AUTHOR=Li Pingping , Jiang Jing , Zhang Guogen , Miao Siyu , Lu Jingbing , Qian Yukang , Zhao Xiuqin , Wang Wensheng , Qiu Xianjin , Zhang Fan , Xu Jianlong 

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

JOURNAL=Frontiers in Plant Science

VOLUME=13

YEAR=2023

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2022.1102938

DOI=10.3389/fpls.2022.1102938

ISSN=1664-462X

ABSTRACT=<sec><title>Introduction</title><p>Rice (<italic>Oryza sativa L.</italic>) 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.</p></sec><sec><title>Methods</title><p>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). </p></sec><sec><title>Results</title><p>Among the six detected loci, <italic>qHT7</italic> harbored the strongest association signal and the most associated SNPs. By comparing the transcriptomes of two representative accessions with contrasting heat tolerance, <italic>LOC_Os07g48710</italic> (<italic>OsVQ30</italic>) was selected as a promising candidate gene in <italic>qHT7</italic> due to the significant difference in its expression level between the two accessions. Haplotype 4 (Hap4) of <italic>LOC_Os07g48710</italic> was determined as the favorable haplotype for heat tolerance via the gene-based haplotype analysis. The heat-tolerant haplotype <italic>LOC_Os07g48710</italic>Hap4 is highly enriched in the tropical <italic>Geng/Japonica</italic> accessions, and its frequency has decreased significantly during the improvement process of rice varieties. </p></sec><sec><title>Discussion</title><p>Based on the GWAS and transcriptomics integrated results, a hypothetical model modulated by <italic>qHT7</italic> in response to heat stress was proposed. Our results provide valuable candidate genes for improving rice heat tolerance through molecular breeding. </p></sec>