WorldWideScience

Sample records for byelorussian ssr

  1. Important contribution of Byelorussian scientists into radioecology

    International Nuclear Information System (INIS)

    Paper presents a review of radioactive contamination of the Byelorussian flora (in the context of the Chernobyl NPP accident) publication signed a large number of experts and edited by V.I., Parphenov and B.I. Yakushev in the book Mn: Navuka i tekhnika, 1995 and of Fauna in the area impacted by the Chernobyl NPP accident. Published edited by L.M. Susheni, M.M. Pikulin, A.E. Plenin in the book Mn.: Navuka i tekhnika, 1995. The mentioned papers represent the result of complex many year research activities conducted in research institutions of the Byelorussian Academy of Sciences. The first book sums up to results of 10-years research activities devoted to the effect of ionizing radiation in the flora and radionuclide migration in soil-plant mantle, the second one - represents a generalizing report concerning animal radioecology. The drawbacks and advantages of both books are pointed out

  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. DNA Fingerprinting Eastern Redbud Cultivars (Cercis canadensis) Using SSR Markers

    Science.gov (United States)

    In this study we present data for a subset of SSR loci, 76 out of the 130 high-quality loci, which were selected out of hundreds of SSR loci identified from a SSR-enriched library. SSR markers are abundant in eukaryotic genomes and are highly reproducible. Previously, we have used SSR markers to e...

  4. 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...

  5. 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.

  6. 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

  7. 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.

  8. 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.

  9. 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.

  10. Strawberry cultivar identification based on hypervariable SSR markers

    OpenAIRE

    Honjo, Masanori; Nunome, Tsukasa; Kataoka, Sono; Yano, Takayoshi; Yamazaki, Hiromichi; Hamano, Megumi; Yui, Susumu; Morishita, Masami

    2011-01-01

    We genotyped strawberry cultivars by two newly selected and two previously reported SSR markers. All four markers produced interpretable electropherograms from 75 accessions consisting of 72 Fragaria × ananassa cultivars or lines and three octoploid Fragaria species accessions. These SSR markers were highly polymorphic; in particular, one of the newly developed markers, FxaHGA02P13, was capable of distinguishing all of the accessions except for a mutant strain that was derived from another ac...

  11. 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,...

  12. 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)

  13. 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.

  14. 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...

  15. 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

  16. Strawberry cultivar identification based on hypervariable SSR markers.

    Science.gov (United States)

    Honjo, Masanori; Nunome, Tsukasa; Kataoka, Sono; Yano, Takayoshi; Yamazaki, Hiromichi; Hamano, Megumi; Yui, Susumu; Morishita, Masami

    2011-12-01

    We genotyped strawberry cultivars by two newly selected and two previously reported SSR markers. All four markers produced interpretable electropherograms from 75 accessions consisting of 72 Fragaria × ananassa cultivars or lines and three octoploid Fragaria species accessions. These SSR markers were highly polymorphic; in particular, one of the newly developed markers, FxaHGA02P13, was capable of distinguishing all of the accessions except for a mutant strain that was derived from another accession in the set. When two markers were combined, all 48 full-sib individuals could be distinguished. Fingerprinting patterns were reproducible between multiple samples, including the leaves, sepals, and fruit flesh of the same accession. Principal-coordinate analysis of the 75 accessions detected several groups, which reflect taxon and breeding site. Together with other available markers, these SSR markers will contribute to the management of strawberry genetic resources and the protection of breeders' rights. PMID:23136480

  17. 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.

  18. 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.

  19. Development of genomic and EST-SSR markers in radish (Raphanus sativus L.)

    OpenAIRE

    Nakatsuji, Ryoichi; Hashida, Tomoko; Matsumoto, Naoko; Tsuro, Masato; Kubo, Nakao; Hirai, Masashi

    2011-01-01

    Radish (Raphanus sativus L.) belongs to Brassicaceae family and is a close relative of Brassica. This species shows a wide morphological diversity, and is an important vegetable especially in Asia. However, molecular research of radish is behind compared to that of Brassica. For example, reports on SSR (simple sequence repeat) markers are limited. Here, we designed 417 radish SSR markers from SSR-enriched genomic libraries and the cDNA data. Of the 256 SSR markers succeeded in PCR, 130 showed...

  20. 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.

  1. 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...

  2. 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...

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

    Directory of Open Access Journals (Sweden)

    Antonietta Di Maio

    2013-01-01

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

  4. 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...

  5. EST and EST-SSR marker resources for Iris

    Directory of Open Access Journals (Sweden)

    Taylor Christopher A

    2009-06-01

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

  6. 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.

  7. 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.

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

    OpenAIRE

    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...

  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. Thermal hydraulic test apparatus to develop advanced BWR fuel bundles with spectral shift rods (SSR)

    International Nuclear Information System (INIS)

    An advanced water rod (WR) called the spectral shift rod (SSR), which replaces a conventional WR in a BWR fuel bundle, enhances the BWR's merit of uranium saving through the spectral shift operation. The SSR consists of an inlet hole, a wide ascending path, a narrow descending path and an outlet hole. The inlet hole locates below a lower tie plate (LTP) and the outlet hole is set above it. In the SSR, water boils by neutron and gamma-ray heating and water level is formed in the ascending path. This SSR water level can be controlled by core flow rate, which amplifies core void fraction change, resulting in the amplified spectral shift effect. Steady state and transient tests were conducted to evaluate SSR thermal-hydraulic characteristics under BWR operation condition. The several types of SSR configuration were tested, which covers SSR design in both next generation and conventional BWRs. In this paper, the test apparatus overview and measurement systems especially two phase water level measures in the SSR are presented. (author)

  13. 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 ...

  14. Use of SSR markers for DNA fingerprinting and diversity analysis of Pakistani sugarcane (Saccharum spp. hybrids) cultivars

    Science.gov (United States)

    In recent years SSR markers have been used widely for genetic analysis. The objective of this study was to use an SSR-based marker system to develop the molecular fingerprints and analyze the genetic relationship of sugarcane cultivars grown in Pakistan. Twenty-one highly polymorphic SSR markers wer...

  15. 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

  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. PMID:27504250

  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. 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

  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 markers in characterization of sweet corn inbred lines

    Directory of Open Access Journals (Sweden)

    Srdić Jelena

    2008-01-01

    Full Text Available Sweet corn differs from field corn in many important traits. So its breeding although includes some standard procedures demand application of techniques that are important for determining special traits, all because of the specificity of its usage. Application of molecular markers becomes almost a necessity for the breeding of sweet corn, especially because this is the type of maize in which still no definitive heterotic patterns have been determined. So getting to know genetic divergence of the sweet corn inbred lines is of great importance for its breeding. In this paper we analyzed genetic similarity of six sweet corn inbreds based on SSR markers. 40 SSR primers were used in DNA amplification. Results were compared and correlated with the data on specific combining ability, obtained by the diallel analysis. The results of SCA were in concurrence with genetic similarity. Values of rank correlation coefficient were negative, indicating that more similar inbred lines had smaller estimates of SCA, and lines that were less similar had higher estimates of SCA. Rank correlation coefficient between SCA and GS according to Dice coefficient was between -0,16 and -0,57*.

  2. 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

  3. 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.

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. 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...

  10. DNA fingerprinting of groundnut (Arachis hypogaea L.) varieties of Tirupati using SSR markers

    OpenAIRE

    Y. Amaravathi, R.P. Vasanthi, E. Siva Kumar, M. Purushotham and T. Giridhara Krishna

    2014-01-01

    Unambiguous identification of varieties is important for registration and certification of newly released varieties. Molecular markers are powerful tools, which help in differentiating plant varieties at the DNA level and have been widely used for fingerprinting in a number of crop varieties. In the present study, a set of 12 groundnut varieties released from Regional Agricultural Research Station, Tirupati were fingerprinted employing SSR markers. A total of 300 SSR were screened and fifteen...

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

    OpenAIRE

    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 wer...

  12. 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...

  13. 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...

  14. 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

  15. 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.

  16. 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...

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

    Directory of Open Access Journals (Sweden)

    Jana Ondroušková

    2013-04-01

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

  18. 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)

  19. SSR Markers Associated with Proline in Drought Tolerant Wheat Germplasm.

    Science.gov (United States)

    Iqbal, Muhammad Javid; Maqsood, Yasir; Abdin, Zain Ul; Manzoor, Atif; Hassan, Muhammad; Jamil, Amer

    2016-03-01

    Water stress causes major agricultural loss throughout the world as survival of the crops remained under stress and loss in yield. Plants respond to drought stress by means of different adaptive mechanisms such as accumulation of osmoprotectants to counteract the water stress. Amino acid proline is known to occur widely in higher plants and normally accumulates in large quantities as an osmolyte in response to environmental stresses. Biochemical estimation of proline was done in the drought-affected wheat genotypes by spectrophotometric method. Proline promoted a positive effect as root/shoot ratio was enhanced in wheat germplasm under drought stress. SSR primer pairs (45) were tested for polymorphism among selected wheat genotypes. The dendrogram results have shown the wheat genotype association with the levels of proline during induced drought stress. The relationship between pattern of drought responsive biochemical attributes and DNA markers in the selected wheat genotypes was recognized to select drought tolerant genotypes for sowing in drought affected areas of the country. PMID:26637362

  20. 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.

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

    Directory of Open Access Journals (Sweden)

    Li Yujun

    2011-10-01

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

  2. 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.

  3. 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. PMID:18956020

  4. 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.

  5. DNA fingerprinting of groundnut (Arachis hypogaea L. varieties of Tirupati using SSR markers

    Directory of Open Access Journals (Sweden)

    Y. Amaravathi, R.P. Vasanthi, E. Siva Kumar, M. Purushotham and T. Giridhara Krishna

    2014-12-01

    Full Text Available Unambiguous identification of varieties is important for registration and certification of newly released varieties. Molecular markers are powerful tools, which help in differentiating plant varieties at the DNA level and have been widely used for fingerprinting in a number of crop varieties. In the present study, a set of 12 groundnut varieties released from Regional Agricultural Research Station, Tirupati were fingerprinted employing SSR markers. A total of 300 SSR were screened and fifteen potential markers were employed for fingerprinting of groundnut varieties. The SSR markers generated alleles ranging from 2 to 7 with an average of four per locus. The polymorphism information content (PIC values ranged from 0 to 0.85. The genotypic data from all the loci provided unique SSR allelic fingerprints which helped in varietal identification of groundnut. Core set of highly informative primers viz., PM 377, TC1A02, TC5A06 and GM1489 identified in this study has the potential to identify most of the groundnut varieties. Cluster analysis using SSR marker grouped 12 groundnut varieties into two major clusters. Finger printing of the groundnut genotypes provide information about phylogenetic relationships and assists groundnut breeders in varietal registration and protection of intellectual property rights.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

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

    Directory of Open Access Journals (Sweden)

    Singh M.K.

    2014-01-01

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

  11. 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.

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

    Directory of Open Access Journals (Sweden)

    Xiaofeng Zhuang

    2013-01-01

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

  13. The transferability of SSR and EST-SSR markers of different origins in Elymus and Roegneria in the Triticeae (Poaceae)%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

    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

  14. 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.

  15. 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 ...

  16. Evaluation of genetic diversity and pedigree within crapemyrtle (Lagerstroemia spp.) cultivars using simple sequence repeat (SSR) markers

    Science.gov (United States)

    Genetic diversity was estimated for 93 crapemyrtle (Lagerstroemia spp.) cultivars (51 L. indica cultivars, 5 L. fauriei cultivars, and 37 interspecific hybrids) using 78 simple sequence repeat (SSR) markers. SSR loci were highly variable among the cultivars, detecting an average of 6.6 alleles per l...

  17. 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.

  18. 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

  19. Genetic Diversity and Identification of Chinese-Grown Pecan Using ISSR and SSR Markers

    Directory of Open Access Journals (Sweden)

    Zhong-Ren Guo

    2011-12-01

    Full Text Available Pecan is an important horticultural nut crop originally from North America and now widely cultivated in China for its high ecological, ornamental and economic value. Currently, there are over one hundred cultivars grown in China, including introduced American cultivars and Chinese seedling breeding cultivars. Molecular markers were used to assess the genetic diversity of these cultivars and to identify the pedigrees of fine pecan plants with good characteristics and no cultivar-related data. A total of 77 samples grown in China were studied, including 14 introduced cultivars, 12 domestic seedling breeding cultivars, and 49 fine pecan plants with no cultivar data, together with Carya cathayensis and Juglans nigra. A total of 77 ISSR and 19 SSR primers were prescreened; 10 ISSR and eight SSR primers were selected, yielding a total of 94 amplified bands (100% polymorphic in the range of 140–1,950 bp for the ISSR and 70 amplified bands (100% polymorphic in the range of 50–350 bp for SSR markers. Genetic diversity analyses indicated Chinese-grown pecan cultivars and fine plants had significant diversity at the DNA level. The dengrograms constructed with ISSR, SSR or combined data were very similar, but showed very weak grouping association with morphological characters. However, the progeny were always grouped with the parents. The great diversity found among the Chinese cultivars and the interesting germplasm of the fine pecan plants analyzed in this study are very useful for increasing the diversity of the pecan gene pool. All 77 accessions in this study could be separated based on the ISSR and SSR fingerprints produced by one or more primers. The results of our study also showed that ISSR and SSR techniques were both suitable for genetic diversity analyses and the identification of pecan resources.

  20. 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...

  1. 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。

  2. Analysis of esterase isozyme and SSR for mutagenic progenies induced by space mutation in mustard

    International Nuclear Information System (INIS)

    Seeds of five mustard (Brassica juncea Coss) varieties were carried into outer space by 'Shijian No.8' satellite. After five years' consecutive planting and selection, ten relatively stable mutant lines were obtained, which had significant variation in agronomic and economic characters. The mutant lines and their original varieties without space mutation treatment as control were studied by esterase isozyme and SSR analyses. Electrophoresis analysis of esterase isozymes indicated that there were differences between mutant lines and their controls in enzyme types and enzyme activity. Different mustard varieties had different enzymographs, and so did the mutants induced by space mutation, which shows different sensitivity among different mustard varieties. The SSR analysis showed that large differences were found in the SSR loci between mutant lines and their original variety, the variation frequency was between 9.52% and 57.14% with an average frequency of 26.19% for all the mutant lines. Among the mutant SSR loci, about 56.36% showed changes in band number and 43.64% in molecular weight. These results indicated that the ten mutant lines had large genetic difference in phenotype, genomic sequence and gene expression, and the outer space mutation would be an effective method to develop new mustard germplasm and variety. (authors)

  3. 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.

  4. 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.

  5. 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...

  6. Molekularna karakterizacija starog stabla masline Olea europea na Brijunima analizom SSR markera

    OpenAIRE

    Miljković, Ivo; Žužić, Italo; Pucci, Claudio; Baldoni, L.; Mariotti, M.; Cultrera, N.G.M.

    2010-01-01

    Istraživanja obuhvaćaju molekularnu karakterizaciju 1600 godina starog stabla masline Olea europea na Brijunima analizom SSR markera. Provedene su izmjere svojstava ploda i lišća starog stabla masline Brijunke i standardne istarske sorte Buga (Buža). Rezultati istraživanja obrađeni su varijacijsko-statistički.

  7. 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

  8. 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

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

    Directory of Open Access Journals (Sweden)

    Zhao Yongli

    2012-07-01

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

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

    Science.gov (United States)

    Wang, Tiegu; Huang, Qunce; Feng, Weisen

    2007-10-01

    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, s1, opt-16, and f14, were significantly associated with the muticate trait, while three SSR markers, Rht8 (Xgwm261), Rht-B1b, and Rht-D1b, 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.

  11. 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

  12. 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.

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

    International Nuclear Information System (INIS)

    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, s1, opt-16, and f14, were significantly associated with the muticate trait, while three SSR markers, Rht8 (Xgwm261), Rht-B1b, and Rht-D1b, 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

  14. SsrA-mediated tagging and proteolysis of LacI and its role in the regulation of lac operon

    OpenAIRE

    Abo, Tatsuhiko; INADA, TOSHIFUMI; Ogawa, Kazuko; AIBA, HIROJI

    2000-01-01

    SsrA RNA of Escherichia coli, also known as 10Sa RNA or tmRNA, acts both as tRNA and mRNA when ribosomes are paused at the 3′ end of an mRNA lacking a stop codon. This process, referred to as trans-translation, leads to the addition of a short peptide tag to the C-terminus of the incomplete nascent polypeptide. The tagged polypeptide is then degraded by C-terminal-specific proteases. Here, we focused on endogenous targets for the SsrA system and on a potential regulatory role of SsrA RNA. Fir...

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

    OpenAIRE

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

    2012-01-01

    Species-specific simple sequence repeat (SSR) markers are favored for genetic studies and marker-assisted selection (MAS) breeding for oil palm genetic improvement. This report characterizes 20 SSR markers from an Elaeis oleifera genomic library (gSSR). Characterization of the repeat type in 2000 sequences revealed a high percentage of di-nucleotides (63.6%), followed by tri-nucleotides (24.2%). Primer pairs were successfully designed for 394 of the E. oleifera gSSRs. Subsequent analysis show...

  16. 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.

  17. 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

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

    OpenAIRE

    Jia Baoguang; Lin Qing; Zhang Lin; Tan Xiaofeng; Lei Xiaolin; Hu Xiaoyi; Shao Fenggong

    2014-01-01

    Oil-tea tree is one of the most important woody edible oil plants; however, lack of useful molecular markers hinders current genetic research. We performed transcriptome sequencing of developing seeds and characterized microsatellites from transcriptome sequences to identify valuable markers for C. oleifera molecular genetics research. A total of 69,798 unigenes were identified, in which 6,949 putative SSR motifs from 6,042 SSR-containing unique putative tr...

  19. 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.

  20. Effect of space flight mutation on eggplant and analysis of genetic diversity by ssr molecular marker

    International Nuclear Information System (INIS)

    Seeds of three eggplant varieties (05 - 7, 05 - 9 and 05 - 18) were carried byShijian 8satellite for space flight treatment. The space flight mutation effects on eggplant were studied and the genetic diversity of mutant lines was analyzed using SSR markers. The results showed that space flight had obvious effects on the seed germination in eggplant SP1 generation and other characters such as plant height, plant type, leaf shape, fruit shape in the second generation. Most of the mutated characters could stably inherit in the third generation. The results also indicated that different eggplant genotypes resporded different to the space flight mutation; the long eggplant 05 - 18 was much more sensitive than other two varieties. Great variation between variant lines and their original varieties were detected by SSR markers, suggesting that space flight could induce molecular variation in eggplant. (authors)

  1. 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)

  2. 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.

  3. Molecular Screening of Blast Resistance Genes in Rice using SSR Markers

    OpenAIRE

    Singh, A.K.; Singh, P. K.; Arya, Madhuri; Singh, N K; U S Singh

    2015-01-01

    Rice Blast is the most devastating disease causing major yield losses in every year worldwide. It had been proved that using resistant rice varieties would be the most effective way to control this disease. Molecular screening and genetic diversities of major rice blast resistance genes were determined in 192 rice germplasm accessions using simple sequence repeat (SSR) markers. The genetic frequencies of the 10 major rice blast resistance genes varied from 19.79% to 54.69%. Seven accessions I...

  4. Phylogeny and sequence variability of the Sarcocystis singaporensis Zaman and Colley, (1975) 1976 ssrDNA

    Czech Academy of Sciences Publication Activity Database

    Šlapeta, Jan Roger; Kyselová, Iveta; Richardson, A. O.; Modrý, David; Lukeš, Julius

    2002-01-01

    Roč. 88, č. 9 (2002), s. 810-815. ISSN 0932-0113 R&D Projects: GA ČR GA524/00/P015; GA AV ČR KSK6005114 Institutional research plan: CEZ:AV0Z6022909 Keywords : Sarcocystis * phylogeny * ssrDNA Subject RIV: GJ - Animal Vermins ; Diseases, Veterinary Medicine Impact factor: 1.046, year: 2002

  5. 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

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

    Directory of Open Access Journals (Sweden)

    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.

  7. 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.

  8. An EST-SSR Linkage Map of Raphanus sativus and Comparative Genomics of the Brassicaceae †

    OpenAIRE

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

    2011-01-01

    Raphanus sativus (2n = 2x = 18) is a widely cultivated member of the family Brassicaceae, for which genomic resources are available only to a limited extent in comparison to many other members of the family. To promote more genetic and genomic studies and to enhance breeding programmes of R. sativus, we have prepared genetic resources such as complementary DNA libraries, expressed sequences tags (ESTs), simple sequence repeat (SSR) markers and a genetic linkage map. A total of 26 606 ESTs hav...

  9. Assessment of genetic variation in Bulgarian tomato (Solanum lycopersicum L.) genotypes, using fluorescent SSR genotyping platform

    OpenAIRE

    TODOROVSKA, Elena; IVANOVA, Albena; Daniela GANEVA; Galina PEVICHAROVA; Molle, Emil; Bojinov, Bojin; Radkova, Mariana; Danailov, Zhivko

    2014-01-01

    Genetic variability in modern crops is limited due to domestication and selection processes. Genetic variation in eight Bulgarian tomato varieties and breeding lines (variety Plovdivska karotina, variety IZK Alya, L21β, L53β, L1140, L1116, L975, L984) differing in their morphological and biochemical composition was assessed using a highly efficient and low-cost fluorescent simple sequence repeat (SSR) genotyping platform. Genotyping was conducted with 165 publicly available microsatellite mar...

  10. Correlation between heterosis and genetic distance based on SSR markers in sunflower (Helianthus annuus L.)

    OpenAIRE

    Gvodzenović Sandra; Panković-Saftić Dejana; Jocić Siniša; Radić Velimir

    2009-01-01

    The objective of this study was to determine the correlation between SSR based genetic distance (GD) of new NS sunflower inbred lines and heterosis for six agronomic traits. Twenty three sunflower inbred lines (20 restorer lines and three female lines used as testers) and their hybrids were examined for plant height, head diameter, thousand seed mass, oil content, seed yield per plant and oil yield per plant. Significant heterosis was observed in hybrid combinations for all examined traits ex...

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

    Directory of Open Access Journals (Sweden)

    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.

  12. 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.

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

    Directory of Open Access Journals (Sweden)

    A. Imamovic

    2015-11-01

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

  14. 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℃.

  15. SSR-based molecular analysis of economically important Turkish apricot cultivars.

    Science.gov (United States)

    Akpinar, A E; Koçal, H; Ergül, A; Kazan, K; Selli, M E; Bakir, M; Aslantaş, S; Kaymak, S; Saribaş, R

    2010-01-01

    Turkey is not only the main apricot (Prunus armeniaca) producer and exporter in the world, but it also has a wide variety of apricot germplasms, owing to its close proximity to the centers of apricot origin. However, there is little or no genetic information on many apricot cultivars that are extensively cultivated in Turkey. We examined the genetic relatedness of 25 Turkish and four exotic apricot cultivars using SSR (simple sequence repeat) markers that were either previously developed for apricot, or for peach (P. persica), a close relative of apricot. Allele diversity (with an average allele number of 6.37) at the SSR loci and the heterozygosity rates (with an average Ho value of 0.648) of these cultivars were found to be higher than in previous studies that used the same loci for apricot. This fact might be attributed to the analysis of different numbers of accessions in the different studies. No correlations were found between the genetic relatedness and the geographical distributions of these cultivars. The data reported here will assist in the prevention of confusions in the apricot propagation and breeding in Turkey. The findings can also be directly compared with other studies that used the same SSR markers on apricot. PMID:20198588

  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. 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

    2016-03-01

    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 from 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.

