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Open Access Research article

Detection of copy number variations and their effects in Chinese bulls

Liangzhi Zhang1, Shangang Jia14, Mingjuan Yang1, Yao Xu1, Congjun Li2, Jiajie Sun1, Yongzhen Huang1, Xianyong Lan1, Chuzhao Lei1, Yang Zhou1, Chunlei Zhang3, Xin Zhao1 and Hong Chen1*

Author Affiliations

1 College of Animal Science and Technology, Northwest A & F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, China

2 United States Department of Agriculture-Agricultural Research Service, Bovine Functional Genomics Laboratory, Beltsville, Maryland, USA

3 Institutes of Cellular and Molecular Biology, Jiangsu Normal University, Xuzhou, Jiangsu, China

4 Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia

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BMC Genomics 2014, 15:480  doi:10.1186/1471-2164-15-480

Published: 17 June 2014

Abstract

Background

Copy number variations (CNVs) are a main source of genomic structural variations underlying animal evolution and production traits. Here, with one pure-blooded Angus bull as reference, we describe a genome-wide analysis of CNVs based on comparative genomic hybridization arrays in 29 Chinese domesticated bulls and examined their effects on gene expression and cattle growth traits.

Results

We identified 486 copy number variable regions (CNVRs), covering 2.45% of the bovine genome, in 24 taurine (Bos taurus), together with 161 ones in 2 yaks (Bos grunniens) and 163 ones in 3 buffaloes (Bubalus bubalis). Totally, we discovered 605 integrated CNVRs, with more “loss” events than both “gain” and “both” ones, and clearly clustered them into three cattle groups. Interestingly, we confirmed their uneven distributions across chromosomes, and the differences of mitochondrion DNA copy number (gain: taurine, loss: yak & buffalo). Furthermore, we confirmed approximately 41.8% (253/605) and 70.6% (427/605) CNVRs span cattle genes and quantitative trait loci (QTLs), respectively. Finally, we confirmed 6 CNVRs in 9 chosen ones by using quantitative PCR, and further demonstrated that CNVR22 had significantly negative effects on expression of PLA2G2D gene, and both CNVR22 and CNVR310 were associated with body measurements in Chinese cattle, suggesting their key effects on gene expression and cattle traits.

Conclusions

The results advanced our understanding of CNV as an important genomic structural variation in taurine, yak and buffalo. This study provides a highly valuable resource for Chinese cattle’s evolution and breeding researches.

Keywords:
Copy number variations; Bos taurus; Bos grunniens; Bubalus bubalis; Gene expression