A global analysis of CNVs in diverse yak populations using whole-genome resequencing

BackgroundGenomic structural variation represents a source for genetic and phenotypic variation, which may be subject to selection during the environmental adaptation and population differentiation. Here, we described a genome-wide analysis of copy number variations (CNVs) in 16 populations of yak based on genome resequencing data and CNV-based cluster analyses of these populations.ResultsIn total, we identified 51,461 CNV events and defined 3174 copy number variation regions (CNVRs) that covered 163.8Mb (6.2%) of yak genome with more loss events than both gain and both events, and we confirmed 31 CNVRs in 36 selected yaks using quantitative PCR. Of the total 163.8Mb CNVR coverage, a 10.8Mb region of high-confidence CNVRs directly overlapped with the 52.9Mb of segmental duplications, and we confirmed their uneven distributions across chromosomes. Furthermore, functional annotation indicated that the CNVR-harbored genes have a considerable variety of molecular functions, including immune response, glucose metabolism, and sensory perception. Notably, some of the identified CNVR-harbored genes associated with adaptation to hypoxia (e.g., DCC, MRPS28, GSTCD, MOGAT2, DEXI, CIITA, and SMYD1). Additionally, cluster analysis, based on either individuals or populations, showed that the CNV clustering was divided into two origins, indicating that some yak CNVs are likely to arisen independently in different populations and contribute to population difference.ConclusionsCollectively, the results of the present study advanced our understanding of CNV as an important type of genomic structural variation in yak, and provide a useful genomic resource to facilitate further research on yak evolution and breeding.