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

    Directory of Open Access Journals (Sweden)

    Abdul Majid Ansari, and Y. V. Singh

    2014-12-01

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

  19. 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.

  20. Genetic diversity in Fusarium solani f. sp. pisi based on SSR markers

    Directory of Open Access Journals (Sweden)

    Ni Xiang

    2012-11-01

    Full Text Available 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 ofalleles 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 phylogeneticanalysis. 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.

  1. 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 .

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

    Science.gov (United States)

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

    2012-01-01

    Species-specific simple sequence repeat (SSR) markers are favored for genetic studies and marker-assisted selection (MAS) breeding for oil palm genetic improvement. This report characterizes 20 SSR markers from an Elaeis oleifera genomic library (gSSR). Characterization of the repeat type in 2000 sequences revealed a high percentage of di-nucleotides (63.6%), followed by tri-nucleotides (24.2%). Primer pairs were successfully designed for 394 of the E. oleifera gSSRs. Subsequent analysis showed the ability of the 20 selected E. oleifera gSSR markers to reveal genetic diversity in the genus Elaeis. The average Polymorphism Information Content (PIC) value for the SSRs was 0.402, with the tri-repeats showing the highest average PIC (0.626). Low values of observed heterozygosity (H(o)) (0.164) and highly positive fixation indices (F(is)) in the E. oleifera germplasm collection, compared to the E. guineensis, indicated an excess of homozygosity in E. oleifera. The transferability of the markers to closely related palms, Elaeis guineensis, Cocos nucifera and ornamental palms is also reported. Sequencing the amplicons of three selected E. oleifera gSSRs across both species and palm taxa revealed variations in the repeat-units. The study showed the potential of E. oleifera gSSR markers to reveal genetic diversity in the genus Elaeis. The markers are also a valuable genetic resource for studying E. oleifera and other genus in the Arecaceae family. PMID:22605966

  3. 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.

  4. 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.

  5. 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.

  6. QTL mapping for yield and lodging resistance in an enhanced SSR-based map for tef.

    Science.gov (United States)

    Zeid, M; Belay, G; Mulkey, S; Poland, J; Sorrells, M E

    2011-01-01

    Tef is a cereal crop of cultural and economic importance in Ethiopia. It is grown primarily for its grain though it is also an important source of fodder. Tef suffers from lodging that reduces both grain yield and quality. As a first step toward executing a marker-assisted breeding program for lodging resistance and grain yield improvement, a linkage map was constructed using 151 F(9) recombinant inbred lines obtained by single-seed-descent from a cross between Eragrostis tef and its wild relative Eragrostis pilosa. The map was primarily based on microsatellite (SSR) markers that were developed from SSR-enriched genomic libraries. The map consisted of 30 linkage groups and spanned a total length of 1,277.4 cM (78.7% of the genome) with an average distance of 5.7 cM between markers. This is the most saturated map for tef to date, and for the first time, all of the markers are PCR-based. Using agronomic data from 11 environments and marker data, it was possible to map quantitative trait loci (QTL) controlling lodging, grain yield and 15 other related traits. The positive effects of the QTL identified from the wild parent were mainly for earliness, reduced culm length and lodging resistance. In this population, it is now possible to combine lodging resistance and grain yield using a marker-assisted selection program targeting the QTL identified for both traits. The newly developed SSR markers will play a key role in germplasm organization, fingerprinting and monitoring the success of the hybridization process in intra-specific crosses lacking distinctive morphological markers. PMID:20706706

  7. 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.

  8. 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

  9. 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.

  10. Development of EST-SSR Markers to Assess Genetic Diversity in Elettaria Cardamomum Maton

    Directory of Open Access Journals (Sweden)

    N Anjali

    2015-06-01

    Full Text Available Elettaria cardamomum Maton is one of the most ancient and valuable spice crops. Cardamom is cultivated following intensive pesticide usage where alleles present in the wild cardamom genotypes could positively contribute towards genetic improvement of the cultivars. However, the genetic map or whole-genome sequence of E. cardamomum is not available and very limited information on simple sequence repeat (SSR markers are publicly available. We have tested whether SSRs from Curcuma longa can be used to analyze genetic diversity E. cardamomum.

  11. 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...

  12. 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。

  13. 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.

  14. 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.

  15. 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.

  16. 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.

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

    Directory of Open Access Journals (Sweden)

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

    2014-09-01

    Full Text Available 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 genetic variation within and between the species of amaranthus and suggest that cultivated varieties of Amaranthus have significant genetic variation. The differences generated by the markers can be used as fingerprints for detecting the varieties. This is the first report of the utilization of legume microsatellite markers in Amaranthus.

  18. 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

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

    DEFF Research Database (Denmark)

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

    2013-01-01

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

  20. Use of Simple Sequence Repeat (SSR) markers for DNA fingerprinting and diversity analysis of sugarcane (Saccharum spp.) cultivars resistant and susceptible to red rot

    Science.gov (United States)

    In recent years SSR markers have been used widely for the genetic analysis. The objective of present research was to use SSR markers to develop DNA-based genetic identification and analyze genetic relationship of sugarcane cultivars grown in Pakistan either resistant or susceptible to red rot. Twent...

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

    DEFF Research Database (Denmark)

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

    2014-01-01

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

  2. 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

  3. 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.

  4. Development of Simple Sequence Repeat (SSR Markers of Sesame (Sesamum indicum from a Genome Survey

    Directory of Open Access Journals (Sweden)

    Xin Wei

    2014-04-01

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

  5. 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.

  6. 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)

  7. 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)

  8. 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.

  9. 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.  

  10. Genetic diversity of the Bambara groundnut (Vigna subterranea (L.) Verdc.) as assessed by SSR markers.

    Science.gov (United States)

    Somta, P; Chankaew, S; Rungnoi, O; Srinives, P

    2011-11-01

    Bambara groundnut ( Vigna subterranea (L.) Verdc.) is an important African legume crop. In this study, a collection consisting of 240 accessions was analyzed using 22 simple sequence repeat (SSR) markers. In total, 166 alleles were detected, with a mean of 7.59 alleles per locus. Allelic and gene diversities were higher in the west African and Cameroon/Nigeria regions with 6.68 and 6.18 alleles per locus, and 0.601 and 0.571, respectively. The genetic distance showed high similarity between west African and Cameroon/Nigeria accessions. Principal coordinate analyses and neighbor-joining analysis consistently revealed that the majority of west African accessions were grouped with Cameroon/Nigeria accessions, but they were differentiated from east African, central African, and southeast Asian accessions. Population structure analysis showed that two subpopulations existed, and most of the east African accessions were restricted to one subpopulation with some Cameroon/Nigeria accessions, whereas most of the west African accessions were associated with most of the Cameroon/Nigeria accessions in the other subpopulation. Comparison with SSR analysis of other Vigna cultigens, i.e., cultivated azuki bean ( Vigna angularis ) and mungbean ( Vigna radiata ), reveals that the mean gene diversity of Bambara groundnut was lower than azuki bean but higher than mungbean. PMID:22017518

  11. 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

  12. 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.

  13. 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

  14. Comparative Analysis of SSR and SRAP Sequence Divergence in Citrus Germplasm

    Directory of Open Access Journals (Sweden)

    Mohamed Hamdy Amar

    2012-01-01

    Full Text Available In the present study, we sought to determine whether one simple criterion, sequence divergence, can reasonably guide in phylogenetic across a broad scale in Citrus germplasm. Comparative investigation on the performance of the SSR and SRAP markers was conducted in phylogenetic analysis across sequence analysis of the PCR product in the genus Citrus and its relatives. The maximum composite likelihood model was used for pairwise distance calculation. To determine whether there is a difference depending on the method of choice. Somehow, phylogenetic trees were constructed using two algorithms Neighbor Joining (NJ and Maximum Parsimony (MP via MEGA 4 software. In contrast some differences in the positioning of some genotypes were observed in the phylogenetic trees created using the two models and the dendrogram from MP across SRAP sequence was the most congruent with Swingle and Reeces treatment of the subfamily Aurantioideae. The results of the present study suggest that evaluation of SRAP variation at the sequence level can be effective than SSR variation in exploring the evolutionary relationships among Citrus species. These results were the new information for future study on Citrus breeding programs such as germplasm characterization, screening of zygotic and nuclear seedlings and developing sequence divergence in Citrus and its relatives.

  15. 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

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

    Science.gov (United States)

    2013-03-22

    ... Federal Register on February 20, 2013. (78 FR 11939). On page 11940, in the first column, under the... From the Federal Register Online via the Government Publishing Office SOCIAL SECURITY ADMINISTRATION Social Security Ruling, SSR 13-2p; Titles II and XVI: Evaluating Cases Involving Drug...

  17. 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

  18. 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 ...

  19. 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.

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

    Directory of Open Access Journals (Sweden)

    Jia Baoguang

    2014-01-01

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

  1. 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…

  2. 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...

  3. 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...

  4. Mining and validating grape (Vitis L.) ESTs to develop EST-SSR markers for genotyping and mapping

    Science.gov (United States)

    Ninety-six new primer pairs, used to identify disease resistance in grapes were created. The newly identified EST-derived SSRs are being used to conduct analyses of grape functional diversity and in the development of grape SSR-EST genetic and physical maps. A pipeline including several computation...

  5. Mapping a stripe rust resistance gene YrC591 in wheat variety C591 with SSR and AFLP markers.

    Science.gov (United States)

    Li, Y; Niu, Y C; Chen, X M

    2009-01-01

    Stripe rust, caused by Puccinia striiformis Westend. f. sp. tritici (PST), is one of the most destructive diseases of common wheat (Triticum aestivum L.). To determine inheritance of stripe rust resistance and map the resistance gene(s) in wheat variety C591, F(1), F(2,) and F(3) progenies derived from the Taichung 29 x C591 cross were inoculated with Chinese PST race CY32 in the greenhouse. Genetic analysis identified a single dominant gene, temporarily designated YrC591. A total of 178 SSR and 130 AFLP markers were used to test the parents and resistant and susceptible bulks. From the bulk segregant analysis, seven polymorphic SSR and two AFLP markers were selected for genotyping the F(2) population. SSR marker Xcfa2040-7B, and SCAR marker SC-P35M48 derived from AFLP marker P35M48 ( 373 ) were identified to be closely linked to the resistance gene with genetic distances of 8.0 and 11.7 cM, respectively. The SSR markers mapped the resistance gene on chromosome arm 7BL. In the seedling test with five PST races, the reaction patterns of C591 were different from wheat cultivars or lines carrying Yr2 or Yr6 that also are found on chromosome 7B. The results indicate that YrC591 is probably a novel stripe rust resistance gene. PMID:18946654

  6. 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.

  7. 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

  8. 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

  9. 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

  10. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-01-01

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

  12. 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.

  13. 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.

  14. Data acquisition and display system for the 14 MW SSR TRIGA Reactor from INR Pitesti

    International Nuclear Information System (INIS)

    This paper briefly describes the data acquisition system used for almost ten years at the 14 MW SSR TRIGA Reactor in INR Pitesti. Starting with a small system for the reactor thermal power evaluation, the system was developed to cover multiple experiment monitoring requirements. With a relative large number of channels (280) it satisfies now the necessity of monitoring both the 14 MW Reactor and different irradiation experiments for the steady-state mode at high resolution (10 μV, equivalent to 0.25 deg C for type K thermocouples) in a noisy environment. The user interface allows multiple user-configuration displays and both predefined and/or user-defined printouts. A real time system and multi-user capabilities offers both fast response and a very flexible data processing system. (authors)

  15. Comparing failure rates in different research reactors including Romanian TRIGA SSR Reactor

    International Nuclear Information System (INIS)

    Probabilistic Safety Assessment (PSA) is a tool for evaluating and enhancing the safety of a nuclear reactor. In general, the PSA is used to support the system design, configuration decisions and the operational safety management of the plant. Ideally, the failure data used for safety and reliability analyses should be based on site-specific data. The paper presents failure rates for some components, both stand-alone taken from Romanian TRIGA SSR Reactor Data Collection and in comparison with other research reactors, as well as statistics pertaining to the failures and failure modes of the investigated components. Most of the work in the purpose of obtaining reliability data for Romanian TRIGA as well as for different research reactors was performed during IAEA Coordinated Research Project: 'Update and Expand Reliability database for research reactors for PSA use' (2000-2004). (authors)

  16. Overview of probabilistic safety assessment activity for Romanian TRIGA SSR 14 MW reactor

    International Nuclear Information System (INIS)

    Current international approach of Probabilistic Safety Assessment (PSA) is not only for Nuclear Power Plants but also for Research Reactors. Recently commissioned Research Reactors use PSA in the process of licensing. In case of the Institute for Nuclear Research Pitesti, PSA for TRIGA Research Reactor was developed with a scientific aim joint to the Deterministic Analysis, covering the qualitative and quantitative approach of safety. The paper presents the PSA activity related to TRIGA SSR 14 MW reactor starting with raw data collection for obtaining a historical view of the reactor operation and to obtain reliability data used in PSA. Further on, an overall presentation of the PSA model (Initiating Events, Event Trees and Fault Trees) is made. (authors)

  17. 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.

  18. Genetic Diversity in Southeast European Soybean Germplasm Revealed by SSR Markers

    Directory of Open Access Journals (Sweden)

    Daniela Ristova

    2010-03-01

    The objective of this study was to assess genetic diversity and relationships of 23 soybean genotypes representing several independent breeding sources from Southeastern Europe and five plant introductions from Western Europe and Canada using 20 SSR markers. In total 80 alleles were detected among 28 genotypes with an average of four alleles per locus and an average marker diversity of 0.585. Allele frequency distribution was characterised with a high proportion of alleles at very low frequencies with 11 % of unique alleles. Cluster analysis clearly separated all genotypes from each other assigning them into three major clusters, which largely corresponded to their origin. Results of clustering were mainly in accordance with the known pedigrees.

  19. Development and Integration of an SSR-Based Molecular Identity Database into Sugarcane Breeding Program

    Directory of Open Access Journals (Sweden)

    Yong-Bao Pan

    2016-04-01

    Full Text Available Sugarcane breeding is very difficult and it takes 12 to 14 years to develop a new cultivar for commercial production. This is because sugarcane varieties are highly polyploid, inter-specific hybrids with 100 to 130 chromosomes that may vary across geographical areas. Other obstacles/constraints include the small size of flowers that may not synchronize but may self-pollinate, difficulty in distinguishing hybrids from self progenies, extreme (G × E interactive effect, and potential variety mis-identification during vegetative propagation and varietal exchange. To help cane breeders circumvent these constraints, a simple sequence repeats (SSR-based molecular identity database has been developed at the United States Department of Agriculture-Agricultural Research Service, Sugarcane Research Unit in Houma, LA. Since 2005, approximately 2000 molecular identities have been constructed for clones of sugarcane and related Saccharum species that cover geographical areas including Argentina, Australia, Bangladesh, China, Colombia, India, Mexico, Pakistan, South Africa, Thailand, USA (Louisiana, Florida, Texas, and Hawaii, and Venezuela. The molecular identity database is updated annually and has been utilized to: (1 provide molecular descriptors to newly registered cultivars; (2 identify in a timely fashion any mislabeled or unidentifiable clones from cross parents and field evaluation plots; (3 develop de novo clones of energy cane with S. spontaneum cytoplasm; (4 provide clone-specific fingerprint information for assessing cross quality and paternity of polycross; (5 determine genetic relatedness of parental clones; (6 select F1 hybrids from (elite × wild or (wild × elite crosses; and (7 investigate the inheritance of SSR markers in sugarcane. The integration of the molecular identity database into the sugarcane breeding program may improve the overall efficacy of cultivar development and commercialization.

  20. 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.

  1. 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.

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

    Directory of Open Access Journals (Sweden)

    Jian-Wei Zong

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

  3. 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.

  4. 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)

  5. 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.

  6. 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

  7. 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.

  8. 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.

  9. A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study

    OpenAIRE

    Durand, J; Bodénès, C.; Chancerel, E; Frigerio, J.M.; Vendramin, G.; Sebastiani, F.; Buonamici, A.; Gailing, O.; Koelewijn, H. P.; Villani, F.; Mattioni, C.; Cherubini, M.; Goicoechea, P.G.; Herrán, A.; Ikaran, Z.

    2010-01-01

    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) ma...

  10. A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study

    OpenAIRE

    Cherubini Marcello; Mattioni Claudia; Villani Fiorella; Koelewijn Hans-Peter; Gailing Oliver; Buonamici Anna; Sebastiani Federico; Vendramin Giovanni; Frigerio Jean-Marc; Chancerel Emilie; Bodénès Catherine; Durand Jérôme; Goicoechea Pablo G; Herrán Ana; Ikaran Ziortza

    2010-01-01

    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 ...

  11. Development of expressed sequence tag resources for Vanda Mimi Palmer and data mining for EST-SSR.

    Science.gov (United States)

    Teh, Seow-Ling; Chan, Wai-Sun; Abdullah, Janna Ong; Namasivayam, Parameswari

    2011-08-01

    Vanda Mimi Palmer (VMP) is a highly sought as fragrant-orchid hybrid in Malaysia. It is economically important in cosmetic and beauty industries and also a famous potted ornamental plant. To date, no work on fragrance-related genes of vandaceous orchids has been reported from other research groups although the analysis of floral fragrance or volatiles have been extensively studied. An expressed sequence tag (EST) resource was developed for VMP principally to mine any potential fragrance-related expressed sequence tag-simple sequence repeat (EST-SSR) for future development as markers in the identification of fragrant vandaceous orchids endemic to Malaysia. Clustering, annotation and assembling of the ESTs identified 1,196 unigenes which defined 966 singletons and 230 contigs. The VMP dbEST was functionally classified by gene ontology (GO) into three groups: molecular functions (51.2%), cellular components (16.4%) and biological processes (24.6%) while the remaining 7.8% showed no hits with GO identifier. A total of 112 EST-SSR (9.4%) was mined on which at least five units of di-, tri-, tetra-, penta-, or hexa-nucleotide repeats were predicted. The di-nucleotide motif repeats appeared to be the most frequent repeats among the detected SSRs with the AT/TA types as the most abundant among the dimerics, while AAG/TTC, AGA/TCT-type were the most frequent trimerics. The mined EST-SSR is believed to be useful in the development of EST-SSR markers that is applicable in the screening and characterization of fragrance-related transcripts in closely related species. PMID:21116862

  12. 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...

  13. 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.

  14. 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

  15. 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

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

    Science.gov (United States)

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

    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. PMID:20861564

  17. 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

  18. 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%.

  19. 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.

  20. 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

  1. 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.

    2016-01-01

    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

  2. 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.

  3. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2008-10-29

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

  5. 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

  6. Correlation between heterosis and genetic distance based on SSR markers in sunflower (Helianthus annuus L.

    Directory of Open Access Journals (Sweden)

    Gvodzenović Sandra

    2009-01-01

    Full Text Available The objective of this study was to determine the correlation between SSR based genetic distance (GD of new NS sunflower inbred lines and heterosis for six agronomic traits. Twenty three sunflower inbred lines (20 restorer lines and three female lines used as testers and their hybrids were examined for plant height, head diameter, thousand seed mass, oil content, seed yield per plant and oil yield per plant. Significant heterosis was observed in hybrid combinations for all examined traits except oil content. Genetic distance between pairs of tested sunflower inbred lines ranged from 0.13 to 0.8. There was no significant positive correlation between genetic distance and mid- and better-parent heterosis, specific combining ability and mean value in any of the examined traits for all 60 hybrids. A highly significant negative correlation was found between GD and mean oil percentage (r=-0.33 p<0.01. Although GD was generally a poor predictor of heterosis, better results are obtained if hybrid combinations for each tester and each trait are analyzed separately.

  7. 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.

  8. Лимнологический аспект водохозяйственной рекультивации нарушенных земель

    OpenAIRE

    Хомич, Светлана Александровна

    1987-01-01

    In the Byelorussian SSR the depleted quarries of such mineral resources as clay, sand and limestone gradually become filled with water, which prevents the afforestation or cultivation of these areas. But if we level the bottom of such quarries, strighten their shoreline and cover the bottom with earth, the resulting artificial water-bodies can be used for breeding fish.

  9. SSR markers to detect gene flow from upland to mocó cotton Marcadores SSR para detecção de fluxo gênico de algodoeiro herbáceo para algodoeiro mocó

    Directory of Open Access Journals (Sweden)

    Ana Carolina Assis Dantas

    2012-03-01

    Full Text Available Mocó cotton was the most important crop in Northeastern Brazil. Local varieties had been developed before governmental breeding programs, which should be identified and preserved as a genetic resource. The aim of this work was to select SSR markers which can be used to monitor gene flow from herbaceous to mocó cotton plants, using non transgenic upland cotton as a pollen source. Unique mocó cotton feral populations were identified in the state of Rio Grande do Norte, and mother plants and their seeds were collected. Allele frequencies were studied among fifteen plants from these populations using 64 SSR primer pairs. Ten SSR markers, with alleles exclusive to mocó or upland genotypes, were selected to monitor gene flow by paternity analysis (BNL3627; 2960; 2572; 3261; 3398; 3948; 3502; 3646 and CIR 094; 097. The collected seeds had none of the upland cotton alleles. The absence of exclusive alleles from upland cotton in the offspring showed that gene flow to mocó cotton was absent or lower than the analysis could detect. Among the mother plants, the number of homozygous individuals at four polymorphic loci was greater than expected, showing that reproduction occurs preferentially by self-fertilization or crossing among related individuals. Paternity analysis is an accurate measure of gene flow, and the methodology can be used for monitor these populations or others. Preservation of the plants is spoiled mainly by drought.O algodoeiro mocó foi a planta cultivada mais importante do Nordeste do Brasil. Variedades locais desenvolvidas anteriormente aos programas de melhoramento governamentais devem ser identificadas e preservadas como recurso genético. O objetivo deste trabalho foi selecionar marcadores SSR para monitorar o fluxo de genes do algodoeiro herbáceo para o mocó, usando plantas de algodoeiro herbáceo não transgênicas como fonte de pólen. Populações ferais de algodoeiro mocó raras foram identificadas no estado Rio Grande do

  10. 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.

  11. 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.)

  12. 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.

  13. 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.

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

    Directory of Open Access Journals (Sweden)

    Matsumoto Takashi

    2010-04-01

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

  15. Molecular diversity of Cuban cassava (Manihot esculenta Crantz cultivars assessed by simple sequences repeats (SSR

    Directory of Open Access Journals (Sweden)

    Beovides, Y.

