Construction Of Genetic Linkage Map Based On SSR Marker And Mapping Of QTLs Related To Rice Cadmium Content Using A RIL Population In Rice

Cadmium is a widespread contaminant. Cadmium moves into human body by way of food chains, causing genotoxicity, cytotoxicity, and finally inhibition of cell proliferation and apoptosis. Therefore, it’s of great importance to minimize cadmium in human diet, with the use of molecular marker-assisted breeding to cultivate crop varieties with low-Cd accumulation. In this study, we constructed a genetic linkage map using recombinant inbred lines with corresponding microsatellite markers(SSR), which derived from Nipponbare and 9311, for the purpose of analyzing QTLs related to brown rice cadmium content. The nucleotide sequences of seven cadmium associated genes in rice were determinated, with many discrepancy sites to be found, genotype of parts of the groups were identified. We also analyzed the relationship between SSR and brown rice cadmium content, to provide molecular markers for cultivating crop varieties with low-Cd accumulation. The main results are as follows: 1、Total 614 SSR(Simple Sequence Repeat)markers were used to screen the Polymorphism between two Parents(Nipponbare and 9311). Among 278 pairs markers with Polymorphism, 123 were finally used to construct a genetic linkage map in a Population of 96 lines. It spans 2424.01 c M in length covering all 12 chromosomes, with an average density of 19.71 c M. 2、Three QTLs were detected, associated with brown rice cadmium. one were mapped on chromosomes 6 between RM 1370 and RM 4608. The other were mapped on chromosomes 7 between F14 and F21. The third one were mapped on chromosomes 9 by ST 6062. 3、The nucleotide sequences of seven cadmium associated genes in rice were determinated, with many discrepancy sites, sequence and Amino acids variations to be found between Nipponbare and 9311. 24 rice RIL populations were analyzed with sequence-based typing. 4、Ten genes related to cadmium brown rice were analyzed directly by bioinformatics, in order to figure out the multiple differences sites between Nipponbare and 9311. Therefore specific primers were designed for genotyping a group of 96 rice RIL materials. Thus we found that gene Os HMA3 and Os NRAMP5 are of high correlation with brown rice cadmium content. 5、Thirteen SSR markers associated with brown rice cadmium were detected, mapped on chromosomes 2, 3, 5, 6, 7, 8, 9, 10. Among them, the greatest positive effect is RM 3805, with effect of 0.225. The greatest negative effect is S7-25049, with effect of-0.083.