,统计得到三核苷酸重复类型47种,六核苷酸重复类型113种.利用部分EST-SSR序列设计49对SSR引物,其中40对引物有扩增产物,占所设计引物总数的81.63%.进一步用这些引物在24个大麻品种进行多态性检测,29对引物显示多态性,占可扩增引物的72.5%.利用E-7、E-8、E-11、E-18、E-21、E-39及E-48共7对引物构建了24份供试材料的SSR指纹图谱.本研究结果证明了基于大麻EST信息建立SSR标记是一种有效而又可行的方法,并且为这些品种的真伪鉴定和保护提供科学依据.

  10. 中国328个玉米品种(组合)SSR标记遗传多样性分析%Genetic Diversity Analysis of 328 Maize Varieties (Hybridized Combinations) Using SSR Markers

    Institute of Scientific and Technical Information of China (English)

    王凤格; 田红丽; 赵久然; 王璐; 易红梅; 宋伟; 高玉倩; 杨国航

    2014-01-01

    。参试品种主坐标分析显示各区试组划分、对照品种设置起到了育种导向的作用。%[Objective] The objective of this study is to analyze the genetic diversity of 328 maize varieties from breeding years, planting regions, and to research the genetic differentiation characteristics of all the varieties from every appropriate planting region. This study will provide a theoretical basis for the maize regional trial, validation management and breeding strategic adjustment.[Method] Forty core SSR primers covering the entire maize genome were used to scan 328 samples by high-throughput 10-plex capillary electrophoresis platform. The polymorphism of 40 SSR loci and genetic diversity of 328 samples were evaluated via the software Power-Marker ver.3.25, and the Principal Coordinate Analysis (PCoA) of these samples from every regional trial groups was executed using statistical analysis software MVSP ver.3.13. [Result] The detected alleles of 40 SSR primers ranged from 3 to 16, with an average of 8.10, the polymorphism information index (PIC) ranged from 0.18 to 0.85, with an average of 0.63. There were no significant genetic diversity changes among varieties from different years, and all the PIC values were about 0.60. The total allele and gene-type number of 8 regional trial groups ranged from 170 to 262 and from 200 to 511. The varieties from Jing-Jin-Tang and Xi-Nan displayed the minimum and maximum values. The varieties from Jing-Jin-Tang group displayed the lowest PIC value of 0.51, and the remaining groups were near 0.60, and the average heterozygosity was about 0.60. Principal coordinate analysis (PCoA) of varieties from eight regional trial groups showed that the genetic distribution of varieties from Xian-Shi (maize for table use) and Ji-Zao-Shu (very early maturity maize) groups deviated from the common maize region, displayed an obvious germplasm specificity. As the common maize varieties were used as control samples at early stage, the

  11. Study on Genetic Diversity of 54 Sweet Corn Inbred Lines by SSR Markers%54份甜玉米自交系的SSR遗传多样性分析

    Institute of Scientific and Technical Information of China (English)

    黄君; 冯发强; 王青峰; 张晶; 周鹏; 李小琴

    2012-01-01

    利用SSR标记对54份甜玉米自交系进行了遗传多样性分析,从150对引物中筛选出了56对扩增条带清晰、稳定性好的引物.结果表明:56对引物在54份甜玉米自交系中共检测到155个位点的等位基因变异,平均每对引物检测出的等位基因变异为2.77个,变异范围为2~5个,平均多态性信息含量为0.42,变异范围为0.13 ~0.71.UPGMA聚类结果表明,可将甜玉米自交系划分为三大类,其划分结果与系谱分析基本一致.%The technique of SSR markers was used to study the genetic diversity of the sweet corn inbred lines, 56 pairs of primers selected from 150 pairs of primers. A total of 155 polymorphic bands, an average of 2. 77 alleles per primer, variation of 2 -5 alleles for each primer, mean polymorphic information content of 0. 42 and its range from 0. 13 to 0. 71 were detected. Clustering analysis in UPGMA classified the sweet corn inbred lines into 3 groups, which were similar to germplasmic genealogy.

  12. Analysis of Genomic Microsatellite Sequence and Development of SSR Markers in Metasequoia glyptostroboides%水杉基因组微卫星分析及标记开发

    Institute of Scientific and Technical Information of China (English)

    张新叶; 张亚东; 彭婵; 宋丛文; 杨彦伶

    2013-01-01

    In this paper, the partial genome of Metasequoia glyptostroboides, a rare plant, was sequenced by using the ROCHE-454 GLX high-throughput sequencing platform. Through sequence assembly and microsatellite finding, 1 965 microsatellite loci were obtained in the sequence and the repeat unit length was 2 - 5 base pairs, by which 921 pairs of primer were designed with the Primer 3 Plus software. Analysis of these microsatellite sequences showed that tetranucleotide microsatellite was the most abundant, accounting for 38.8% of the total repeat sequences, followed by dinucleotide (31.8%), trinucleotide (22%) and pentanucleotide (7.4%) in the M. glyptostroboides genome. Among the dinucleotide repeat types, AG type was the most, accounting for 13.9% of total repeats and 43.8% of dinucleotide repeats. In the eight trinucleotide repeat types, AAG type accounted for 8.3% of total repeats and 37.7% of trinucleotide repeats, followed by ATG (23.1%), AAC (16.%) and AAT (13.0%). The analysis of different lengths of the microsatellite repeat unit showed that the most abundant variants were dinucleotide microsatellite and there were 23 different types of repeat lengths, followed by the tetranucleotide repeat (10 types), trinucleotide repeat (8 types) and pentanucleotide repeat (3 types). The validation of SSR markers showed that, 87 pairs brought about clear products and 46 pairs had polymorphic products, accounting for 62. 14% and 32.86% out of the 140 primer pairs,respectively.

  13. 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

    Directory of Open Access Journals (Sweden)

    Polovka S.N.

    2014-12-01

    Full Text Available 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 expeditions (surface and submarine fleet and displayed in terms of the further development of the geology of the oceans and seas in Ukraine. attempt in the 50th anniversary of the end of the first Ukrainian official for marine geologists USSR Academy of Sciences (NAS of Ukraine expedition, which took place during the twelfth flight NDS "Mikhail Lomonosov" in the tropical Atlantic, recreate the historical course of events that led to this sea expedition and recall the scientific community on the official start investigations bottom waters of the oceans Ukrainian researchers. It is shown that the knowledge of Ukrainian researchers waters of the oceans using conventional methods and techniques that have been in service in Oceanology of the USSR, but in addition, they have developed methodological and instrumental principles of nuclear-physical methods of geological studies of sediments waters (apparatus and methods for determining water-physical properties of sediments and pore waters hydrochemistry study and created and improved methods. According its history, the geology of the oceans and seas experienced its heyday in the USSR. The current phase of the complex, ambiguous and has a different assessment scientists. Some estimate it as a naval expeditions stagnation and decline of theoretical research. Other developing the idea of rethinking the strategic approach to the development of this field of science in our country, synthesis of theoretical and practical

  14. Analysis of Genetic Diversity of Wheat Varieties in Yunnan Province Using SSR Markers%利用SSR分析云南省小麦资源的遗传多样性

    Institute of Scientific and Technical Information of China (English)

    程加省; 于亚雄; 勾宇宏; 杨金华; 刘丽; 胡银星; 程耿

    2009-01-01

    本研究利用微卫星(SSR)分子标记对云南铁壳麦、地方品种和推广品种遗传多样性进行研究比较分析.20对SSR引物对102份材料进行PCR扩增,共扩增出54条带,平均2.7条带.其中有52条具有多态性,每个多态性引物可扩增出1~5条带.云南铁壳麦、地方品种、推广品种的平均遗传距离分别为0.143 9、0.183 8、0.201 3; Nei's基因多样性指数(H)平均为0.233 6、0.230 1、0.222 4;Shannon信息指数(I)平均为0.351 9、0.349 8、0.333 8;多态位点百分率分别为72.22%、81.48%、68.52%.采用类平均法 (UPGMA)聚类分析,在域值为0.31处被聚为6类,云南铁壳麦聚为一类,地方品种聚为4类,推广品种29份聚为一类,一份单独聚为一类.根据上述指标和聚类分析得:云南铁壳麦在DNA分子水平上有一定多样性,大于推广品种但低于地方品种.

  15. Genetic Diversity of Ganpi Series Beer Barley Varieties(Lines) and Imported Varieties by SSR%甘啤系列啤酒大麦品种(系)与国外引进品种间遗传多样性的SSR分析

    Institute of Scientific and Technical Information of China (English)

    杨振华; 漆燕玲; 蒋玮

    2009-01-01

    The genetic relationship among 35 beer barley varieties, including 10 Gansu and 25 foreign varieties were investigated by SSR. The results showed that among the 49 pairs of SSR primers used, 32 pairs of SSR primers detected polymorphisms. Clustering analysis showed that the range of between genetic similarity coefficient (GS) located in between 0.0500~0.6667. At the level of 0.26 GS, these varieties could be clustered into 4 groups, the majority of Ganpi series varieties (lines) were located in the same group, indicated that the genetic basis was rather narrow. The imported varieties had relatively wide range, indicated that their genetic basis is more extensive.%为了解甘啤系列啤酒大麦品种(系)与国外引进品种间的遗传关系,利用SSR标记技术对10个甘啤系列啤酒大麦品种(系)和25个国外引进品种的遗传背景进行了遗传多样性分析.结果表明,所用49对SSR引物中,有32对有多态性.这些品种遗传相似系数(GS)的分布范围较小,处于0.0500~0.6667之间.通过聚类分析,在GS值为0.26的水平上,这些品种被聚为4大类,大多数甘啤系列品种(系)分在同一类中,表明其遗传距离较近,遗传基础较狭窄;国外引进品种的分布范围相对较宽,表明其遗传基础较广泛.

