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

IntroductionRice (Oryza sativa L.) 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. MethodsWe 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 similar to 2.8 million single nucleotide polymorphisms (SNPs). ResultsAmong the six detected loci, qHT7 harbored the strongest association signal and the most associated SNPs. By comparing the transcriptomes of two representative accessions with contrasting heat tolerance, LOC_Os07g48710 (OsVQ30) was selected as a promising candidate gene in qHT7 due to the significant difference in its expression level between the two accessions. Haplotype 4 (Hap4) of LOC_Os07g48710 was determined as the favorable haplotype for heat tolerance via the gene-based haplotype analysis. The heat-tolerant haplotype LOC_Os07g48710Hap4 is highly enriched in the tropical Geng/Japonica accessions, and its frequency has decreased significantly during the improvement process of rice varieties. DiscussionBased on the GWAS and transcriptomics integrated results, a hypothetical model modulated by qHT7 in response to heat stress was proposed. Our results provide valuable candidate genes for improving rice heat tolerance through molecular breeding.

Automated summary

In this study, 620 diverse rice accessions were evaluated for heat tolerance at the seedling stage, and six loci associated with heat tolerance were identified through a genome-wide association study. Among these loci, qHT7 showed the strongest association signal and the most associated SNPs. By comparing the transcriptomes of two representative accessions, LOC_Os07g48710 was identified as a promising candidate gene in qHT7, and its Hap4 was determined to be the favorable haplotype for heat tolerance. This study provides valuable candidate genes for improving rice heat tolerance through molecular breeding.