Theoretical and Applied Genetics

, Volume 132, Issue 11, pp 2947–2963 | Cite as

Genome-wide association study of pre-harvest sprouting tolerance using a 90K SNP array in common wheat (Triticum aestivum L.)

  • Yulei Zhu
  • Shengxing Wang
  • Wenxin Wei
  • Hongyong Xie
  • Kai Liu
  • Can Zhang
  • Zengyun Wu
  • Hao Jiang
  • Jiajia Cao
  • Liangxia Zhao
  • Jie Lu
  • Haiping ZhangEmail author
  • Cheng ChangEmail author
  • Xianchun Xia
  • Shihe Xiao
  • Chuanxi Ma
Original Article


Key message

Three major loci for pre-harvest sprouting tolerance (PHST) were mapped on chromosomes 1AL, 3BS, and 6BL, and two CAPS and one dCAPS markers were validated. Sixteen lines with favorable alleles and increased PHST were identified.


Pre-harvest sprouting (PHS) significantly affects wheat grain yield and quality. In the present study, the PHS tolerance (PHST) of 192 wheat varieties (lines) was evaluated by assessment of field sprouting, seed germination index, and period of dormancy in different environments. A high-density Illumina iSelect 90K SNP array was used to genotype the panel. A genome-wide association study (GWAS) based on single- and multi-locus mixed linear models was used to detect loci for PHST. The single-locus model identified 23 loci for PHST (P < 0.0001) and explained 6.0–18.9% of the phenotypic variance. Twenty loci were consistent with known quantitative trait loci (QTLs). Three single-nucleotide polymorphism markers closely linked with three major loci (Qphs.ahau-1A, Qphs.ahau-3B, and Qphs.ahau-6B) on chromosomes 1AL, 3BS, and 6BL, respectively, were converted to two cleaved amplified polymorphic sequences (CAPS) and one derived-CAPS markers, and validated in 374 wheat varieties (lines). The CAPS marker EX06323 for Qphs.ahau-6B co-segregated with a novel major QTL underlying PHST in a recombinant inbred line population raised from the cross Jing 411 × Wanxianbaimaizi. Linear regression showed a clear dependence of PHST on the number of favorable alleles. Sixteen varieties showing an elevated degree of PHST were identified and harbored more than 16 favorable alleles. The multi-locus model detected 39 marker–trait associations for PHST (P < 0.0001), of which five may be novel. Six loci common to the two models were identified. The combination of the two GWAS methods contributes to efficient dissection of the complex genetic mechanism of PHST.



This work was supported by grants from the National Natural Science Foundation of China (31871608, 31401372), The National Key Research and Development Plan “Breeding new wheat varieties with high-yielding, high-quality and water-saving in the south of Huang-Huai River winter wheat area”—the breeding of new wheat germplasm and varieties with resistance to adversity (2017YFD0100703), the China Agriculture Research System (CARS-03), the Natural Science Foundation of Anhui Province (1508085MC57), the Wheat genetics and breeding research platform innovation team of Anhui's University (2015-), Jiangsu Collaborative Innovation Center for Modern Crop Production (JCIC-MCP), and the Agriculture Research System of Anhui Province (AHCYTX-02). We thank Robert McKenzie, PhD, from Liwen Bianji, Edanz Group China (, for editing the English text of a draft of this manuscript.

Compliance with ethical standardas

Conflict of interest

We declare no conflicts of interest in regard to this manuscript.

Ethical standards

The experiments conducted in this study comply with the current laws of China.

Supplementary material

122_2019_3398_MOESM1_ESM.docx (2.4 mb)
Supplementary file1 (DOCX 2412 kb)
122_2019_3398_MOESM2_ESM.xlsx (103 kb)
Supplementary file2 (XLSX 103 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Yulei Zhu
    • 1
  • Shengxing Wang
    • 1
  • Wenxin Wei
    • 1
  • Hongyong Xie
    • 1
  • Kai Liu
    • 1
  • Can Zhang
    • 1
  • Zengyun Wu
    • 1
  • Hao Jiang
    • 1
  • Jiajia Cao
    • 1
  • Liangxia Zhao
    • 1
  • Jie Lu
    • 1
  • Haiping Zhang
    • 1
    Email author
  • Cheng Chang
    • 1
    Email author
  • Xianchun Xia
    • 1
    • 2
  • Shihe Xiao
    • 2
  • Chuanxi Ma
    • 1
  1. 1.College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement On Southern Yellow and Huai River ValleyMinistry of AgricultureHefeiChina
  2. 2.Institute of Crop Sciences, National Wheat Improvement CenterChinese Academy of Agricultural Sciences (CAAS)BeijingChina

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