  16. Development of 25 SSR Markers and Their Uses in Evaluating Genetic Diversity of Oil Palm Germplasm Resources%25个油棕 SSR标记的开发及应用这些标记评估油棕资源的遗传多样性

    Institute of Scientific and Technical Information of China (English)

    肖勇; 杨耀东; 夏薇; 沈雁; 雷新涛; 马子龙

    2013-01-01

    The research mined SSR loci according to EST sequences published in NCBI website , and designed primers based on the sequences flanking these SSR loci .Then, PCR amplification of the DNAs from 18 oil palm germplasm resources was carried out to test their diversity .The amplification results showed that:among the PCR amplification with 72 pairs of primers , that with 25 pairs of primers obtained polymorphic bands , and their heterozygosity varied from 0.1049 to 0.6605, with the average of 0.4702, indicating these markers had an intermediate level of genetic variance .Meanwhile , these polymorphic SSR markers were used to e-valuate the genetic diversity and population structure of these oil palm germplasm resources .The results showed that the oil palm germplasm resources from Coconut Research Institute had the richest genetic diversity .Clustering analysis demonstrated that there was a significant genetic difference among these oil palm resources from different regions .The developed SSR markers in this re-search will have an immediate application in the genetic breeding of oil palm .%应用NCBI网站上公布的EST序列,挖掘SSR位点,并根据SSR位点的侧翼序列设计引物,对18份油棕资源的DNA进行了PCR扩增,扩增结果显示,在72对引物的PCR扩增中,25对引物具有多态性特征,并且其杂合度在0.1049和0.6605之间,平均杂合度为0.4702,这暗示了这些标记具有中度的多样性。同时,应用这些有多态性的标记评估了这些油棕资源的遗传多样性和群体结构,分析结构显示:椰子研究所油棕资源圃的遗传多样性最为丰富,此外,聚类分析表明不同位置来源的油棕资源展现了显著的遗传差异。本研究开发的SSR标记将能被应用到油棕的遗传育种研究中。

  17. Genetic Diversity and Population Structure of Quercus serrata var. brevipetiolata Revealed by nSSR Markers%基于核微卫星的短柄枹栎居群遗传多样性和遗传结构

    Institute of Scientific and Technical Information of China (English)

    王雁红; 俞琦; 杨佳; 赵鹏; 李忠虎; 赵桂仿

    2015-01-01

    [Objective]Quercus serrata var. brevipetiolata as one of the important forest tree species in south China has degenerated due to recent human influences. Study of genetic diversity and genetic structure,as well as correlation between genetic structure and geographical distributions can help to develop sound conservation strategies for Q. serrata var. brevipetiolata. [Method]In this study,a total of 398 individuals of 24 Q. serrata var. brevipetiolata natural populations across the species distribution were collected. Eight nuclear microsatellite ( nSSR ) markers with rich polymorphism were used to analyze the genetic diversity of each population,and genetic differentiation was estimated with analysis of molecular variance ( AMOVA) . Genetic structure at species level and correlation between genetic structure and geographical elements of Q. serrata var. brevipetiolata were evaluated using STRUCTURE and Alleles In Space programs.[Result]Results indicated rich genetic diversity of the species ( He =0. 43,Ho =0. 28,Na =3. 67,Ne =1. 96,I =0. 66,PPL =82. 81%). Analysis of molecular variance (AMOVA) showed that genetic variation mainly existed within populations (FST = 0. 22,P < 0. 001),and the genetic diversity differed among different populations. Two groups containing the east and the west populations were plotted based on the Bayesian clustering analysis( STRUCTURE) ,and gene flow existed among these populations ( Nm =1. 88 ) . Great genetic differentiation existed between the two groups containing the east and west geographical populations of the species (FST = 0.25,P < 0.001),while the genetic variations was relatively low among the populations of each group. The Landscape Shape Interpolation analysis ( AIS) also suggested great genetic differentiation between the east and west populations,which was consistent with the STRUCTURE cluster results. No correlation was found between the genetic distance and geographical distance ( R2 = 0. 011,P =0. 07).[Conclusion

  18. 东北粳稻分蘖期耐冷性鉴定及SSR标记关联分析%Association Analysis of Rice Cold Tolerance at Tillering Stage with SSR Markers in japonica Cultivars in Northeast China

    Institute of Scientific and Technical Information of China (English)

    张艳梅; 邹德堂

    2012-01-01

    The cold tolerance of rice at the tillering stage was evaluated with 140 rice cultivars(lines) from Northeast China as materials and association analysis was conducted among 96 selected materials which differed in cold tolerance with 84 SSR markers. The experimental results showed: there were 20. 0% of rice materials with better cold tolerance,30. 71 % with intermediate cold tolerance and 49. 28% with worse cold tolerance! Correlation analysis showed that rice cold tolerance at the tillering stage was significantly positively correlated with seed setting rate and single panicle weight. Rice cold tolerance at the tillering stage and growth duration were significantly negatively correlated) Eighteen markers associated with rice cold tolerance were detected through the association analysis, markers like RM214,RM445,RM5O6,RM1O6,RM215,RM182,RM27O and RM229 were mutual authentication with family-based linkage mapping. These markers can be used for selection of rice cold tolerance resources in Northeast China. Finally, a serial of elite alleles, loci and their carrier materials were screened out by anglicizing these associated markers.%以140份东北粳稻品种(系)为材料进行分蘖期耐冷鉴定,用84个SSR标记对耐冷性差异较大的96份材料进行基于SSR标记的关联分析.结果表明,供试材料强耐冷品种(系)占20%,中间型(系)占30.71%,不耐冷品种(系)占49.28%;分蘖期耐冷性与结实率和单株穗重呈极显著正相关,与生育期呈极显著负相关;关联分析得到18个位点与分蘖期耐冷性关联,其中标记RM214,RM445,RM506,RM106.RM215,RM182,RM270和RM229与前人研究获得的水稻耐冷性QTL定位结果吻合.这些标记可作为东北粳稻耐冷性资源筛选重点选择的标记.还通过优异等位基因的挖掘,得到一系列的优异等位变异及载体材料.

  19. 用SSR分子标记研究大豆属种间亲缘进化关系%Phylogenetic Analysis of Interspecies in Genus Glycine Through SSR Markers

    Institute of Scientific and Technical Information of China (English)

    吴晓雷; 贺超英; 陈受宜; 庄炳昌; 王克晶; 王学臣

    2001-01-01

    利用SSR标记技术对大豆属11个种37份材料的遗传多样性进行分析,不同位点在种间的等位基因数为6~29,平均每个位点15.9个等位基因,Soja亚属的等位基因数是Glycine亚属的71.5%,并且Glycine亚属种间指纹图谱的差异大于Soja亚属种间的指纹图谱。SSR等位基因的主成分分析结果表明,大豆属中的Glycine亚属和Soja亚属的分类界限是比较明确的,利用第一主成分和第二主成分可较明显地区分开Glycine亚属和Soja亚属。通过UPGMA方法构建了大豆属11个种的遗传进化关系,Soja亚属中G.max、G.soja和G.gracilis3个种在系统分化树上界限是比较明显的,由此看来这3个种是独立存在的。%The genetic diversity among 11 species of genus Glycine (altogether 37 accessions) was evaluated through SSR analysis. The number of alleles in different loci ranges from 6 to 29, averaging 15.9 per locus; alleles of subgenus soja account for 71.5% of those in subgenus Glycine, and the fingerprinting among subgenus Glycine is more divergent than that of subgenus soja. Principal factor analysis shows that the first and the second principal factor can classify genus Glycine into two groups which represent subgenus Glycine and subgenus soja. The results of UPGMA indicate that G. mas, G. soja and G. gracilis in subgenus soja are different species.

