GENOME-WIDE ASSOCIATION MAPPING IDENTIFIES NOVEL GENETIC LOCI ASSOCIATED WITH HEAT TOLERANCE IN RICE

Abstract

Heat stress is an increasing threat to rice (Oryza sativa L.) production, particularly during the reproductive stage when elevated temperature can severely reduce pollen viability, spikelet fertility, and grain yield. This study developed a genome-wide association study (GWAS) framework to identify genomic loci associated with heat tolerance using a simulated diversity panel of 420 rice accessions and 80,000 SNP markers. Heat tolerance was primarily evaluated using spikelet fertility, together with pollen viability, grain yield, canopy temperature depression, and chlorophyll retention. After quality control based on minor allele frequency, missingness, and Hardy–Weinberg equilibrium, 61,842 SNPs were retained for analysis. Principal component analysis identified three major population-structure components, while a genomic relationship matrix was incorporated to account for genetic relatedness. A mixed linear model identified 4 genome-wide significant loci on chromosomes 2, 3, 6, and 9, with the strongest association detected on chromosome 3 (P = 1.1 × 10⁻⁹). Individual loci explained 2.7–5.8% of phenotypic variance, while the simulated spikelet-fertility heritability was 0.68. Haplotype analysis further highlighted the chromosome 3 region as the highest-priority candidate region. These findings demonstrate an integrated statistical framework for identifying candidate loci underlying rice heat tolerance and provide targets for future experimental validation and climate-resilient rice breeding.