Genome-wide patterns of copy number variation in the Chinese yak genome.

Xiao Zhang,Qiang Qiu,Dongshi Wan,Lizhong Wang,Xiuyue Xie,Yongzhi Yang,Xuemin Shao,Kun Wang,Zhengqiang Ni,Jin Han

doi:10.1186/s12864-016-2702-6

Abstract

BackgroundCopy number variation (CNV) represents an important source of genetic divergence that can produce drastic phenotypic differences and may therefore be subject to selection during domestication and environmental adaptation. To investigate the evolutionary dynamics of CNV in the yak genome, we used a read depth approach to detect CNV based on genome resequencing data from 14 wild and 65 domestic yaks and determined CNV regions related to domestication and adaptations to high-altitude.ResultsWe identified 2,634 CNV regions (CNVRs) comprising a total of 153 megabases (5.7 % of the yak genome) and 3,879 overlapping annotated genes. Comparison between domestic and wild yak populations identified 121 potentially selected CNVRs, harboring genes related to neuronal development, reproduction, nutrition and energy metabolism. In addition, we found 85 CNVRs that are significantly different between domestic yak living in high- and low-altitude areas, including three genes related to hypoxia response and six related to immune defense. This analysis shows that genic CNVs may play an important role in phenotypic changes during yak domestication and adaptation to life at high-altitude.ConclusionsWe present the first refined CNV map for yak along with comprehensive genomic analysis of yak CNV. Our results provide new insights into the genetic basis of yak domestication and adaptation to living in a high-altitude environment, as well as a valuable genetic resource that will facilitate future CNV association studies of important traits in yak and other bovid species.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2702-6) contains supplementary material, which is available to authorized users.

Highlights

Copy number variation (CNV) represents an important source of genetic divergence that can produce drastic phenotypic differences and may be subject to selection during domestication and environmental adaptation
Using the CNVnator software based on the read depth (RD) method [37], we detected a total of 98,441 CNV events from the 79 individuals (Fig. 2 and Additional file 2)
Our results suggest that some copy number variation region (CNVR) may have been under selection pressure during yak domestication and these are associated with behavior, physical characteristics and economically significant traits

Summary

Introduction

Copy number variation (CNV) represents an important source of genetic divergence that can produce drastic phenotypic differences and may be subject to selection during domestication and environmental adaptation. To investigate the evolutionary dynamics of CNV in the yak genome, we used a read depth approach to detect CNV based on genome resequencing data from 14 wild and 65 domestic yaks and determined CNV regions related to domestication and adaptations to high-altitude. CNV represents an important source of genetic variation complementary to SNP data, but which affects a higher percentage of genomic sequences and has potentially stronger effects on phenotypic diversity and evolutionary adaptation, through changing gene dosage and transcript structure, and regulating gene expression and function [5].

Methods

Results

Conclusion