  20. Consequences of the nuclear power plant accident at Chernobyl

    International Nuclear Information System (INIS)

    The Chernobyl Nuclear Power Plant accident, in the Ukrainian Soviet Socialist Republic (SSR), on April 26, 1986, was the first major nuclear power plant accident that resulted in a large-scale fire and subsequent explosions, immediate and delayed deaths of plant operators and emergency service workers, and the radioactive contamination of a significant land area. The release of radioactive material, over a 10-day period, resulted in millions of Soviets, and other Europeans, being exposed to measurable levels of radioactive fallout. Because of the effects of wind and rain, the radioactive nuclide fallout distribution patterns are not well defined, though they appear to be focused in three contiguous Soviet Republics: the Ukrainian SSR, the Byelorussian SSR, and the Russian Soviet Federated Socialist Republic. Further, because of the many radioactive nuclides (krypton, xenon, cesium, iodine, strontium, plutonium) released by the prolonged fires at Chernobyl, the long-term medical, psychological, social, and economic effects will require careful and prolonged study. Specifically, studies on the medical (leukemia, cancers, thyroid disease) and psychological (reactive depressions, post-traumatic stress disorders, family disorganization) consequences of continued low dose radiation exposure in the affected villages and towns need to be conducted so that a coherent, comprehensive, community-oriented plan may evolve that will not cause those already affected any additional harm and confusion

  1. Study on the Genetic Diversity and Association Analysis of Yield and Agronomic Traits with SSR Primers in Waxy Maize Inbred Lines%糯玉米自交系遗传多样性及其产量、农艺性状与SSR分子标记的关联研究

    Institute of Scientific and Technical Information of China (English)

    蒋思霞; 倪正斌; 印志同; 徐志英; 邓德祥

    2012-01-01

    [目的]研究糯玉米自交系的遗传多样性,确定其亲缘关系远近,为糯玉米的新品种选育提供依据.[方法]以84个糯玉米自交系为试验材料,利用分布在玉米全基因组上的71个SSR标记对供试材料的遗传多样性进行分析,并对其产量及农艺性状与SSR标记进行了关联分析.[结果]150对SSR引物中有71对在糯玉米自交系中能扩增出多态性条带,共检测到342个等位基因,每对引物可检测到2~11个数目不等的等位基因,多态性信息量为0.249 ~0.876;糯玉米自交系间的遗传距离为0.02~0.32,均值为0.17,84个自交系可划分为8个组别;玉米10个连锁群上71个SSR位点的2485个组合,都存在一定程度的连锁不平衡;共检测出21个SSR座位与10个产量、农艺性状显著相关.[结论]该试验阐明了所选糯玉米自交系的遗传多样性及相互间的亲缘关系,为有目的的组配糯玉米杂交种及其新品种选育提供了参考.%[Objective]To study the genetic diversity of waxy maize inbred lines and determine their genetic relationship,so as to provide references for the new varieties breeding of waxy maize. [ Method] A total of 84 waxy corn inbred lines were used as experimental materials. Seventy one SSR markers in maize 10 chromosomes were adopted to explore the genetic diversity of waxy maize. The association of the agronomic and yield traits of waxy corn with the SSR primers was analyzed. [ Result]Of the 150 SSR primers,71 could obtain polymorphic bands among waxy corn inbred lines. Seventy one pairs of primers in maize 10 chromosomes detected 342 alleles. The number of detected alleles was within a range of 2 -11. Polymorphism information content (PIC) value ranged from 0. 249 to 0. 876, the genetic distance among the inbred lines was 0.02 -0. 32 with an average of 0.17; 84 waxy maize inbred lines could be divided into 8 groups. The 2 485 combinations of 71 SSR primers at 10 linkage group were in linkage

  2. Complete the Blank Section with SSR Markers on Linkage Group C1 of Public Genetic Map in Soybean%大豆公共遗传图谱C1连锁群SSR标记空白区段的填补

    Institute of Scientific and Technical Information of China (English)

    雷雅坤; 闫龙; 杨春燕; 宋晓昆; 张孟臣; 黄占景

    2012-01-01

    为进一步饱和大豆公共图谱SSR标记,以大豆育成品种冀豆12×地方品种ZDD03651组合的211个F6株系为作图群体,以Kosambi作图函数构建SSR标记遗传连锁图谱.结果表明,栽培大豆冀豆12与大豆地方品种ZDD03651间SSR标记多态率为44.6%,遗传图谱包含21个连锁群,117个SSR标记,遗传距离总长度1 501 cM,标记间平均距离15.6 cM,其中包含8个偏分离标记.与公共遗传图谱相比,位点间排列顺序、遗传距离和偏分离位点比例基本相同.将SSR新标记Barcsoyssr_4_1181、Barcsoyssr_4_1201、Barcsoyssr_4_1235和Barcsoyssr_5_1266整合到C1连锁群上,填补了国际大豆公共遗传图谱中C1连锁群94.62 ~120.12 cM之间的SSR标记空白区段.%Cross was made using bred varieties Jidou 12 × landrace soybean ZDD03651 ,get F6 RIL population with 211 single plants as the mapping population, construction of a SSR genetic linkage map with Kosambi mapping function, In order to saturate with SSR markers on public genetic map in the further. The polymorphic ratio was 44. 6% of SSR markers between Jidou 12 and ZDD03651. A total of 117 pairs of SSR markers on genetic linkage map,including 8 pairs distorted SSR markers,The resulting genetic linkage map covered 1 501 cM,with an average inter-marker distance of 15.6 cM, including 21 linkage groups. Compared with public genetic map, the order between points, genetic distance and the proportion of distorted markers basically the same. And eventually the development of new molecular markers Barcsoyssr_4_l 181 , Barcsoyssr_4_1201, Barcsoyssr_4_1235 , Barcsoyssr_5_1266 linked to the Cl linkage map,in order to complete the blank section on linkage group Cl between 94.62 cM and 120. 12 cM in the international.

  3. Earthquake Damage, Armenian SSR, December 7, 1988

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — On December 7, 1988, at 11:41 A.M. local time a magnitude 6.9 earthquake shook northwestern Armenia and was followed four minutes later by a magnitude 5.8...

  4. cpSSR: a New Tool to Analyze Chloroplast Genome of Citrus Somatic Hybrids%叶绿体S S R标记:柑橘体细胞杂种胞质遗传分析的一种新方法

    Institute of Scientific and Technical Information of China (English)

    程运江; 郭文武; 邓秀新

    2003-01-01

    Chloroplast simple sequence repeat (cpSSR) markers in Citrus were developed and success-fully used to analyze chloroplast genome inheritance of Citrus somatic hybrids. Twenty-two previouslyreported cpSSR primer pairs from pine (Pinus thunbergii Parl.), rice (Oryza sativa L.) and tobacco (Nicotianatabacum L.) were tested in Citrus, nine of which could amplify intensive PCR products by agarose gelelectrophoresis. Chloroplast genome inheritance of Citrus somatic hybrids from nine fusions was thenanalyzed, and five of the nine pre-screened primer pairs showed polymorphisms by polyacrylamide gelelectrophoresis. The results revealed the random inheritance nature of chloroplast genome in all analyzedCitrus somatic hybrids, which was in agreement with previous reports based on RFLP or CAPS analyses. Itwas also shown that cpSSR is a more efficient tool in chloroplast genome analyses of somatic hybrids inhigher plants, compared with the conventional RFLP or CAPS analyses.%从水稻(Oryza sativa L.)、烟草(Nicotiana tabacum L.)和黑松(Pinus thunbergiiParl.)等植物的22对叶绿体SSR引物中筛选出 5对能用于柑橘叶绿体SSR分析的引物,应用这5对引物对9个组合的柑橘体细胞杂种的叶绿体遗传进行了分析.结果表明:这些组合再生的杂种中叶绿体都呈现随机分离,该现象与以前报道的RFLP分析结果一致,而且其可靠性已被CAPS分析所证实.表明柑橘叶绿体SSR同RFLP及CAPS一样可靠,并且更简单高效、易于操作,特别适合对柑橘等植物体细胞杂种进行早期胞质遗传组成分析.

  5. 大叶藻居群微卫星遗传多样性研究%GENETIC DIVERSITY IN POPULATIONS OF ZOSTER MARINA L.INFERRED FROM NUCLEAR SSR MARKERS

    Institute of Scientific and Technical Information of China (English)

    孙典荣; 李渊; 李文涛; 高天翔

    2013-01-01

    Seagrasses are angiosperms that are thought to have become adaptive to aquatic environment independently. The marine, monocotyledonous Zostera marina is a species of Zosteraceae using traditional classifications, which widely distributes from subtropical to subfrigid coastal oceans. Seven natural populations of Z. marina (Lidao, Tian'ehu, Qingdao Bay, Dalian, Naepo, Tokyo Bay and Finavarra) were used in this study. To study the mechanism of the genetic diversity and population structure of the seven populations, microsatellite marker (SSR) analysis was done. A total of 57 alleles were identified in 148 individuals across the four microsatellite primers analyzed, with a mean value of 6 alleles per locus. The mean expected heterozygosity (He) and observed heterozygosity (Ho) across all populations were 0.687 and 0.417, respectively, and a higher level of diversity was found in the population from the Qingdao Bay (A=l.750, AR=1.043) than other populations. The minimum Fst value was 0.051 between the populations from the Qingdao Bay and Dalian. The maximum Fsl value was 0.261 between the populations from Tian'ehu and Finavarra. The Fsl values suggested moderate genetic differentiation within most of the Z. marina populations. From the UPGMA tree, four populations in China (Lidao, Tian'ehu, Qingdao Bay and Dalian) clustered together, and the genetic relationships may be attributed to eelgrass meadow fragmentation. The geographic distance was responsible for the genetic differentiation from large-scale among populations in China (Lidao, Tian'ehu, Qingdao Bay and Dalian), Korea (Naepo), Japan (Tokyo Bay) and Ireland (Finavarra). Results of possible number of clusters supported that this seagrass species originated from East Asia. The population from the Qingdao Bay has higher genetic diversity, suggesting that populations in this region demand prioritized conservation and utilization for breeding programs.%采用4对微卫星引物对大叶藻的7个地理居群进行了

