Tall fescue genomic SSR markers: development and transferability across multiple grass species

Saha, Malay C.; Cooper, J.D.H.; Mian, M. A. Rouf; Chekhovskiy, Konstantin; May, Gregory D.

doi:10.1007/s00122-006-0391-2

Cited by 116 publications

(96 citation statements)

References 45 publications

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“…It has been reported that EST-SSR markers show lower polymorphism compared to genomic SSR markers (Saha et al, 2006). In our research, a total of 9 EST-SSR markers have been found polymorphic from 49 EST-SSRs, giving a polymorphism rate of 18%, compared with the 72% polymorphism rate found by Burstin et al (2001).…”

Section: Discussionmentioning

confidence: 53%

Developing new SSR markers from ESTs of pea (Pisum sativum L.)

Gong

Mao

et al. 2010

J. Zhejiang Univ. Sci. B

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Abstract:The development of expressed sequence tags (ESTs) from pea has provided a useful source for mining novel simple sequence repeat (SSR) markers. In the present research, in order to find EST-derived SSR markers, 18 552 pea ESTs from the National Center for Biotechnology Information (NCBI) database were downloaded and assembled into 10 086 unigenes. A total of 586 microsatellites in 530 unigenes were identified, indicating that merely 5.25% of sequences contained SSRs. The most abundant SSRs within pea were tri-nucleotide repeat motifs, and among all the tri-nucleotide repeats, the motif GAA was the most abundant type. In total, 49 SSRs were used for primer design. EST-SSR loci were subsequently screened on 10 widely adapted varieties in China. Of these, nine loci showed polymorphic profiles that revealed two to three alleles per locus. The polymorphism information content value ranged from 0.18 to 0.58 with an average of 0.41. Furthermore, transferable analysis revealed that some of these loci showed transferability to faba bean. Because of their polymorphism and transferability, these nine novel EST-SSRs will be valuable tools for marker-assisted breeding and comparative mapping of pea in the future.

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Section: Discussionmentioning

confidence: 53%

Developing new SSR markers from ESTs of pea (Pisum sativum L.)

Gong

Mao

et al. 2010

J. Zhejiang Univ. Sci. B

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“…The PCR products were analyzed with ABI 3730 DNA Analyzer (Applied Biosystems) following the protocol suggested by Saha et al [31]. ABI data were scored as present (1) or absent (0) with GeneMapper Software v 3.7.…”

Section: Genotyping and Sequencingmentioning

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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“…Moreover, due to their association with coding sequences, EST-SSRs can also lead to the direct gene tagging for QTL mapping of agronomically important traits and increase the efficiency of marker-assisted selection [15]. In addition, EST-SSRs show a higher level of transferability to closely related species than genomic SSR markers [13,16-18] and can be served as anchor markers for comparative mapping and evolutionary studies [19,20]. …”

Section: Introductionmentioning

confidence: 99%

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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Tall fescue genomic SSR markers: development and transferability across multiple grass species

Cited by 116 publications

References 45 publications

Developing new SSR markers from ESTs of pea (Pisum sativum L.)

Developing new SSR markers from ESTs of pea (Pisum sativum L.)

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

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

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