, Volume 212, Issue 2, pp 173–185 | Cite as

Genome-wide association study for kernel weight-related traits using SNPs in a Chinese winter wheat population

  • Guangfeng Chen
  • Han Zhang
  • Zhiying Deng
  • Rugang Wu
  • Dongmei Li
  • Mingyou Wang
  • Jichun TianEmail author


Genome-wide association studies have become a wide spread method of quantitative trait locus identification for many crops, including wheat (Triticum aestivum L.). Its benefit over traditional biparental mapping approaches depends on the extent of linkage disequilibrium (LD) in natural populations. We estimated the genetic diversity, population structure, and LD decay rate in a winter wheat association mapping panel (n = 205) and identified markers associated with thousand-kernel weight (TKW) and related traits. The panel was genotyped with a high-density Illumina iSelect 90 K single nucleotide polymorphism assay. PIC values were 0.047–0.375 with a mean of 0.277. Structural analysis suggested the association mapping panel contained four subpopulations. LD decay rates extended to longer genetic distances within the D genome (11.0 cM) relative to the A and B genomes (1.5 and 1.8 cM, respectively). A total of 271 marker-trait associations (MTAs) were identified for TKW and related traits, explaining 5.49–9.86 % of variation in individual traits. Among them, 11 highly significant markers (p < 0.0001), eight stable markers and twelve multi-trait MTAs were detected. Two stable markers, Ku_c9210_105 for KL and BS00023893_51 for TKW, were detected in three environments. These MTAs could be used for developing cleaved amplified polymorphic sequence markers for molecular marker-assisted selection in wheat breeding programs.


Wheat Association mapping Population structure Linkage disequilibrium Thousand-kernel weight 



This research was supported by the Shandong Provincial Agriculture Liangzhong Project Foundation of China (2014 No. 96) and National Natural Science Foundation of China (No. 31171554 and 31301315).

Supplementary material

10681_2016_1750_MOESM1_ESM.xlsx (30 kb)
Supplementary material 1 (XLSX 29 kb)


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Copyright information

© Springer Science+Business Media Dordrecht 2016

Authors and Affiliations

  • Guangfeng Chen
    • 1
    • 2
  • Han Zhang
    • 1
    • 3
  • Zhiying Deng
    • 1
  • Rugang Wu
    • 4
  • Dongmei Li
    • 2
  • Mingyou Wang
    • 2
  • Jichun Tian
    • 1
    Email author
  1. 1.State Key Laboratory of Crop BiologyGroup of Quality Wheat Breeding of Shandong Agricultural UniversityTai’anChina
  2. 2.College of Ecology and Garden ArchitectureDezhou UniversityDezhouChina
  3. 3.Crop Research InstituteShandong Academy of Agricultural SciencesJinanChina
  4. 4.Dezhou Academy of Agricultural SciencesDezhouChina

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