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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	[ Hide all but 1 of 76 ] GBM1023 GBM1036 GBM1001 GBM1002 GBM1003 GBM1004 GBM1005 GBM1006 GBM1007 GBM1008 GBM1011 GBM1013 GBM1015 GBM1016 GBM1017 GBM1019 GBM1020 GBM1021 GBM1022 GBM1024 GBM1025 GBM1026 GBM1027 GBM1029 GBM1031 GBM1032 GBM1034 GBM1035 GBM1038 GBM1039 GBM1040 GBM1044 GBM1047 GBM1048 GBM1049 GBM1051 GBM1052 GBM1053 GBM1055 GBM1057 GBM1058 GBM1060 GBM1061 GBM1062 GBM1064 GBM1068 GBM1069 GBM1071 GBM1073 GBM1075 GBM1076 GBM1042 GBM1030 GBM1070 GBM1072 GBM1066 GBM1012 GBM1010 GBM1074 GBM1014 GBM1043 GBM1037 GBM1056 GBM1059 GBM1050 GBM1046 GBM1028 GBM1067 GBM1009 GBM1018 GBM1041 GBM1045 GBM1054 GBM1063 GBM1033 GBM1065
Probe	GBM1023 [ Show all 77 ]
Keyword	allele [ Show all 36 ]

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