Integrating GWAS and transcriptomics to identify candidate genes conferring heat tolerance in rice.

INTRODUCTION

Rice () production is being challenged by global warming. Identifying new loci and favorable alleles associated with heat tolerance is crucial to developing rice heat-tolerant varieties.

METHODS

We evaluated the heat tolerance at the seedling stage using 620 diverse rice accessions. A total of six loci associated with heat tolerance were identified by a genome-wide association study (GWAS) with ~2.8 million single nucleotide polymorphisms (SNPs).

RESULTS

Among the six detected loci, harbored the strongest association signal and the most associated SNPs. By comparing the transcriptomes of two representative accessions with contrasting heat tolerance, () was selected as a promising candidate gene in due to the significant difference in its expression level between the two accessions. Haplotype 4 (Hap4) of was determined as the favorable haplotype for heat tolerance via the gene-based haplotype analysis. The heat-tolerant haplotype Hap4 is highly enriched in the tropical accessions, and its frequency has decreased significantly during the improvement process of rice varieties.

DISCUSSION

Based on the GWAS and transcriptomics integrated results, a hypothetical model modulated by in response to heat stress was proposed. Our results provide valuable candidate genes for improving rice heat tolerance through molecular breeding.