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. 2021 Oct 7;1(1):10.
doi: 10.1007/s44154-021-00011-4.

Genome-wide association study revealed genetic variations of ABA sensitivity controlled by multiple stress-related genes in rice

Lei Peng #  1 , Tingting Xie #  2 , Zilong Guo  1 , Xiaokai Li  1 , Yu Chang  1 , Haifu Tu  1 , Shengchang Wang  1 , Nai Wu  1 , Yilong Yao  1 , Lizhong Xiong  3
Affiliations

Genome-wide association study revealed genetic variations of ABA sensitivity controlled by multiple stress-related genes in rice

Lei Peng et al. Stress Biol. .

Abstract

Abscisic acid (ABA) is a critical phytohormone that regulates multiple physiological processes including plant growth and stress tolerance. The core ABA signaling pathway has been well established, but genetic variations mediating ABA responses remain largely unknown. In this study, we performed genome-wide association study (GWAS) to identify loci and genes associated with ABA sensitivity (reflected by seed germination inhibition by ABA) in a panel of 425 rice accessions. The seed germination assay revealed that Aus and indica rice had stronger ABA sensitivity than japonica rice. A total of 48 non-redundant association loci were detected in the indica subpopulation and whole population, and 386 genes in these loci were responsive to ABA or abiotic stresses. Eight association loci were overlapped with previously reported loci for yield under drought stress or for drought-indicative image traits. Haplotype analyses of important candidate genes such as OsSAPK6, a key component in the ABA signaling core, were performed to identify key SNPs/InDels that may affect gene functions through promoter activity regulation, amino acid variation, or gene splicing. These results provide insights into the genetic basis of ABA sensitivity related to stress responses.

Keywords: ABA sensitivity; Rice; Seed germination; Stress response.

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Conflict of interest statement

Author LX is a member of the Editorial Board, but was not involved in the journal's review of, or decisions related to, this manuscript.

Figures

Fig. 1
Fig. 1
Population structure analysis and seed germination rate variation within the subpopulations and whole population. a Principal component (PC) analysis for all 425 accessions, including indica (Ind), japonica (Jap), Aus (Aus), and some intermediate (VI and Admix). b Some representative images of ABA inhibited seed germination phenotypes and corresponding REG. c Variation and statistical analysis for seed germination rate of CK group (CKG) and ABA-treated group (ABAG), and the relative germination rate (REG, ABAG/CKG × 100%) in the subpopulations and whole population
Fig. 2
Fig. 2
GWAS for seed germination rate in the indica subpopulation and whole population. Manhattan and Quantile-quantile plots are shown for ABAG in the indica (a), REG in the indica (b), ABAG in the whole populations (c), and REG in the whole population (d) using FaST-LMM. Red arrows indicate the genes are considered to be important candidates related to ABA sensitivity. Dashed horizontal line for each population indicates the suggestive threshold (P = 1.0 × 10− 6)
Fig. 3
Fig. 3
Gene analysis within the association loci. a. Chromosomal distribution of 590 genes in the loci associated with ABA sensitivity. Color scale indicates the number of genes in the associated loci. b. Venn diagram showing the distribution of the genes in the associated loci for ABAG in the indica subpopulations (Ind_ABAG) and whole population (Whole_ABAG), and the genes in the associated loci for REG in the indica subpopulations (Ind_REG) and whole population (Whole_REG). c. Venn diagram showing the number of the genes from the association loci are responsive (threshold of 2-fold-change) to ABA, drought, and/or osmotic stresses. The relative expression levels of these genes in the treatment of ABA and drought or osmotic stress were extracted from a public database (https://tenor.dna.affrc.go.jp)
Fig. 4
Fig. 4
Haplotype and expression level analysis of the three candidate genes. Locations of key SNPs used for haplotype analysis are shown for the three genes including OsSAPK6 (LOC_Os02g34600, a), OsbZIP60 (LOC_Os07g44950, d), and OsBAK1–8 (LOC_Os11g39370, g). The REG of hap1 (303 accessions) and hap2 (121 accessions) in OsSAPK6 (b), hap1 (288 accessions) and hap2 (129 accessions) in OsbZIP60 (e), hap1 (387 accessions) and hap2 (45 accessions) in and OsBAK1–8 (h) in the whole population are shown. The relative expression levels of hap1 group (16 accessions) and hap2 group (13 accessions) in OsSAPK6 (c), hap1 group (18 accessions) and hap2 group (11 accessions) in OsbZIP60 (f), and hap1 group (21 accessions) and hap2 group (8 accessions) in OsBAK1–8 (i) in response to ABA at 0 h and 6 h are presented
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