Identification of candidate genes for heat tolerance in rice by genome-wide association study and transcriptome sequencing

Heat stress during the heading stage has a particularly negative impact on rice. In this study, we employed 159 core rice germplasms as materials, set up high-temperature and normal-temperature treatments during the heading stage, and measured the phenotypic traits such as the seed-setting rate, the number of grains per panicle, and the thousand-grain weight. Combining the results and data from whole-genome sequencing, we employed genome-wide association study (GWAS) to identify the heat tolerance-related genes or QTLs in rice. Additionally, we selected two heat-tolerant and two heat-intolerant varieties for transcriptome sequencing after high-temperature treatment during the heading stage, and further screened and analyzed the candidate genes based on GWAS and transcriptome sequencing. As a result, a total of 206 genes related to heat tolerance during rice heading were detected by GWAS, and 57 genes were co-detected by GWAS and transcriptome sequencing. Further gene function annotation and haplotype analysis identified five important candidate genes related to heat tolerance, including LOC_Os03g18010, LOC_Os07g43700, LOC_Os10g22980, LOC_Os10g41660, and LOC_Os11g39020. qRT-PCR verified that the trends of relative expression of these five genes were highly consistent with the RNA-seq data. The findings may lay an important foundation for mining and cloning heat-tolerant genes in rice for biotechnological improvement.