Development of Elytrigia repens EST-SSR markers and its application

To develop new simple sequence repeat (SSR) markers for Elytrigia repens, EST-SSR primers of E. repens were designed using the EST sequences of E. repens in NCBI database.The genetic diversity of 47 Elytrigia samples were analyzed using EST-SSR markers to determine the function of EST-SSR in E. repens. Results showed that: From the 27891 Elytrigia EST sequences released in NCBI, 1 068 SSRs were searched. Among those EST-SSRs, the frequency of hexamer motifs was the highest, which is 53.83% of the total number of SSRs,whereas the frequency of dimer, trimer tetramer, pentamer, hexamer were AC/TG(2.72%), CGC/GCG(1.87%), CGAC/GCTG(5.24%), CCGCC/GGCGG(0.37%), CAGCTC/GTCGAG (3.37%), respectively. 105 pairs of EST-SSR primers were designed and synthesized, and 64 pairs (60.95%) of EST-SSR primers led to PCR amplification products. 18 EST-SSR primers were randomly selected and used to analyze the genetic diversity of 47 Elytrigia samples. The results showed that the polymorphic percentage was 78.64%,polymorphic information content (PIC) was in the range of 0.22~0.83. Taken together, all results indicate that the EST-SSR markers of E. repens developed in this study is highly effective and valuable, and they can be used in the research of genetic diversity and association analysis for important trait in E. repens.