LARGE-SCALE DEVELOPMENT OF PIP AND SSR MARKERS AND THEIR COMPLEMENTARY APPLIED IN Nicotiana

摘要

PIP (Potential Intron Polymorphism) and SSR (Simple Sequence Repeats) were used in many species, but large-scale development and combined use of these two markers have not been reported in tobacco. In this study, a total of 12,388 PI P and 76,848 SS Rmarkers were designed and uploaded to a web-accessible database (http://yancao.sdau.edu.cn/tgb/). E-PCR analysis showed that PIP and SSR rarely overlapped and were strongly complementary in the tobacco genome. The density was 3.07 PIP and 1.72 SSR markers per 10 kb of the known sequences. A total of 153 and 166 alleles were detected by 22 PIP and 22 SSR markers in 64 Nicotiana accessions. SSR produced higher PIC (polymorphism information content) values and identified more alleles than PIP, whereas PIPcould identify larger numbers of rare alleles. Mantel testing demonstrated a high correlation coefficient (r= 0.949, P< 0.001) between PIPand SSR. The UPG MA dendrogram created from the combined PIP and SSR markers was clearer and more reliable than theindividual PIP or SSR dendrograms. It suggested that PIP and SSR can make up the deficiency of molecular markers not only in tobacco but other plant.