Development of SSR markers from ESTs of gramineous species and their chromosome location on wheat

A total of 407,663 expressed sequence tags (ESTs) of wheat, barley, maize, rice and sorghum, obtained from GenBank/dbEST, were used to search for simple sequence repeats (SSRs). A total of 10,253 EST-SSRs, which accounted for 2.52% of all the ESTs, were identified. Using Primer Premier 5.0, software 1,367 EST-SSR primer pairs were designed, of which 715 with high quality were synthesized. The 715 primer pairs were tested on wheat, rice, maize, cotton and soybean under the same PCR-conditions, and the effective primer pairs in the five crops were 500 (69.93%), 383 (53.57%), 452 (63.22%), 357 (49.93%) and 388 (56.27%), respectively. This indicated a high transferability of EST-SSR markers between far-ranging species. In addition, 139 EST-SSR primer pairs with 240 loci were localized on all the 21 wheat chromosomes by using Chinese Spring nulli-tetrasomic lines of wheat.