Abstract
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 163.8 Mb (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 163.8 Mb CNVR coverage, a 10.8 Mb region of high-confidence CNVRs directly overlapped with the 52.9 Mb 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.
Highlights
Genomic structural variation represents a source for genetic and phenotypic variation, which may be subject to selection during the environmental adaptation and population differentiation
Using CNVnator software based on the RD method [34], we detected a total of 51,461 copy number variations (CNVs) events from the 48 individuals (Fig. 1, Additional file 4), the average number of CNVs per individual was 1072 with an average of 557 gain and 515 loss events, and the average number of specific CNV events per individual was 107
It is worth noting that a series of Discussion In this study, we detected and verified Copy number variation region (CNVR) using whole-genome resequencing and Quantitative PCR (qPCR), the results showed that the CNVRs occupied 163.8 Mb or 6.2% of the yak genome, which is slightly higher than the value determined in previous study that examined 14 wild and 65 domestic yaks (153 Mb, 5.7%) via resequencing [33] and considerably higher that than determined for two yak individuals (33 Mb, 1.25%) based on a comparative genomic hybridization (CGH) array approach [29]
Summary
Genomic structural variation represents a source for genetic and phenotypic variation, which may be subject to selection during the environmental adaptation and population differentiation. Given the ubiquitous distribution of CNVs and their importance, advances in CNV detection have extended to livestock and poultry species, including pigs [16], goats [17], sheep [18], cattle [19], and chicken [20] These animal datasets provide a very valuable resource for evolution and genetic improvement research. Apolipophorin 3 and fatty acid-binding protein 2, two genes involved in lipid transport and metabolism, are highly duplicated in the beef breeds [26] These findings indicate that multiple beneficial CNVs may have been naturally selected in livestock during adaptation to different environments and could be associated with population diversity and economic characteristics
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