  6. 吉林省玉米新品种SSR标记指纹数据库的构建及其分析%Construction and Analysis of the SSR-based Fingerprinting Database for New Maize Varieties in Jilin Province

    Institute of Scientific and Technical Information of China (English)

    高玉倩; 田红丽; 王凤格; 赵久然; 陈学军; 王璐; 易红梅; 原亚萍

    2012-01-01

    A DNA fingerprinting database containing 174 new maize varieties authorized by Jilin Province from 2005 to 2009 was constructed using 20 SSR loci. The genetic difference among different years was analyzed based on the number and frequency of alleles and polymorphism information content(PIC). Through the analysis, we can see that the average number of alleles of 174 new maize varieties from 2005 to 2009 was a fell slightly trend, but there is not apparent change in the average index of polymorphism information. The change of individual allele frequency is apparent in corn varieties of different years. According to the analysis, the remains maybe because of the strong directional selection putting in breeding process analysis. That means as the change of the year, the individual rare alleles may be decreased, but the genetic diversity is no lower. This also shows the reflection of polymorphism information index should be more objective when we evaluate the change of corn genetic diversity. Overall, there is no apparent change in genetic diversity among Jilin corn varieties of different years, which means the com varieties authorized by Jilin province in recent years have no large fluctuations in breeding resources, breeding mode, and the breeding direction.%以SSR标记为技术手段,利用20对核心引物,构建吉林省2005~2009年审定的174份普通玉米新品种的DNA指纹数据库,同时分析不同年份间审定品种的等位基因频率、等位基因数目、多态性信息指数的变化.结果表明,2005~2009年供试174份材料的平均等位基因数目略有下降,但平均多态性信息指数没有明显变化,不同年份间玉米品种的个别等位基因频率变化比较明显,分析可能在育种过程中人为施加了较强的定向选择而保留了下来,说明随着年份的变化,个别稀有等位基因可能在减少,但遗传多样性并没有降低.同时说明在评价玉米品种遗传多样性变化时,多态性信息

  7. Genetic Diversity Analysis of Tibetan Wild Barley Using SSR Markers%应用微卫星标记研究西藏野生大麦的遗传多样性

    Institute of Scientific and Technical Information of China (English)

    冯宗云; 刘仙俊; 张义正; 凌宏清

    2006-01-01

    以西藏不同地区的106份野生大麦为材料,其中包括50份野生二棱大麦(HS),27份野生瓶形大麦(HL)和29份野生六棱大麦(HA),用Liu等(1996)发表的SSR连锁图的每个连锁群的两个臂的不同位置上选取3~5个共30个SSR标记,研究了西藏3类野生大麦的遗传多样性.结果表明,这3类野生大麦在遗传组成及等位变异频率分布上存在着明显的遗传分化.在总样本中,共检测到229个等位变异,平均每个SSR位点检测到7.6个等位变异,其中70个为这3类野生大麦间共同的等位变异,等位变异数在这3类野生大麦间有明显的差异,亚种间的遗传多样性明显高于亚种内的遗传多样性.其遗传多样性大小顺序为HS>HL>HA.聚类分析表明,野生二棱大麦、野生六棱大麦分别聚在不同的两类,而野生瓶形大麦中各有约50%的材料分别聚在这两类.根据本研究及前人研究结果,我们认为中国栽培大麦是从野生二棱大麦经野生瓶形大麦向野生六棱大麦进化的.该结果支持了栽培大麦起源的"野生二棱大麦单系起源论"的观点.%One hundred and six accessions of wild barley collected from Tibet, China, including 50 entries of the two-rowed wild barley Hordeum vulgare ssp. spontaneum (HS), 29 entries of the six-rowed wild barley Hordeum vulgare ssp. agriocrithon (HA),and 27 entries of the six-rowed wild barley Hordeum vulgare ssp. agriocrithon var. lagunculiforme (HL), were analyzed using 30 SSR markers selected from the seven barley linkage groups for studying genetic diversity and evolutionary relationship of the three subspecies of Tibetan wild barley to cultivated barley in China. Over the 30 genetic loci that were studied, 229 alleles were identified among the 106 accessions, of which 70 were common alleles. H. vulgare ssp. spontaneum possesses about thrice more private alleles (2.83 alleles/locus) than HS (0.93 alleles/locus), whereas almost no private alleles were detected

  8. Cytological and SSR Analysis on Cold-tolerant Gene Introgression Lines from Dongxiang Wild Rice%东乡野生稻耐冷渐渗系的细胞学观察及SSR分析

    Institute of Scientific and Technical Information of China (English)

    曹娟芳; 罗向东; 邓晓娟; 戴亮芳; 胡标林; 张帆涛; 谢建坤

    2012-01-01

    Two previously identified strong cold-tolerant introgression lines of IL5243 and IL5335 from Dongxiang wild rice (Oryza rufipogon Griff. ) were used to investigate the meiosis behavior,chromosome recombination and the molecular evidence of alien genes introgression. The results showed that the rate of pollen mother cells (PMC) with normal meiotic behavior in the IL5243 and IL5335 was to 89. 93% and 90. 22% .respectively. And they finally formed the normal mature pollen;The rates of pollen germination in vitro were (83. 03±2. 82)% and (81. 96±1. 73)%,respectively. There were no significant differences between the cold-tolerant introgression lines and their parents. However,at meiosis I, the low frequency of abnormal chromosome behavior was observed in IL5243 and lL5335,such as univalent,8-shape bivalent, multivalent and some PMCs (3. 95%~5. 15%) exist lagging chromosomes at anaphase I and so on, which suggested that there were genetic exchange and recombination between cultivated rice and common wild rice. In addition, the high frequency of double nucleoli was observed at pachytene in the two cold tolerance introgression lines (IL5335 and IL5243 were 38. 9% and 27. 0% .respectively) .while their parents only had one nucleolus. Through SSR markers and structure analysis, we further confirmed that introgression of some Dongxiang wild rice DNA fragments in the strong cold resistance introgression lines through chromosome exchange and recombination between the cultivated rice and the wild rice. These results laid a foundation for further excavating and using this rice cold-tolerant gene in the future.%以前期鉴定筛选的2个东乡野生稻强耐冷渐渗系(IL5243和IL5335)为试材,研究其减数分裂时期的染色体行为特征及外源基因的渗入分子证据.结果表明:(1)IL5243和IL5335中正常减数分裂的花粉母细胞分别达89.93%和90.22%,最终形成正常的成熟花粉粒,花粉离体萌发率分别为(83.03±2.82)%和(81.96±1

  9. Development of EST-SSR Markers from Jatropha curcas (Euphorbiaceae) and Their Application in Genetic Diversity Analysis among Germplasms%小桐子EST-SSR分子标记的开发与种质遗传多样性分析

    Institute of Scientific and Technical Information of China (English)

    杨春; 刘爱忠

    2011-01-01

    Jatropha curcas ( Euphorbiaceae) has created tremendous interest all over the world for the use of its seed oil as a commercial source of biodiesel. Based on 9843 ESTs available from the developing seeds of Jatropha curcas, we identified 1009 SSRs in 4640 unigenes and developed 11 polymorphic EST-SSR markers which exhibited a low level of genetic diversity among germplasms, I. E. Allele number varied from 2 to 3, with a average of 2. 45; Het-erozygosity (He) ranged from 0.0887-0.5128, with a average of 0.2736; Polymorphic Information Content (PIC) ranged from 0.0847-0.4031, with a average of 0. 2313. Further, we analyzed the genetic relationships among 24 germplasms collected from different areas in southern China, northern Vietnam, and India using the 11 EST-SSR markers. The results showed that there was no a geographic pattern of genotypes across the collection areas of Jatropha curcas. The EST-SSR markers developed in current study is useful for both genetic diversity analysis and identification of genetic relationships among germplasms in Jatropha curcas.%小桐子(Jatropha curcas)适应性强,不择土壤,种子油脂性能适宜生物柴油的生产,是重要的生物柴油植物.基于小桐子种子发育过程中的EST序列,采用生物信息学方法,从4640个EST非冗余序列上鉴别了1009个SSR位点并分析其分布特征;开发了11对多态的EST-SSR分子标记,并利用这些分子标记调查了24个不同地理种源的遗传多样性,从每个位点的等位基因数目(2~3,平均为2.45)、期望杂合度(He为0.0887 ~0.5128,平均是0.2736)、多态信息含量(PIC为0.0847~0.4031,平均是0.2313)等方面反映了小桐子种质的遗传多样性低.进一步分析显示不同地理种源的遗传关系缺乏明显的地理结构.作者开发的EST-SSR分子标记不仅有助于小桐子种质的遗传多样性研究,也有助于小桐子种质间的遗传关系鉴别.

  10. NCBI和cDNA文库中栽培花生EST-SSR分子标记的开发及其特点%Development and Characterization of EST-SSR Markers from NCBI and cDNA Library in Cultivated Peanut (Arachis hypogaea L.)