    2015-01-01

    Full Text Available A total of 36 microsatellites (SSR markers were used to analyze the genetic diversity of 163 accessions of cultivated cassava (Manihot esculenta Crantz, 94 accessions of them from the Cuban Cassava Germplasm Collection and 69 genotypes from different countries and conserved at the International Center for Tropical Agriculture (Colombia. This study was carried out to determine genetic diversity within and between all accessions to promote their better use and conservation strategies. Thirty-four of those markers were used for the genetic diversity study based on their higher polymorphism. The Cuban cultivars showed the highest average allele number per loci with 5.8 and 100% of the loci were polymorphic, as well as those from Guatemala. The average proportion of individual heterozygocity observed (HO was high (0.5918 ± 0.0351, while the highest HO rates were observed in groups of genotypes from Cuba (0.6016 and Tanzania (0.6459. The total heterozygocity (HT was high (0.6538 ± 0.1770, but only 7.4% (GST = 0.0740 ± 0.0377 was due to differences between the five countries studied. Genetic differentiation coefficients (estimated by F-statistics were low to moderate (FST > 0.04 and 17 unique alleles with low frequency were found in Cuban cultivars. The results provide the first molecular characterization of Cuban cassava genotypes and showed a wide diversity among landraces from Cuba. Application of this valuable information can be used for genetic diversity conservation and genotype identification studies for the genetic breeding program of cassava.

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

    Directory of Open Access Journals (Sweden)

    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.

  17. 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)

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

    Directory of Open Access Journals (Sweden)

    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.

  19. 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.

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

    Science.gov (United States)

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

    2016-05-01

    The complete plastome sequencing is an efficient option for increasing phylogenetic resolution and evolutionary studies, as well as may greatly facilitate the use of plastid DNA markers in plant population genetic studies. Merostachys and Guadua stand out as the most common and the highest potential utilization bamboos indigenous of Brazil. Here, we sequenced the complete plastome sequences of the Brazilian Guadua chacoensis and Merostachys sp. to perform full plastome phylogeny and characterize the occurrence, type, and distribution of SRRs using 20 Bambuseae species. The determined plastome sequence of Merostachys sp. and G. chacoensis is 136,334 and 135,403 bp in size, respectively, with an identical gene content and typical quadripartite structure consisting of a pair of IRs separated by the LSC and SSC regions. The Maximum Likelihood and Bayesian Inference analyses produced phylogenomic trees identical in topology. These trees supported monophyly of Paleotropical and Neotropical Bamboos clades. The Neotropical bamboos segregated into three well-supported lineages, Chusqueinae, Guaduinae, and Arthrostylidiinae, with the last two forming a well-supported sister relationship. Paleotropical bamboos segregated into two well-supported lineages, Hickeliinae and Bambusinae + Melocanninae. We identified 141.8 cpSSR in Bambuseae plastomes and an inferior value (38.15) for plastome coding sequences. Among them, we identified 16 polymorphic SSR loci, with number of alleles varying from 3 to 10. These 16 polymorphic cpSSR loci in Bambuseae plastome can be assessed for the intraspecific level of polymorphism, leading to innovative highly sensitive phylogeographic and population genetics studies for this tribe. PMID:26643654

  1. Development of EST-SSR markers and construction of a linkage map in faba bean (Vicia faba)

    OpenAIRE

    El-Rodeny, Walid; Kimura, Mitsuhiro; Hirakawa, Hideki; Sabah, Attia; SHIRASAWA, KENTA; Sato, Shusei; Tabata, Satoshi; Sasamoto, Shigemi; Watanabe, Akiko; Kawashima, Kumiko; Kato, Midori; Wada, Tsuyuko; Tsuruoka, Hisano; Takahashi, Chika; Minami, Chiharu

    2014-01-01

    To develop a high density linkage map in faba bean, a total of 1,363 FBES (Faba bean expressed sequence tag [EST]-derived simple sequence repeat [SSR]) markers were designed based on 5,090 non-redundant ESTs developed in this study. A total of 109 plants of a ‘Nubaria 2’ × ‘Misr 3’ F2 mapping population were used for map construction. Because the parents were not pure homozygous lines, the 109 F2 plants were divided into three subpopulations according to the original F1 plants. Linkage groups...

  2. Common cause failure data collection and analysis for safety-related components of TRIGA SSR-14MW Pitesti, Romania

    International Nuclear Information System (INIS)

    This paper presents a study performed on the set of common cause failures (CCF) of safety-related components of the research reactor TRIGA SSR-14 MW Pitesti. The data collected cover a period of 20 years, from 1979 to 2000. The sources of data are Shift Supervisor Reports, Work Authorizations, and Reactor Log Books. Events collected are analyzed by failure mode and degrees of failure. Qualitative analysis of root causes, coupling factors and corrective actions and quantitative analysis of CCF events are studied. The objective of this work is to develop qualitative insights in the nature of the reported events and to build a site-specific common cause events database. (author)

  3. Application of the GERB shock absorbers for seismic protection of pipelines and equipment at NPPs in ChSSR

    International Nuclear Information System (INIS)

    Operation principle of the GERB viscons friction shock absorbers intended for the NPP equipment and pipeline protection against damages and displacements caused by external dynamic loads, is described. Dynamic calculation of pipeline systems equipped with viscous friction shock absorbers is performed. The GERB shock absorbers are about 3 times cheaper than hydraulic or mechanical ones. Their application in the first coolant circuit of the Mochovce WWER-440 reactor (ChSSR) provides for a reliable equipment operation under the maximum calculated earthquake of 6 points

  4. 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...

  5. 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

  6. 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

  7. 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.

  8. 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.

  9. Multiplex SSR-PCR approaches for semi-automated genotyping and characterization of loci linked to blast disease resistance genes in rice.

    Science.gov (United States)

    Ashkani, Sadegh; Rafii, Mohd Yusop; Shabanimofrad, Mahmoodreza; Foroughi, Majid; Azizia, Parisa; Akhtar, Mohd Sayeed; Sahebi, Mahbod; Harun, Abd Rahim; Nasehi, Abbas

    2015-11-01

    In the present study, 63 polymorphic microsatellite markers related to rice blast resistance genes were fluorescently labelled at the 5'-end with either 6-FAM or HEX using the G5 dye set and incorporated into a multiplex SSR-PCR for the detection of fragments using an automated system. For rice F3 families obtained from crosses between Pongsu Seribu 2 (Malaysian blast resistant cultivar) and Mahsuri (a susceptible rice cultivar), the genotypes for 13 designated multiplex SSR panels were determined. The genotyping assays were performed using a capillary-based ABIPRISM 3100 genetic analyser. The sizes of the SSRs alleles observed in the range from 79 to 324 bp. The observed marker segregation data were analysed using the Chi(2) test. A genetic linkage map covering ten chromosomes and comprising 63 polymorphic SSR markers was constructed, and the distorted loci were localised to linkage groups. The results indicated that distorted loci are presented on eight chromosomes. PMID:26318048

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. 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

  15. 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.

  16. 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.

  17. 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.

  18. 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)

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

    Directory of Open Access Journals (Sweden)

    Tao Yang

    Full Text Available 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.

  20. 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...

  1. 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

  2. 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.

  3. 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

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

    Science.gov (United States)

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

    2016-01-01

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

  5. 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.

  6. 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

  7. 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.

  8. 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

  9. A high-density SSR genetic map constructed from a F2 population of Gossypium hirsutum and Gossypium darwinii.

    Science.gov (United States)

    Chen, Haodong; Khan, M Kashif Riaz; Zhou, Zhongli; Wang, Xingxing; Cai, Xiaoyan; Ilyas, M Kashif; Wang, Chunying; Wang, Yuhong; Li, Yuqiang; Liu, Fang; Wang, Kunbo

    2015-12-15

    The cultivated allotetraploid species Gossypium hirsutum, accounts for 90% of the world cotton production, has narrow genetic basis that's why its yield, quality or stress resistance breeding is stagnant. It is therefore, essential to explore desirable genes from Gossypium darwinii which has enviable traits such as high fiber fineness, drought tolerance, fusarium and verticillium resistance. We used G. darwinii as primary plant materials in this study not only to enrich the genetic diversity of exiting germplasm but also to better understand its genome structure. An interspecific high density linkage map of allotetraploid cotton was constructed using F2 population (G. hirsutum×G. darwinii). The map was based entirely on genome-wide simple sequence repeat (SSR) markers. A total of 2763 markers were mapped in 26 linkage groups (chromosomes) covering a genome length of 4176.7cM with an average inter-locus distance of 1.5cM. The length of the chromosomes ranged from 84.7 to 238.5cM with an average length of 160.6cM. At subgenome length was 2160.7cM with an average distance of 1.6cM, where as Dt genome length was 2016cM with an average distance of 1.4cM. There were 601 distorted SSR loci. Less number of segregation distortion loci were located in At subgenome than in Dt subgenome. Two post-polyploidization reciprocal translocations of "A2/A3 and A4/A5" were suggested by 44 pairs of duplicate loci. PMID:26275937

  10. 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.

  11. 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.

  12. 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.

  13. 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)

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

    Science.gov (United States)

    Singh, Ram K; Jena, Satya N; Khan, Suhail; Yadav, Sonia; Banarjee, Nandita; Raghuvanshi, Saurabh; Bhardwaj, Vasudha; Dattamajumder, Sanjay K; Kapur, Raman; Solomon, Sushil; Swapna, M; Srivastava, Sangeeta; Tyagi, Akhilesh K

    2013-07-25

    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

  16. 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

  17. 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...

  18. High polymorphism in Est-SSR loci for cellulose synthase and β-amylase of sugarcane varieties (Saccharum spp.) used by the industrial sector for ethanol production.

    Science.gov (United States)

    Augusto, Raphael; Maranho, Rone Charles; Mangolin, Claudete Aparecida; Pires da Silva Machado, Maria de Fátima

    2015-01-01

    High and low polymorphisms in simple sequence repeats of expressed sequence tag (EST-SSR) for specific proteins and enzymes, such as β-amylase, cellulose synthase, xyloglucan endotransglucosylase, fructose 1,6-bisphosphate aldolase, and fructose 1,6-bisphosphatase, were used to illustrate the genetic divergence within and between varieties of sugarcane (Saccharum spp.) and to guide the technological paths to optimize ethanol production from lignocellulose biomass. The varieties RB72454, RB867515, RB92579, and SP813250 on the second stage of cutting, all grown in the state of Paraná (PR), and the varieties RB92579 and SP813250 cultured in the PR state and in Northeastern Brazil, state of Pernambuco (PE), were analyzed using five EST-SSR primers for EstC66, EstC67, EstC68, EstC69, and EstC91 loci. Genetic divergence was evident in the EstC67 and EstC69 loci for β-amylase and cellulose synthase, respectively, among the four sugarcane varieties. An extremely high level of genetic differentiation was also detected in the EstC67 locus from the RB82579 and SP813250 varieties cultured in the PR and PE states. High polymorphism in SSR of the cellulose synthase locus may explain the high variability of substrates used in pretreatment and enzymatic hydrolysis processes, which has been an obstacle to effective industrial adaptations. PMID:25351629

  19. 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

  20. 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

  1. 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.

  2. 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

  3. 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.

  4. 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.

  5. A new resource for the development of SSR markers: Millions of loci from a thousand plant transcriptomes1

    Science.gov (United States)

    Hodel, Richard G. J.; Gitzendanner, Matthew A.; Germain-Aubrey, Charlotte C.; Liu, Xiaoxian; Crowl, Andrew A.; Sun, Miao; Landis, Jacob B.; Segovia-Salcedo, M. Claudia; Douglas, Norman A.; Chen, Shichao; Soltis, Douglas E.; Soltis, Pamela S.

    2016-01-01

    Premise of the study: The One Thousand Plant Transcriptomes Project (1KP, 1000+ assembled plant transcriptomes) provides an enormous resource for developing microsatellite loci across the plant tree of life. We developed loci from these transcriptomes and tested their utility. Methods and Results: Using software packages and custom scripts, we identified microsatellite loci in 1KP transcriptomes. We assessed the potential for cross-amplification and whether loci were biased toward exons, as compared to markers derived from genomic DNA. We characterized over 5.7 million simple sequence repeat (SSR) loci from 1334 plant transcriptomes. Eighteen percent of loci substantially overlapped with open reading frames (ORFs), and electronic PCR revealed that over half the loci would amplify successfully in conspecific taxa. Transcriptomic SSRs were approximately three times more likely to map to translated regions than genomic SSRs. Conclusions: We believe microsatellites still have a place in the genomic age—they remain effective and cost-efficient markers. The loci presented here are a valuable resource for researchers.

  6. 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.

  7. Development and validation of 697 novel polymorphic genomic and EST-SSR markers in the American cranberry (Vaccinium macrocarpon Ait.).

    Science.gov (United States)

    Schlautman, Brandon; Fajardo, Diego; Bougie, Tierney; Wiesman, Eric; Polashock, James; Vorsa, Nicholi; Steffan, Shawn; Zalapa, Juan

    2015-01-01

    The American cranberry, Vaccinium macrocarpon Ait., is an economically important North American fruit crop that is consumed because of its unique flavor and potential health benefits. However, a lack of abundant, genome-wide molecular markers has limited the adoption of modern molecular assisted selection approaches in cranberry breeding programs. To increase the number of available markers in the species, this study identified, tested, and validated microsatellite markers from existing nuclear and transcriptome sequencing data. In total, new primers were designed, synthesized, and tested for 979 SSR loci; 697 of the markers amplified allele patterns consistent with single locus segregation in a diploid organism and were considered polymorphic. Of the 697 polymorphic loci, 507 were selected for additional genetic diversity and segregation analyses in 29 cranberry genotypes. More than 95% of the 507 loci did not display segregation distortion at the p 0.25. This comprehensive collection of developed and validated microsatellite loci represents a substantial addition to the molecular tools available for geneticists, genomicists, and breeders in cranberry and Vaccinium. PMID:25633331

  8. Development and Validation of 697 Novel Polymorphic Genomic and EST-SSR Markers in the American Cranberry (Vaccinium macrocarpon Ait.

    Directory of Open Access Journals (Sweden)

    Brandon Schlautman

    2015-01-01

    Full Text Available The American cranberry, Vaccinium macrocarpon Ait., is an economically important North American fruit crop that is consumed because of its unique flavor and potential health benefits. However, a lack of abundant, genome-wide molecular markers has limited the adoption of modern molecular assisted selection approaches in cranberry breeding programs. To increase the number of available markers in the species, this study identified, tested, and validated microsatellite markers from existing nuclear and transcriptome sequencing data. In total, new primers were designed, synthesized, and tested for 979 SSR loci; 697 of the markers amplified allele patterns consistent with single locus segregation in a diploid organism and were considered polymorphic. Of the 697 polymorphic loci, 507 were selected for additional genetic diversity and segregation analyses in 29 cranberry genotypes. More than 95% of the 507 loci did not display segregation distortion at the p < 0.05 level, and contained moderate to high levels of polymorphism with a polymorphic information content >0.25. This comprehensive collection of developed and validated microsatellite loci represents a substantial addition to the molecular tools available for geneticists, genomicists, and breeders in cranberry and Vaccinium.

  9. De novo characterization of Larimichthys crocea transcriptome for growth-/immune-related gene identification and massive microsatellite (SSR) marker development

    Science.gov (United States)

    Han, Zhaofang; Xiao, Shijun; Liu, Xiande; Liu, Yang; Li, Jiakai; Xie, Yangjie; Wang, Zhi Yong

    2016-04-01

    The large yellow croaker, Larimichthys crocea is an important marine fish in China with a high economic value. In the last decade, the stock conservation and aquaculture industry of this species have been facing severe challenges because of wild population collapse and degeneration of important economic traits. However, genes contributing to growth and immunity in L. crocea have not been thoroughly analyzed, and available molecular markers are still not sufficient for genetic resource management and molecular selection. In this work, we sequenced the transcriptome in L. crocea liver tissue with a Roche 454 sequencing platform and assembled the transcriptome into 93 801 transcripts. Of them, 38 856 transcripts were successfully annotated in nt, nr, Swiss-Prot, InterPro, COG, GO and KEGG databases. Based on the annotation information, 3 165 unigenes related to growth and immunity were identified. Additionally, a total of 6 391 simple sequence repeats (SSRs) were identified from the transcriptome, among which 4 498 SSRs had enough flanking regions to design primers for polymerase chain reactions (PCR). To access the polymorphism of these markers, 30 primer pairs were randomly selected for PCR amplification and validation in 30 individuals, and 12 primer pairs (40.0%) exhibited obvious length polymorphisms. This work applied RNA-Seq to assemble and analyze a live transcriptome in L. crocea. With gene annotation and sequence information, genes related to growth and immunity were identified and massive SSR markers were developed, providing valuable genetic resources for future gene functional analysis and selective breeding of L. crocea.

  10. 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.

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

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    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.

  12. 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

  13. 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)

  14. 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

  15. 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

  16. Construction of an integrated genetic linkage map for the A genome of Brassica napus using SSR markers derived from sequenced BACs in B. rapa

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    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.

  17. 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.

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

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    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.

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

    OpenAIRE

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

    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 for the cross Holiday x Korona. We used the previously published MADCE method to obtain full haplotype information for both of the parental cultivars, facilitating in-depth studies on their genomic o...

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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。

  5. 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

  6. 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.

  7. 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.

  8. Identification of microsatellite markers (SSR linked to a new bacterial blight resistance gene xa33(t in rice cultivar ‘Ba7’

    Directory of Open Access Journals (Sweden)

    Theerayut Toojinda

    2009-05-01

    Full Text Available This study attempts to identify a new source of bacterial blight (BB resistance gene and microsatellite makers (SSR linked to it. A total number of 139 F2 progenies generated from a cross between the resistant donor ‘Ba7’and ‘Pin Kaset’ were developed and used for this study. A Thai Xoo isolate, TXO16, collected from Phitsanulok province, was used to evaluate the resistance reaction in the F2 population. The segregation ratio of resistance (R and susceptibility (S was statistically fitted to 1R:3S model indicating single recessive gene segregation. Twenty F2 individuals consisting of 10 resistant and 10 susceptible plants were chosen for DNA analysis. Sixty-two polymorphic markers covering all rice chromosomes were used to identify the location and linked markers of the resistance gene. Four SSR markers, viz. RM30, RM7243, RM5509 and RM400, located on the long arm of rice chromosome 6, could clearly discriminate between resistant and susceptible phenotypes, and 161 BC2F2:3 individuals carrying BB resistance gene were developed through MAS using these SSR markers. This population was inoculated with TXO16 to validate and confirm the location of the gene and linked markers. The segregation ratio was statistically fitted to 1R:3S model confirming a recessive nature of the gene action in this germplasm. Phenotypic-genotypic association including five additional markers suggested that RM20590 was tightly linked to this resistance gene (R2=59.12 %. The BB phenotype was controlled by a recessive gene with incomplete dominance of susceptible allele providing intermediate resistance to Xoo pathogen in heterozygotes. The location of the gene was in the vicinity of a dominant gene, Xa7, which was previously reported. However, the resistance gene identified here was different from Xa7 because of the different nature of gene action. Consequently, this gene was tentatively designated as xa33(t. The resistance gene from rice cultivar ‘Ba7’ and the

  9. 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

  10. 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.

  11. The results of the IFIN-HH and INR Pitesti cooperation in obtaining radioisotopes at TRIGA -- SSR-14 MW reactor

    International Nuclear Information System (INIS)

    A short history is presented about the radioisotope production at the 2 MW WWRS reactor of the Institut of Atomic Physics Bucharest, beginning with July 1957. In 1967 a catalogue was issued, containing 44 products, radioisotopes and labelled combinations produced by the laboratory for radioisotope preparation (CPR). Later, in 1971 the Technical Report Series nr. 128, issued by IAEA, mentioned 10 Romania technologies for preparation of radioactive products. During 1994-1998 obtaining the 99m Tc ROMTEC generated from fission 99 Mo was one of the main objective of the CPR. After the WWRS reactor shutdown on December 21, 1997 the radioisotope production developed by the TRIGA -- SSR-14 MW reactor, at Pitesti. Two important radioisotopes used in medicine on therapy purposes focused our main attention: 131 I used as pharmaceutical, 1'31 INa solution and gelatine capsules and 192 Ir used as brachytherapy sources. The following radionuclides were produced: 99 Mo and 198 Au used as radiopharmaceuticals, 32 P, 51 Cr for life sciences and 134 Cs, 60 Co, 110m Ag for industrial applications. The designing of new targets to be irradiated as the irradiation conditions were different from those of the WWRS reactor both as geometry and neutron flux values. The chosen solutions were adapted for two different irradiation zones: the reactor core zone, with high flux values of (8-12) x 1013 n/cm2s and maximum imposed external diameter of the irradiation capsule of 12 mm, and the reflector zone with (2-5) x 1013 n/cm2s flux values and external diameter of maximum 25 mm. New types of aluminium (of nuclear purity) capsules, sealed by electron beam welding, were prepared. The primary package was chosen according to the irradiated materials, such as: - small aluminium capsules in the case of powder targets and small quartz vials for iridium needles. By difference of the past WWRS reactor situation, when about 80 g weight targets were prepared in order to obtain 131 I and 99 Mo, in this

  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. 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.

  14. 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 S; Hansen, Henrik H;

    2008-01-01

    Recent studies have demonstrated that amyloid-beta1-42 (Abeta1-42) binds to the nicotinergic alpha7 acetylcholine receptor (alpha7 nAChR) and that the application of Abeta1-42 to cells inhibits the function of the alpha7 nAChR. The in vivo consequences of the pharmacological activation of the alp...... that clinical trials testing alpha7 nAChR agonists should be related to the content of Abeta peptides in the patient's nervous system....... 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...

  15. 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

  16. Ultrastructure and ssrRNA sequencing of Myxidium amazonense n. sp. a myxosporean parasite of Corydoras melini from the Rio Negro river, Amazonas state, Brazil.

    Science.gov (United States)

    Mathews, Patrick D; Silva, Marcia R M; Maia, Antônio A M; Adriano, Edson A

    2015-12-01

    In a survey of myxozoan parasites of ornamental freshwater fish from the Rio Negro river, it was found that seven of 30 (23.3 %) Corydoras melini specimens examined had plasmodia of a new Myxidium species (Myxidium amazonense n. sp.) in the gallbladder. The fish were caught in the Rio Negro river, in the municipality of Santa Isabel do Rio Negro, in the state of Amazonas, Brazil. The plasmodia had a tubular shape, which was organized as a spiral spring with several turns in the gallbladder. The development of the myxospores was asynchronic, with disporic pansporoblasts. Mature myxospores were elongated, with 17.0 ± 0.9 (16.1-17.9) μm in length and 3.7 ± 0.7 (3.0-4.4) μm in width, and lightly arcuate from the valval view, with their bodies tapering slowly until ending in rounded extremities. The valval surface had nine to ten grooves in each valve. The polar capsules, one at either end of the spore, had a length of 5.4 ± 0.5 (4.9-5.9) μm and a width of 3.4 ± 0.6 (2.8-4.0) μm. Ultrastructural analysis showed that the wall of the plasmodia had numerous microvilli-like structures, pinocytotic canals, and cytoplasmic bridges connecting the pansporoblasts to each other and to the ectoplasm zone. Phylogenetic analysis, based on a small subunit ribosomal RNA (ssrRNA), identified the new species as a sister species of Myxidiumceccarelli, the unique South American Myxidium species whose ssrRNA sequence is available in the NCBI database. This study is the first description of Myxidium species in ornamental freshwater fish from Amazon. PMID:26341802

  17. 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.

