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

作者：Li, Pingping; Jiang, Jing; Zhang, Guogen; Miao, Siyu; Lu, Jingbing; Qian, Yukang; Zhao, Xiuqin; Wang, Wensheng; Qiu, Xianjin^*; Zhang, Fan^*; Xu, Jianlong^*

来源：Frontiers in Plant Science, 2023, 13: 1102938.

DOI：10.3389/fpls.2022.1102938

• GWAS
• transcriptome analysis
• heat stress
• candidate genes
• germplasm resource
• 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.