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.