Identification of novel and useful EST-SSR markers from de novo transcriptome sequence of wheat (Triticum aestivum L.).

Simple sequence repeats (SSRs) are highly informative, polymorphic, and co-dominant Mendelian markers that provide an important genomic resource for genetic research. Recently, the use of large-scale transcriptome sequence has become a reliable and efficient approach for the identification and development of new EST-SSR markers. In this study, 8389 potential SSRs with a minimum of five repetitions for all motifs were identified from 121,210 unigenes. Gene ontology analysis indicated that the unigenes containing SSR loci participate in various biological processes of regulation, growth, development, metabolism, and apoptosis in wheat. As in many other plants, trinucleotide repeats were found to be the most abundant repeat units with a frequency of 62.33%. A subset of 300 EST-SSRs was randomly selected for the applicability of EST-SSRs to be evaluated. Of the 300 primer pairs tested, 177 (59%) yielded unambiguous PCR products among five wheat cultivars. Using the Chinese Spring nulli-tetrasomic line, 131 of the 177 EST-SSR primer pairs yielded products and 178 loci were found to be located on all the 21 wheat chromosomes. These findings suggest that the novel EST-SSR markers, as a basis for future genetic linkage and gene tagging analysis, are a valuable tool for genetic mapping, marker assisted selection, and comparative genome analysis.