    Institute of Scientific and Technical Information of China (English)

    王金彦; 潘丽娟; 杨庆利; 禹山林

    2009-01-01

    86 132 ESTs downloaded from GenBank in NCBI and 12 501 ESTs from cDNA library constructed by high-oil linoleic acid accession E 12 were analysed. After the preprocession, there were 18 051 singletons and 9 972 contigs in the GenBank of NCBI and cDNA library. Totally 3 104 SSR loci had been screened by MISA software, accounting for 11.08% for these non-redundant ESTs. All SSR loci are divided into di-nucleotide, thi-nucleotide, tetra-nucleotide, penta-nucleotide, hexa-nucleotide and multi-nucleotide etc., and thi-nucleotide motif is the most motifs and the frequency was 43.0% and 56.8% in NCBI and cDNA libraray, respectively. The number of di-and penta-nucleotide motifs were second and third in all motifs. And the hexa-nucleotide was the least mo-tif both in NCBI and cDNA library. In all repeat motifs nucleotide, AG/TC was the most motifs and accounted for 8.65% and 13.42% in NCBI and cDNA library, respectively. Among the tri-nucleotide repeats, CTT/GAA was the most frequent motif, accounting for 6.7% and 13.42%, respectively. The repeat unit number of SSR loci is from 4 to 51.%本研究利用NCBI的GenBank数据库中公布的花生86 132条EST序列以及利用高油酸品种E12所创建的cDNA文库中的12 501条EST序列,对这些序列进行前期处理,总共获得非冗余且拼接较长的singleton 11 260条,contig 9 972条.通过MISA软件分析发现两个EST库中共包含有3 104个SSR位点,占到总共非冗余序列的11.08%.这些SSR位点被分成二核苷酸重复、三核苷酸重复、四核苷酸重复、五核苷酸重复、六核苷酸重复以及混合核苷酸重复等,其中三核苷酸重复占的比例最多,分别占到NCBI和cDNA文库的43.0%和56.8%,二核苷酸和五核苷酸重复占到所有重复位点的第二位和第三位,六核苷酸重复的比例最少.在所有重复基序中,AG/TC重复的数量最多,分别占到NCBI和cDNA文库的8.65%和13.42%.在三核苷酸重复中,CTT/GAA出现的频率最大,分别占到6.7%

  11. COMPARISON OF EMBRYONIC DEVELOPMENT AND SSR ANALYSIS OF GYNOGENESIS IN PSEUDOSCIAENA CROCEA INDUCED BY HOMO- AND HETEROLOGOUS SPERM%同源和异源精子诱导大黄鱼(Pseudosciaena crocea)雌核发育的胚胎发育比较及子代SSR遗传标记分析

    Institute of Scientific and Technical Information of China (English)

    苗亮; 王天柱; 李明云; 汤先念; 王曙; 安钦; 徐万土

    2011-01-01

    以紫外灭活的同源(大黄鱼)精子和未灭活的异源(鱿鱼)精子为激活源,采用冷休克处理的方法诱导了大黄鱼雌核发育二倍体,进行胚胎发育和SSR标记分析的比较研究。结果表明,异源组的受精率和孵化率高于同源组,但存活率低于同源组;两组中经冷休克处理未能恢复倍性的胚胎发育畸形而陆续死亡,恢复倍性的胚胎在发育程序上均与普通大黄鱼相同,但各阶段出现时间较对照组滞后:SSR分析显示同源组子代中有16.7%出现父本条带,异源组子代均未出现父本条带。以灭活的同源(大黄鱼)精子和未经灭活的异源(鲍鱼)精子诱导大黄鱼雌核发育各有优缺点,需根据具体情况选择使用。%Gynogenesis was induced in Pseudosciaena crocea with heterologous (Miichthys miiuy) sperm and UV-irradiated homologous sperm, and the embryonic development and SSR patterns were compared. The fertilization and hatching rates of hetero-gynogenesis were higher than homo-gynogenesis, although the survival rate was lower. In the two gynogenesis groups, the embryos which failed to inhibit the extrusion of polar body showed obvious haploid syndrome, the embryos which were successful diploidized had the same process with the normal diploid embryos. However, the developing speed of gynogenetic diploid was slower than the control group. The delay may be due to the disturbance to the cell division cycle caused by cold shock. In homo-gynogenesis, SSR analysis at loci KPC9 and KPC45 showed in 24 tested offsprings, with four individuals showing the paternal bands, suggesting that there were genetic leakage of the paternal fish In hetero-gynogenesis, SSR analysis at locus KPC43 showed 18 tested offsprings with all individuals showing the maternal specific band only, indicating that the heterologous sperm can avoid paternal gene inflowing to the offspring. In the gynogenesis induction studies, the

  12. In vitro culture and identification of polyembryos from polyembryonic seeds in Manju x Yanxiwanlu Ponkan by leaf morphology and SSR analysis%单胚槾橘×多胚岩溪晚芦槿柑多胚种子的胚分离培养及后代的叶形态和SSR鉴定

    Institute of Scientific and Technical Information of China (English)

    彭祝春; 龚桂芝; 马喜军; 洪棋斌

    2012-01-01

    继首次报道单胚清见与多胚桠柑杂交产生高比例多胚种子后,在单胚棱橘(Citrus tardiferax Hort.ex Tan)与多胚岩溪晚芦桠柑(Citrus reticulata Blanco)的杂交组合中,又发现高比例多胚种子,其比例一般为30%左右。为探明多胚来源,对多胚进行了分胚组织培养,获得同一种子来源的多胚苗。选取多组多胚苗进行叶形态比较分析。结果表明.同种子来源的多数多胚苗及亲本间叶形指数差异显著,但5胚苗中有3株跟母本相似,难以判断来源。筛选来自9个柑橘不同连锁群上的特异SSR引物对多胚苗进行标记分析,结果显示。多胚苗在多个标记上与母本不同,不可能为无性后代(珠心胚来源),均可能是有性苗;同组多胚苗之间既有部分在全部检查位点完全相同,表明其可能由同一合子胚分裂而来,也有部分在多个检查位点明显不同,可能来源于多卵受精形成的不同合子胚。%Following the first report of high ratio polyembryonic seeds in monoembryonic Kiyomi x polyembryonic Ponkan, polyembryonic seeds were found in the cross monoembryonic Manju (Citrus tardiferax Hort. ex Tan) x polyembryonie Yanxiwanlu Ponkan (C. reticulata Blanco) also. The ratio of polyembryonic seeds was about 30% generally. To investigate the origin of polyembryos, the embryos from polyembryonie seeds were cultured in vitro. Polyembryonic seedlings from one seed were selected and analysed by leaf morphology and SSR markers. The result of leaf morphology analysis showed that most of the polyembryonic seedlings were significantly different to both parents and indicated zygotic origins, but three seedlings in the 5 seedlings group were similar to the seed parent and it is difficult to determine their origins. Nine specific SSR markers from different citrus linkage groups were screened and used in SSR analysis. Four or more markers were found to show different

  13. Research Progress of Tea Genetic Evolution and the Application Prospects of SSR in Tea Genetic Evolution%茶树遗传演化研究进展及SSR在茶树遗传演化研究中的应用前景

    Institute of Scientific and Technical Information of China (English)

    周炎花; 姚明哲; 陈亮; 孙威江

    2009-01-01

    Tea plant [Camellia sinensis (L.) O. Kuntze], which originated in the southwest of China, took place a series of evolution from the level of morphology to the cytology level and to molecular level as it spread from the original center to other parts of China and elsewhere in the world. The research on the tea genetic evolution is not only a fundamental issue of tea biology but also an important aspect of the study of tea genetic resources. In the recent years, new technologies and methods have been widely applied in the study of the genetic evolution of tea plant. Some significant progress had been made so far. In this paper, we summarized the studies on the tea genetic evolution in the aspects of morphology, cytology, biochemistry and molecular biology of tea plant. The applications of SSR markers in genetic evolution of plants and its prospects in tea plant were discussed. The purpose is to provide some references for further study of the genetic diversity of tea in China and related analysis of the evolution.%茶树[Camellia sinensis(L.)O.Kuntze]起源于中国的西南地区,在由起源地向中国其他地区和世界其他地区传播的过程中,发生了从形态学水平到细胞水平再到分子水平的一系列演化.对茶树遗传演化的研究,是茶树基础生物学的一个基本问题,也是茶树种质资源研究的重要方面.近年来,各种新技术、新方法被广泛应用于研究荼树遗传演化关系,取得了一定的进展.从形态学、细胞学、生物化学、分子生物学方面对茶树遗传演化研究取得的进展进行了综述,分析了SSR(Simple Sequence Repeat)标记在植物遗传演化中的应用,探讨了SSR标记在茶树遗传演化研究中的应用前景,旨为进一步深入研究中国茶树遗传多样性、亲缘关系及演化路径分析提供参考.

