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GrainGenes Reference Report: TAG-106-411

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Reference	TAG-106-411
Title	Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.)
Journal	Theoretical and Applied Genetics
Year	2003
Volume	106
Pages	411-422
Author	Thiel T Michalek W Varshney RK Graner A
Abstract	Summary: A software tool was developed for the identification of simple sequence repeats (SSRs) in a barley (Hordeum vulgare L.) EST (expressed sequence tag) database comprising 24,595 sequences. In total, 1,856 SSR-containing sequences were identified. Trimeric SSR repeat motifs appeared to be the most abundant type. A subset of 311 primer pairs flanking SSR loci have been used for screening polymorphisms among six barley cultivars, being parents of three mapping populations. As a result, 76 EST-derived SSR-markers were integrated into a barley genetic consensus map. A correlation between polymorphism and the number of repeats was observed for SSRs built of dimeric up to tetrameric units. 3'-ESTs yielded a higher portion of polymorphic SSRs (64%) than 5'-ESTs did. The estimated PIC (polymorphic information content) value was 0.45 +/- 0.03. Approximately 80% of the SSR-markers amplified DNA fragments in Hordeum bulbosum, followed by rye, wheat (both about 60%) and rice (40%). A subset of 38 EST-derived SSR-markers comprising 114 alleles were used to investigate genetic diversity among 54 barley cultivars. In accordance with a previous, RFLP-based, study, spring and winter cultivars, as well as two- and six-rowed barleys, formed separate clades upon PCoA analysis. The results show that: (1) with the software tool developed, EST databases can be efficiently exploited for the development of cDNA-SSRs, (2) EST-derived SSRs are significantly less polymorphic than those derived from genomic regions, (3) a considerable portion of the developed SSRs can be transferred to related species, and (4) compared to RFLP-markers, cDNA-SSRs yield similar patterns of genetic diversity
External Databases	Pubmed: 12589540
Locus	GBM1023 [ Show all 76 ]
Probe	GBM1023 [ Show all 77 ]
Keyword	[ Hide all but 1 of 36 ] allele allele variation barley diversity diversity analysis dna dna fragment est fragment length polymorphism fragments genetic diversity genetic mapping genome genomic genomic regions hordeum linkage maps locus map mapping microsatellite marker parents polymorphism polymorphism information content (pic) region rflp rice rye screening sequence simple sequence repeats (ssrs) ssr ssr marker tool winter yield

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