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

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

doi:10.3389/fpls.2022.1102938

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

Front Plant Sci. 2023 Jan 9:13:1102938. doi: 10.3389/fpls.2022.1102938. eCollection 2022.

Authors

Pingping Li¹, Jing Jiang², Guogen Zhang³, Siyu Miao², Jingbing Lu², Yukang Qian², Xiuqin Zhao², Wensheng Wang^{2

3}, Xianjin Qiu¹, Fan Zhang^{2

3}, Jianlong Xu^{2

4}

Affiliations

¹ Ministry of Agriculture and Rural Affairs (MARA) Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou, China.
² Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
³ College of Agronomy, Anhui Agricultural University, Hefei, China.
⁴ Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.

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.

Keywords: GWAS; candidate genes; germplasm resource; heat stress; rice; transcriptome analysis.

Grants and funding

This work was funded by the National Natural Science Foundation of China (U21A20214), the Key Research and Development Project of Hainan Province (ZDYF2021XDNY128), and the Agricultural Science and Technology Innovation Program and the Cooperation and Innovation Mission (CAAS-ZDXT202001).