Integrating GWAS, QTL, mapping and RNA-seq to identify candidate genes for seed vigor in rice (Oryza sativa L.)

Seed vigor is an important seed quality trait in rice (Oryza sativa L.) that profoundly affects seedling morphogenesis in different environments. Generally, highly vigorous seeds have many advantages in agricultural production, such as resistance to adverse stresses, rapid emergence, and yield improvement. In the present study, one germplasm collection and one recombinant inbred line (RIL) population were used to identify quantitative trait loci (QTLs) for seed vigor. A total of 19 single nucleotide polymorphisms (SNPs) were found to be significantly associated with seed vigor (−log10(P) > 6) in the germplasm collection, which consisted of 200 rice cultivars. Nine loci responsible for seed vigor were identified via QTL mapping by using a high-density bin map. To screen the candidate genes more efficiently, we selected six loci that were co-localized in GWAS and QTL mapping, overlapped previous reports, repeat detected across two seasons, or high contribution rate as reliable loci. A total of 44 differentially expressed genes were obtained from the reliable loci via gene expression profile analysis. Among these 44 genes, Os06g0108600, Os06g0110200, Os06g0253100, Os06g0282000, Os07g0583600, Os07g0592600, and Os09g0432300 were the most promising candidates associated with seed vigor.