  18. Sequence composition of BAC clones and SSR markers mapped to Upland cotton chromosomes 11 and 21 targeting resistance to soil-borne pathogens

    Science.gov (United States)

    Wang, Congli; Ulloa, Mauricio; Shi, Xinyi; Yuan, Xiaohui; Saski, Christopher; Yu, John Z.; Roberts, Philip A.

    2015-01-01

    Genetic and physical framework mapping in cotton (Gossypium spp.) were used to discover putative gene sequences involved in resistance to common soil-borne pathogens. Chromosome (Chr) 11 and its homoeologous Chr 21 of Upland cotton (G. hirsutum) are foci for discovery of resistance (R) or pathogen-induced R (PR) genes underlying QTLs involved in response to root-knot nematode (Meloidogyne incognita), reniform nematode (Rotylenchulus reniformis), Fusarium wilt (Fusarium oxysporum f.sp. vasinfectum), Verticillium wilt (Verticillium dahliae), and black root rot (Thielaviopsis basicola). Simple sequence repeat (SSR) markers and bacterial artificial chromosome (BAC) clones from a BAC library developed from the Upland cotton Acala Maxxa were mapped on Chr 11 and Chr 21. DNA sequence through Gene Ontology (GO) of 99 of 256 Chr 11 and 109 of 239 Chr 21 previously mapped SSRs revealed response elements to internal and external stimulus, stress, signaling process, and cell death. The reconciliation between genetic and physical mapping of gene annotations from new DNA sequences of 20 BAC clones revealed 467 (Chr 11) and 285 (Chr 21) G. hirsutum putative coding sequences, plus 146 (Chr 11) and 98 (Chr 21) predicted genes. GO functional profiling of Unigenes uncovered genes involved in different metabolic functions and stress response elements (SRE). Our results revealed that Chrs 11 and 21 harbor resistance gene rich genomic regions. Sequence comparisons with the ancestral diploid D5 (G. raimondii), A2 (G. arboreum) and domesticated tetraploid TM-1 AD1 (G. hirsutum) genomes revealed abundance of transposable elements and confirmed the richness of resistance gene motifs in these chromosomes. The sequence information of SSR markers and BAC clones and the genetic mapping of BAC clones provide enhanced genetic and physical frameworks of resistance gene-rich regions of the cotton genome, thereby aiding discovery of R and PR genes and breeding for resistance to cotton diseases. PMID

  19. 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

  20. Construction of an interspecific genetic map based on InDel and SSR for mapping the QTLs affecting the initiation of flower primordia in pepper (Capsicum spp..

    Directory of Open Access Journals (Sweden)

    Shu Tan

    Full Text Available Re-sequencing permits the mining of genome-wide variations on a large scale and provides excellent resources for the research community. To accelerate the development and application of molecular markers and identify the QTLs affecting the flowering time-related trait in pepper, a total of 1,038 pairs of InDel and 674 SSR primers from different sources were used for genetic mapping using the F2 population (n = 154 derived from a cross between BA3 (C. annuum and YNXML (C. frutescens. Of these, a total of 224 simple PCR-based markers, including 129 InDels and 95 SSRs, were validated and integrated into a map, which was designated as the BY map. The BY map consisted of 13 linkage groups (LGs and spanned a total genetic distance of 1,249.77 cM with an average marker distance of 5.60 cM. Comparative analysis of the genetic and physical map based on the anchored markers showed that the BY map covered nearly the whole pepper genome. Based on the BY map, one major and five minor QTLs affecting the number of leaves on the primary axis (Nle were detected on chromosomes P2, P7, P10 and P11 in 2012. The major QTL on P2 was confirmed based on another subset of the same F2 population (n = 147 in 2014 with selective genotyping of markers from the BY map. With the accomplishment of pepper whole genome sequencing and annotations (release 2.0, 153 candidate genes were predicted to embed in the Nle2.2 region, of which 12 important flowering related genes were obtained. The InDel/SSR-based interspecific genetic map, QTLs and candidate genes obtained by the present study will be useful for the downstream isolation of flowering time-related gene and other genetic applications for pepper.

  1. Comparison of PCR-RFLP Based on Ribosomal Regions and SSR Markers in Genetic Diversity of Pistachio Die-Back Caused by Paecilomyces variotii

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    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.

  2. Synthesis and carbon-11-labeling of p-MeO-SSR180575, a novel indoleacetamide-based candidate for PET imaging of the peripheral benzodiazepine receptor (TSPO 18 kDa)

    International Nuclear Information System (INIS)

    Complete text of publication follows: Objectives: The 3-iso-quinolinecarboxamide [11C]PK11195, despite its low brain uptake and high level of nonspecific binding, is still the most widely used PET-radioligand for the in vivo imaging of the peripheral benzodiazepine receptor (PBR or TSPO 18 kDa). Several new PBR radioligands are currently developed to replace [11C]PK11195, e.g the pyrazolo[1, 5-a]pyrimidine-acetamides [11C]DPA-713 and [18F]DPA-714, the imidazo[1, 2-a]pyridine-acetamides [11C]CLINME and [18F]PBR111 and the N-benzyl-N-(2-phenoxy-aryl)- acetamides [11C]PBR28 and [18F]FEDAA1106. Another attractive newly identified chemical class of structures are the indole-acetamides and notably compounds derived from the lead compound SSR180575. Herein are reported the synthesis and the labelling with the positron-emitter carbon-11 (half-life: 20.38 min) of a novel derivative of SSR180575, bearing a para methoxy function on its phenyl ring. Methods: p-MeO-SSR180575 (1) was synthesized from commercially available 4-chloro-2-nitrotoluene in 10 steps. O-demethylation, performed with a boron tribromide solution in dichloromethane at low temperature, afforded the free phenol derivative 2. Carbon-11 labeling of p-MeO-SSR180575 (1) was performed using a TRACERLab FX-C Pro synthesizer (GEMS) and comprised (1) trapping of [11C]MeOTf at -10 C in acetone (0.3 mL) containing the nor-derivative 2 (O-demethylated, 0.6-0.9 mg) and aq. 3N NaOH (8 μL); (2) heating at 110 C for 2 min; (3) concentration to dryness and taking up the residue in 1.0 mL of the HPLC mobile phase; (4) purification using semi-preparative reversed-phase HPLC (Waters Symmetry C-18 - eluent: CH3CN / H2O / TFA: 50 / 50 / 0.1 (v:v:v) - flow rate: 5 mL/min - detection at 254 nm) and (5) SepPakR Plus C-18-based formulation for i.v. injection. Results: p-MeO-SSR180575 (1) was obtained in 10% overall yield. The tricky and low-yielding step in our approach was the pyridazine ring formation reaction that proceeded

  3. 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

  4. 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

  5. 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。

  6. 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

  7. 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

  8. 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.

  9. Evaluation of a novel real-time PCR test based on the ssrA gene for the identification of group B streptococci in vaginal swabs

    Directory of Open Access Journals (Sweden)

    Barry Thomas

    2009-09-01

    Full Text Available Abstract Background Despite the implementation of prevention guidelines, early-onset group B streptococci (GBS disease remains a cause of neonatal morbidity and mortality worldwide. Strategies to identify women who are at risk of transmitting GBS to their infant and the administration of intrapartum antibiotics have greatly reduced the incidence of neonatal GBS disease. However, there is a requirement for a rapid diagnostic test for GBS that can be carried out in a labour ward setting especially for women whose GBS colonisation status is unknown at the time of delivery. We report the design and evaluation of a real-time PCR test (RiboSEQ GBS test for the identification of GBS in vaginal swabs from pregnant women. Methods The qualitative real-time PCR RiboSEQ GBS test was designed based on the bacterial ssrA gene and incorporates a competitive internal standard control. The analytical sensitivity of the test was established using crude lysate extracted from serial dilutions of overnight GBS culture using the IDI Lysis kit. Specificity studies were performed using DNA prepared from a panel of GBS strains, related streptococci and other species found in the genital tract environment. The RiboSEQ GBS test was evaluated on 159 vaginal swabs from pregnant women and compared with the GeneOhm™ StrepB Assay and culture for the identification of GBS. Results The RiboSEQ GBS test is specific and has an analytical sensitivity of 1-10 cell equivalents. The RiboSEQ GBS test was 96.4% sensitive and 95.8% specific compared to "gold standard" culture for the identification of GBS in vaginal swabs from pregnant women. In this study, the RiboSEQ GBS test performed slightly better than the commercial BD GeneOhm™ StrepB Assay which gave a sensitivity of 94.6% and a specificity of 89.6% compared to culture. Conclusion The RiboSEQ GBS test is a valuable method for the rapid, sensitive and specific detection of GBS in pregnant women. This study also validates the

  10. Evaluation of a novel real-time PCR test based on the ssrA gene for the identification of group B streptococci in vaginal swabs.

    LENUS (Irish Health Repository)

    Wernecke, Martina

    2009-01-01

    BACKGROUND: Despite the implementation of prevention guidelines, early-onset group B streptococci (GBS) disease remains a cause of neonatal morbidity and mortality worldwide. Strategies to identify women who are at risk of transmitting GBS to their infant and the administration of intrapartum antibiotics have greatly reduced the incidence of neonatal GBS disease. However, there is a requirement for a rapid diagnostic test for GBS that can be carried out in a labour ward setting especially for women whose GBS colonisation status is unknown at the time of delivery. We report the design and evaluation of a real-time PCR test (RiboSEQ GBS test) for the identification of GBS in vaginal swabs from pregnant women. METHODS: The qualitative real-time PCR RiboSEQ GBS test was designed based on the bacterial ssrA gene and incorporates a competitive internal standard control. The analytical sensitivity of the test was established using crude lysate extracted from serial dilutions of overnight GBS culture using the IDI Lysis kit. Specificity studies were performed using DNA prepared from a panel of GBS strains, related streptococci and other species found in the genital tract environment. The RiboSEQ GBS test was evaluated on 159 vaginal swabs from pregnant women and compared with the GeneOhm StrepB Assay and culture for the identification of GBS. RESULTS: The RiboSEQ GBS test is specific and has an analytical sensitivity of 1-10 cell equivalents. The RiboSEQ GBS test was 96.4% sensitive and 95.8% specific compared to "gold standard" culture for the identification of GBS in vaginal swabs from pregnant women. In this study, the RiboSEQ GBS test performed slightly better than the commercial BD GeneOhm StrepB Assay which gave a sensitivity of 94.6% and a specificity of 89.6% compared to culture. CONCLUSION: The RiboSEQ GBS test is a valuable method for the rapid, sensitive and specific detection of GBS in pregnant women. This study also validates the ssrA gene as a suitable and

  11. 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

  12. 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

  13. 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

  14. 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.

  15. 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

  16. Background characteristics of the underground laboratory of the Hydrogeology and Engineering-Geology Section of the Academy of Sciences of the Georgian SSR

    International Nuclear Information System (INIS)

    A low-background underground laboratory outfitted with equipment for determining ultra-small amounts of radionuclides in rock and water samples and in the structural materials of nuclear-radiation detectors has been built in the Hydrogeology and Engineering-Geology Section (SGIG) of the Academy of Sciences of the Georgian SSR. A detector based on a NaI(T1) crystal 100 mm in diameter and 100 mm long with a well 33 mm in diameter and 60 mm long was used to measure the background gamma radiation. The crystal was connected to an FEU-100 photomultiplier through a quartz optical waveguide. The body of the scintillation unit was made of grade M1 copper, which was then chrome plated. The energy resolution of the detector is 9.5 ± 0.1% for the 137Cs peak. Primary measurements were made with an AI-1024 analyzer. The measurement time for multiple exposures was 1000 sec outside passive shielding, while the measurement time in the shielding was 7 h of operating time daily for half a year. The results of the measurements were compared with data obtained from a similar detector in one of the low-background facilities of the Baksan Neutrino Observatory (BNO) of the Academy of Sciences of the USSR. The content of natural radionuclides in samples taken from the rocks surrounding the low-background loaboratories BNO and SGIG is shown in a table

  17. 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

  18. 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.

  19. 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.

  20. 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

  1. 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.

  2. 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

  3. 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

  4. 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.

  5. 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 to56th 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.

  6. 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.

  7. Molecular implications from ssr markers for stripe rust (puccinia striiformis F.Sp. tritici) resistance gene in bread wheat line N95175

    International Nuclear Information System (INIS)

    Stripe rust caused by Puccinia striiformis f. sp. tritici is one of the most devastating diseases of wheat in China as well as in Pakistan. In the present studies F2 population was established by crossing N95175 resistant to stripe rust race CYR32 with two susceptible lines Huixianhong and Abbondanza to molecularly tag resistance gene existing in wheat line N95175. The segregation of phenotype was accorded with an expected 3:1 ratio in both combinations studied and fit the model of a single dominant gene controlling stripe rust resistance in N95175. Thirty five SSR primer pairs were screened on the parents and bulks and also on individuals since resistance gene to be located in chromosome 1B. The result indicated that most of resistant plants amplified same band as resistant parent while susceptible plants amplified same as susceptible parents studied and considered that markers co-segregated with resistant loci in N95175. This yellow rust resistance gene was considered to be Yr26 originally thought to be also located in chromosome arm 1BS linked to marker loci Xgwm273 and Xgwm11 with genetic distances ranging from 1.075cM to 2.74cM in both combinations studied. However, the closest loci were observed 2.67cM for Xgwm273 and 1.075cM for Xgwm11 in Huixianhong XN95175 and Abbondanza XN95175 crosses respectively. Hence, it has been concluded that the PCR-based micro satellite markers Xgwm273 and Xgwm11 located in chromosome 1B were shown to be very effective for the detection of Yr26 gene in segregating population and can be applied in future wheat breeding strategies. (author)

  8. 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)

  9. 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

  10. La implementación de la política pública de salud sexual y reproductiva (SSR) en el Eje Cafetero colombiano: el caso del embarazo adolescente

    OpenAIRE

    Sara E. del Castillo Matamoros; André-Noël Roth Deubel; Clara Inés Wartski Patiño; Ricardo Rojas Higuera; Orlando Arnulfo Chacón Barliza

    2008-01-01

    La política nacional de salud sexual y reproductiva (SSR) definida en Colombia en 2002 por el Ministerio de la Protección Social para los años 2002 a 2006 señala los temas prioritarios en este campo: maternidad segura, planificación familiar, salud sexual y reproductiva de las y los adolescentes, cáncer de cuello uterino, infecciones de transmisión sexual y reproductiva, VIH/SIDA, y violencia doméstica y sexual. La investigación que se reporta se ha focalizado en el análisis cuantitativo y cu...

  11. 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.

  12. 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.

  13. 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

  14. 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.

  15. 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

  16. 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

  17. 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.

  18. 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

  19. 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

  20. 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.

  1. 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

  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. 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

  4. 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.

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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。

  11. 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.

  12. On the functional status of the hypophysis-adrenal medulla system of adaptation by Byelorussian children exposed to low-level radiation after Chernobyl disaster

    International Nuclear Information System (INIS)

    The analysis of the status of sympatho-adrenal hypophysis-adrenal medulla systems of adaptation in children living in territories contaminated by radionuclides was carried out. A decrease in the catecholamine level in children's urine and hyperactivity of the hormonal response of adrenal medulla to endogenous ACTH indicated the reduced ability of adaptation and decreased resistance of children's organisms to stress factors of the environment

  13. 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.

  14. 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。

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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.

  20. 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.

  1. 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。

  2. 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

  3. Radioactive contamination in Byelorussia, and its effects

    International Nuclear Information System (INIS)

    This report presents scientific data on radioactive contamination and its effects upon soil, vegetation, cattle and man four years after the Chernobyl accident. Data were collected during a fact- finding mission to the Byelorussian SSR in June 1990. Many research establishments and hospitals were visited including communication with scientists, physicians and lay people. Field measurements were performed and various samples were collected for analysis in Norway. A survey is given of the collected information on magnitue and distribution of the fallout, combined with own measurements. Many areas far from the official exclusion zone around Chernobyl have an unexpected high level of deposition, partly present as particles. The high external dose commitment motivates the evacuation/relocation of relatively large areas. At present the transfer of cesium from soil to agricultural products is relatively low. However, weathering of particles could provide the potential for a mobilization of radionuclides. The possibility of increased uptake in the biosphere is of great concern to the Byelorussian experts. Biological effects on vegetation and cattle have already been observed. Health effects are evaluated, especially in children. It is, however, too early to draw general conclusions on long term consequences. Apparently, an increase in thyroid hyperplasia has been observed, whereas data on thyroid cancer are less clear. There is no definite increase in leukemia occurrence in humans, although an increase of leukemia/leucosis has been observed in cattle. Changes in dietary habits have resulted in iron deficiency anemia. Many reports on vegetative dystonia were presented. 12 refs., 1 fig., 4 tabs

  4. 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...

  5. SSR TRIGA 14 MW thermal hydraulic analysis

    Energy Technology Data Exchange (ETDEWEB)

    Negut, G.; Mladin, M.; Preda, M.; Ciocanescu, M. (Institute for Nuclear Research, Pitesti (Romania))

    1999-12-15

    TRIGA research reactor requires periodic licensing by the Romania's Comitee for Nuclear Activities Control (CNCAN). The documents needed involve reactor safety analysis. In due process we made thermalhydraulic reactor core analysis. There were required reactor natural convection and loss of flow accident documentation to prove that the facility can cope and mitigate the adverse phenomena. There were used validated computer codes for TRIGA reactors. There were analyzed the natural convection tests made during start-up tests and the computed results compared with that from Safety Analysis Report. The Loss of Flow Accident LOFA), determined by the primary coolant pumps with the similar analysis made with other computer codes and compared with the LOFA test made during startup. The results proved to be satisfactory and the reactor operation was approved. (orig.)

  6. 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.

  7. 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

  8. 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

  9. 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

  10. Consequences of the nuclear power plant accident at Chernobyl

    Energy Technology Data Exchange (ETDEWEB)

    Ginzburg, H.M.; Reis, E. (Health Resources and Services Administration, Rockville, MD (USA))

    1991-01-01

    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.

  11. 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

  12. 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

  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. 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

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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

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

    Directory of Open Access Journals (Sweden)

    Márcia de Nazaré Oliveira Ribeiro

    2011-01-01

    Full Text Available The aim of this study was to characterize and estimate the genetic similarity among 93 cassava accessions. The DNAamplification was performed with 14 microsatellite primers. The amplification products were separated by a polyacrylamide gelelectrophoresis, showing a polymorphism formation, through which the accessions were discriminated against. The genetic similarityamong accessions of cassava was estimated by the Dice coefficient. Cluster analysis was carried out using the UPGMA method. Thepolymorphic primers amplified a total of 26 alleles with 2-4 alleles per loci. The genetic similarity ranged from 0.16 to 0.96. Theaverage values for observed and expected heterozygosity were 0.18 and 0.46, respectively. Twenty genetic similarity clusters weredetermined, demonstrating diversity among accessions, suggesting the possibility of heterotic hybrid generation.

  2. 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.

  3. 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)

  4. SSR markers in characterization of sweet corn inbred lines

    OpenAIRE

    Srdić Jelena; Nikolić Ana; Pajić Zorica

    2008-01-01

    Sweet corn differs from field corn in many important traits. So its breeding although includes some standard procedures demand application of techniques that are important for determining special traits, all because of the specificity of its usage. Application of molecular markers becomes almost a necessity for the breeding of sweet corn, especially because this is the type of maize in which still no definitive heterotic patterns have been determined. So getting to know genetic divergence of ...

  5. 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, ...

  6. TRIGA SSR 14 MW data acquisition and monitoring system

    International Nuclear Information System (INIS)

    According to national and international regulations and laws, which refer to: Increase of the nuclear safety level through physical and electrical separation of the operation system vs. safety system, ensuring the reliability of the components and systems with implication in nuclear safety, extending the reactor facility lifetime, increase of the irradiation capability and capacity, quantification of the processes with impact on environment and population, ICN has issued and implemented a program for reactor systems upgrading. The upgrading program allows: - On-line monitoring of operating parameters of the systems; - Real-time data processing; - Data evaluation and taking the proper decision to prevent events occurrence. (authors)

  7. [SSR mapping of stripe rust resistance gene from Ae. tauschii].

    Science.gov (United States)

    Zhang, Hai-Quan; Jia, Ji-Zeng; Yang, Hong; Zhang, Bao-Shi

    2008-04-01

    A dominant wheat stripe rust resistance gene, temporarily designated as YrY201, was identified in an accession Y201 of Aegilops tauschii. By bulk segregation analysis, three microsatellite markers Xgwm273b, Xgwm37 and Wmc14 were found to be linked to YrY201 with genetic distance of 11.5, 5.8 and 10.9 cM , respectively. According to the locations of the linked markers, the resistance gene was located on chromosome 7DL. Based on the chromosomal location and the resistance pattern of the gene, we proposed that YrY201 was a novel stripe rust resistance gene, and could be selected by marker-assisted selection. PMID:18424421

  8. 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.

  9. 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

    2016-01-01

    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 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

  10. PlantFuncSSR: Integrating First and Next Generation Transcriptomics for Mining of SSR-Functional Domains Markers

    Science.gov (United States)

    Sablok, Gaurav; Pérez-Pulido, Antonio J.; Do, Thac; Seong, Tan Y.; Casimiro-Soriguer, Carlos S.; La Porta, Nicola; Ralph, Peter J.; Squartini, Andrea; Muñoz-Merida, Antonio; Harikrishna, Jennifer A.

