Abstract:

【Objective】 The objective of this study was to develop new simple sequence repeat (SSR) markers from EST (Expressed sequence tag) sequences (EST-SSR markers) for wheat. 【Method】 The wheat EST sequences from GenBank/dbEST (from April 18, 2006 to February 4, 2007) were used to search for SSRs, EST-SSR primer pairs were designed using Primer5.0 software, the validity of primer pairs were detected using three wheat varieties, and the marker loci were mapped using RIL population and Mapmaker/Exp3.0 software.【Result】From the 265 362 wheat EST sequences released in GenBank/dbEST, 6 314 SSRs were found which amounts to 2.38% of the total number of ESTs. Among those EST-SSRs, the most motifs were dinucleotides and trinucleotides, which were 2 237 (35.43%) and 2 084 (33.01%), respectively. For dinucleotides, GA/CT (17.85%) and AG/TC (10.37%) were the most frequent repeat, followed by CA/GT (4.07%) and AC/TG (2.53%); and for trinucleotides, CAA/GTT (3.93%), CGG/GCC (3.83%), CGC/GCG (3.36%), GGC/CCG (3.14%), CTT/GAA (2.53%) and TGC/ACG (2.27%) appeared high frequency. Based on these EST-SSR sequences, 596 EST-SSR primer pairs were designed, 194 of which were synthesized, and 165（85%）led to PCR amplification products. Using a RIL population, the polymorphism of 21 EST-SSR primer pairs with 26 loci were detected, and 23 of those loci were integrated on the wheat genetic map. 【Conclusion】 A total of 165 new wheat EST-SSR markers have been developed. EST sequences are important sources for developing SSR markers.

Key words: wheat, EST-SSR, molecular marker, RIL, genetic map