| Drought-resistance is one of the major quantitative traits of rice, whose relative genes turn out to be in quantitative trait loci (QTL) in the rice genome. A large number of mapping information of the drought-resistance QTL has been accumulated along all the 12 chromosomes in rice. And the key to reveal the essence of these QTLs is to improve the mapping resolution. In view of the broad and successful application of association analysis in the fine mapping of complex traits, it should be feasible to apply it in the QTL analysis. And the understanding of Single-nucleotide polymorphisms as well as the structure of linkage disequilibrium in target loci plays an important fundamental role in this area.Fifty-one DNA fragments in the region of drought-resistance QTL, in total of 32,150 bp, were sequenced in all of the 80 cultivated rice accessions including 40 accessions of indica group and 40 of japonica group. 189 SNPs, including 165 single-base substitution and 24 indels were found. Of the 165 single-base substitution, transitions accounted for 113 (68%) and transversions for 52 (32%), with the ratio of 2.1:1 corresponding to the theoretical value of 2:1.142 and 136 SNPs were found respectively in indica group and japonica group, the SNPs frequency (0w) is 1.10×10-3 in indica group and 1.07×10-3 in japonica group, suggesting that both indica group and japonica group has abundant single-nucleotide polymorphisms.Distinct structures of linkage disequilibrium were detected in the three investigated drought-resistance QTL regions. Each regions show different pattens of LD , the physical distance between sites can range from 200kb to 3000kb or even more, but LD in japonica group appears to extend over a longer distance than they are in indica group. It indicates that different pattens of LD would not only be detected in different chromosomal regions but also in the same area.How to take a modest number of SNPs and full advantage of linkage disequilibrium information on genome-wide association analysis was discussed at the end of this paper. |
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