Genome-wide Association Study Of Rice Seed Dormancy

The dormancy and strength of rice seeds directly affect the yield and quality of rice.Strong dormancy varieties that cannot be released from dormancy after sowing will have a low emergence rate and an irregular emergence,while weak dormancy varieties or non-dormancy varieties are prone to panicle germination,which will lead to a decrease in yield and seed quality.In order to explore the key genes of rice seed dormancy and select new rice germplasm resources with moderate dormancy,198 rice core germplasm from 82countries and 164 rice core germplasm resources from 3K were used as experimental materials and planted in Hainan,Liuyang and Changsha,Hunan,respectively.To not break the dormancy of seed germination rate after treatment and breaking dormancy germination rate as the rate of seed dormancy phenotype,the difference between the analysis of different varieties and dormancy characteristic between each subgroup,and combining with genotype GWAS analysis was carried out on the rice seed dormancy,reuse of haplotype analysis of candidate genes for validation,the main results were as follows:1.By TASSEL5.2 software analysis,with P=10^-4or P=10^-3as the significance threshold,a total of 50 significantly associated SNP sites were detected in 3 environments.A total of 34SNP loci associated with dormancy were detected in Hainan,4 significant SNP loci were detected in Liuyang,and 12 significant SNP loci were detected in Changsha.Among them,two identical sites were detected in Hainan and Changsha,named qsdo7-1 and qsdo5-1.2.We analyzed candidate genes for QTLs qsdo7-1 and qsdo5-1,which were jointly detected in two environments,Hainan and Changsha,Hunan.By screening the significant sites Chr5＿5991867,Chr7＿20001456,Chr5＿5817741,and Chr7＿20113643 within the range of 200 Kb,4 candidate genes were screened in qsdo7-1 and qsdo5-1,a total of 8 candidate genes.3.Through haplotype analysis of the candidate genes of QTLs qsdo7-1 and qsdo5-1,we found that none of the candidate genes of qsdo7-1 can have a significant association with the phenotype,and the locus of qsdo5-1 has the haplotype of LOC＿Os05g10830 and LOC＿Os05g10620 can be significantly correlated with the phenotype,indicating that these two genes may be candidate genes for the locus of qsdo5-1.