    2016-01-01

    Analysis of repetitive DNA sequence content and divergence among the repetitive functional classes is a well-accepted approach for estimation of inter- and intra-generic differences in plant genomes. Among these elements, microsatellites, or Simple Sequence Repeats (SSRs), have been widely demonstrated as powerful genetic markers for species and varieties discrimination. We present PlantFuncSSRs platform having more than 364 plant species with more than 2 million functional SSRs. They are provided with detailed annotations for easy functional browsing of SSRs and with information on primer pairs and associated functional domains. PlantFuncSSRs can be leveraged to identify functional-based genic variability among the species of interest, which might be of particular interest in developing functional markers in plants. This comprehensive on-line portal unifies mining of SSRs from first and next generation sequencing datasets, corresponding primer pairs and associated in-depth functional annotation such as gene ontology annotation, gene interactions and its identification from reference protein databases. PlantFuncSSRs is freely accessible at: http://www.bioinfocabd.upo.es/plantssr. PMID:27446111

  11. 基于SSR和RSAP的龙须菜作图群体多态性标记开发与亲本间遗传距离的估计与比较%Development of polymorphic markers and estimation and comparison of genetic distances among parents of mapping population of Gracilariopsis lemaneiformis (Rhodophyta) based on SSR and RSAP analysis

    Institute of Scientific and Technical Information of China (English)

    郭伟华; 隋正红; 胡依依; 李彬彬

    2015-01-01

    遗传连锁图谱的构建是实现分子标记辅助育种与数量性状定位的必要手段,为构建龙须菜(Gracilariopsis lemaneiformis)遗传连锁图谱提供多态性分子标记,本实验共采用400对SSR引物和91对RSAP引物对组合,对龙须菜两个F1代配子体作图群体的亲本进行了多态性标记筛选,并对4个亲本间的遗传距离进行了评估.得到的SSR多态性标记在GL-F3/GL-M8间为15个,GL-F6/GL-M9间为8个;多态性RSAP标记在GL-F3/GL-M8间为88个;GL-F6/GL-M9间为93个.分析了基于SSR、RSAP技术的两对亲本间的遗传距离,SSR结果显示GL-F3/GL-M8间遗传距离为0.071 2,GL-F6/GL-M9间的遗传距离为0.043 6;RSAP结果显示GL-F3/GL-M8间遗传距离为0.228 4,GL-F6/GL-M9间的遗传距离为0.253 7.结果表明,在引物组合平均覆盖的位点和引物组合平均产生的多态性方面,RSAP均远高于SSR,在GL-F3/GL-M8间RSAP分别是SSR的4.48与12.13倍,在GL-F6/GL-M9间RSAP分别是SSR的5.81与25.5倍,RSAP标记更适合应用于龙须菜的遗传距离估计和资源的遗传多样性研究.本研究揭示出作图群体亲本间遗传多样性特征,SSR与RSAP分子标记的开发为龙须菜遗传连锁图谱的构建奠定了基础.

  12. Genetic Diversity and Differentiation of Eelgrass Zostera marina along Yantai and Weihai Coasts by Simple Sequence Repeat (SSR), in Reference to Conservation and Remediation of Seagrass Bed%烟威沿海大叶藻居群遗传多样性研究及对海草场修复的启示

    Institute of Scientific and Technical Information of China (English)

    田萍萍; 李晓捷; 张立楠; 江鑫; 潘金华; 于深辉; 彭捷

    2014-01-01

    Seventeen pairs of Simple Sequence Repeat (SSR) primers selected from 26 primers in a total of 57 individuals of eelgrass Zostera marina were applied to study genetic diversity and genetic differentiation in 3 populations of the eelgrass along Yantai and Weihai coasts (Chudao Peninsula ,RZM ;Danzi Island , DZM ;Gulf of Yudai Hill ,YZM) .The 17 loci were all found to be polymorphism ,and the alleles (Na) had 120 in number ,with an average of 7 alleles per locus .There were average effective number of alleles (Ne) of 2 .30 ,expected heterozygosity (He) of 0 .4743 ,observed heterozygosity (Ho) of 0 .4128 and Nei’ s gene diversity (H) of 0 .4700 ,the maximal genetic diversity in RZM population ,followed by YZM and the minimum in DZM population .The value of Fst (the average of genetic differentiation) was ranged from 0 .0534 to 0 .1226 and Nm (gene flow ) from 1 .7895 to 4 .4344 among the 3 populations ,indicating that the genetic differentiation may be attributed to meadow fragmentation in history .The AMOVA (analysis of molecular variance) showed that there was 89 .51% of genetic variation within populations ,and 10 .49%among populations . The result of UPGMA (unweighted pair-group method with arithmetic means ) dendrogram of the 3 seagrass populations was found to be consistent with results of the genetic distance among them .Overall ,the relatively lower genetic diversity in YZM population implied that the population needed sufficient conservation and remediation to increase the adaptive capacity to environmental changes and evolutionary potentials .The relatively lowest genetic diversity in DZM population was found to be attributed to the unsuitability of local substrate .Otherwise ,RZM population showed relatively higher genetic diversity and differentiation ,w hich is supposed to provide materials for transplantation of seagrass and supplement of seeds to other population in Yantai and Weihai coasts .%采用微卫星引物对烟威沿海3个大叶藻居群进

  13. 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

  14. Experience of operating and decommissioning of the research IRT-M reactor

    International Nuclear Information System (INIS)

    The nuclear reactor of IRT-type was being operated during 25 years at the Institute of Power Engineering Problems /Academy of Sciences of Belarus (the former Institute of Nuclear Power Engineering/Academy of Sciences of Byelorussian SSR). The reactor with the designed power of 2000 kW was put into operation in April 1962 . With the same level of power the reactor was under operation up to 1971 with using rod fuel elements of 10%- enrichment as to U-235 as fuel and a side graphite reflector. As the research works have been developed, it became clear that comparatively small power of the reactor and, as the consequence of this, low level of neutron flux in experimental channels were insufficient for further development of the investigations. Besides, the reactor core with downwards upwards circulation of the coolant has led to vibrations of fuel assemblies, suspended in up going flow of the coolant. Hood-baffle plate of water flow and assembly-holder above the core, which are necessary in the scheme of cooling given, restricted the accessibility to the core for carrying out experiments there. In 1971 the modernization of the reactor was done directed to the increasing of its power up to 4000 kW and improving its design but with preserving the main designed principles peculiar to a basin-type reactor. Experience of Operating and Decommissioning of the IRT-M Reactor are presented. (author)

  15. Present state and prospects of development of methods and facilities of the radioimmunological microanalysis in the USSR

    International Nuclear Information System (INIS)

    In the USSR, more than 300 research establishments have used in vitro radiodiagnostic kits for determination of 89 compounds. The laboratory equipped with standard Soviet radiometric apparatus permits to carry out up to 500 tests within one working day. The work on the problems related to the application of in vitro investigation methods in medical practice is carried out at the leading establishments, such as the Institute of Bioorganic Chemistry of Academy of Sciences of the Byelorussian SSR and CIAMS of the Ministry of Public Health of the USSR. In accordance with the adopted scientific and technical program of research on radioimmunological analysis in the USSR, the work is conducted in the following basic directions: radioimmunological analyses in (a) endocrinology, (b) oncology, (c) cardiology, (d) the evaluation of reproductive function of human beings, and (e) pediatrics. In this report, these five issues are discussed in detail. It is stressed that radioimmunological analysis would contribute to not only all branches of medicine but also public health services. (Namekawa, K.)

  16. ОПТИМИЗАЦИЯ ВЫДЕЛЕНИЯ ДНК ЗАРАЗИХИ (OROBANCHE CUMANA WALLR.) И ВЫЯВЛЕНИЕ ПОЛИМОРФНЫХ RAPDИ SSR-ЛОКУСОВ ДЛЯ ГЕНОТИПИРОВАНИЯ ПАРАЗИТА

    OpenAIRE

    Гучетль, С.; Челюстникова, Т.; Антонова, Т.

    2013-01-01

    Оптимизирована методика выделения ДНК из свежих и высушенных тканей растений заразихи Orobanche cumana Wallr., находящихся на разных стадиях онтогенеза. Наиболее оптимальным было признано выделение ДНК из свежих замороженных соцветий методом Doyle J.J. and J.L. Doyle (1987) с добавлением 1 % поливинилпирролидона в экстракционный буфер. Отобрано три RAPDи 10 SSR-праймеров, инициирующих амплификацию полиморфных фрагментов ДНК. Выявлены стабильно воспроизводящиеся фрагменты амплифицированной ДНК...

  17. Records of the 11. regular session (26 September - 2 October 1967) 116. plenary meeting

    International Nuclear Information System (INIS)

    Statements by the delegates of: Federal Republic of Germany Turkey Byelorussian Soviet Socialist Republic Ukrainian Soviet Socialist Republic Iran Pakistan Bolivia Peru Brazil Czechoslovakia Paragraphs 151 1 belarus ukraine csech republic

  18. Identification of Introgressed Lines by the SSR Markers and Agronomic Traits

    Institute of Scientific and Technical Information of China (English)

    ZHANG Jie; LIU Xiao-jie; SUN Jun-ling; DU Xiong-ming

    2008-01-01

    @@ The wild cotton cultivars and species have abundant genetic polymorphisms,and they possess lots of excellent genes,such as drought resistance,insect resistance,fine and strong fiber,and so on.So cotton breeding experts have widely carried out interspecific hybridization and obtained more than 20 types of advanced generation hybrids with good quality and stable traits between wild resources and upland cotton.

  19. Development of EST-SSR and TRAP markers from transcriptome sequencing data of the mango.

    Science.gov (United States)

    Luo, C; Wu, H X; Yao, Q S; Wang, S B; Xu, W T

    2015-01-01

    Mango is one of the most commercially important fruit crops in tropical and subtropical regions. To increase the efficiency of breeding strategies, two EST-derived marker systems were developed in the present study using information from the mango fruit transcriptome. Using simple sequence repeats, 218 of 230 primer pairs showed stable amplification for 7 mango genotypes with amplicons ranging from 84 to 160 bp; 93 of the primer pairs yielded polymorphic products. The proportion of polymorphic bands ranged from 16.67 to 100%, with a mean of 55.64%. In contrast, 86 primer pairs exhibited good amplification with clear bands for target region amplification polymorphism analysis, and a total of 66 primer combinations were polymorphic. These two novel sets of EST-derived markers will be of use in future studies of genetic diversity, genetic map construction, and marker-assisted selection in mango. PMID:26214472

  20. Identification of expressed resistance gene analogs (RGA and development of RGA-SSR markers in tobacco

    Directory of Open Access Journals (Sweden)

    Yuan Qinghua

    2015-01-01

    Full Text Available Tobacco is an important cash crop and an ideal experimental system for studies of plant-pathogen interactions. Identification of tobacco resistance (R genes and resistance gene analogs (RGAs is propitious to elucidate the underlying resistant mechanisms. In recent years, the public tobacco EST (expressed sequence tags data set, which provides a rich source for identifying expressed RGAs, has enlarged substantially. In this study, 149606 Uni-ESTs were assembled from 412325 tobacco ESTs available in GenBank, scanned with 112 published plant R-genes protein sequences, and 1113 Nicotiana (tobacco RGAs (NtRGAs were identified. The majority of them comprised the common R-genes domains, such as NBS-LRR, LRR-PK, LRR, PK and Mlo, while we were unable to identify 109 RGAs using published domains of R-genes. Upon sequence alignment, 1079 NtRGAs were allocated on 712 loci within the Nicotiana benthamiana genome. A total of 78 simple sequence repeats (SSRs were identified from 72 NtRGAs, and out of 64 newly designed primer pairs, 54 primer pairs generated clear bands upon PCR amplification using tobacco genomic DNA. Only nine primer pairs displayed polymorphism in 24 varieties of tobacco, with 2-4 alleles per locus (2.56 alleles on average, while 41 primer pairs were able to detect polymorphisms in six wild species of genus Nicotiana, with 2-4 alleles per locus (2.61 alleles on average.

  1. SSR-based Genetic Analysis of “Candidatus Liberibacter asiaticus” isolates from Multiple Continents.

    Science.gov (United States)

    Huanglongbing (HLB) is one of the most devastating citrus diseases that threaten citrus production worldwide. The causal agents are believed to be Candidatus Liberibacter spp. Although substantial efforts have been made toward detection of the presumed pathogens, information regarding to the patho...

  2. Interpreting lineaments in the southern slope of the greater Caucasus (within the Azerbaijan SSR)

    Energy Technology Data Exchange (ETDEWEB)

    Budagov, B.A.; Aliyev, A.S.; Mikailov, A.Ya.

    1982-01-01

    Faults and block morphostructures of the southern slope of the greater Caucasus are revealed by interpreting space photographs. A plan of lineaments is compiled. Interpretation signs of the most important faults are described.

  3. Inferred origin of several Native American potatoes from the Pacific Northwest using SSR markers

    Science.gov (United States)

    Certain Native Americans from the Pacific Northwest and Alaska of the USA have grown potatoes in their gardens for many generations. However, the origin of these potatoes was unclear. In this study, the origin of several potatoes collected from Native gardens, including two potatoes, “Ozette” (fro...

  4. Clonal diversity and genetic differentiation revealed by SSR markers in wild Vaccinium macrocarpon and Vaccinium oxycoccos

    Science.gov (United States)

    American cranberry (Vaccinium macrocarpon Ait.) is a perennial, woody plant species, native to North American bogs and wetlands. Cranberries represent one of the few agriculturally important native plants in which wild gene pools are still readily available within the undeveloped wetlands the northe...

  5. Identification and functional annotation of expressed sequencetags based SSR markers of Stevia rebaudiana

    OpenAIRE

    Kaur, Rajinder; Sharma, Neha; RAINA, RAVINDER

    2015-01-01

    Stevia rebaudiana Bertoni, a perennial herb belonging to the family Asteraceae, is a tropical as well as subtropical plant of medicinal importance. Despite being an important medicinal plant and in fact proving a boon to diabetics, it has remained almost ignored by molecular biologists. A systematic molecular evaluation of stevia germplasm and molecular breeding work are sparsely reported mainly due to the limited specific molecular markers available. Expressed sequence tags (ESTs) are a valu...

  6. Genetic Diversity and Linkage Disequilibrium in Chinese Bread Wheat (Triticum aestivum L.) Revealed by SSR Markers

    OpenAIRE

    Hao, Chenyang; Wang, Lanfen; Ge, Hongmei; Dong, Yuchen; Zhang, Xueyong

    2011-01-01

    Two hundred and fifty bread wheat lines, mainly Chinese mini core accessions, were assayed for polymorphism and linkage disequilibrium (LD) based on 512 whole-genome microsatellite loci representing a mean marker density of 5.1 cM. A total of 6,724 alleles ranging from 1 to 49 per locus were identified in all collections. The mean PIC value was 0.650, ranging from 0 to 0.965. Population structure and principal coordinate analysis revealed that landraces and modern varieties were two relativel...

  7. Full conversion of materials and nuclear fuel research and test - TRIGA SSR 14 MW

    International Nuclear Information System (INIS)

    This article presents the HEU (high enrichment uranium) to LEU (low enrichment uranium) conversion of the TRIGA reactor at the Institute for Nuclear Research (Pitesti, Romania). This process began in 1992 when the first 4 LEU (23% U235 enrichment) fuel bundles integrated the reactor core in replacement of 4 HEU fuel bundles. By March 2004, the mixed reactor core had 18 LEU and 17 HEU fuel bundles by HEU-LEU replacement through successive steps of fueling. In 2006 the conversion process was completed and now we have a standard reactor core of 29 LEU fuel bundles

  8. Use of EST-SSR loci flanking regions for phylogenetic analysis of genus Arachis

    Science.gov (United States)

    All wild peanut collections in the genus Arachis were assigned to nine taxonomy sections on the bases of cross-compatibility and morphologic character clustering. These nine sections consist of 80 species from the most ancient to the most advanced, providing a diverse genetic resource for phylogenet...

  9. Kontakte zwischen ČSSR- und DDR- Bürgern 1968-1989

    Czech Academy of Sciences Publication Activity Database

    Vilímek, Tomáš

    2007-01-01

    Roč. 4, č. 2 (2007), s. 285-300. ISSN 1612-9008 R&D Projects: GA AV ČR KJB800630703 Institutional research plan: CEZ:AV0Z80630520 Keywords : opposition - DDR - Czechoslovakia Subject RIV: AB - History

  10. Reliability data collection and processing for Romanian TRIGA-SSR 14MW

    International Nuclear Information System (INIS)

    The use of site specific reliability data for PSA use is highly recommended because it enhances the accurateness and credibility of the risk analysis. In order to obtain the database statistic items for the reactor components it is necessary to: Develop a brief reactor operation history; Identify the components which can be monitored and their specific failure modes: Clearly define the component boundary; Select and run through the sources of recorded information related to failures and operational details; Process the data; The paper presents how these steps are completed for obtaining failure rates and confidence intervals limits (95% and 5%) for a series of Romanian TRIGA components such as: pumps, motors, valves, compressors, fans, etc. The identification of component boundary and failure rates modes is performed according to the IAEA guides for research reactors database. (author)

  11. A SSR Marker for Leaf Rust Resistance Gene Lr19 in Wheat

    Institute of Scientific and Technical Information of China (English)

    LI Xing; YANG Wen-xiang; LI Ya-ning; LIU Da-qun; YAN Hong-fei; MENG Qing-fang; ZHANG Ting

    2006-01-01

    Microsatellite was carried out in Thatcher, six near-isogenic lines and F2 progeny of TcLr19×Thatcher to develop molecular markers for leaf rust resistance gene Lr19. Thirteen primer pairs were screened, of which one primer pair Xgwm44 displayed polymorphsim in the population of TcLr19, Thatcher, and their F2 generations. One marker closed linked to Lr19 resistance trait was obtained, and was named Xgwm44139 bp with the genetic distance 0.9 cM. The research shows that Lr19 has more potential in marker-assisted breeding programs in wheat and provides a step stone for mapping genetic map, physical map and the eventual cloning.

  12. QTL Analysis of Agronomic Traits in Rice Using SSR and AFLP Markers

    Directory of Open Access Journals (Sweden)

    Dina KEBRIYAEE

    2012-05-01

    Full Text Available A quantitative trait is a measurable trait that depends on the cumulative action of many genes and their interaction with the environment that can vary among individuals over a given range to produce a continuous distribution of phenotypes. The identification and mapping of QTLs for such traits has great significance for rice breeders. In this study, a genetic analysis of quantitative trait loci (QTLs affecting 11 agronomical traits was performed using an F2 population of a cross between two Oryza sativa ssp. indica type cultivars, �Domsiah� and �IR44�, comprising 160 plants. A total of 22 QTLs were detected for 11 traits, including two for plant height (PH, one for full grain per panicle (FG, two for flag leaf width (FLW, three for 1000-grain weight (TGW, two for number of panicles per plant (NP, three for flag leaf length (FL, two for peduncle length (Pd, one for panicle exertion (PE, two for grain yield (GY, two for basal panicle length (BPL and two for awn length (AL.

  13. Chloroplast SSR polymorphisms in the Compositae and the mode of organellar inheritance in Helianthus annuus.

    Science.gov (United States)

    Wills, David M; Hester, Melissa L; Liu, Aizhong; Burke, John M

    2005-03-01

    Because organellar genomes are often uniparentally inherited, chloroplast (cp) and mitochondrial (mt) DNA polymorphisms have become the markers of choice for investigating evolutionary issues such as sex-biased dispersal and the directionality of introgression. To the extent that organellar inheritance is strictly maternal, it has also been suggested that the insertion of transgenes into either the chloroplast or mitochondrial genomes would reduce the likelihood of gene escape via pollen flow from crop fields into wild plant populations. In this paper we describe the adaptation of chloroplast simple sequence repeats (cpSSRs) for use in the Compositae. This work resulted in the identification of 12 loci that are variable across the family, seven of which were further shown to be highly polymorphic within sunflower (Helianthus annuus). We then used these markers, along with a novel mtDNA restriction fragment length polymorphism (RFLP), to investigate the mode of organellar inheritance in a series of experimental crosses designed to mimic the initial stages of crop-wild hybridization in sunflower. Although we cannot rule out the possibility of extremely rare paternal transmission, our results provide the best evidence to date of strict maternal organellar inheritance in sunflower, suggesting that organellar gene containment may be a viable strategy in sunflower. Moreover, the portability of these markers suggests that they will provide a ready source of cpDNA polymorphisms for use in evolutionary studies across the Compositae. PMID:15690173

  14. Development and Characterization of EST-SSR Markers in the Chinese Medicinal Plant Callerya speciosa (Fabaceae

    Directory of Open Access Journals (Sweden)

    Li Li

    2013-06-01

    Full Text Available Premise of the study: The first microsatellite primers were developed for Callerya speciosa, an important traditional medicinal plant with island-mainland distributions in China, to further investigate its genetic variability and population structure. Methods and Results: The microsatellite-containing sequences were selected from a cDNA library of C. speciosa. In total, 58 primer pairs were designed, and 25 of the corresponding loci showed clear amplification. Polymorphisms were assessed in two different natural populations. The mean number of alleles per locus ranged from two to nine. Observed and expected heterozygosity per loci ranged from 0.067 to 0.938 and 0.064 to 0.836, respectively. One out of 25 loci showed departure from Hardy–Weinberg equilibrium expectations in both populations, and three pairs of loci showed significant linkage disequilibrium after Bonferroni correction. Conclusions: These microsatellite markers will be useful tools for genetic and conservation studies and to understand the evolutionary processes in Callerya species.

  15. Activities of national and local government bodies of the Ukrainian SSR

    International Nuclear Information System (INIS)

    Paper deals with the activity of the Ukrainian Republican and local authorities linked with the elimination of the Chernobyl accident consequences. Attention is focused on the radiation monitoring, on the evacuation and migration of people, on the agriculture and local economy activities in the contaminated areas, on efforts to decontaminate buildings and installations, on health protection of people. The main problems stipulated in the complex program on the elimination of the Chernobyl NPP accident consequences in the Ukraine are discussed. 3 figs.; 2 tabs

  16. Genetic variation of Garra rufa fish in Kermanshah and Bushehr provinces, Iran, using SSR microsatellite markers

    Directory of Open Access Journals (Sweden)

    Ali Shabani

    2013-09-01

    Full Text Available Six highly variable microsatellite loci were used to investigate the genetic diversity and population structure of the Garra rufa in Kermanshah and Bushehr provinces, Iran. All of the 6 microsatellite loci screened in this study showed polymorphism. A total of 90 individual fish from 3 populations were genotyped and 60 alleles were observed in all loci. The number of alleles per locus ranged from 6 to14. The average allelic number of these polymorphic markers was 10. The averages of observed (Ho and expected heterozygosity (He was 0.529 and 0.826, respectively. The genetic distance values ranged between 0.235-0.570. The UPGMA dendrogram based on genetic distance resulted in three clusters: Gamasiab population alone was classified as one and the other two populations as the second cluster. This study revealed a fairly high level of genetic variation in the microsatellite loci within the three populations, and identified distinct population groups of Garra rufa. This study gains significance for the analysis of the populations’ genetic diversity as well as the management of this important fish resource.

