| We choose representative Chinese and foreign cultivated rice including accessions of indica and japinica for the study of single nucleotide polymorphisms (SNPs) and linkage disequilibrium (LD), to explore the feasibility of association analysis in finding rice drought-resistant gene. The mainly results are as follows:1. Ninety eight DNA fragments which distribution on six drought-resistance QTL of Oryza sativa L. were successfully sequenced in 42 Indica and 28 Japonica. The total length of the sequence is 46895 bp.455 single-base changes (SNPs) were found. There were 306 transitions and 149 transversions in all single-base changes (SNPs). And TslTv was 2.05:1, which is consistent with the theoretical ratio 2:1. There are 371 SNPs in Indica, the SNPs frequencies (θw) in indica is 1.84×10-3,πis 1.74×10-3. There are 271 SNPs in japonica, the SNPs frequencies (θw) in japonica is 1.49×10-3,πis 0.76×10-3, the SNPs frequencies in indica are higher than in japonica. The SNPs frequencies in the six QTL region are significantly different. In indica, QTL QRT10 has the highest SNPs frequency (0w=2.31×10-3). QTL QRfp12 has the lowest SNPs frequency (9w=1.15×10-3). In japonica, QTL QRT10 has the highest SNPs frequency (9w=2.70×10-3). QTL QRfp12 has the lowest SNPs frequency (9w=0.48×10-3), a difference of more than five times.2. The most SNPs have Minor SNPs frequency≤10% in Indica and Japonica. the number of SNPs tends to reduce when the Minor SNPs frequency increase. japonica has more rare SNPs, There are 121 SNPs with Minor SNPs frequency (<10%) in 271 SNPs, the frequency is 44.6%. In indica, there are 131 SNPs with Minor SNPs frequency (<10%) in 371 SNPs. the frequency is 35.3%, The number of rare SNPs is different in different QTL regions. In Indica, the proportion of rare SNPs in QTL qDT-5 is 81.1%, the proportion of rare SNPs in QTL QRfp12 is 6.3%. In Japonica, the proportion of rare SNPs in QTL QRT10 is 100%, the proportion of rare SNPs in QTL OA8.1 is 24.1%.3. Linkage disequilibrium structures were detected in the six investigated drought-resistance QTL regions. Each regions show different patterns of LD, The extent of LD in japonica group is500->1500 kb, the extentof LD in indica group is 500-1500 kb. The median R2 values of japonica group is 0.2957, indica group is 0.2473. The extent of LD in japonica is larger than indica. In indica, QTL PRL11.1 has the lowest R2 values (0.0840), QTL qCC-1 has the largest R2 values (0.3535). In japonica, QTL PRL11.1 has the lowest R2 values (0.1334), QTL qDT-5 has the largest R2 values (0.4389). It shows that different QTL regions has different LD structure even in the same group.4. Cluster analysis based on SNPs haplotype shows that indica and japonica clearly clustered into two separate groups, but both in the indica and japonica, the difference of lowland rice and upland rice is not obvious, mixed with each other. It shows that the differences between indica and. japonica are higher than lowland rice and upland rice.5. The association analysis show that QTL qCC-1, qDT-5, OA8.1, PRL11.1 associated with drought-resistance, and the most notable association was on QTL PRL11.1 of chromosome 11. The ratio of QTL linkage analysis agree with association analysis is 67%, it suggests that association analysis in finding rice drought-resistance genes is possible. |
