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, 1367 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.