  17. Environmental radioactivity in the SSR following the Chernobyl nuclear power plant accident

    International Nuclear Information System (INIS)

    Radioactivity monitoring in the air and in foods in the period between May 1986 till the end of 1987 is described. Monitored were especially milk, this both cow and sheep milk, meat, vegetables, fruit, cereals and potatoes. The radiation situation did not require any special measures concerning nutrition or stays in the open. However, milk containing more than 1,000 Bq/l 131I was excluded from the sale, iodine profylaxis was introduced in staff of mountain sheep farms and milking cows were kept on winter feed. Estimates were performed of the population dose and the reliability of delayed effects occurrences in the population of the Slovak republic. (M.D.). figs., 3 tabs., 5 refs

  18. SSR-based identification of genetic groups within European populations of Tuber aestivum Vittad.

    Science.gov (United States)

    Molinier, Virginie; Murat, Claude; Peter, Martina; Gollotte, Armelle; De la Varga, Herminia; Meier, Barbara; Egli, Simon; Belfiori, Beatrice; Paolocci, Francesco; Wipf, Daniel

    2016-02-01

    Tuber species are ectomycorrhizal ascomycetes establishing relationships with different host trees and forming hypogeous fruiting bodies known as truffles. Among Tuber species, Tuber aestivum Vittad. has a wide distributional range being found naturally all over Europe. Here, we performed large-scale population genetic analyses in T. aestivum to (i) investigate its genetic diversity at the European scale, (ii) characterize its genetic structure and test for the presence of ecotypes and (iii) shed light into its demographic history. To reach these goals, 230 ascocarps from different populations were genotyped using 15 polymorphic simple sequence repeat markers. We identified 181 multilocus genotypes and four genetic groups which did not show a clear geographical separation; although, one of them was present exclusively in Southeast France, Italy and Spain. Fixation index values between pairs of genetic groups were generally high and ranged from 0.29 to 0.45. A significant deficit of heterozygosity indicated a population expansion instead of a recent population bottleneck, suggesting that T. aestivum is not endangered in Europe, not even in Mediterranean regions. Our study based on a large-scale population genetic analysis suggests that genetically distinct populations and likely ecotypes within T. aestivum are present. In turn, this study paves the way to future investigations aimed at addressing the biological and/or ecological factors that have concurred in shaping the population genetic structure of this species. Present results should also have implications for the truffle market since defining genetic markers are now possible at least for some specific T. aestivum genetic groups. PMID:26070448

  19. Molecular Characterization and Genetic Structure in Avocado (Persea americana Mill.) Using Simple Sequence Repeat (SSR) Markers

    Science.gov (United States)

    Avocado (Persea americana Mill.) is an economically important tropical fruit native to Mesoamerica. It belongs to the Lauraceae family and is subdivided in three horticultural races (Guatemalan, Mexican, and West Indian) based primarily on ecological adaptation, botanical and physiological traits. T...

  20. Molecular characterization of the Andean blackberry, Rubus glaucus, using SSR markers.

    Science.gov (United States)

    Marulanda, M; López, A M; Uribe, M

    2012-01-01

    The species Rubus glaucus, also known as the Andean or "Castilla" blackberry, is one of nine edible species of this genus that grow naturally in Central and South America. In Colombia, this species is the most important of all Rubus species for agricultural and commercial purposes. We used 20 SSRs developed for other Rubus species to characterize 44 Colombian R. glaucus genotypes, collected from eight different departments, and to look for molecular differences between thornless and thorny cultivated blackberries. Eighty-two bands were obtained from 28 loci. The genotypes were classified into eight populations, corresponding to collection sites. The mean number of polymorphic alleles per locus in all populations and genotypes ranged from 1.857 to 2.393. Samples collected from Valle del Cauca, Quindío, Caldas, and Risaralda departments had the highest heterozygosity values. The finding of exclusive bands from R. glaucus genotypes from Valle del Cauca, Quindío, and Caldas demonstrates genetic and molecular differentiation between thorny and thornless Andean blackberries. PMID:22370934

  1. Full conversion of materials and nuclear fuel research and test - TRIGA SSR 14 MW

    Energy Technology Data Exchange (ETDEWEB)

    Ciocanescu, M.; Preda, M.; Iorgulis, C. [Triga Reactor, Instittute For Nuclear Research Pitesti (Romania)

    2007-07-01

    This article presents the HEU (high enrichment uranium) to LEU (low enrichment uranium) conversion of the TRIGA reactor at the Institute for Nuclear Research (Pitesti, Romania). This process began in 1992 when the first 4 LEU (23% U235 enrichment) fuel bundles integrated the reactor core in replacement of 4 HEU fuel bundles. By March 2004, the mixed reactor core had 18 LEU and 17 HEU fuel bundles by HEU-LEU replacement through successive steps of fueling. In 2006 the conversion process was completed and now we have a standard reactor core of 29 LEU fuel bundles.

  2. Full conversion of materials and nuclear fuel in TRIGA SSR 14 MW research and test reactor

    International Nuclear Information System (INIS)

    During 1952-2005 General Atomics built and commissioned worldwide 62 TRIGA research reactors. Almost all reactors built by General Atomics use Low Enriched Uranium (19,9%). One exception was the TRIGA reactor from ICN Pitesti. The transition from HEU to LEU utilization, called a core conversion, is supported by Department of Energy - USA and Member States in the project 'Reduced Enrichment in Research and Testing Reactors (RERTR)' and by Member States and IAEA through Technical Cooperation programmes. The activities that are related to core conversion are managed and reviewed as refueling operations. This type of activities was performed at least six times from reactor commissioning stage until now. The implied personnel in this type of activities is licensed by CNCAN, the Romanian Regulatory Body and periodically trained. (authors)

  3. Cross-amplification and multiplexing of SSR markers for Alnus glutinosa and A. incana

    Czech Academy of Sciences Publication Activity Database

    Drašnarová, Alena; Krak, Karol; Vít, Petr; Doudová, Jana; Douda, Jan; Hadincová, Věroslava; Zákravský, Petr; Mandák, Bohumil

    2014-01-01

    Roč. 10, č. 4 (2014), s. 865-873. ISSN 1614-2942 R&D Projects: GA ČR(CZ) GAP504/11/0402 Institutional support: RVO:67985939 Keywords : alder * Betulaceae * microcatelites Subject RIV: EF - Botanics Impact factor: 2.451, year: 2014

  4. Germination characteristics and molecular characterizations of some wheat varieties in Sulaimanyah by SSR marker

    OpenAIRE

    TAHIR, Nawroz Abdul-razzak

    2010-01-01

    The genetic diversity of 11 bread and durum wheat varieties was estimated using germination characteristic and molecular analysis. The phenotypic data showed highly significant differences between cultivars for germination speed, germination percentage, seedling length, fresh weight, and dry weight. Simple sequence repeats (SSRs) were used to examine the genomic diversity of wheat (Triticum aestivum L. and Triticum durum L.). Eleven wheat varieties of diverse origins were analyzed with 12 sel...

  5. Construction of an EST-SSR-based interspecific transcriptome linkage map of fibre development in cotton

    Indian Academy of Sciences (India)

    Chuanxiang Liu; Daojun Yuan; Zhongxu Lin

    2014-12-01

    Quantitative trait locus (QTL) mapping is an important method in marker-assisted selection breeding. Many studies on the QTLs focus on cotton fibre yield and quality; however, most are conducted at the DNA level, which may reveal null QTLs. Hence, QTL mapping based on transcriptome maps at the cDNA level is often more reliable. In this study, an interspecific transcriptome map of allotetraploid cotton was developed based on an F2 population (Emian22 × 3-79) by amplifying cDNA using EST-SSRs. The map was constructed using cDNA obtained from developing fibres at five days post anthesis (DPA). A total of 1270 EST-SSRs were screened for polymorphisms between the mapping parents. The resulting transcriptome linkage map contained 242 markers that were distributed in 32 linkage groups (26 chromosomes). The full length of this map is 1938.72 cM with a mean marker distance of 8.01 cM. The functions of some ESTs have been annotated by exploring homologous sequences. Some markers were related to the differentiation and elongation of cotton fibre, while most were related to the basic metabolism. This study demonstrates that constructing a transcriptome linkage map by amplifying cDNAs using EST-SSRs is a simple and practical method as well as a powerful tool to map eQTLs for fibre quality and other traits in cotton.

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

    OpenAIRE

    Yaling Liu; Pengfei Zhang; Meiling Song; Junling Hou; Mei Qing; Wenquan Wang; Chunsheng Liu

    2015-01-01

    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 uni...

  7. Genetic differentiation of watermelon landrace types in Mali revealed by microsatellite (SSR) markers

    DEFF Research Database (Denmark)

    Nantoume, Aminata Dolo; Andersen, Sven Bode; Jensen, Brita Dahl

    2013-01-01

    This study describes the genetic differentiation of a collection of 134 watermelon landrace accessions from Mali, representing red fleshed dessert and white fleshed seed and cooking type watermelons from five regions, plus three commercial dessert type cultivars with red flesh. The material was...... accessions into use groups (dessert, cooking, seed processing) explained 25 % of the variation. When categorising the accessions further into 10 landrace types, differentiated on the basis of use groups, local accession name, flesh colour and seed phenotype, these landrace types explained 26 % of the......-groups. One group included again the red fleshed dessert types with local and commercial origin, while the remaining seven genetic sub-groups comprised the white fleshed landrace types used for seed processing and cooking, as well as white fleshed types of one dessert type. Some of the seed and cooking types...

  8. Diversity of garlic (Allium sativum L.) using SSR, EST and AFLP markers

    Science.gov (United States)

    Germplasm from the center of origin/diversity is important for the breeding and fingerprinting crop plants. In this study we utilized both dominant and co-dominant markers for the characterization of garlic samples from diverse geographic origins to assess the relative utility of these markers to id...

  9. An EST-SSR based linkage map for Persea americana Mill. (avocado)

    Science.gov (United States)

    Recent enhancement of the pool of known molecular markers for avocado has allowed the construction of the first moderate density genetic map for this species. Over 300 microsatellite markers have been characterized and 163 of these were used to construct a map from the cross of two Florida cultivar...

  10. Assessment of genetic diversity among rice (Oryza sativa L. landrace populations under traditional production using microsatellite (SSR markers

    Directory of Open Access Journals (Sweden)

    Santosh Kumar, I.S.Bisht and K.V.Bhat

    2010-07-01

    Full Text Available Despite the surge of support for on farm conservation of plant genetic resources on global scale, no agreed set of scientificprinciples yet exists for its effective implementation. Farming communities in traditional agroecosystem have been playingan important role in conserving agricultural diversity and assessment at genetic level is a prerequisite for understandingdetrimental evolutionary patterns and devising suitable strategies for their conservation and sustainable use. The presentinvestigation was undertaken with the objectives of understanding farmer management of population structure of ricelandraces in traditional farming systems as well as inter- and intra-population molecular diversity at microsatellite loci. Themicrosatellites (STMS markers were used for analysing selected eleven rice landrace populations from various parts ofUttarakhand state in north-western Himalayas. A total number of 98 alleles were recorded, of which 91 were common andseven were rare. The mean number of alleles per locus was 6.13 and for different groups of rice landrace populations, namelyeight populations of common landrace and three populations of rare landraces were 4.96 and 4.37, respectively. The studyalso compared genebank-conserved (ex situ and on-farm-managed (in situ landrace populations of same named commonlandraces Jaulia and Thapachini, and revealed greater number of alleles per locus for on-farm-managed populations ascompared to the populations under static management. Significant number of alleles specific to populations under dynamicmanagement could also be recorded. Changes in yield parameters also seemed affected under dynamic farmer managementfor same rice landrace populations. Further, the rare landraces included in the present study were more diverse than thecommon landrace populations. The rare landraces were distinct entities largely representing locally common alleles. Geneticdifferentiation results from the joint effects of various evolutionary forces, which in turn must operate within the historicaland biological context of the crop. The present investigation about the population genetic structure is therefore helpful inmonitoring diversity loss over time and space, and also for devising a rational conservation plan, particularly on-farmmanagement of farmer landraces under traditional production.

  11. Bayesian analysis of the genetic structure of a Brazilian popcorn germplasm using data from simple sequence repeats (SSR)

    OpenAIRE

    Javier Saavedra; Tereza Aparecida Silva; Freddy Mora; Carlos Alberto Scapim

    2013-01-01

    Several studies have confirmed that popcorn (Zea mays L. var. everta) has a narrow genetic basis, which affects the quality of breeding programs. In this study, we present a genetic characterization of 420 individuals representing 28 popcorn populations from Brazilian germplasm banks. All individuals were genotyped using 11 microsatellite markers from the Maize Genetics and Genomics Database. A Bayesian clustering approach via Monte Carlo Markov chains was performed to examine the genetic dif...

  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

    ...) published by the American Psychiatric Association.\\3\\ See Question 4. In general, the DSM defines Substance... or distress.\\4\\ \\3\\ American Psychiatric Association (APA), Diagnostic and Statistical Manual of..., psychologist, or other appropriate acceptable medical source based on examination of the claimant....

  13. Assessing genetic diversity in java fine-flavor cocoa (theobroma cacao l.) Germplasm by simple sequence repeat (ssr) markers

    Science.gov (United States)

    Indonesia is the 3rd largest cocoa producing countries in the world, with an annual cacao bean production of 572,000 tons. The currently cultivated cacao varieties in Indonesia were inter-hybrids of various clones introduced from the Americas since the 16th century. Among them, “Java cocoa” is a wel...

  14. Interdependent morphostructural analysis of the Dnieper-Donets Basin in relation to its oil and gas content. [Ukrainian SSR

    Energy Technology Data Exchange (ETDEWEB)

    Volkov, N.G.

    1979-01-01

    A new theoretical principle of morphostructural analysis is advanced, the principle of interdependent analysis of the relief, geological structure and heat flux of the depths of the earth as the main energy source of tectonic (neotectonic) movement of the earth's crust. It was used for the first time under conditions of the Dnieper-Donets intraplatform basin and its local morphostructures. Its use made it possible to reveal regional and local causal links between the relief of the modern surface, geological structure, geothermal regime and neotectonic movements, as well as the conditions for formation and laws governing arrangement of oil and gas fields. Grouping of the morphostructural studies with direct geothermal method for prospecting for oil and gas fields made it possible to solve not only structural tasks, but also to advance a hypothesis regarding the presence in the structural traps of oil and gas fields. This promotes further development of the relief-structure-field system.

  15. Proceedings of the Institute of Geology and Geochemistry of Fuel Minerals of the Ukrainian SSR Academy of Sciences, No. 16

    Energy Technology Data Exchange (ETDEWEB)

    Kityk, V.I.

    1981-01-01

    Data are presented on the genesis of transverse dislocations in the central Black Sea region and the role of mud volcanes in the formation of the structure and relief of the Kerchenskiy Peninsula, biostratigraphy of Cretaceous and Paleogene deposits on the southern slope of the Ukrainian Carpathians, nature of arrangement of the buried reefs and bioherms in the lower Permian deposits of the Dnieper-Donets Basin, nature and mechanism of the formation of folded deformations in the sedimentary mass of the central Donbass, substance composition and thickness of the salt deposits of the Transcarpathian trough. Questions are covered of the development of the science on the origin of fossil fuels, evaluation of the coals in the L'vov-Volynskiy basin according to the international classification, geochemistry of carbon containing fluids in magmatic hydrothermal-metasomatic processes, geochemical laws governing metamorphism of organic matter of coal formations in the Ukraine. A number of articles cover the hydrogeology and geophysics of oil-gas and coal geology of the Ukraine and definite scientific-applied developments.

  16. Effect of Acute Gamma Irradiation on Curcuma alismatifolia Varieties and Detection of DNA Polymorphism through SSR Marker

    OpenAIRE

    Sima Taheri; Thohirah Lee Abdullah; Zaiton Ahmad; Nur Ashikin Psyquay Abdullah

    2014-01-01

    The effects of eight different doses (0, 10, 20, 25, 35, 40, 60, and 100 Gy) of acute gamma irradiation on 44 (three varieties of Curcuma alismatifolia: Chiang Mai Red, Sweet Pink, Kimono Pink, and one Curcuma hybrid (Doi Tung 554) individual plants were investigated. Radiation sensitivity tests revealed that the LD50 values of the varieties were achieved at 21 Gy for Chiang Mai Red, 23 Gy for Sweet Pink, 25 Gy for Kimono Pink, and 28 Gy for Doi Tung 554. From the analysis of variance (ANOVA)...

  17. Cross-Species, Amplifiable EST-SSR Markers for Amentotaxus Species Obtained by Next-Generation Sequencing

    Directory of Open Access Journals (Sweden)

    Chiuan-Yu Li

    2016-01-01

    Full Text Available Amentotaxus, a genus of Taxaceae, is an ancient lineage with six relic and endangered species. Four Amentotaxus species, namely A. argotaenia, A. formosana, A. yunnanensis, and A. poilanei, are considered a species complex because of their morphological similarities. Small populations of these species are allopatrically distributed in Asian forests. However, only a few codominant markers have been developed and applied to study population genetic structure of these endangered species. In this study, we developed and characterized polymorphic expressed sequence tag-simple sequence repeats (EST-SSRs from the transcriptome of A. formosana. We identified 4955 putative EST-SSRs from 68,281 unigenes as potential molecular markers. Twenty-six EST-SSRs were selected for estimating polymorphism and transferability among Amentotaxus species, of which 23 EST-SSRs were polymorphic within Amentotaxus species. Among these, the number of alleles ranged from 1–4, the polymorphism information content ranged from 0.000–0.692, and the observed and expected heterozygosity were 0.000–1.000 and 0.080–0.740, respectively. Population genetic structure analyses confirmed that A. argotaenia and A. formosana were separate species and A. yunnanensis and A. poilanei were the same species. These novel EST-SSRs can facilitate further population genetic structure research of Amentotaxus species.

  18. Development of EST-SSR markers in Barringtonia racemosa (Lecythidaceae) and cross-amplification in related species 1

    OpenAIRE

    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 ra...

  19. 78 FR 6168 - Social Security Ruling, SSR 13-1p; Titles II and XVI: Agency Processes for Addressing Allegations...

    Science.gov (United States)

    2013-01-29

    ... Misconduct by Administrative Law Judges, 57 FR 49186 (October 30, 1992). DATES: Effective Date: January 29..., or discrimination undermine public trust and confidence in our administrative process. Our ALJs perform an essential role in ensuring that our administrative process is fair to claimants by...

  20. Development of a high-density cranberry SSR linkage map for comparative genetic analysis and trait detection

    Science.gov (United States)

    Since its domestication 200 years ago, breeding of the American Cranberry (Vaccinium macrocarpon) has relied on phenotypic selection because applicable resources for molecular improvement strategies such as marker-assisted selection (MAS) remain limited. To enable MAS in cranberry, the first high de...

  1. Development and Validation of 697 Novel Polymorphic Genomic and EST-SSR Markers in the American Cranberry (Vaccinium macrocarpon Ait.)

    OpenAIRE

    Brandon Schlautman; Diego Fajardo; Tierney Bougie; Eric Wiesman; James Polashock; Nicholi Vorsa; Shawn Steffan; Juan Zalapa

    2015-01-01

    The American cranberry, Vaccinium macrocarpon Ait., is an economically important North American fruit crop that is consumed because of its unique flavor and potential health benefits. However, a lack of abundant, genome-wide molecular markers has limited the adoption of modern molecular assisted selection approaches in cranberry breeding programs. To increase the number of available markers in the species, this study identified, tested, and validated microsatellite markers from existing nucle...

  2. An analysis of LEU fuel behavior as compared to HEU fuel in the 14 MW TRIGA SSR reactor

    International Nuclear Information System (INIS)

    The paper presents an analysis of the behavior and properties of the fuel loading the 14 MW TRIGA research reactor. Comparison are made between the original highly enriched fuel and the slightly enriched fuel which is loading the reactor at present. Both the highly enriched and the slightly enriched fuels have the same physical and thermal properties but different nuclear properties. Thermal hydraulic analysis of the transient regime behavior of reactivity insertion type was effected, evidencing the different behavior of the fuels with different enrichments. (authors)

  3. De novo assembly and characterization of the transcriptome, and development of SSR markers in wax gourd (Benicasa hispida.

    Directory of Open Access Journals (Sweden)

    Biao Jiang

    Full Text Available BACKGROUND: Wax gourd is a widely used vegetable of Cucuribtaceae, and also has important medicinal and health values. However, the genomic resources of wax gourd were scarcity, and only a few nucleotide sequences could be obtained in public databases. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we examined transcriptome in wax gourd. More than 44 million of high quality reads were generated from five different tissues of wax gourd using Illumina paired-end sequencing technology. Approximately 4 Gbp data were generated, and de novo assembled into 65,059 unigenes, with an N50 of 1,132 bp. Based on sequence similarity search with known protein database, 36,070 (55.4% showed significant similarity to known proteins in Nr database, and 24,969 (38.4% had BLAST hits in Swiss-Prot database. Among the annotated unigenes, 14,994 of wax gourd unigenes were assigned to GO term annotation, and 23,977 were found to have COG classifications. In addition, a total of 18,713 unigenes were assigned to 281 KEGG pathways. Furthermore, 6,242 microsatellites (simple sequence repeats were detected as potential molecular markers in wax gourd. Two hundred primer pairs for SSRs were designed for validation of the amplification and polymorphism. The result showed that 170 of the 200 primer pairs were successfully amplified and 49 (28.8% of them exhibited polymorphisms. CONCLUSION/SIGNIFICANCE: Our study enriches the genomic resources of wax gourd and provides powerful information for future studies. The availability of this ample amount of information about the transcriptome and SSRs in wax gourd could serve as valuable basis for studies on the physiology, biochemistry, molecular genetics and molecular breeding of this important vegetable crop.

  4. 77 FR 43640 - Social Security Ruling, SSR 12-2p; Titles II and XVI: Evaluation of Fibromyalgia

    Science.gov (United States)

    2012-07-25

    ... Determinable Physical and Mental Impairments, and Exertional and Nonexertional Limitations, 61 FR 34488 (July 2... Not ``Acceptable Medical Sources'' in Disability Claims, 71 FR 45593 (August 9, 2006), (also available...: Evaluation of Symptoms in Disability Claims: Assessing the Credibility of an Individual's Statements, 61...

  5. Das magische Jahr 1989. Zu den Ursachen des Umbruchs des kommunistischen Regimes in der ČSSR

    Czech Academy of Sciences Publication Activity Database

    Vilímek, Tomáš

    Graz : Ludwig Boltzmann-Institut für Kriegsfolgen-Forschung, 2009 - (Laussegger, A.; Linke, R.; Perzi, N.), s. 137-142 ISBN 978-3-643-50092-2 Institutional research plan: CEZ:AV0Z80630520 Keywords : democratic revolution 1989 * fall of the communist regime Subject RIV: AB - History

  6. Modulation and SSR tests performed on the BPA 500 kV thyristor controlled series capacitor unit at Slatt substation

    Energy Technology Data Exchange (ETDEWEB)

    Hauer, J.F. [Pacific Northwest Lab., Richland, WA (United States); Mittelstadt, W.A. [Bonneville Power Administration, Portland, OR (United States); Piwko, R.J. [General Electric Co., Schenectady, NY (United States); Damsky, B.L. [Electric Power Research Inst., Palo Alto, CA (United States); Eden, J.D. [Portland General Electric, OR (United States)

    1995-07-01

    Field experience is reported for a thyristor controlled series capacitor (TCSC) recently commissioned at BPA`s Slatt substation. Subsynchronous resonance tests show that TCSC interactions with shaft dynamics of PGE`s Boardman steam generator are well understood and are effectively avoided by normal TCSC valve firing logic. Modulation tests, performed with the Boardman plant off line, show that the TCSC can be a powerful and responsive actuator for swing damping. Security considerations did not permit lightly damped operation of the controlled plant. Close analysis indicates that the TCSC damping contribution, though small, was measurable. The best estimate is that damping for the McNary mode is 7.33% and 8.55%, for the TCSC damper loop open and closed respectively. TCSC testing and monitoring is facilitated by an advanced interactive measurement network representing BPA`s approach to the information requirements of major control systems.

