Genome-Wide Association Study of Kernel Traits in Aegilops tauschii

Qing Wang; Ning Yan; Hao Chen; Sirui Li; Haiyan Hu; Yu Lin; Haoran Shi; Kunyu Zhou; Xiaojun Jiang; Shifan Yu; Caixia Li; Guangdeng Chen; Zisong Yang; Yaxi Liu

doi:10.3389/fgene.2021.651785

Genome-Wide Association Study of Kernel Traits in Aegilops tauschii

Front Genet. 2021 May 28:12:651785. doi: 10.3389/fgene.2021.651785. eCollection 2021.

Authors

Qing Wang^{1

2}, Ning Yan^{1

2}, Hao Chen^{1

2}, Sirui Li³, Haiyan Hu⁴, Yu Lin^{1

2}, Haoran Shi^{1

2}, Kunyu Zhou^{1

2}, Xiaojun Jiang^{1

2}, Shifan Yu^{1

2}, Caixia Li², Guangdeng Chen⁵, Zisong Yang⁶, Yaxi Liu^{1

2}

Affiliations

¹ State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China.
² Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China.
³ Chengdu Foreign Language School, Chengdu, China.
⁴ School of Life Sciences and Technology, Henan Institute of Science and Technology, Xinxiang, China.
⁵ College of Resources, Sichuan Agricultural University, Chengdu, China.
⁶ College of Resources and Environment, Aba Teachers University, Wenchuan, China.

Abstract

Aegilops tauschii is the diploid progenitor of the D subgenome of hexaploid wheat (Triticum aestivum L.). Here, the phenotypic data of kernel length (KL), kernel width (KW), kernel volume (KV), kernel surface area (KSA), kernel width to length ratio (KWL), and hundred-kernel weight (HKW) for 223 A. tauschii accessions were gathered across three continuous years. Based on population structure analysis, 223 A. tauschii were divided into two subpopulations, namely T-group (mainly included A. tauschii ssp. tauschii accessions) and S-group (mainly included A. tauschii ssp. strangulata). Classifications based on cluster analysis were highly consistent with the population structure results. Meanwhile, the extent of linkage disequilibrium decay distance (r ² = 0.5) was about 110 kb and 290 kb for T-group and S-group, respectively. Furthermore, a genome-wide association analysis was performed on these kernel traits using 6,723 single nucleotide polymorphism (SNP) markers. Sixty-six significant markers, distributed on all seven chromosomes, were identified using a mixed linear model explaining 4.82-13.36% of the phenotypic variations. Among them, 15, 28, 22, 14, 21, and 13 SNPs were identified for KL, KW, KV, KSA, KWL, and HKW, respectively. Moreover, six candidate genes that may control kernel traits were identified (AET2Gv20774800, AET4Gv20799000, AET5Gv20005900, AET5Gv20084100, AET7Gv20644900, and AET5Gv21111700). The transfer of beneficial genes from A. tauschii to wheat using marker-assisted selection will broaden the wheat D subgenome improve the efficiency of breeding.

Keywords: Aegilops tauschii; GWAS; SNP; candidate gene; genetic diversity; kernel traits.