  14. 紫扇贝与海湾扇贝通用SSR的检测及其在杂交子代鉴定中的应用%Screening of Transferable SSR Markers in the Peruvian Scallop and the Bay Scallops and Progeny Identification in the Hybrids

    Institute of Scientific and Technical Information of China (English)

    范晓; 李琪; 何庆国; 林国明; 王春德

    2012-01-01

    以紫扇贝DNA为模板,用已开发的147个海湾扇贝微卫星标记引物扩增,结果表明100个微卫星标记能成功扩增,其中有47个表现出多态性,等位基因数目从2到9不等.观测杂合度范围为0.1280~1.0000(平均0.6604),期望杂合度范围为0.5031~0.8621(平均0.6719),有6个位点偏离Hardy-Weinberg平衡(P<0.05).用7对引物分别对紫扇贝、海湾扇贝及其种间正反杂交F1各30个个体进行PCR扩增,发现它们可明确区分紫扇贝与海湾扇贝,且所检测60个杂交子代均同时含海湾扇贝与紫扇贝的相应种特异性条带,证明全部为种间杂交子代.将该7对引物的扩增产物克隆测序,发现这些位点在两种扇贝中的序列同源率为40.22%~91.95%,其中3个位点在紫扇贝中的扩增产物仍然含有微卫星.%In order to investigate transferability of microsatellite markers in genus Argopecten, 147 mi-crosatellite markers developed from the bay scallop (A. irradians), were amplified in 30 Peruvian scallop (A. purpuratus) individuals. One hundred loci can be amplified in the Peruvian scallop, of which 47 loci were found to be polymorphic with the number of alleles per locus ranging from 2 to 9. The observed heterozygos-ity (Ho) of these loci ranged from 0.128 0 to 1.000 0 (with an average of 0.660 4) while the expected het-erozygosity (He) ranged from 0.503 1 to 0.862 1 (with an average of 0.671 9). Six loci were found to be significantly departed from Hardy-Weinberg Equilibrium. Seven loci were selected for progeny identification in the Peruvian scallops, the bay scallops and their hybrids. The results showed that these SSR (simple sequence repeat) markers are able to distinguish between the Peruvian and the bay scallops. Amplification with these SSR markers in 60 hybrids displayed bands from both parents, indicating that these animals were true hybrids. Sequencing of these 7 loci in the Peruvian scallop showed they have 40.22%~91.95% identity with their

  15. Genetic Background Screen of Inter-specific Hybrids between SSR Marker Assisted Chinese Kale and Rapeseed%SSR标记辅助芥蓝×甘蓝型油菜种间杂交后代的遗传背景筛选

    Institute of Scientific and Technical Information of China (English)

    于海龙; 方智远; 杨丽梅; 刘玉梅; 庄木; 李占省; 吕红豪; 张扬勇

    2015-01-01

    To screen the genetic background and increase the back-cross breeding efficiency of the interspecific hybrids and their back-cross offsprings between Chinese kale(Brassica oleracea var.alboglabra, CC,2n=2x=18) and rapeseed(Brassica napus,AACC),the F1 inter-specific hybrids and their BC1 backcross offsprings between Ogu-CMS Chinese kale and rapaseed were obtained through hand pollination combined with embryo rescue technology. A total of 220 SSR primers were used to detect polymorphisms between the parents, in which 51 pairs of SSR primers showed polymorphism. 33 pairs of primers were selected to analyze the genetic background of 3 F1 plants and 35 BC1 plants,with even distribution on 9 chromosomes and stable amplifications. The results of analysis by software NTSYSpc2.11a showed that the similarity coefficients between F1 plants and rapeseed was 0.74,which indicated that the genetic background of F1 plants was closer to rapeseed than to Chinese kale,while the similarity coefficients between BC1 plants and Chinese kale varied from 0.26-0.65,with big genetic background differences among BC1 plants.In all 35 BC1 plants,the genetic background of individual 14Y1 was the closest to Chinese kale,which was further confirmed by morphological observation.Thus,the individual 14Y1 could be used as donor plant for further backcross.%为筛选芥蓝×甘蓝型油菜种间杂交后代的遗传背景,加速回交转育进程,采用蕾期授粉结合胚挽救手段进行远缘杂交,获得芥蓝和甘蓝型油菜的种间杂种F1和BC1群体。利用已有的220对SSR引物对双亲进行多态性筛选,获得多态性引物51对。挑选均匀分布在甘蓝9条染色体上、扩增稳定、条带清晰的33对多态性SSR引物,对3株F1单株和35株BC1单株进行遗传背景筛选。NTSYSpc2.11a分析结果表明:F1植株的遗传背景与亲本甘蓝型油菜更为接近,遗传相似系数为0.74;而BC1植株的遗传背景差异较大,与亲本

  16. SSR标记辅助芥蓝×甘蓝型油菜种间杂交后代的遗传背景筛选%Genetic Background Screen of Inter-specific Hybrids between SSR Marker Assisted Chinese Kale and Rapeseed

    Institute of Scientific and Technical Information of China (English)

    于海龙; 方智远; 杨丽梅; 刘玉梅; 庄木; 李占省; 吕红豪; 张扬勇

    2015-01-01

    To screen the genetic background and increase the back-cross breeding efficiency of the interspecific hybrids and their back-cross offsprings between Chinese kale(Brassica oleracea var.alboglabra, CC,2n=2x=18) and rapeseed(Brassica napus,AACC),the F1 inter-specific hybrids and their BC1 backcross offsprings between Ogu-CMS Chinese kale and rapaseed were obtained through hand pollination combined with embryo rescue technology. A total of 220 SSR primers were used to detect polymorphisms between the parents, in which 51 pairs of SSR primers showed polymorphism. 33 pairs of primers were selected to analyze the genetic background of 3 F1 plants and 35 BC1 plants,with even distribution on 9 chromosomes and stable amplifications. The results of analysis by software NTSYSpc2.11a showed that the similarity coefficients between F1 plants and rapeseed was 0.74,which indicated that the genetic background of F1 plants was closer to rapeseed than to Chinese kale,while the similarity coefficients between BC1 plants and Chinese kale varied from 0.26-0.65,with big genetic background differences among BC1 plants.In all 35 BC1 plants,the genetic background of individual 14Y1 was the closest to Chinese kale,which was further confirmed by morphological observation.Thus,the individual 14Y1 could be used as donor plant for further backcross.%为筛选芥蓝×甘蓝型油菜种间杂交后代的遗传背景,加速回交转育进程,采用蕾期授粉结合胚挽救手段进行远缘杂交,获得芥蓝和甘蓝型油菜的种间杂种F1和BC1群体。利用已有的220对SSR引物对双亲进行多态性筛选,获得多态性引物51对。挑选均匀分布在甘蓝9条染色体上、扩增稳定、条带清晰的33对多态性SSR引物,对3株F1单株和35株BC1单株进行遗传背景筛选。NTSYSpc2.11a分析结果表明:F1植株的遗传背景与亲本甘蓝型油菜更为接近,遗传相似系数为0.74;而BC1植株的遗传背景差异较大,与亲本

  17. 小麦蜡质基因座位上SSR的多态性及其与直链淀粉含量的关系%SSR POLYMORPHISM ON THE WAXY GENE LOCUS AND THEIR RELATIONSHIP TO AMYLOSE CONTENT IN WHEAT

    Institute of Scientific and Technical Information of China (English)

    王芳; 王燕; 赵辉; 王宪泽

    2006-01-01

    分析了蜡质基因(Wx)3'端的一个简单重复序列(SSR)(AT(AT)n AT)在32份小麦中的多态性及其与直链淀粉含量(AC)的关系.这些材料包括了山东省内的不同小麦品种,其AC含量差别较大.在扩增的小麦品种中均出现两条带,一条204bp(Wx-Dla)位于7DS染色体上,另一条225-346bp(Wx-Ala)位于7AS染色体上.也就是说在扩增的小麦品种中均存在Wx-Ala和Wx-Dla基因,并且较长的片段显示了长度多态性.分析表明AC与7D上这个SSR序列基因的多态性呈正相关,高AC小麦品种扩增的片段较长,电泳迁移率较小;相反,低AC小麦品种扩增的片段较短,迁移率较大,不同长度SSR品种间AC差异显著.虽然目前还不能确定这个SSR序列在直链淀粉合成中的直接功能,但SSR变异与AC之间的相关性可作为分子标记直接用于小麦品种改良.

  18. 应用红外荧光和加尾引物法进行向日葵SSR遗传分析中的多聚PCR和多聚凝胶电泳的优化%Optimization of Multiplex PCR and Multiplex Gel Electrophoresis in Sunflower SSR Analysis Using Infrared Fluorescence and Tailed Primers

    Institute of Scientific and Technical Information of China (English)

    张潞生; Vanessa BECQUET; 李绍华; David ZHANG

    2003-01-01

    In an effort to simplify the procedure and to reduce the cost of fluorescence SSR analysis,the conditions of the multiplex PCR and the multiplex gel electrophoresis were optimized in the genetic analysis of sunflower (Helianthus annuus L.) inbred lines. Results indicated that factors for a successful multiplex PCR assay were related to the cycling touchdown annealing temperature, the balance of primer concentration at the various loci, the concentration of PCR buffer and the Taq DNA polymerase. Based on the optimization, a tailed primer strategy was outlined, and the effective ways were proposed to overcome the troubleshootings commonly encountered in the multiplex PCR and the multiplex gel electrophoresis.%在向日葵(Helianthus annuus L.)自交系SSR遗传分析中,为了提高SSR荧光分析效率、简化分析程序和降低研究费用,我们进行了多聚PCR和多聚凝胶电泳两项技术的优化研究.结果表明,优化多聚PCR和多聚凝胶电泳的影响因子(如逐步降低的退火温度的循环数、各个多聚位点引物浓度的平衡、PCR缓冲液浓度以及Taq DNA多聚酶的浓度等)可以收到更好的实验效果.基于以上的优化研究,系统地提出了一套优化的加尾引物法的策略.同时,提出了在多聚PCR和多聚凝胶电泳中常常遇到的技术难题的有效防止和解决的方法.