  7. Modulation and SSR tests performed on the BPA 500 kV thyristor controlled series capacitor unit at Slatt substation

    Energy Technology Data Exchange (ETDEWEB)

    Hauer, J.F. [Pacific Northwest Lab., Richland, WA (United States); Mittelstadt, W.A. [Bonneville Power Administration, Portland, OR (United States); Piwko, R.J. [General Electric Co., Schenectady, NY (United States); Damsky, B.L. [Electric Power Research Inst., Palo Alto, CA (United States); Eden, J.D. [Portland General Electric, OR (United States)

    1996-05-01

    Field experience is reported for a thyristor controlled series capacitor (TCSC) recently commissioned at BPA`s Slatt substation. Subsynchronous resonance tests show that TCSC interactions with shaft dynamics of PGE`s Boardman steam generator are well understood and are effectively avoided by normal TCSC valve firing logic. Modulation tests, performed with the Boardman plant off line, show that the TCSC can be a powerful and responsive actuator for swing damping. Security considerations did not permit lightly damped operation of the controlled plant. Close analysis indicates that the TCSC damping contribution, though small, was measurable. The best estimate is that damping for the McNary mode is 7.33% and 8.55%, for the TCSC damper loop open and closed respectively. TCSC testing and monitoring is facilitated by an advanced interactive measurement network representing BPA`s approach to the information requirements of major control systems.

  8. Analysis of area events as part of probabilistic safety assessment for Romanian TRIGA SSR 14 MW reactor

    International Nuclear Information System (INIS)

    The international experience has shown that the external events could be an important contributor to plant/ reactor risk. For this reason such events have to be included in the PSA studies. In the context of PSA for nuclear facilities, external events are defined as events originating from outside the plant, but with the potential to create an initiating event at the plant. To support plant safety assessment, PSA can be used to find methods for identification of vulnerable features of the plant and to suggest modifications in order to mitigate the impact of external events or the producing of initiating events. For that purpose, probabilistic assessment of area events concerning fire and flooding risk and impact is necessary. Due to the relatively large power level amongst research reactors, the approach to safety analysis of Romanian 14 MW TRIGA benefits from an ongoing PSA project. In this context, treatment of external events should be considered. The specific tasks proposed for the complete evaluation of area event analysis are: identify the rooms important for facility safety, determine a relative area event risk index for these rooms and a relative area event impact index if the event occurs, evaluate the rooms specific area event frequency, determine the rooms contribution to reactor hazard state frequencies, analyze power supply and room dependencies of safety components (as pumps, motor operated valves). The fire risk analysis methodology is based on Berry's method [1]. This approach provides a systematic procedure to carry out a relative index of different rooms. The factors, which affect the fire probability, are: personal presence in the room, number and type of ignition sources, type and area of combustibles, fuel available in the room, fuel location, and ventilation. The flooding risk analysis is based on the amount of piping in the room. For accuracy of the information regarding piping a facility walk-about is necessary. In case of flooding risk analysis some factors contributed to the flooding event: flow index, length index, size index, pressure index, all related to pipes. The flooding impact index takes into account the drainage and vulnerability of the index. With all above information the room specific area event frequency is calculated for each type of area event separately. (author)

  9. Neutronic design and comparative characteristics of new pin type control rod for 14-MW TRIGA-SSR reactor

    Energy Technology Data Exchange (ETDEWEB)

    Iorgulis, C.; Truta, C. [Institute for Nuclear Research, 0300 Pitesti (Romania)

    2001-07-01

    This paper presents the structural changes of the control rods (CR-s) which will be done in order to manufacture new ones and therefore to replace the original rods and to increase the present safety features of TRIGA 14 MW reactor in Pitesti. Few years ago two CR-s became inoperable due to the combined effect of welding corrosion, water penetration into the absorbent section of the CR and finally the swelling caused from the high internal pressure of the radiolysis-generated gases (gases which accelerated welding corrosion, water penetration, etc). Although safe reactor operation is not yet affected a decision to redesign a new CR was taken, entirely suitable to the general reactor design. The new CR will use boron carbide (same absorbent as in the original one); this baron carbide will be packed in a different way. A set of 16 Incoloy pins filled with a column of boron carbide pellets, leak-tight welded, will be manufactured. These 16 pins will be mounted in a square array with 5 pins on each side of the square (corner pins being the same far two sides). Neutronic analysis on the preliminary design was done using specific computer codes (WIMS, DFA, and MCNP). Reactivity worth of this new rod would be slight less (8%) than that of the original one, but still with full compensation capacity. Helium release analysis showed that gas pressure in the Incoloy tube after 15 years of normal operation would not exceed 57 ATM. (author)

  10. Concept and neutronic design on the new pin-type control rods for TRIGA SSR 14 MW-INR Pitesti

    International Nuclear Information System (INIS)

    This paper presents the structural changes of the control rods (CR-s) intended to improve the safety features of TRIGA 14 MW reactor Pitesti. Few years ago two CR-s became inoperable due to the combined effect of welding corrosion, water penetration into the absorbent section of the CR and finally the swelling caused by the high internal pressure of the radiolysis-generated gases (gases which accelerated welding corrosion, water penetration, etc.). Although safe reactor operation is not yet affected, a decision to re-design a new CR was taken, entirely suitable to the general reactor design. The new CR will use boron carbide (same absorbent as in the original one), which will be packed in a different way. A set of 16 Incoloy pins filled with a column of boron carbide pellets, leak-tight welded will be manufactured. These 16 pins will be mounted in a square array with 5 pins on each side. Neutronic analysis on the preliminary design was done using specific computer codes (WIMS, DFA and and MCNP). Reactivity worth of this new rod would be slightly less (8%) than that of the original one, but still with full compensation capacity. Helium leak analysis showed that gas pressure in the Incoloy tube after 15 years of normal operation would not exceed 57 ATM. The new design maintains unchanged all the components of the CR but the shape and the enclosure of the boron carbide absorbent. In conclusion: - same boron carbide is the neutron absorbent as cylindrical pellets of 70% theoretical density; - absorbent pellets are definitely cladded in stainless steel tubes for all the estimated time of use; - the absorbent pins will be disposed in square array, 5 on each side of a standard rod location. So the concept of peripheral absorbent with a central trap is preserved; - all hydraulic and thermal conditions are preserved; - most important, the absorbent structure has to fulfil the major demand of safe operation - shutdown with the most reactive control rod fully withdrawn. (authors)

  11. SSR Markers for Trichoderma virens: Their Evaluation and Application to Identify and Quantify Root-Endophytic Strains

    Directory of Open Access Journals (Sweden)

    Joerg Geistlinger

    2015-11-01

    Full Text Available Using biological fertilizers and pesticides based on beneficial soil microbes in order to reduce mineral fertilizers and chemical pesticides in conventional agriculture is still a matter of debate. In this regard, a European research project seeks to elucidate the role of root-endophytic fungi and to develop molecular tools to trace and quantify these fungi in the rhizosphere and root tissue. To do this, the draft genome sequence of the biocontrol fungus Trichoderma virens (T. virens was screened for simple sequence repeats (SSRs and primers were developed for 12 distinct loci. Primers were evaluated using a global collection of ten isolates where an average of 7.42 alleles per locus was detected. Nei’s standard genetic distance ranged from 0.18 to 0.27 among the isolates, and the grand mean of haploid diversity in AMOVA analysis was 0.693 ± 0.019. Roots of tomato plants were inoculated with different strains and harvested six weeks later. Subsequent PCR amplification identified root-endophytic strains and co-colonization of roots by different strains. Markers were applied to qPCR to quantify T. virens strains in root tissue and to determine their identity using allele-specific melting curve analysis. Thus, the root-endophytic lifestyle of T. virens was confirmed, strains in roots were quantified and simultaneous colonization of roots by different strains was observed.

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

    OpenAIRE

    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 t...

  13. Conservation of nuclear SSR loci reveals high affinity of Quercus infectoria ssp. veneris A. Kern (Fagaceae) to section Robur

    OpenAIRE

    Neophytou, Charalambos; Dounavi, Aikaterini; Aravanopoulos, Filippos A.

    2013-01-01

    Conservation of 16 nuclear microsatellite loci, originally developed for Quercus macrocarpa (section Albae), Q. petraea, Q. robur (section Robur) and Q. myrsinifolia, (subgenus Cyclobalanopsis) was tested in a Q. infectoria ssp. veneris population from Cyprus. All loci could be amplified successfully and displayed allele size and diversity patterns that match those of oak species belonging to the section Robur. At least in one case, limited amplification and high levels of homozygosity suppor...

  14. [Genetic analysis and SSR mapping on an new stem stripe rust resistance gene YrY206 in Aegilops tauschii].

    Science.gov (United States)

    Zhang, Haiquan; Lang, Jie; Ma, Shuqin; Zhang, Baoshi

    2008-08-01

    A wheat stripe rust resistance gene was screened out from Aegilops tauschii which is relative genera of wheat species, broadening the genetic basis of the anti-disease character of wheat species. By hybridizing diversed Ae. Tauschii species, which is either resistant or susceptible to wheat stripe rust, a dominant wheat stripe rust resistance gene was detected from Ae. Tauschii (Coss.) Schmal Y206. The novel gene was temporarily designated as YrY206. By bulk segregation analysis, four microsatellite markers Wmc11a, Xgwm71c, Xgwm161 and Xgwm183 were found to be linked to YrY206 with genetic distances of 4.0, 3.3, 1.5 and 9.3 cM, respectively. According to the locations of the linked markers, the resistance gene was located on chromosome 3DS. Based on the chromosomal location and the resistance pattern of the gene, YrY206 should be a novel stripe rust resistance gene. PMID:18998554

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

    Czech Academy of Sciences Publication Activity Database

    Snow, A. A.; Travis, S. E.; Wildová, Radka; Fér, T.; Sweeney, P. M.; Marburger, J. E.; Windels, S.; Kubátová, B.; Goldberg, D. E.; Mutegi, E.

    2010-01-01

    Roč. 97, č. 12 (2010), s. 2061-2067. ISSN 0002-9122 Institutional research plan: CEZ:AV0Z60050516 Keywords : gene flow * hybrid * introgression * invasive species * molecular markers Subject RIV: EF - Botanics Impact factor: 3.052, year: 2010

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

    OpenAIRE

    Li Shaoxiong; Zhou Guiyuan; Liu Haiyan; Liang Xuanqiang; Chen Xiaoping; Hong Yanbin; Wen Shijie; Holbrook C Corley; Guo Baozhu

    2010-01-01

    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 peanu...

  17. Genetic Structure and Relationship Analysis of an Association Population in Jute (Corchorus spp. Evaluated by SSR Markers.

    Directory of Open Access Journals (Sweden)

    Liwu Zhang

    Full Text Available Population structure and relationship analysis is of great importance in the germplasm utilization and association mapping. Jute, comprised of white jute (C. capsularis L and dark jute (C. olitorius L, is second to cotton in its commercial significance in the world. Here, we assessed the genetic structure and relationship in a panel of 159 jute accessions from 11 countries and regions using 63 SSRs. The structure analysis divided the 159 jute accessions from white and dark jute into Co and Cc group, further into Co1, Co2, Cc1 and Cc2 subgroups. Out of Cc1 subgroup, 81 accessions were from China and the remaining 10 accessions were from India (2, Japan (5, Thailand, Vietnam (2 and Pakistan (1. Out of Cc2 subgroup, 35 accessions were from China, and the remaining 3 accessions were from India, Pakistan and Thailand respectively. It can be inferred that the genetic background of these jute accessions was not always correlative with their geographical regions. Similar results were found in Co1 and Co2 subgroups. Analysis of molecular variance revealed 81% molecular variation between groups but it was low (19% within subgroups, which further confirmed the genetic differentiation between the two groups. The genetic relationship analysis showed that the most diverse genotypes were Maliyeshengchangguo and Changguozhongyueyin in dark jute, BZ-2-2, Aidianyehuangma, Yangjuchiyuanguo, Zijinhuangma and Jute 179 in white jute, which could be used as the potential parents in breeding programs for jute improvement. These results would be very useful for association studies and breeding in jute.

  18. Characterization of the global transcriptome for Pyropia haitanensis (Bangiales, Rhodophyta) and development of cSSR markers

    OpenAIRE

    Xie, Chaotian; Li, Bing; Xu, Yan; Ji, Dehua; Chen, Changsheng

    2013-01-01

    Background Pyropia haitanensis is an economically important mariculture crop in China and is also valuable in life science research. However, the lack of genetic information of this organism hinders the understanding of the molecular mechanisms of specific traits. Thus, high-throughput sequencing is needed to generate a number of transcriptome sequences to be used for gene discovery and molecular marker development. Results In this study, high-throughput sequencing was used to analyze the glo...

  19. An efficient and rapid DNA minipreparation procedure suitable for PCR/SSR and RAPD analyses in tropical forest tree species

    OpenAIRE

    Ana Lilia Alzate-Marin; Marcela Corbo Guidugli; Hilda Hildebrand Soriani; Carlos Alberto Martinez; Moacyr Antônio Mestriner

    2009-01-01

    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 alcoho...

  20. Oppositionists in the ČSSR and the GDR. Mutual Awareness, Exchanges of Ideas and Cooperation, 1968-1989

    Czech Academy of Sciences Publication Activity Database

    Vilímek, Tomáš

    Osnabrück: Fibre Verlag, 2013 - (Brier, R.), s. 55-85. (Einzelveröffentlichungen des DHI Warschau. 31). ISBN 978-3-938400-96-8 R&D Projects: GA ČR GAP410/12/2287 Institutional support: RVO:68378114 Keywords : disent and resistance * Czechoslovakia 1968-1989 * GDR 1968-1989 Subject RIV: AB - History

  1. A polymorphic (GA/CT)n- SSR influences promoter activity of Tryptophan decarboxylase gene in Catharanthus roseus L. Don.

    Science.gov (United States)

    Kumar, Santosh; Bhatia, Sabhyata

    2016-01-01

    Simple Sequence Repeats (SSRs) of polypurine-polypyrimidine type motifs occur very frequently in the 5' flanks of genes in plants and have recently been implicated to have a role in regulation of gene expression. In this study, 2 accessions of Catharanthus roseus having (CT)8 and (CT)21 varying motifs in the 5'UTR of Tryptophan decarboxylase (Tdc) gene, were investigated for its role in regulation of gene expression. Extensive Tdc gene expression analysis in the 2 accessions was carried out both at the level of transcription and translation. Transcript abundance was estimated using Northern analysis and qRT-PCR, whereas the rate of Tdc gene transcription was assessed using in-situ nuclear run-on transcription assay. Translation status of Tdc gene was monitored by quantification of polysome associated Tdc mRNA using qRT-PCR. These observations were validated through transient expression analysis using the fusion construct [CaM35S:(CT)8-21:GUS]. Our study demonstrated that not only does the length of (CT)n -SSRs influences the promoter activity, but the presence of SSRs per se in the 5'-UTR significantly enhances the level of gene expression. We termed this phenomenon as "microsatellite mediated enhancement" (MME) of gene expression. Results presented here will provide leads for engineering plants with enhanced amounts of medicinally important alkaloids. PMID:27623355

  2. Epochenwende 1989/90. Die gesellschaftliche Situation in der ČSSR am Ende der 1980er-Jahre

    Czech Academy of Sciences Publication Activity Database

    Vilímek, Tomáš

    Berlin: Metropol, 2015 - (Apelt, A.; Grünbaum, R.; Gutzeit, M.), s. 106-116 ISBN 978-3-86331-228-2 R&D Projects: GA ČR GAP410/12/2287 Institutional support: RVO:68378114 Keywords : collapse of the communist regime * Czechoslovakia 1989 Subject RIV: AB - History

  3. Мультимедийная поддержка преподавания предметов геоинформатики

    OpenAIRE

    Войтешенко, И. С.; ТАРАНЧУК В.Б.

    2005-01-01

    A system of multi-media support of geoinformatics and GIS-technology training has been considered. The system has been developed at the Byelorussian State University for students of the Geography Department and includes computer presentations and additional resources for lectures, laboratory work and independent study as well as software for computer tests and other components.

  4. Reasons for Errors Done by Belarusian Learners Learning Turkish as a Foreign Language

    Science.gov (United States)

    Tum, Gulden

    2012-01-01

    Teaching Turkish as a Foreign Language (TFL) has gained importance recently and several studies are carried out in this field. Especially, learners of linguistically different communities (Byelorussian/Russian) are observed to make errors while learning Turkish. If making errors is an integral outcome in learning a TFL, then to what extent is it…

  5. Apple and pear rootstock research in Lithuania

    OpenAIRE

    Kviklys, Darius

    2006-01-01

    The paper presents ongoing apple and pear rootstock trials at the Lithuanian Institute of Horticulture. Rootstock research projects are established in following directions: rootstock and location interaction (Baltic fruit rootstock studies where Byelorussian, Estonian, Latvian, Lithuanian and Polish research institutions are involved); budding high effect on rootstock performance; interstock trials; rootstock effect on fruit quality, ripening time and fruit storage; rootstock and tree trainin...

  6. QTL Mapping for Fiber Quality Traits Based on a Dense Genetic Linkage Map with SSR,TRAP,SRAP and AFLP Markers in Cultivated Tetraploid Cotton

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Cotton is one of the most important economic crops in the world,and it provides natural fiber for the textile industry.With the advancement of the textile technology and increased consumption demands on cotton fiber,both cotton yield and quality should be enhanced.However,cotton yield and

  7. QTL Mapping for Fiber Quality Traits Based on a Dense Genetic Linkage Map with SSR,TRAP,SRAP and AFLP Markers in Cultivated Tetraploid Cotton

    Institute of Scientific and Technical Information of China (English)

    YU Ji-wen; YU Shu-xun; ZHANG Jin-fa; ZHAI Hong-hong

    2008-01-01

    @@ Cotton is one of the most important economic crops in the world,and it provides natural fiber for the textile industry.With the advancement of the textile technology and increased consumption demands on cotton fiber,both cotton yield and quality should be enhanced.However,cotton yield and fiber quality are complex quantitative traits and are usually negatively associated that hampers the simultaneous improvement of lint yield and fiber quality by traditional breeding.

  8. Thyroid irradiation doses and organization of endocrinological monitoring for the population in the Ukrainian SSR after the accident at the Chernobyl Nuclear Power Station

    International Nuclear Information System (INIS)

    The paper is devoted to one of the most important aspects of the accident at the Chernobyl Nuclear Power Station: thyroid irradiation in the residents of 8 areas in the Ukrainian SSSR and the town of Pripyat, affected with radioactive iodine. Irradiation doses, prognosis of medical effects of endocrinological monitoring of the affected population were thoroughly considered. The authors proposed a scheme of health care of the population in these areas. They also discussed the structure of data bases for analysis of medicodosimetric information of iodine effects of the accident. The main trends in medicodosimetric problems of the effects of thyroid irradiation were outlined

  9. Construction of an integrated genetic linkage map for the A genome of Brassica napus using SSR markers derived from sequenced BACs in B. rapa

    OpenAIRE

    Xu, Jinsong; Qian, Xiaoju; Wang, Xiaofeng; Li, Ruiyuan; Cheng, Xiaomao; Yang, Yuan; Fu, Jie; Zhang, Shunchang; King, Graham J; Wu, Jiangsheng; Liu, Kede

    2010-01-01

    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 ...

  10. Development of a Low-cost and High-throughput Polyacrylamide Gel System for Peanut Genotyping with Simple Sequence Repeat (SSR) Markers.

    Science.gov (United States)

    Traditionally, peanut cultivar development has been dominated by conventional breeding methods, which have greatly increased yield and will continue to play an important role in peanut genetic improvement. Applications of MAS (marker-assisted selection) in plant breeding have been shown to increase ...

  11. High-level genetic diversity and complex population structure of Siberian apricot (Prunus sibirica L. in China as revealed by nuclear SSR markers.

    Directory of Open Access Journals (Sweden)

    Zhe Wang

    Full Text Available Siberian apricot (Prunus sibirica L., an ecologically and economically important tree species with a high degree of tolerance to a variety of extreme environmental conditions, is widely distributed across the mountains of northeastern and northern China, eastern and southeastern regions of Mongolia, Eastern Siberia, and the Maritime Territory of Russia. However, few studies have examined the genetic diversity and population structure of this species. Using 31 nuclear microsatellites, we investigated the level of genetic diversity and population structure of Siberian apricot sampled from 22 populations across China. The number of alleles per locus ranged from 5 to 33, with an average of 19.323 alleles. The observed heterozygosity and expected heterozygosity ranged from 0.037 to 0.874 and 0.040 to 0.924 with average values of 0.639 and 0.774, respectively. A STRUCTURE-based analysis clustered all of the populations into four genetic clusters. Significant genetic differentiation was observed between all population pairs. A hierarchical analysis of molecular variance attributed about 94% of the variation to within populations. No significant difference was detected between the wild and semi-wild groups, indicating that recent cultivation practices have had little impact on the genetic diversity of Siberian apricot. The Mantel test showed that the genetic distance among the populations was not significantly correlated with geographic distance (r = 0.4651, p = 0.9940. Our study represents the most comprehensive investigation of the genetic diversity and population structure of Siberian apricot in China to date, and it provides valuable information for the collection of genetic resources for the breeding of Siberian apricot and related species.

  12. Insights into the Genetic Relationships and Breeding Patterns of the African Tea Germplasm Based on nSSR Markers and cpDNA Sequences.

