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

Authors: LIU, MEI - Northwest Agriculture And Forestry University; LI, BO - Northwest Agriculture And Forestry University; SHI, TAO - Northwest Agriculture And Forestry University; HUANG, YONGZEN - Northwest Agriculture And Forestry University; Liu, Ge - George; LAN, XIANYONG - Northwest Agriculture And Forestry University; LEI, CHUZHAO - Northwest Agriculture And Forestry University; CHEN, HONG - Northwest Agriculture And Forestry University

Submitted to: Journal of Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/29/2019
Publication Date: 4/17/2019
Citation: Liu, M., Li, B., Shi, T., Huang, ., Liu, G., Lan, X., Lei, C., Chen, H. 2019. Copy number variation of bovine SHH gene is associated with body conformation traits in Chinese beef cattle. Journal of Applied Genetics. 60(2):199–207. https://doi.org/10.1007/s13353-019-00496-w.
DOI: https://doi.org/10.1007/s13353-019-00496-w

Interpretive Summary: Copy number variation (CNV) represents a major source of genomic variation. By studying the distributions of copy number changes of the Sonic Hedgehog gene in 648 individuals from 11 Chinese cattle populations, we investigated their impacts on gene expressions and cattle growth traits. These results fill our knowledge gaps and provide the foundation for future studies of CNV role in ruminants. Farmers, scientist, and policy planners who need improve animal health and production based on genome-enable animal selection will benefit from this study.

Technical Abstract: 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 expressions 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 had higher median copy numbers, suggesting the diversity of SHH-CNV could be implicated in 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 on bovine fat formation. Association analysis of SHH-CNV and body size traits were conducted in five breeds. The results revealed that the copy number gain type of SHH-CNV exhibited significant better body weight, body length, body height, chest girth, chest breadth, chest depth, hip height, hip width, hucklebone width, and rump length in adult Qinchuan cattle, and better body weight, body length and chest girth in Nanyang cattle, whereas the copy number median had superior phenotype in Jinnan cattle (P<0.05 or P<0.01). In summary, this research uncovered meaningful effects of SHH-CNV on gene expressions and cattle phenotypic traits, indicating its potential applications for genetic improvement of beef cattle.