Journal of Applied Genetics

, Volume 60, Issue 2, pp 199–207 | Cite as

Copy number variation of bovine SHH gene is associated with body conformation traits in Chinese beef cattle

  • Mei Liu
  • Bo Li
  • Tao Shi
  • Yongzhen Huang
  • George E. Liu
  • Xianyong Lan
  • Chuzhao Lei
  • Hong ChenEmail author
Animal Genetics • Original Paper


Sonic Hedgehog (Shh) regulates many key developmental processes during vertebrate limb development, fat formation, and skeletal tissue regeneration. Current whole genome sequencing data have identified a copy number variation mapping to bovine Sonic Hedgehog gene (SHH-CNV). The object of this study was to characterize the SHH-CNV distributions in 648 individuals from 11 Chinese cattle populations and further to investigate the associations of the copy number changes with gene expression and cattle growth traits. The SHH-CNV showed a high variance within Chinese indigenous yellow cattle. Compared to yak and dairy cattle, the beef cattle like Luxi and Xianan breed had significantly higher median copy numbers, suggesting the diversity of SHH-CNV in beef cattle selections. The negative correlation of SHH-CNV with SHH transcriptional level in adult adipose tissue (P < 0.01) indicated the dosage effects of SHH-CNV related to bovine fat formation. Association analysis of SHH-CNV and body size traits was conducted in five breeds. The results revealed that the copy number gain type of SHH-CNV exhibited significantly better chest depth in 24 months old Qinchuan cattle, and better body weight, body length, and chest girth in 18 months old Nanyang cattle, whereas the normal copy number had superior chest girth and body weight in adult Jinnan cattle (P < 0.05 or P < 0.01). In summary, this research uncovered meaningful effects of SHH-CNV on gene expression and cattle phenotypic traits, indicating its potential applications for genetic improvement of beef cattle.


Cattle Copy number variation Sonic Hedgehog Growth trait Associations 



We acknowledge Dr. Yao Xu’s help in providing the RNA sample for tissues of QC cattle and the guidance for designing this research. We acknowledge Dr. Shaoqiang Wang’s help in providing the DNA sample for YAK population. We acknowledge Dr. Xinglei Qi’s help in sampling the blood sample for Xianan cattle. We acknowledge Dr. Shijun Li’s help in association analysis.


This study was funded by the National Natural Science Foundation of China (No. 31772574) and the Program of National Beef Cattle and Yak Industrial Technology System (CARS-37).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

The China Council on Animal Care and the Experimental Animal Management Committee of Northwest A&F University approved the procedures and protocols of all experiments in this study.

Consent for publication

Written consent was obtained for use of all animal data.

Supplementary material

13353_2019_496_MOESM1_ESM.docx (308 kb)
Supplementary Figure S1 Correlations between the SHH-CNV and associated body traits in QC and NY cattle. The SHH-CNV was positively associated with chest depth of QC cattle aged 24 months (A. r = 0.19, P = 0.13) and positively associated with chest girth (B. r = 0.24, P = 0.05), body length (C. r = 0.19, P = 0.14), and body weight (D. r = 0.29, P = 0.02) of NY cattle aged 18 months (DOCX 307 kb)
13353_2019_496_MOESM2_ESM.docx (5.1 mb)
Supplementary Figure S2 Pairwise Pearson correlation coefficients for the body conformation and growth traits in QC (A, 24 months old; B, 36 months old), NY (C, 18 months old; D, 24 months old), and JN (E, 24 months old) breeds (DOCX 5270 kb)
13353_2019_496_MOESM3_ESM.docx (182 kb)
Supplementary Figure S3 Expression profiling of SHH gene in three periods of Qinchuan cattle. The mRNA levels of SHH gene in tissues of fetal (A), calf and adult (B) cattle were normalized to the housekeeping gene (GAPDH); the kidney group in each stage was selected as the control group. Error bars represents standard deviations of three different biological replicates (DOCX 181 kb)
13353_2019_496_MOESM4_ESM.docx (22 kb)
ESM 1 (DOCX 21 kb)


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Copyright information

© Institute of Plant Genetics, Polish Academy of Sciences, Poznan 2019

Authors and Affiliations

  • Mei Liu
    • 1
    • 2
  • Bo Li
    • 1
  • Tao Shi
    • 1
  • Yongzhen Huang
    • 1
  • George E. Liu
    • 2
  • Xianyong Lan
    • 1
  • Chuzhao Lei
    • 1
  • Hong Chen
    • 1
    Email author
  1. 1.College of Animal Science and Technology, Shaanxi Key Laboratory of Molecular Biology for AgricultureNorthwest A&F UniversityYanglingPeople’s Republic of China
  2. 2.Animal Genomics and Improvement Laboratory, BARC, Agricultural Research ServiceUSDABeltsvilleUSA

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