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

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 4

Candidate gene analysis of qHT7. (A) Local Manhattan plot (top) and LD analysis (bottom) of 150-kb upstream and downstream around the lead SNP rs7_29140282. The red dot is the lead SNP, and its LD block region is marked by the black dotted lines. (B) Relative expression of 14 annotated genes in qHT7. *** FDR < 0.001, ** FDR < 0.01, * FDR < 0.05. G1: F64_Control vs PK_Control; G2: F64_HS vs F64_Control; G3: F64_HS vs PK_HS; G4: PK_HS vs PK_Control. (C) Haplotype of LOC_Os07g48710, which is the promising candidate gene of qHT7. (D) The distribution of SR in the whole population for the four major haplotypes (n > 40 accessions) of LOC_Os07g48710. Different letters above each boxplot indicate significant differences among haplotypes (P < 0.05, Duncan’s multiple range post-hoc test). (E) Verification of the relative expression of LOC_Os07g48710 in F64 and PK under heat stress 24 h by qRT-PCR. UBQ was used as an internal control. The figure presents the relative expression levels of LOC_Os07g48710 relative to that under control conditions in each accession. Bars represent standard deviation of three biological replicates. ***P < 0.001 (two-tailed Student’s t-test). (F, G) Frequency of the four major haplotypes of LOC_Os07g48710 in the GWAS panel (F) and in 3K RG (G). (H) Haplotype frequency distribution of LOC_Os07g48710 in landrace and modern variety of 3K RG. The type of each accession was from the metadata of 3K RG (Wang et al., 2018). (I) Haplotype network of LOC_Os07g48710 retrieved from MBKbase (Peng et al., 2019) (http://www.mbkbase.org/rice/, query date: October 25^th, 2022). Circle size of a given haplotype is proportioned to its number of accessions. Letter n indicates the number of rice accessions belonging to the corresponding haplotype in D and I, subpopulation in F and G, or variety type in H, respectively.