Influence of microsatellite DNA sequence integrity to polymorphism

• 1、Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture & Forestry University

Abstract：IMicrosatellites are tandem repeats with 1-6bp for a repeat unit. SSR concludes perfect SSR and imperfect SSR. Imperfect SSRs refer the tandem repeats allowing for some mismatch bases. The polymorphism of SSR is very important for its application. In this study, two model plants rice and Arabidopsis were used to analyze the relationship between SSR integrity and polymorphism. We searched SSR sequences in Oryza sative Nipponbare and Arabidopsis thaliana Columbia genome sequence, and designed primers in the flanking sequence of SSR, then used these primers to run e-PCR upon O.sativa 93-11 and A. thaliana Lansberg genome sequences. After blasting and comparing, polymorphism primers were founded and analyzed. 245 pairs primers in Magnaporthe grisea genome were also used to recomfirm the results through experiments. The results showed that in rice, Arabidopsis and M. grisea genomes the polymorphism of imperfect SSR were lower obviously than perfect SSR expect for pentermers. However this tendency related to the integrity of SSR sequence. When the identity of SSR is larger than 95%, the polymorphism of imperfect SSR increased distinctly, even higher than perfect SSR. This phenomenon is particular obvious in Arabidopsis genome. Therefore, imperfect SSR with identity larger than 95% should be pay attention when analyzing SSR sequence. The information obtained in this study will lay the foundations for studying the variation mechanism of SSR and facilitate the study of genome evolution and the development of SSR markers in other plants.

Keywords： Rice Arabidopsis M.grisea, perfect SSR imperfect SSR polymorphism