Date Published: September 27, 2018
Publisher: Public Library of Science
Author(s): Maria Giuseppina Strillacci, Erica Gorla, Maria Cristina Cozzi, Mario Vevey, Francesca Genova, Kathy Scienski, Maria Longeri, Alessandro Bagnato, Qin Zhang.
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.
The use of genomic information in dairy cattle breeding has taken high priority in recent years, as genomic selection has been adopted to improve genetic gain for production traits such as milk production  and meat quality  in cattle breeding programs. In the last 50 years, artificial and natural selection has provoked changes within the cattle genome, causing relevant phenotypic and genetic variability and resulting in the adaptation to local environments .
Although recent studies on CNVs in cattle breeds using high-density SNP chips have been performed, limited knowledge regarding genetic variability and CNV characterization in local populations like the VRP is available. This study is the first CNV scan on the VRP using a high-density SNP chip, and provides valuable information of the structural genomic variation able to enrich the Bovine CNV map. A total of 6,784 CNVs were detected in the autosomes of 108 VRP bulls, and breed-specific regions were identified comparing CNVs mapped here and those available from previously published studies for IBS (n = 164)  and HOL (n = 124)  populations. We observed a similar number of duplications (gain state) and deletions (loss state) in VRP and IBS, while the number of deletions (loss state) is superior to the number of duplications (gain state) in the HOL breed. The latter result was previously reported for the Holstein breed in several studies based on SNPs  and whole genome sequencing . These results suggest the existence of high genetic variability among these breeds.
In this project, we performed the first CNV mapping in an autochthonous cattle population, the Valdostana Red Pied breed, using high-density SNP genotypes. The study permitted to disclose a CNV map in a local population well adapted to a harsh environment., and to compare it with 2 cosmopolitan populations, the Holstein and the Brown Swiss. One of the major indication of this study is that the directional selection occurring in population is affecting the genome in term of CNVs. Particularly the comparison among a very selected and specialized population, the HOL, a population as the Italian Brown Swiss where a directional selection occurred only recently, and a population under a very limited selection pressure for milk and meat but maintained adapted to environment as the VPR, discloses differentiated CNVRs where genes and QTL related to their selection history are annotated.