Tall fescue EST-SSR markers with transferability across several grass species

Saha, Malay C.; Mian, M. A. Rouf; Eujayl, Imad A.; Zwonitzer, John C.; Wang, Liangjiang; May, Gregory D.

doi:10.1007/s00122-004-1681-1

Cited by 276 publications

(224 citation statements)

References 43 publications

(52 reference statements)

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“…Of these, 897 primer pairs (84.6%) yielded amplicons in the two parents of our mapping population. This result was similar to EST-SSR amplification rate in sweetpotato [26,28] and many other studies in which a success rate of 60-90% amplification has also been reported [37,40-43]. In those studies (except [26]), they also reported a similar success rate of amplification for both genomic SSRs and EST-SSRs.…”

Section: Discussionsupporting

confidence: 90%

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

et al. 2011

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BackgroundCurrently 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.ResultsIn 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.ConclusionThis 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 be useful for qualitative and quantitative trait mapping, marker-assisted selection, evolution and genetic diversity studies in cultivated sweetpotato and related Ipomoea species.

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Section: Discussionsupporting

confidence: 90%

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

et al. 2011

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“…The EST-SSRs derived from fiber tissues showed high level of transferability in diploid genomes, confirming the presence of fiber related genes in all the cotton genomes. Phenomenon of transferability has also been reported in other crop species (Kuleung et al 2004;Saha et al 2004).…”

Section: Performance Of Microsatellite Between a D And Ad-genome Spementioning

confidence: 58%

Pros and cons of using genomic SSRs and EST-SSRs for resolving phylogeny of the genus Gossypium

2013

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The genus Gossypium is comprised of 50 diverse cotton species representing eight different genomes (A through G and K), however, phylogenetic relationship using various DNA marker types such as RAPD and SSRs was determined on limited number of cotton species. In this report, we have demonstrated the application of genomic SSRs (gSSRs) and EST-SSRs, and after combining both the data sets, for resolving the phylogenies of 36 cotton species including seven races. Out of the 100 primer pairs surveyed (50 for gSSRs and 50 for ESTSSRs), 75 produced scorable amplification products in all species. Out of these, 73 were found to be polymorphic and amplified 135 alleles ranging from 1 to 5 alleles per SSR marker (average 2.87 alleles per marker). The gSSRs amplified higher number of alleles (72) compared to the EST-SSRs (63). In total 22 highly informative SSRs with PIC values C0.5 were identified. Genomic SSRs containing di-while EST-SSRs containing tri-nucleotide repeats exhibited high polymorphism compared to the other nucleotide repeats containing gSSRs/EST-SSRs. Number of tandem repeats and polymorphism were positively correlated. Neither the type of chromosome nor the location of the SSRs showed association with the polymorphism. Gossypium herbaceum var. africanum (Watt) Hutch. ex and Ghose and Gossypium robinsonii F. Muell. were found the most genetically diverse, while among races of Gossypium hirsutum L. ''yucatanense'' and G. hirsutum ''punctatum'' were found genetically diverse. Of the three data sets, clustering analysis based on EST-SSRs and combined data sets, revealed parallel results reported in earlier studies. This study further confirmed that Gossypium darwinii Watt has close relationship with Gossypium barbadense L. Moreover, Gossypium raimondii Ulbr. and G. herbaceum/Gossypium arboreum L. are close living relatives of the ancestor allotetraploid species. Our studies suggest that for resolving phylogenetic relationship among the various plant species EST-SSRs could be a better choice. This information can be instrumental in transferring novel alleles or loci from the wild species into the cultivated cotton species which would set a stage for cultivating genetically diverse cultivars-a way to achieve sustainable cotton production in changing climate.

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“…Polymorphisms in the forms of insertions, deletions, and substitutions are fairly common within SSR motifs and their flanking regions [30]. Sequences from six loci had revealed no variations, suggesting the solidity of these primers in the microsatellites and in the flanking regions.…”

Section: Discussionmentioning

confidence: 97%

“…Microsatellite or simple sequence repeat markers have proven useful for genetic diversity analysis in different crop species [20,30]. Only a few SSR markers have been developed for the genetic analysis of Jatropha [5,37].…”

Section: Discussionmentioning

confidence: 99%

Molecular Characterization of Jatropha curcas Resources and Identification of Population-Specific Markers

et al. 2011

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Jatropha curcas L. is cited as one of the best candidates for future oil and biodiesel production. It is widespread in many tropical and subtropical countries but has not yet received much genetic improvement. The objective of this study was to collect Jatropha germplasm and characterize it with molecular markers. A total of 64 genotypes, collected from seven geographic locations on two continents, were analyzed with 32 simple sequence repeat and two candidate gene-specific primers (ISPJ-1 gene and Curcin-P2 gene promoter). In general, markers were found to be highly conserved, and many (40%) were monomorphic in the studied populations. Polymorphic primers, which amplified population-specific fragments, were identified. The polymorphic information content of the polymorphic markers ranged from 0.03 to 0.47. Genetic similarity analysis identified two distinct groups at 0.73 DICE similarity coefficient. Group I included germplasm collected from the islands of Cuba and Cape Verde, and group II consisted of Brazil, Mozambique, and Senegal populations. Island genotypes were found to be very distinct compared to their mainland counterparts. Sequencing of monomorphic fragments identified single nucleotide polymorphism (SNP) between these two groups. Highresolution melting analysis of the SNP in the Jcps9 locus further confirmed the two gene pools. Sequencing of polymorphic fragments of the Jc03 locus identified a deletion in a (GT) 4 repeat motif in the genotypes in group II. Several population-specific microsatellites and SNP markers have been recognized. The distinct Jatropha genotypes and the population-specific molecular markers identified in this study will be valuable resources in breeding programs.

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Tall fescue EST-SSR markers with transferability across several grass species

Cited by 276 publications

References 43 publications

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

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

Pros and cons of using genomic SSRs and EST-SSRs for resolving phylogeny of the genus Gossypium

Molecular Characterization of Jatropha curcas Resources and Identification of Population-Specific Markers

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