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

Yindeng Ding; Hui Fang; Yonghong Gao; Guiqiang Fan; Xiaolei Shi; Shan Yu; Sunlei Ding; Tianrong Huang; Wei Wang; Jikun Song

doi:10.3389/fpls.2023.1296197

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

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

Authors

Yindeng Ding¹, Hui Fang¹, Yonghong Gao¹, Guiqiang Fan¹, Xiaolei Shi², Shan Yu³, Sunlei Ding², Tianrong Huang¹, Wei Wang⁴, Jikun Song⁵

Affiliations

¹ Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, China.
² Institute of Crop Variety Resources, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, China.
³ College of Agriculture, Xinjiang Agricultural University, Urumqi, Xinjiang, China.
⁴ Department of Computer Science and Information Engineering, Anyang Institute of Technology, Anyang, China.
⁵ Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, China.

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.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. The present study was funded by the Xinjiang Academy of Agricultural Sciences Youth Science and Technology Backbone Innovation Ability Training Project (xjnkq-2020005); Xinjiang Academy of Agricultural Sciences Youth Science and Technology Backbone Innovation Ability Training Project (xjnkq-2021006); Xinjiang Uygur Autonomous Region Department of Agriculture and Rural Affairs 2022 “Unveiling and Hanging the Marshal” Research Project; Major Science and Technology Special Project of Xinjiang Autonomous Region (2021A02001-1).