  19. 中国西藏与中东地区近缘野生大麦遗传多样性的SSR标记分析%Genetic Diversity of Wild Close Relatives of Barley from Tibet of China and Middle East Region Based on SSR Markers

    Institute of Scientific and Technical Information of China (English)

    于智勇; 丁毅

    2007-01-01

    应用简单重复序列(SSR)标记方法对90个近缘野生大麦样本进行了遗传多样性分析,其中包括45份中国西藏近缘野生大麦样本和45份中东地区近缘野生大麦样本.从大麦的7个连锁群中选取27对引物用于PCR扩增,结果有11对引物扩增出有效多态性片段.11对引物共检测到126个等位变异位点,每对引物检测到5~22个SSR等位变异位点,平均每对引物检测到11.45个等位变异位点.中国西藏近缘野生大麦比中东地区近缘野生大麦平均每对引物多检测出2个位点.SSR结果采用NTSYS软件进行相似性系数计算,POPGNEN32软件进行遗传多样性系数计算,算术平均的非加权成对分组法(UPGMA法)构建聚类树状图,结果表明中国西藏近缘野生大麦样本比中东地区近缘野生大麦样本具有更高的遗传多样性,这为大麦的东方起源学说提供了新的佐证.

  20. Development of SSR Markers in Giant Lobelia (Lobelia deckenii) Based on Next-generation High-throughput Sequencing%基于新一代高通量测序技术开发巨人半边莲Lobelia deckenii的SSR标记

    Institute of Scientific and Technical Information of China (English)

    米奇; 龙志成; Muchuku John Kamau; 陈进明; 王青锋

    2015-01-01

    为了开发东非半边莲属特有植物的微卫星分子标记(SSR),本研究基于Illumina-HiSeq 2000测序平台对巨人半边莲Lobelia deckenii的基因组进行高通量测序.利用MISA软件对获得的基因组数据库进行搜索与分析,共鉴别出58 966个SSR位点,并利用Primer软件成功设计出3558对特异性的SSR引物.利用L.deckenii3个居群的6个样品对随机挑选的40对SSR引物进行扩增效率检验,发现有32对重复性好且可扩增出清晰条带.利用筛选出的32对SSR引物对来自肯尼亚山居群的24株个体进行PCR扩增并采用荧光分型技术检测多态性,结果显示有14对可扩增出稳定的多态性条带,共有86个等位基因,各SSR位点的等位基因数(NA)为4~9个,观测杂合度(H.)和期望杂合度(He)分别为0.000~1.000和0.625 ~ 0.854.本研究结果表明,通过高通量测序技术开发东非特有植物巨人半边莲的SSR标记是一种简单而高效的途径,这些新的SSR分子标记为巨人半边莲的居群遗传多样性、遗传结构以及对其开展保护生物学研究提供了工具.

  1. High-throughput discovery of SSR genetic markers in the mealybug,Phenacoccus solenopsis (Hemiptera: Pseudococcidae), from its transcriptome database%基于转录组数据高通量发掘扶桑绵粉蚧微卫星引物

    Institute of Scientific and Technical Information of China (English)

    罗梅; 张鹤; 宾淑英; 林进添

    2014-01-01

    [目的]扶桑绵粉蚧Phenacoccus solenopsis Tinsley是我国重要的检疫性害虫.简单重复序列(simple sequence repeat,SSR)研究在遗传图谱和物理图谱的构建、分子标记辅助育种、品种鉴定、基因定位、遗传多样性、动植物分类和进化等方面具有重要意义.筛选的SSR引物将为扶桑绵粉蚧遗传多样性分析、进化分析及入侵生物学等奠定基础.[方法]利用高通量搜索的方法对扶桑绵粉蚧转录组中28 120条unigenes的数据进行搜索.[结果]共找到1 781个SSR位点.扶桑绵粉蚧转录组中SSRs的主要重复类型是单核苷酸重复,占SSR总数的89.44%;其次是三核苷酸重复,占SSR总数的7.52%.单核苷酸重复里主要是A/T基序,占了总量的87.42%.基于筛选的SSRs,运用Primer 3软件进行引物的批量设计,共有481个unigenes成功设计引物,共设计出1 228对引物.[结论]研究表明利用扶桑绵粉蚧转录组数据开发SSR标记是可行的,本研究开发的引物将为扶桑绵粉蚧遗传多样性分析、进化分析及入侵生物学等奠定基础.

  2. 基于新一代高通量测序技术开发巨人半边莲Lobelia deckenii的SSR标记%Development of SSR Markers in Giant Lobelia (Lobelia deckenii) Based on Next-generation High-throughput Sequencing

    Institute of Scientific and Technical Information of China (English)

    米奇; 龙志成; Muchuku John Kamau; 陈进明; 王青锋

    2015-01-01

    为了开发东非半边莲属特有植物的微卫星分子标记(SSR),本研究基于Illumina-HiSeq 2000测序平台对巨人半边莲Lobelia deckenii的基因组进行高通量测序.利用MISA软件对获得的基因组数据库进行搜索与分析,共鉴别出58 966个SSR位点,并利用Primer软件成功设计出3558对特异性的SSR引物.利用L.deckenii3个居群的6个样品对随机挑选的40对SSR引物进行扩增效率检验,发现有32对重复性好且可扩增出清晰条带.利用筛选出的32对SSR引物对来自肯尼亚山居群的24株个体进行PCR扩增并采用荧光分型技术检测多态性,结果显示有14对可扩增出稳定的多态性条带,共有86个等位基因,各SSR位点的等位基因数(NA)为4~9个,观测杂合度(H.)和期望杂合度(He)分别为0.000~1.000和0.625 ~ 0.854.本研究结果表明,通过高通量测序技术开发东非特有植物巨人半边莲的SSR标记是一种简单而高效的途径,这些新的SSR分子标记为巨人半边莲的居群遗传多样性、遗传结构以及对其开展保护生物学研究提供了工具.

  3. Assessment of Genetic Diversity in Chinese Sorghum Landraces Using SSR Markers as Compared with Foreign Accessions%中国高粱地方品种遗传多样性评价及中、外高粱遗传变异水平比较

    Institute of Scientific and Technical Information of China (English)

    张晗; 王建成; 王东建; 姚凤霞; 许金芳; 宋国安; 管延安; 李汝玉

    2011-01-01

    The genetic variation of 184 Chinese sorghum landraces (Sorghum bicolor L.) from a broad geographic area and representing different phenotypes, and 69 representative foreign cultivated sorghum accessions (world sorghum), was assessed using 32 nuclear SSR primer pairs. Overall, lower level of genetic diversity was detected in Chinese sorghum than in world sorghum. The allelic richness (Rs) and Nei's allele diversity (He) for Chinese sorghum and world sorghum were 9.81 and 0.629, and 11.52 and 0.745, respectively. Fewer unique alleles were detected in Chinese sorghum than in world sorghum. Chinese sorghum had a genetic diversity level lower than accessions from East Africa (He=0.732), North America (He=0.707) and South Asia (He=0.712);and was only comparable to those from South African accessions (He=0.609). Marked differences in level of genetic variation were revealed between Chinese sorghum landraces from 12 provinces, with Rs ranging from 3.64 to 4.88 and He from 0.517 to 0.714. Accessions from Jihn Province exhibited the highest level of genetic diversity among all regions in China, which was comparable to the sorghum in East Africa. The results indicated a strong divergence of Chinese sorghum from world sorghum, but a weak differentiation among Chinese sorghum both on regional and type bases. Principal component analysis (PCA) clearly separated Chinese sorghum from world accessions but could not separate Chinese sorghum into discrete geographical or phenotypic groups. Analysis of molecular variance (AMOVA) indicated that 20.43% of the total genetic variation was attributable to the difference between world and Chinese sorghum and 79.57% occurred among Chinese and world sorghum accessions. For Chinesesorghum, partitioning the total variation revealed that genetic diversity mainly existed among accessions within regions (91.94%)or eco-regions (94.97%) rather than among regions (8.06%) or eco-regions (5.03%). Similarly, a large portion (97.93%) of the total

  4. Identification of Wheat-Aegilops Ovata Derivatives Using SSR Markers and Evaluation of Their Powdery Mildew Resistance%小麦-卵穗山羊草衍生后代的SSR分子标记鉴定和白粉病抗性评价

    Institute of Scientific and Technical Information of China (English)

