Plant Molecular Biology Reporter

, Volume 36, Issue 4, pp 605–617 | Cite as

Genome-Wide Association Studies of Soybean Seed Hardness in the Chinese Mini Core Collection

  • Xing Zhang
  • Jinming Zhao
  • Yuanpeng Bu
  • Dong Xue
  • Zhangxiong Liu
  • Xiangnan Li
  • Jing Huang
  • Na Guo
  • Haitang Wang
  • Han XingEmail author
  • Lijuan Qiu
Original Paper


Soybean seed hardness is an important quality character in soybean food processing. Both vegetable soybean and natto require soft seeds to achieve a desirable sensory experience and for effective processing. In this study, we used a texture analyzer to measure the seed hardness of Chinese mini core collection via two indexes over 4 years and found significant correlations among the seed hardness, seed oil content, and germplasm eco-region. Based on 1514 SNPs, genome-wide association studies (GWAS) were conducted using a mixed linear model (MLM). Seventeen SNPs were identified to be associated with seed hardness in at least two environments. Among them, one locus, designated Q-15-0087770, was associated with two indexes, and 13 putative genes were confirmed based on their annotations in SoyBase. This research provides new insights into advanced marker-assisted selections for breeding soybeans for seed hardness and oil content.


Soybean mini core collection Soybean seed hardness Seed oil content GWAS 



This work was supported by the National Natural Science Foundation of China (31471519), Modern Agro-industry Technology Research System of China (CARS-004-PS10), and Jiangsu Collaborative Innovation Center for Modern Crop Production.

Authors’ Contributions

All authors have read and approved the manuscript. Han Xing conceived the work. Lijun Qiu, Jinming Zhao, Zhangxiong Liu, Na Guo, and Haitang Wang conducted the planting of soybean materials. Xing Zhang, Yuanpeng Bu, Dong Xue, and Xiangnan Li measured and analyzed the phenotyping data. Xing Zhang, Jinming Zhao, Yuanpeng Bu, and Jing Huang performed genome-wide association studies. Xing Zhang wrote the manuscript.

Compliance with Ethical Standards

Competing Interests

The authors declare that they have no competing interests.

Supplementary material

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Fig. S1

Measurements of Fm and H using a texture analyzer. (PNG 195 kb)

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High resolution image (TIF 349 kb)
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Fig. S2

Frequency distributions of the Fm mean (A) and BLUP (B) and H mean (C) and BLUP (D). (PNG 124 kb)

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High resolution image (TIF 6834 kb)
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Fig. S3

The seven eco-regions of the soybean mini core collection in China include: the Northeast spring (NESp), the North spring (NSp), the Huanghuai spring (HSp), the Huanghuai summer (HSu), the South spring (SSp), the South summer (SSu) and the South autumn (SA). (PNG 554 kb)

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High resolution image (TIF 5986 kb)
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Fig. S4

Changes in Fm and H over seven eco-regions (A, B) and two subgroups (C, D) over 4 years. (PNG 198 kb)

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High resolution image (TIF 5380 kb)
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Fig. S5

Frequency distributions of the mean values of seed protein content (A), moisture (B), and oil content (C) over the three years and oil content in 2012 (D), 2013 (E) and 2014 (F). (PNG 97 kb)

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Fig. S6

Changes in seed protein content, oil content and moisture over seven eco-regions (A, B, C) and two subgroups over 3 years (D, E, F). (PNG 202 kb)

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High resolution image (TIF 6159 kb)
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Fig. S7

Manhattan plots and QQ plots of Fm (A, B, C, D) and H (E, F, G, H) over 4 years in the MLM model. (PNG 2149 kb)

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High resolution image (TIF 9700 kb)


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Xing Zhang
    • 1
  • Jinming Zhao
    • 1
  • Yuanpeng Bu
    • 1
  • Dong Xue
    • 1
  • Zhangxiong Liu
    • 2
  • Xiangnan Li
    • 1
  • Jing Huang
    • 1
  • Na Guo
    • 1
  • Haitang Wang
    • 1
  • Han Xing
    • 1
    Email author
  • Lijuan Qiu
    • 2
  1. 1.National Center for Soybean Improvement/National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of AgricultureNanjing Agricultural UniversityNanjingPeople’s Republic of China
  2. 2.The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA)Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijingPeople’s Republic of China

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