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GrainGenes Reference Report: TAG-104-286

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Reference	TAG-104-286
Title	Characterization of trinucleotide SSR motifs in wheat
Journal	Theoretical and Applied Genetics
Year	2002
Volume	104
Pages	286-293
Author	Song QJ Fickus EW Cregan PB
Abstract	Summary: Length differences among trinucleotide-based microsatellite alleles can be more easily detected and frequently produce fewer 'stutter bands' as compared to dinucleotide-based microsatellite markers. Our objective was to determine which trinucleotide motif(s) would be the most-polymorphic and abundant source of trinucleotide microsatellite markers in wheat (Triticum aestivum L.). Four genomic libraries of cultivar 'Chinese Spring' were screened with nine trinucleotide probes. Based on the screening of 28550 clones, the occurrences of (CTT/GAA)n, (GGA/CCT)n, (TAA/ATT)n, (CAA/GTT)n, (GGT/CCA)n, (CAT/GTA)n, (CGA/GCT)n, (CTA/GAT)n, and (CGT/GCA)n repeats were estimated to be 5.4x10(4), 3.5x10(4), 3.2x10(4), 1.2x10(4), 6.3x10(3), 4.9x10(3), 4.5x10(3), 4.5x10(3) and 3.6x10(3), i.e., once every 293 kbp, 456 kbp, 500 kbp, 1.3 Mbp, 2.6 Mbp, 3.2 Mbp, 3.6 Mbp, 3.6 Mbp and 4.5 Mbp in the wheat genome, respectively. Of 236 clones selected for sequencing, 38 (93%) (TAA/ATT)n, 30 (43%) (CTT/GAA)n, 16 (59%) (CAA/GTT)n, 3 (27%) (CAT/GTA)n and 2 (4%) (GGA/CCT)n clones contained microsatellites with eight or more perfect repeats. From these data, 29, 27 and 16 PCR primer sets were designed and tested to the (TAA/ATT)n, (CTT/GAA)n and (CAA/GTT)n microsatellites, respectively. A total of 12 (41.4%) primers designed to (TAA/ATT)n, four (14.8%) to (CTT/GAA)n, and two (12.5%) to (CAA/GTT)n resulted in polymorphic markers. The results indicated that (TAA/ATT)n microsatellites would provide the most-abundant and the most-polymorphic source of trinucleotide microsatellite markers in wheat
External Databases	http://link.springer-ny.com/link/service/journals/00122/bibs/2104002/21040286.htm
Keyword	[ Hide all but 1 of 36 ] 30 allele bread wheat chinese chinese spring chromosome substitution lines clone cultivar gene genome genomic library human genome library linkage map marker microsatellite microsatellite dna markers microsatellite marker molecular markers motif pcr polymorphic primer probes repeat rice screening sequence repeat markers sequencing simple sequence repeat (ssr) source spring ssr trinucleotide motifs triticum triticum aestivum

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