Abstract
Copy number variations (CNVs) are defined as deletions, insertions, and duplications between two individuals of a species. To investigate the diversity and population-genetic properties of CNVs and their diverse selection patterns, we performed a genome-wide CNV analysis using high density SNP array in Chinese native cattle. In this study, we detected a total of 13,225 CNV events and 3,356 CNV regions (CNVRs), overlapping with 1,522 annotated genes. Among them, approximately 71.43 Mb of novel CNVRs were detected in the Chinese cattle population for the first time, representing the unique genomic resources in cattle. A new Vi statistic was proposed to estimate the region-specific divergence in CNVR for each group based on unbiased estimates of pairwise VST. We obtained 12 and 62 candidate CNVRs at the top 1% and top 5% of genome-wide Vi value thresholds for each of four groups (North, Northwest, Southwest and South). Moreover, we identified many lineage-differentiated CNV genes across four groups, which were associated with several important molecular functions and biological processes, including metabolic process, response to stimulus, immune system, and others. Our findings provide some insights into understanding lineage-differentiated CNVs under divergent selection in the Chinese native cattle.
Highlights
In recent years, many studies have revealed genomic diversity could be generated by the differential selection of Copy number variations (CNVs) in specific environments for adaptations[30,31,32,33]
Many studies regarding CNV discovery had been reported for various cattle populations using aCGH, SNP array and generation sequencing[25,28,31,39,44,45,46,47,48]
Some previous studies carried out CNV analysis in world-wide cattle including taurine, indicine, and mixed cattle population from African using both BovineSNP50 and BovineHD SNP array[26,44]
Summary
Many studies have revealed genomic diversity could be generated by the differential selection of CNVs in specific environments for adaptations[30,31,32,33]. Investigations of population genetic properties and selection patterns involved with CNVs have gradually become an emerging research topic for farm animals. Bickhart et al further explored the diversity and population genetics of both taurine and indicine cattle based on CNV using generation sequencing and showed hundreds of copy number variable genes were breed-specific[31]. A few studies have been carried out to investigate CNV in Chinese cattle[41,42,43], genome-wide CNV landscapes and its population-genetic properties in Chinese cattle adapted for local specific environments are largely unknown. The objectives of this study were to 1) Generate a comprehensive CNV landscape in Chinese cattle populations; 2) Investigate and compare the diversity and population-genetic properties of CNVs; 3) Explore the diverse selection patterns involved with CNV genes for local adaptation in Chinese native cattle
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