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

Front Plant Sci.; 2023 Jan 9:13:1102938. doi: 10.3389/fpls.2022.1102938.

Abstract

Introduction: Rice (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.

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, 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.

Discussion: Based 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.

See https://pubmed.ncbi.nlm.nih.gov/36699845/

Figure 1. Phenotypic variations of heat tolerance and identification of loci associated with heat tolerance by GWAS in 620 rice accessions. (A) Box-plots of survival rate (SR) for the whole population, Xian/Indica (XI), and Geng/Japonica (GJ) subpopulations. (B) Box-plots of SR among GJ-adm, GJ-subtropical (GJ-sbtrp), GJ-temperate (GJ-tmp), GJ-tropical (GJ-trp), XI-1A, XI-1B, XI-2, XI-3, and XI-adm accessions. (C) Box-plots of leaf score of heat tolerance (SHT) for the whole population, XI and GJ subpopulations. (D) Box-plots of SHT among GJ-adm, GJ-sbtrp, GJ-tmp, GJ-trp, XI-1A, XI-1B, XI-2, XI-3, and XI-adm accessions. (E) Manhattan plots of GWAS results for SR. (F) Manhattan plots of GWAS results for SHT. (G) Genome-wide significant loci for SR and SHT. In A-D, different letters indicate significant differences (P < 0.05, Duncan’s multiple range post-hoc test). In E, F, the horizontal blue lines represent the suggestive significant threshold (P = 2.29E-6).