A copy number variant scan in the autochthonous Valdostana Red Pied cattle breed and comparison with specialized dairy populations

Abstract

Copy number variants (CNVs) are an important source of genomic structural variation, recognized to influence phenotypic variation in many species. Many studies have focused on identifying CNVs within and between human and livestock populations alike, but only few have explored population-genetic properties in cattle based on CNVs derived from a high-density SNP array. We report a high-resolution CNV scan using Illumina’s 777k BovineHD Beadchip for Valdostana Red Pied (VRP), an autochthonous Italian dual-purpose cattle population reared in the Alps that did not undergo strong selection for production traits. After stringent quality control and filtering, CNVs were called across 108 bulls using the PennCNV software. A total of 6,784 CNVs were identified, summarized to 1,723 CNV regions (CNVRs) on 29 autosomes covering a total of ~59 Mb of the UMD3.1 assembly. Among the mapped CNVRs, there were 812 losses, 832 gains and 79 complexes. We subsequently performed a comparison of CNVs detected in the VRP and those available from published studies in the Italian Brown Swiss (IBS) and Mexican Holstein (HOL). A total of 171 CNVRs were common to all three breeds. Between VRP and IBS, 474 regions overlapped, while only 313 overlapped between VRP and HOL, indicating a more similar genetic background among populations with common origins, i.e. the Alps. The principal component, clustering and admixture analyses showed a clear separation of the three breeds into three distinct clusters. In order to describe the distribution of CNVs within and among breeds we used the pair VST statistic, considering only the CNVRs shared to more than 5 individuals (within breed). We identified unique and highly differentiated CNVs (n = 33), some of which could be due to specific breed selection and adaptation. Genes and QTL within these regions were characterized.

Functional and population genetic features of copy number variations in two dairy cattle populations

“…Furthermore, when rare CNVs were filtered for both of the populations, which means CNVRs were present in both populations with more than 5 copies, the correlation coefficient was 0.81. This number is slightly lower than 0.9, which was shown in human CNV study [49]. These findings underline high concordance of Fst and Vst when CNVRs are present in both populations with sufficient MAF.…”

“…4 and Additional file 2: Table S6). Among the 17 intergenic CNVRs with high population Subsequently, we calculated Vst statistic, which is a widely used statistic in CNV studies [23,49]. This statistic is analogous to Fst, but using LRR values instead of allele frequencies [28].…”

Functional and population genetic features of copy number variations in two dairy cattle populations

“…Subsequently, we calculated Vst statistic, which is a widely used statistic in CNV studies [23,49]. This statistic is analogous to Fst, but using LRR values instead of allele frequencies [50].…”

Functional and population genetic features of copy number variations in two dairy cattle populations

“…Interestingly, these CNVRs are duplications and have a high allele frequency in JER (MAF = 0.08-0.37), and a low allele frequency in HOL (MAF = 0-0.06). Subsequently, we calculated Vst statistic, which is a widely used statistic in CNV studies [23,49]. This statistic is analogous to Fst, but using LRR values instead of allele frequencies [28].…”