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. 2023 Dec 1:14:1296197.
doi: 10.3389/fpls.2023.1296197. eCollection 2023.

Genome-wide association analysis of time to heading and maturity in bread wheat using 55K microarrays

Yindeng Ding  1 , Hui Fang  1 , Yonghong Gao  1 , Guiqiang Fan  1 , Xiaolei Shi  2 , Shan Yu  3 , Sunlei Ding  2 , Tianrong Huang  1 , Wei Wang  4 , Jikun Song  5
Affiliations

Genome-wide association analysis of time to heading and maturity in bread wheat using 55K microarrays

Yindeng Ding et al. Front Plant Sci. .

Abstract

To investigate the genetic mechanisms underlying the reproductive traits (time to flowering and maturity) in wheat and identify candidate genes associated, a phenotypic analysis was conducted on 239 wheat accessions (lines) from around the world. A genome-wide association study (GWAS) of wheat heading and maturity phases was performed using the MLM (Q+K) model in the TASSLE software, combined with the Wheat 55K SNP array. The results revealed significant phenotypic variation in heading and maturity among the wheat accessions across different years, with coefficients of variation ranging from 0.96% to 1.97%. The phenotypic data from different years exhibited excellent correlation, with a genome-wide linkage disequilibrium (LD) attenuation distance of 3 Mb. Population structure analysis, evolutionary tree analysis, and principal component analysis indicated that the 239 wheat accessions formed a relatively homogeneous natural population, which could be divided into three subgroups. The GWAS results identified a total of 293 SNP marker loci that were significantly associated with wheat heading and maturity stages (P ≤ 0.001) in different environments. Among them, nine stable SNP marker loci were consistently detected in multiple environments. These marker loci were distributed on wheat chromosomes 1A、1B、2D、3A、5B、6D and 7A. Each individual locus explained 4.03%-16.06% of the phenotypic variation. Furthermore, through careful analysis of the associated loci with large phenotypic effect values and stable inheritance, a total of nine candidate genes related to wheat heading and maturity stages were identified. These findings have implications for molecular marker-assisted selection breeding programs targeting specific wheat traits at the heading and maturity stages. In summary, this study conducted a comprehensive GWAS of wheat heading and maturity phases, revealing significant associations between genetic markers and key developmental stages in wheat. The identification of candidate genes and marker loci provides valuable information for further studies on wheat breeding and genetic improvement targeted at enhancing heading and maturity traits.

Keywords: GWAS; candidate genes; heading; maturity; wheat.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Distribution of traits in different environments (A) Germination-spike and germination-maturity in E1 and E2 environments; (B) Germination-spike and germination-maturity in E3 and E4 environments. E1: 2020 Zepu, Xinjiang; E2: 2021 Zepu, Xinjiang E3: 2021 Anning Drain, Xinjiang E4: 2022 Zepu, Xinjiang; S1: heading stage; S2: maturity stage.
Figure 2
Figure 2
Correlation plots of germination-sprouting and germination-maturity traits in different environments.
Figure 3
Figure 3
Population structure analysis of 239 wheat accessions. (A) Population structure analysis; (B) Neighbor-joining method evolutionary tree; (C) Principal component analysis.
Figure 4
Figure 4
GWAS of reproductive traits in different environments. (A) Manhattan and quantile-quantile plots for S1 in different environments. (B) Manhattan and quantile-quantile plots for S2 in different environments. E1: 2020 Zepu, Xinjiang; E2: 2021 Zepu, Xinjiang E3: 2021 Anning Drain, Xinjiang E4: 2022 Zepu, Xinjiang; S1: heading stage; S2: maturity stage.
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