Mammalian Genome

, Volume 27, Issue 5–6, pp 246–255 | Cite as

Genome-wide association study identifies loci and candidate genes for meat quality traits in Simmental beef cattle

  • Jiangwei Xia
  • Xin Qi
  • Yang Wu
  • Bo Zhu
  • Lingyang Xu
  • Lupei Zhang
  • Xue Gao
  • Yan Chen
  • Junya LiEmail author
  • Huijiang GaoEmail author


Improving meat quality is the best way to enhance profitability and strengthen competitiveness in beef industry. Identification of genetic variants that control beef quality traits can help breeders design optimal breeding programs to achieve this goal. We carried out a genome-wide association study for meat quality traits in 1141 Simmental cattle using the Illumina Bovine HD 770K SNP array to identify the candidate genes and genomic regions associated with meat quality traits for beef cattle, including fat color, meat color, marbling score, longissimus muscle area, and shear force. In our study, we identified twenty significant single-nucleotide polymorphisms (SNPs) (p < 1.47 × 10−6) associated with these five meat quality traits. Notably, we observed several SNPs were in or near eleven genes which have been reported previously, including TMEM236, SORL1, TRDN, S100A10, AP2S1, KCTD16, LOC506594, DHX15, LAMA4, PREX1, and BRINP3. We identified a haplotype block on BTA13 containing five significant SNPs associated with fat color trait. We also found one of 19 SNPs was associated with multiple traits (shear force and longissimus muscle area) on BTA7. Our results offer valuable insights to further explore the potential mechanism of meat quality traits in Simmental beef cattle.


Principle Component Analysis Meat Quality Significant SNPs Meat Quality Trait Meat Color 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



This work was supported by Cattle Breeding Innovative Research Team (cxgc-ias-03), the 12th “Five-Year” National Science and Technology Support Project (2011BAD28B04) Basic Research Fund Program, the National High Technology Research and Development Program of China (863 Program 2013AA102505-4), Chinese Academy of Agricultural Sciences Fundamental Research Budget Increment Projects (2013ZL031 and 2014ZL006), Chinese Academy of Agricultural Sciences Foundation (2014ywf-yb-4), Beijing Natural Science Foundation (6154032), and the National Natural Science Foundations of China (31472079, 31372294, 31402039 and 31201774).

Author Contributions

HJG and JYL conceived and designed the experiments. JWX and QX conducted the experiments. BZ and YW analyzed the data. XG, YC, LPZ, and LYX helped conduct the experiments. HJG and JYL supervised the study. JWX wrote the manuscript. All authors have read and approved the final manuscript

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.


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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  • Jiangwei Xia
    • 1
  • Xin Qi
    • 1
  • Yang Wu
    • 1
  • Bo Zhu
    • 1
  • Lingyang Xu
    • 1
  • Lupei Zhang
    • 1
  • Xue Gao
    • 1
  • Yan Chen
    • 1
  • Junya Li
    • 1
    Email author
  • Huijiang Gao
    • 1
    Email author
  1. 1.Institute of Animal ScienceChinese Academy of Agricultural ScienceBeijingChina

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