Population-genetic properties of differentiated copy number variations in cattle

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.

Figure 1. Eight diverse cattle breeds were grouped into four clusters in this heatmap based on the mean segment LRR of 257 CNVs, including European taurine in green (TAU), indicine in red (IND), and African taurine in blue (AFR).

As expected, SHK in pink was located between AFR and IND. Cattle were clustered horizontally according to their breeds, and CNV were vertically arranged by the clustering method.

Figure 2. Population genetic analyses of eight diverse cattle breeds based on 184 deletion CNVs.

Four distinct groups include the European taurine (TAU) group containing HOL, ANG, HFD, and BWS; the second indicine (IND) group containing BRM and NEL; the third group African taurine (AFR) containing NDA; and the fourth group formed by the hybrid SHK. (A) MDS analysis of 205 individuals. Individuals were plotted according to their coordinates on the first two components. (B) Clustering of 205 individuals from eight breeds based on 184 deletion CNVs when K = 2–6. Individuals were shown as a thin vertical line colored in proportion to their estimated ancestry. (C) Neighbor-joining tree of the 205 individuals. The tree was constructed using genetic sharing distances. Edges were labeled according to the breed of origin.

Figure 3

Genome wide V_ST value plots for CNVs in the following comparisons: (A) TAU vs. IND; (B) TAU vs. AFR; (C) IND vs. AFR; and (D) HOL vs. ANG.