Data Mining for SSRs in EST Rescources and EST-SSR Markers Development in Radish
A total of 287 349 ESTs of radish were downloaded from NCBI database. After preprocessing, 58 105 non-redundant ESTs with the total length of 38 622.476 kb were obtained. By using the MISA program, a total of 3 718 SSRs were observed in 3 523 ESTs and the average distance between SSRs was 10.39 kb. 265 types of motifs were found in radish＇s ESTs and the dominant motifs types are dinucleotide, trinucleotide and exanucleotide repeats. AG/CT was the main motifs type （91.34%） in dinucleotide repeats; AAG/CTT was the main motifs type （ 35.86%） in trinucleotide; AAGGAG/CCTCTT and AAGAGG/CCTTCT were two main motifs types （total 12.78%） in exanucleotide. Comprehensively analysis indicated that EST-SSRs of radish with high frequency and rich motifs types were potential for the development of polymorphic primers. Using the primer 3.0, 183 primers were designed and synthesized based on different dominant motifs types, and verified with 12 typical radish germplasms for polymorphism and one pair of parents and their F1 for codominance. The results showed that the products of 159 primers are clear and effective, 64 pairs were polymorphic among the germplasms and 27 were codominant between the parents and their hybrids.
NETL
NSTL
万方数据
维普