    Science.gov (United States)

    Wambulwa, Moses C; Meegahakumbura, Muditha K; Kamunya, Samson; Muchugi, Alice; Möller, Michael; Liu, Jie; Xu, Jian-Chu; Ranjitkar, Sailesh; Li, De-Zhu; Gao, Lian-Ming

    2016-01-01

    Africa is one of the key centers of global tea production. Understanding the genetic diversity and relationships of cultivars of African tea is important for future targeted breeding efforts for new crop cultivars, specialty tea processing, and to guide germplasm conservation efforts. Despite the economic importance of tea in Africa, no research work has been done so far on its genetic diversity at a continental scale. Twenty-three nSSRs and three plastid DNA regions were used to investigate the genetic diversity, relationships, and breeding patterns of tea accessions collected from eight countries of Africa. A total of 280 African tea accessions generated 297 alleles with a mean of 12.91 alleles per locus and a genetic diversity (H S) estimate of 0.652. A STRUCTURE analysis suggested two main genetic groups of African tea accessions which corresponded well with the two tea types Camellia sinensis var. sinensis and C. sinensis var. assamica, respectively, as well as an admixed "mosaic" group whose individuals were defined as hybrids of F2 and BC generation with a high proportion of C. sinensis var. assamica being maternal parents. Accessions known to be C. sinensis var. assamica further separated into two groups representing the two major tea breeding centers corresponding to southern Africa (Tea Research Foundation of Central Africa, TRFCA), and East Africa (Tea Research Foundation of Kenya, TRFK). Tea accessions were shared among countries. African tea has relatively lower genetic diversity. C. sinensis var. assamica is the main tea type under cultivation and contributes more in tea breeding improvements in Africa. International germplasm exchange and movement among countries within Africa was confirmed. The clustering into two main breeding centers, TRFCA, and TRFK, suggested that some traits of C. sinensis var. assamica and their associated genes possibly underwent selection during geographic differentiation or local breeding preferences. This study represents the first step toward effective utilization of differently inherited molecular markers for exploring the breeding status of African tea. The findings here will be important for planning the exploration, utilization, and conservation of tea germplasm for future breeding efforts in Africa. PMID:27625655

  13. Determination of the 90Sr and 137Cs concentration factor by some cereals and root crops in the region of the Lithuanian SSR

    International Nuclear Information System (INIS)

    Effect of natural-soil conditions on 90Sr and 137Cs accumulation factor (AF) in barley plants is studied at the Lithuanian republican chemization station. It is shown that in most cases AF is higher in barley grown in the Eastern part of Lithuania and in the Mid-Lithuanian lowland. Study of effect of continuous utilization of fertilizers on radionuclide accumulation in sugar beet has demonstrated an increase of 90Sr and 137Cs content in the soil (up to 1.5 times) and in sugar beet (up to 2 times) as compared to the section under control. 3 refs.; 1 tab

  14. Der „Weg in den Dissent“ in der ČSSR und in der DDR im Vergleich (1968-1989)

    Czech Academy of Sciences Publication Activity Database

    Vilímek, Tomáš

    Leipzig : Edition Kirchhof & Franke, 2013 - (Řezník, M.; Rosenbaum, K.), s. 31-48 ISBN 978-3-933816-61-0. - (Studien zur europäischen Regionalgeschichte. 2) R&D Projects: GA ČR GAP410/12/2287 Institutional support: RVO:68378114 Keywords : disent and resistance * Czechoslovakia 1968-1989 * GDR 1968-1989 Subject RIV: AB - History

  15. Empirical evaluation of DArT, SNP, and SSR marker-systems for genotyping, clustering, and assigning sugar beet hybrid varieties into populations

    NARCIS (Netherlands)

    Simko, I.; Eujayl, I.; Hintum, van T.J.L.

    2012-01-01

    Dominant and co-dominant molecular markers are routinely used in plant genetic research. In the present study we assessed the success-rate of three marker-systems for estimating genotypic diversity, clustering varieties into populations, and assigning a single variety into the expected population. A

  16. 可可全基因组SSR标记的开发及分析%LARGE-SCALE DEVELOPMENT OF SSR MARKERS IN THE GENOME OF CACAO

    Institute of Scientific and Technical Information of China (English)

    曹恒春; 王毅; 黄莉莎; 王玉军; 于元杰; 杨龙

    2013-01-01

    SSR标记是一种广泛应用的分子标记技术,在可可基因组的研究中发挥了重要的作用.本研究运用生物信息学的方法,对可可全基因组进行了扫描,共得到10,4653个SSR区段.对这些SSR区段进行分析,发现含有碱基数目不同的重复单元之间具有较大的差异:含有七核苷酸的重复单元最多,为70,414个,占所有重复单元总数的67.3%;其次为二核苷酸重复单元,为23,272个,占总数的22.2%.在各类SSR单元中,不同核苷酸重复单元出现的频率有明显的差异,其中富含A/T重复单元的SSR单元数目最多,占总数的67%;而C/G重复单元的SSR单元数目较少,约占总数的0.02%.利用SSR单元的位点信息,设计出了65,861对引物,并在可可基因组中进行了电子PCR扩增验证,结果显示100%的引物均能扩增出产物条带.在可可基因组中大规模开发的SSR标记,将为可可的进化、分类和遗传多样性研究提供参考.

  17. Development and identification of SSR markers associated with starch properties and β-carotene content in the storage root of sweet potato (Ipomoea batatas L.)

    OpenAIRE

    Kai eZhang; Zheng-dan eWu; Dao-bin eTang; Chang-wen eLv; Kai eLuo; Yong eZhao; Xun eLiu; Yuan-xin eHuang; Ji-chun eWang

    2016-01-01

    Sweet potato (Ipomoea batatas L.) is a nutritious food crop and, based on the high starch content of its storage root, a potential bioethanol feedstock. Enhancing the nutritional value and starch quantity of storage roots are important goals of sweet potato breeding programs aimed at developing improved varieties for direct consumption, processing, and industrial uses. However, developing improved lines of sweet potato is challenging due to the genetic complexity of this plant and the lack of...

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

    OpenAIRE

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

    2016-01-01

    Sweet potato (Ipomoea batatas L.) is a nutritious food crop and, based on the high starch content of its storage root, a potential bioethanol feedstock. Enhancing the nutritional value and starch quantity of storage roots are important goals of sweet potato breeding programs aimed at developing improved varieties for direct consumption, processing, and industrial uses. However, developing improved lines of sweet potato is challenging due to the genetic complexity of this plant and the lack of...

  19. Transcriptome Profile of the Asian Giant Hornet (Vespa mandarinia) Using Illumina HiSeq 4000 Sequencing: De Novo Assembly, Functional Annotation, and Discovery of SSR Markers

    OpenAIRE

    Bharat Bhusan Patnaik; So Young Park; Se Won Kang; Hee-Ju Hwang; Tae Hun Wang; Eun Bi Park; Jong Min Chung; Dae Kwon Song; Changmu Kim; Soonok Kim; Jae Bong Lee; Heon Cheon Jeong; Hong Seog Park; Yeon Soo Han; Yong Seok Lee

    2016-01-01

    Vespa mandarinia found in the forests of East Asia, including Korea, occupies the highest rank in the arthropod food web within its geographical range. It serves as a source of nutrition in the form of Vespa amino acid mixture and is listed as a threatened species, although no conservation measures have been implemented. Here, we performed de novo assembly of the V. mandarinia transcriptome by Illumina HiSeq 4000 sequencing. Over 60 million raw reads and 59,184,811 clean reads were obtained. ...

  20. Empirical evaluation of DArT, SNP, and SSR marker-systems for genotyping, clustering, and assigning sugar beet hybrid varieties into populations

    Science.gov (United States)

    Dominant and co-dominant molecular markers are routinely used in plant genetic diversity research. In the present study we assessed the success-rate of three marker-systems for estimating genotypic diversity, clustering varieties into populations, and assigning a single variety into the expected pop...

  1. DNA sequences and composition from 12 BAC clones-derived MUSB SSR markers mapped to cotton (Gossypium Hirsutum L. x G. Barbadense L.)chromosomes 11 and 21

    Science.gov (United States)

    To discover resistance (R) and/or pathogen-induced (PR) genes involved in disease response, 12 bacterial artificial chromosome (BAC) clones from cv. Acala Maxxa (G. hirsutum) were sequenced at the Clemson University, Genomics Institute, Clemson, SC. These BACs derived MUSB single sequence repeat (SS...

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

    OpenAIRE

    Tranbarger Timothy; Kluabmongkol Wanwisa; Sangsrakru Duangjai; Morcillo Fabienne; Tregear James W; Tragoonrung Somvong; Billotte Norbert

    2012-01-01

    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 th...

  3. Transcriptome Profile of the Asian Giant Hornet (Vespa mandarinia) Using Illumina HiSeq 4000 Sequencing: De Novo Assembly, Functional Annotation, and Discovery of SSR Markers.

    Science.gov (United States)

    Patnaik, Bharat Bhusan; Park, So Young; Kang, Se Won; Hwang, Hee-Ju; Wang, Tae Hun; Park, Eun Bi; Chung, Jong Min; Song, Dae Kwon; Kim, Changmu; Kim, Soonok; Lee, Jae Bong; Jeong, Heon Cheon; Park, Hong Seog; Han, Yeon Soo; Lee, Yong Seok

    2016-01-01

    Vespa mandarinia found in the forests of East Asia, including Korea, occupies the highest rank in the arthropod food web within its geographical range. It serves as a source of nutrition in the form of Vespa amino acid mixture and is listed as a threatened species, although no conservation measures have been implemented. Here, we performed de novo assembly of the V. mandarinia transcriptome by Illumina HiSeq 4000 sequencing. Over 60 million raw reads and 59,184,811 clean reads were obtained. After assembly, a total of 66,837 unigenes were clustered, 40,887, 44,455, and 22,390 of which showed homologous matches against the PANM, Unigene, and KOG databases, respectively. A total of 15,675 unigenes were assigned to Gene Ontology terms, and 5,132 unigenes were mapped to 115 KEGG pathways. The zinc finger domain (C2H2-like), serine/threonine/dual specificity protein kinase domain, and RNA recognition motif domain were among the top InterProScan domains predicted for V. mandarinia sequences. Among the unigenes, we identified 534,922 cDNA simple sequence repeats as potential markers. This is the first transcriptomic analysis of the wasp V. mandarinia using Illumina HiSeq 4000. The obtained datasets should promote the search for new genes to understand the physiological attributes of this wasp. PMID:26881195

  4. Genetic variation and phylogeography of Stauracanthus (Fabaceae, Genisteae) from the Iberian Peninsula and northern Morocco assessed by chloroplast microsatellite (cpSSR) markers.

    Science.gov (United States)

    Pardo, Cristina; Cubas, Paloma; Tahiri, Hikmat

    2008-01-01

    The tribe Genisteae includes genera of great ecological importance in Mediterranean countries because they are dominant elements of many plant communities. Genetic variation and diversification patterns in Stauracanthus (Genisteae) provide information relevant for the study of the processes of diversification in relation to the environmental history of the western Mediterranean. Nineteen populations of S. boivinii and S. genistoides were assessed by 11 chloroplast microsatellite markers, revealing 44 haplotypes. Both species had different haplotypes and contrasting patterns of karyological, morphological, and genetic variation. In the minimum spanning tree of the haplotypes, AMOVA analysis, and nested clade analysis, S. boivinii had high levels of differentiation and restricted gene flow among populations. Allopatric differentiation occurred between the Moroccan and Iberian populations of S. genistoides, although S. genistoides subsp. spectabilis and subsp. vicentinus had high levels of differentiation among populations (F(ST)), whereas S. genistoides subsp. genistoides had a low F(ST). Genetic patterns are discussed in relation to the Messinian salinity crisis (MSC): hard conditions drove plants to refuge habitats along the Atlantic coast and higher altitude areas in the Moroccan mountains (S. genistoides subsp. spectabilis and S. boivinii). After the MSC, S. boivinii underwent polyploidization and expansion, whereas S. genistoides expanded and continued diversifying into S. genistoides subspp. genistoides and vicentinus. PMID:21632320

  5. Harnessing the sorghum genome sequence:development of a genome-wide microsattelite (SSR) resource for swift genetic mapping and map based cloning in sorghum

    Science.gov (United States)

    Sorghum is the second cereal crop to have a full genome completely sequenced (Nature (2009), 457:551). This achievement is widely recognized as a scientific milestone for grass genetics and genomics in general. However, the true worth of genetic information lies in translating the sequence informa...

  6. Highly Informative Single-Copy Nuclear Microsatellite DNA Markers Developed Using an AFLP-SSR Approach in Black Spruce (Picea mariana) and Red Spruce (P. rubens)

    OpenAIRE

    Yong-Zhong Shi; Natascha Forneris; Rajora, Om P

    2014-01-01

    Background 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)...

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

    OpenAIRE

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

    2014-01-01

    Background The oil palm (Elaeis guineensis, 2n = 32) has the highest oil yield of any crop species, as well as comprising the richest dietary source of provitamin A. For the tropical species, the best mean growth temperature is about 27°C, with a minimal growth temperature of 15°C. Hence, the plantation area is limited into the geographical ranges of 10°N to 10°S. Enhancing cold tolerance capability will increase the total cultivation area and subsequently oil productivity of this tropical sp...

  8. Transcriptome Profile of the Asian Giant Hornet (Vespa mandarinia Using Illumina HiSeq 4000 Sequencing: De Novo Assembly, Functional Annotation, and Discovery of SSR Markers

    Directory of Open Access Journals (Sweden)

    Bharat Bhusan Patnaik

    2016-01-01

    Full Text Available Vespa mandarinia found in the forests of East Asia, including Korea, occupies the highest rank in the arthropod food web within its geographical range. It serves as a source of nutrition in the form of Vespa amino acid mixture and is listed as a threatened species, although no conservation measures have been implemented. Here, we performed de novo assembly of the V. mandarinia transcriptome by Illumina HiSeq 4000 sequencing. Over 60 million raw reads and 59,184,811 clean reads were obtained. After assembly, a total of 66,837 unigenes were clustered, 40,887, 44,455, and 22,390 of which showed homologous matches against the PANM, Unigene, and KOG databases, respectively. A total of 15,675 unigenes were assigned to Gene Ontology terms, and 5,132 unigenes were mapped to 115 KEGG pathways. The zinc finger domain (C2H2-like, serine/threonine/dual specificity protein kinase domain, and RNA recognition motif domain were among the top InterProScan domains predicted for V. mandarinia sequences. Among the unigenes, we identified 534,922 cDNA simple sequence repeats as potential markers. This is the first transcriptomic analysis of the wasp V. mandarinia using Illumina HiSeq 4000. The obtained datasets should promote the search for new genes to understand the physiological attributes of this wasp.

  9. Test results and initial operating experience for the BPA 500 kV thyristor controlled series capacitor-modulation, SSR and performance monitoring

    Energy Technology Data Exchange (ETDEWEB)

    Hauer, J.F. [Pacific Northwest Lab., Richland, WA (United States); Mittelstad, W.A. [Bonneville Power Administration, Portland, OR (United States); Piwko, R.J. Sr. [General Electric Co., Schenectady, NY (United States)] [and others

    1995-12-31

    Field experience is reported for a thyristor controlled series capacitor (TCSC) recently commissioned at BPA`s Slatt substation. Subsynchronous resonance tests show that TCSC interactions with shaft dynamics of PGE`s Boardman steam generator are well understood and are effectively avoided by normal TCSC valve firing logic. Modulation tests, performed with the Boardman plant off line, show that the TCSC can be a powerful and responsive actuator for swing damping. Security considerations did not permit lightly damped operation of the controlled plant. Close analysis indicates that the TCSC damping contribution, though small, was measurable. The best estimate is that damping for the McNary mode is 7.33% and 8.55%, for the TCSC damper loop open and closed respectively. TCSC testing and monitoring is facilitated by an advanced interactive measurement network representing BPA`s approach to the information requirements of major control systems.

  10. High-density genetic linkage map construction and identification of fruit-related QTLs in pear using SNP and SSR markers

    OpenAIRE

    Wu, Jun; Li, Lei-Ting; Li, Meng; Khan, M. Awais; Li, Xiu-Gen; Chen, Hui; Yin, Hao; Zhang, Shao-Ling

    2014-01-01

    Pear (Pyrus spp) is an important fruit crop, grown in all temperate regions of the world, with global production ranked after grape and apples among deciduous tree crops. A high-density linkage map is a valuable tool for fine mapping quantitative trait loci (QTL) and map-based gene cloning. In this study, we firstly constructed a high-density linkage map of pear using SNPs integrated with SSRs, developed by the rapid and robust technology of restriction-associated DNA sequencing (RADseq). The...

  11. Application of ERT and SSR to Detect the shallow subsurface cracks under buildings of District No. 27 at 15th May City, Helwan, Egypt.

    Science.gov (United States)

    Basheer Mohammed, A. A.; Abdalla, M. A.

    2012-09-01

    15th May City, 12 km to the southeast of Helwan city, is one of promised cities planned in 1986 by the Egyptian government through its program to withdraw the population from the condensed central Nile valley to the side parts of the Nile valley Egypt. The present study runs on the district No. 27. at 15th May city. The main target of this study is to detect the cracks in the shallow subsurface layer under buildings and estimate its displacement to reach its causes. This study embraces, two dimension electrical resistivity, and shallow seismic refraction surveys. The two dimension electrical imaging technique was interpreted in terms of depths and thicknesses of the geoelectric layers, on this regard, it suggests a succession of three layers, and in addition, the boundaries of the crack could be sensed. The shallow seismic refraction technique results revealed a succession of three seismic layers. These layers illustrated from both techniques are dried limestone "calcite to dolomite" layer, and the second is wetted to semi-wetted "Marley limestone". On the other hand, these parameters allow for separating the area into layers of different competence nature and consequently different appropriateness. Five cracks sites have been detected with its directions in the study area, the main reason of these crack reveal to the irrigation water which used in garden's watering among the buildings.

  12. Molecular cloning of an SSR marker associated with resistance to Sclerotinia blight in peanut and sequence variation among resistant and susceptible plant lines

    Science.gov (United States)

    The production of cultivated peanut, an important agronomic crop throughout the United States and the world, is consistently threatened by various diseases and pests. Specifically, peanut production in Oklahoma, Texas, North Carolina, and Virginia is challenged by fungal disease such as Sclerotinia...

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

    OpenAIRE

    Yang Jun-Bo; Tian Bo; Yang Chun; Qiu Lijun; Liu Aizhong

    2010-01-01

    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...

  14. A combined functional and structural genomics approach identified an EST-SSR marker with complete linkage to the Ligon lintless-2 genetic locus in cotton (Gossypium hirsutum L.)

    Science.gov (United States)

    Cotton fiber length is an important quality attribute to the textile industry and longer fibers can be more efficiently spun into yarns to produce superior fabrics. There is typically a negative correlation between yield and fiber quality traits such as length. An understanding of the regulatory me...

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

    DEFF Research Database (Denmark)

    Studer, Bruno; Kölliker, Roland; Muylle, Hilde;

    2010-01-01

    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 ma...

  16. Full conversion of the core of a research, nuclear fuel testing and material testing reactor of TRIGA SSR 14 MW type

    International Nuclear Information System (INIS)

    All the TRIGA type reactors have power levels between 100 kW and 14 MW and use a nuclear fuel formed of a uranium - hydride zirconium alloy. The reactor cores made of this fuel are intrinsically secure against any accident of reactivity insertion. This type of fuel presents a low coefficient of fission product release and a remarkable stability to the temperature cycling up to high burnups. All the TRIGA type reactors except the 14 MW reactors, as the type of the TRIGA reactor of INR Pitesti is, make use of low enrichment uranium (19.9%), LEU. Due to the international policy of non-proliferation and nuclear safeguard requirements as well, the highly enriched uranium fuel fabrication ceased in 1978. Subsequently, only LEU type fuel continued to be used. The process of using LEU fuel instead of HEU fuel, coined as conversion, was supported by DOE of USA and the IAEA member states in the frame of the 'Reduced Enrichment in Research and Testing Reactors' (RERTR project) together with the technical cooperation projects (TC) between IAEA and the member states. INR Pitesti enjoyed the both forms of international support since 1984. The conversion process at the TRIGA reactor of INR Pitesti began in 1992 by feeding the reactor core with LEU fuel produced by General Atomics. The report of General Atomics from 1998, titled 'Final Results from TRIGA - LEU fuel Postirradiation Examination and Evaluation following Long-term Irradiation Testing in the OAK Ridge Reactor (ORR)' (UZR-22) presents the results of irradiation testing of the LEU f 13,22 fuel for a burnup of about 65% and an irradiation period of about 900 FPD (full power days). The report confirmed the reliability of the LEU fuel replaced in the conversion process. Similar results were obtained by irradiation of LEU fuel, produced by General Atomics, in the 14 MW TRIGA reactor of INR Pitesti and by post irradiation examination of some fuel element selected from the batch of fuel provided by the Argonne National Laboratory. On the basis of these results and of some neutronic and thermal-hydraulic analyses as well, it can be estimated that the completion of conversion process will be accomplished by June 2007 and the reactor will be operational for the next 20 years

  17. 利用SSR标记分析藜麦品种的遗传多样性%Genetic Diversity of Quinoa Germplasm Assessed by SSR Markers

    Institute of Scientific and Technical Information of China (English)

    陆敏佳; 蒋玉蓉; 陆国权; 陈国林; 毛前

    2015-01-01

    为了解藜麦种质资源的多样性,本研究利用SSR引物对所搜集的41个藜麦种质的多态性及其亲缘关系进行了分析.结果表明,从54对SSR引物中筛选出了16对能明显扩增出稳定的多态性条带的引物,共检测出139个等位基因条带,每一对引物的等位基因个数为3 ~13,平均为8.7;16对引物的多态信息含量(PIC)变幅为0.208 ~0.432,平均为0.366.UPGMA聚类分析显示,41份材料的遗传相似系数(GS)在0.374 ~0.906之间,平均相似系数为0.626.在阀值(GS)约为0.665时,41份材料可分为4大类.其中614929与B.B.Quinoa浙Ⅰ间的遗传相似系数最小,为0.374,表明来源于不同地区的遗传距离较远,遗传基础较广泛.藜麦品种资源间的亲缘关系的揭示为藜麦资源保存和新品种选育提供了理论依据.

  18. 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-ter...... a subset of neurons in the rat prefrontal cortex and this activation likely is important for the attentional effects of this new class of drugs....

  19. De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas)

    OpenAIRE

    Huang Lifei; Luo Zhongxia; Zhang Xiongjian; Chen Jingyi; Fang Boping; Wang Zhangying; Chen Xinliang; Li Yujun

    2010-01-01

    Abstract Background The tuberous root of sweetpotato is an important agricultural and biological organ. There are not sufficient transcriptomic and genomic data in public databases for understanding of the molecular mechanism underlying the tuberous root formation and development. Thus, high throughput transcriptome sequencing is needed to generate enormous transcript sequences from sweetpotato root for gene discovery and molecular marker development. Results In this study, more than 59 milli...

  20. 大麦品种资源遗传多样性的SSR标记评价%Genetic Diversity Assessment of Barley Germplasm Resources Using SSR Markers

    Institute of Scientific and Technical Information of China (English)

    张赤红; 张京

    2008-01-01

    为了有效利用大麦种质资源,利用49对SSR引物,对中国240份和国外60份大麦品种资源进行了遗传多样性研究.结果表明,大麦7条染色体中第五和第六条染色体遗传多样性较高,第三、四、七条染色体遗传多样性比较低.300份材料中,遗传多样性最丰富的是非洲、亚洲和中东的大麦资源;中国西藏、四川、云南及育成品种的遗传多样性较为丰富.基于SSR数据,对300份大麦材料进行了聚类分析,结果聚为三组,来自土库曼斯坦(TKM)的一份材料划分为一组, 43份国外材料划分为一组,其他材料为一组,同一栽培地区的品种基本聚在同一组中.