Abstract
While single nucleotide polymorphism (SNP) is typically the variant of choice for population genetics, copy number variation (CNV) which comprises insertion, deletion and duplication of genomic sequence, is an informative type of genetic variation. CNVs have been shown to be both common in mammals and important for understanding the relationship between genotype and phenotype. However, CNV differentiation, selection and its population genetic properties are not well understood across diverse populations. We performed a population genetics survey based on CNVs derived from the BovineHD SNP array data of eight distinct cattle breeds. We generated high resolution results that show geographical patterns of variations and genome-wide admixture proportions within and among breeds. Similar to the previous SNP-based studies, our CNV-based results displayed a strong correlation of population structure and geographical location. By conducting three pairwise comparisons among European taurine, African taurine, and indicine groups, we further identified 78 unique CNV regions that were highly differentiated, some of which might be due to selection. These CNV regions overlapped with genes involved in traits related to parasite resistance, immunity response, body size, fertility, and milk production. Our results characterize CNV diversity among cattle populations and provide a list of lineage-differentiated CNVs.
Highlights
AMY1 copy number enables the better digestion of starchy foods[26]
While all 257 Copy number variations (CNVs) were used for frequency and VST calculations, only the 184 deletion CNV regions were used in all other subsequent population genetics analyses
We provided additional evidence to support CNVs as genetic markers that can be used to study the across population diversity and capture the subspecies relationships
Summary
AMY1 copy number enables the better digestion of starchy foods[26]. An indel polymorphism in gene APOBEC3b has been associated with malaria susceptibility[27]. The human UGT2B17 gene shows significant copy-number diversity among populations from Africa, Europe, and East Asia, which displays region-specific differences in the metabolism of steroid hormones and a large number of xenobiotics[28]. Another well-known example is the olfactory receptor (OR) genes, which are frequently found to be copy-number variable in most mammalian species. We demonstrated that CNVs can be used for the investigation of population genetics in cattle, as we observed CNVs with significant diversity across groups that might be associated with breed and sub-species specific selection signatures
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