    吴红坡; 王亚娟; 王长有; 吉万全

    2012-01-01

    Aegilops species carrying the U or/and M genomes represent a prominent source of useful genes for wheat breeding. We generated 19 wheat-Aegilops ovata derivatives through hybridization between common wheat and Aegilops ovata. Four hundred SSR (simple sequence repeat) markers were used to investigate the polymorphisms among parental lines, Chinese Spring, Shaanyou 225 and Aegilopsovata, of which 341 markers (85.25%) could amplify bands in Aegilopsovata, and 20 of them (5%) showed specific bands in Aegilopsovata, and were applied to investigate germplasm in- heritance of Aegilops ovata in wheat-Aegilops ovata derivatives. The results showed that 10 markers could amplify specific bands in the 19 derivatives, indicating that all these 19 derivatives inherited germplasms from Aegilops ovata and these 10 SSR markers could be used in further identification of next generations. We also conducted powdery mildew resistance evaluation on the 19 derivatives, and 16 of them are immune to powdery mildew like Aegilops ovata, one of their parents, but not like the other two parental lines, Chinese Spring and Shaanyou 225, which are highly susceptible to powdery mildew, indicating that the powdery mildew resistance in the 16 derivatives were explicitly inherited from Aegilops ovata.%山羊草属植物是普通小麦改良过程中重要的有益基因来源,小麦的许多抗病虫、抗逆基因都来源于山羊草属植物。本研究利用杂交和回交的方法,成功获得了19株小麦-卵穗山羊草衍生后代,实验选取均匀分布于小麦各条染色体的SSR标记400个,对三个亲本(中国春、卵穗山羊草和陕优225)以及19株衍生后代进行分子标记特异性分析,结果表明,341个标记可以在卵穗山羊草中扩增出条带,说明SSR标记在山羊草中位点丰富;20个标记可以在卵穗山羊草中扩增出特异条带,说明在卵穗山羊草中有不同于另外两个亲本的特异SSR位点;将20个在卵穗山羊

  5. International Chernobyl project - input from the Commission of the European Communities to the evaluation of the relocation policy adopted by the former Soviet Union

    International Nuclear Information System (INIS)

    In October 1989, the Government of the USSR formally requested the International Atomic Energy Agency (IAEA) to carry out: '...an international experts' assessment of the concept which the USSR has evolved to enable the population to live safely in areas affected by radioactive contamination following the Chernobyl accident, and an evaluation of the effectiveness of the steps taken in those areas to safeguard the health of the population'. The response to this request was a proposal for a multinational team to undertake an assessment of the radiological situation in the three affected Soviet Republics - the Ukrainian Soviet Socialist Republic (UKrSSR), the Byelorussian Soviet Socialist Republic (BSSR) and the Russian Soviet Federative Socialist Republic (RSFSR). The International Chernobyl Project was established for this purpose with the participation of the Commission of the European Communities (CEC), the Food and Agriculture Organization of the United Nations (FAO), the International Labour Office (ILO), the United Nations Scientific Committee on the Effects of Atomic Radiation (UNSCEAR), the World Health Organization (WHO) and the World Meteorological Organization (WMO). An International Advisory Committee, comprising scientists from 10 countries and seven international organizations, was established to direct the Project and be responsible for its findings. The results of the Project have been published in two reports - an overview and a technical report -prepared by the International Advisory Committee

  6. Overview on radioisotope production at TRIGA-SSR 14 MW

    International Nuclear Information System (INIS)

    The paper presents the technical support provided at Institute for Nuclear Research (INR) Pitesti to accomplish various services concerning isotope production. Also it is presented the study to produce, in collaboration with Institute for Physics and Nuclear Engineering (IFIN) Bucharest, I-131, Au-198, Mo-99, Ir-192 isotopes for medical uses. There is presented neutron physics computation for the TRIGA core to establish the proper experimental locations to accomplish the radioisotope production. (authors)

  7. A radome for air traffic control SSR radar systems

    Science.gov (United States)

    A new generation of monopulse and discrete interrogation systems has evolved for air traffic control applications that presents significant challenges to total system design and performance. Reliable operation of the antenna system is essential in today's ever increasing air traffic congestion. An important component of the total system is a radome to protect the antenna from the environment and to enable consistent, reliable electromagnetic performance. The various types of radomes that have been employed over the years to protect antennas are discussed and evaluated relative to the air traffic control radar application. The sandwich radome is selected as the best option and a detailed design analysis is presented which considers the vital characteristics of transmissivity, boresight error, and sidelobe perturbations.

  8. Development prospects of the Eastern Donbass. [USSR - Ukrainian SSR

    Energy Technology Data Exchange (ETDEWEB)

    Denshchikov, N.A. (Rostovgiproshakht (USSR))

    1990-09-01

    Reviews the production situation of coal mines in the Rostov region (Zhukovugol' and Rostovugol' associations). In 1989 fourteen mines noted a production shortfall of 2.2 Mt anthracite in respect to production targets. Six mines are planned to be shut down by 2000 in conjuncion with exhausted coal reserves, production costs have risen from 12.8 to 24.8 rubles/t and productivity has fallen from 49.2 to 38.4 t/miner shift. Industrial reserves of 1,300 Mt anthracite were explored and made available in the Nesvetaevo-Shakhtinsk, Sulino-Sadkinsk and other regions where 9 mines with a capacity of 14 Mt/a can be constructed. However, it is still necessary to build four mines with a production capacity of 9 Mt/a each to reach the 32-33 Mt/a level (as in 1975). Design features of the Oktyabr'skaya-Yuzhnaya and Obukhovskaya mines are described. Mining-geological conditions and economic aspects of several other mines planned to be constructed or reconstructed by 2005 are discussed.

  9. Rationalization of a genebank cucumber collection with SSR markers

    NARCIS (Netherlands)

    Dooijeweert, van W.; Treuren, van R.

    2012-01-01

    The CGN cucumber (Cucumis sativus) collection consists of 937 accessions. The majority of accessions originated from the working collection of the former Institute for Horticultural Plant Breeding (IVT), where they were used for breeding. The collection mainly includes old cultivars received from Du

  10. Investigation of SSR characteristics of unified power flow controller

    OpenAIRE

    Padiyar, KR; Prabhu, Nagesh

    2005-01-01

    The unified power flow controller (UPFC) is the most versatile flexible ac transmission system (FACTS) controller which can be used to control active and reactive power flows in a transmission line in addition to the bus voltage. The active series compensation is provided by injecting series reactive voltage. The voltage at the two ports of UPF Care regulated by control of shunt current and series real voltage. It also has several operating control modes such as voltage and power regulation, ...

  11. Assessment of genetic diversity in Brazilian barley using SSR markers.

    Science.gov (United States)

    Ferreira, Jéssica Rosset; Pereira, Jorge Fernando; Turchetto, Caroline; Minella, Euclydes; Consoli, Luciano; Delatorre, Carla Andréa

    2016-03-01

    Barley is a major cereal grown widely and used in several food products, beverage production and animal fodder. Genetic diversity is a key component in breeding programs. We have analyzed the genetic diversity of barley accessions using microsatellite markers. The accessions were composed of wild and domesticated barley representing genotypes from six countries and three breeding programs in Brazil. A total of 280 alleles were detected, 36 unique to Brazilian barley. The marker Bmag120 showed the greatest polymorphism information content (PIC), with the highest mean value found on chromosome three, and the lowest on chromosomes four and six. The wild accessions presented the highest diversity followed by the foreign genotypes. Genetic analysis was performed using Principal Coordinates Analysis, UPGMA clustering, and Bayesian clustering analysis implemented in Structure. All results obtained by the different methods were similar. Loss of genetic diversity has occurred in Brazilian genotypes. The number of alleles detected in genotypes released in 1980s was higher, whereas most of the cultivars released thereafter showed lower PIC and clustered in separate subgroups from the older cultivars. The use of a more diverse panel of genotypes should be considered in order to exploit novel alleles in Brazilian barley breeding programs. PMID:27007902

  12. Assessment of genetic diversity in Brazilian barley using SSR markers

    OpenAIRE

    Jéssica Rosset Ferreira; Jorge Fernando Pereira; Caroline Turchetto; Euclydes Minella; Luciano Consoli; Carla Andréa Delatorre

    2016-01-01

    Abstract Barley is a major cereal grown widely and used in several food products, beverage production and animal fodder. Genetic diversity is a key component in breeding programs. We have analyzed the genetic diversity of barley accessions using microsatellite markers. The accessions were composed of wild and domesticated barley representing genotypes from six countries and three breeding programs in Brazil. A total of 280 alleles were detected, 36 unique to Brazilian barley. The marker Bmag1...

  13. Assessment of genetic diversity in Brazilian barley using SSR markers

    Directory of Open Access Journals (Sweden)

    Jéssica Rosset Ferreira

    2016-03-01

    Full Text Available Abstract Barley is a major cereal grown widely and used in several food products, beverage production and animal fodder. Genetic diversity is a key component in breeding programs. We have analyzed the genetic diversity of barley accessions using microsatellite markers. The accessions were composed of wild and domesticated barley representing genotypes from six countries and three breeding programs in Brazil. A total of 280 alleles were detected, 36 unique to Brazilian barley. The marker Bmag120 showed the greatest polymorphism information content (PIC, with the highest mean value found on chromosome three, and the lowest on chromosomes four and six. The wild accessions presented the highest diversity followed by the foreign genotypes. Genetic analysis was performed using Principal Coordinates Analysis, UPGMA clustering, and Bayesian clustering analysis implemented in Structure. All results obtained by the different methods were similar. Loss of genetic diversity has occurred in Brazilian genotypes. The number of alleles detected in genotypes released in 1980s was higher, whereas most of the cultivars released thereafter showed lower PIC and clustered in separate subgroups from the older cultivars. The use of a more diverse panel of genotypes should be considered in order to exploit novel alleles in Brazilian barley breeding programs.

  14. NOTE - Genetic variability among cassava accessions based on SSR markers

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