Massive screening of copy number population-scale variation in Bos taurus genome

Abstract

BackgroundCopy number variations (CNVs) represent a significant source of genomic structural variation. Their length ranges from approximately one hundred to millions of base pair. Genome-wide screenings have clarified that CNVs are a ubiquitous phenomenon affecting essentially the whole genome. Although Bos taurus is one of the most important domestic animal species worldwide and one of the most studied ruminant models for metabolism, reproduction, and disease, relatively few studies have investigated CNVs in cattle and little is known about how CNVs contribute to normal phenotypic variation and to disease susceptibility in this species, compared to humans and other model organisms.ResultsHere we characterize and compare CNV profiles in 2654 animals from five dairy and beef Bos taurus breeds, using the Illumina BovineSNP50 genotyping array (54001 SNP probes). In this study we applied the two most commonly used algorithms for CNV discovery (QuantiSNP and PennCNV) and identified 4830 unique candidate CNVs belonging to 326 regions. These regions overlap with 5789 known genes, 76.7% of which are significantly co-localized with segmental duplications (SD).ConclusionsThis large scale screening significantly contributes to the enrichment of the Bos taurus CNV map, demonstrates the ubiquity, great diversity and complexity of this type of genomic variation and sets the basis for testing the influence of CNVs on Bos taurus complex functional and production traits.

Genome-wide identification of copy number variations in Holstein cattle from Baja California, Mexico, using high-density SNP genotyping arrays

“…CNVs can be associated with changes in gene structure, alteration of gene regulation, and exposure of recessive alleles among other effects (Bovine Genome Sequencing and Analysis Consortium et al, 2009;Zhang et al, 2009). Phenotypic variations caused by CNVs are the subject of study in many domestic animals, such as cows (Fadista et al, 2010;Liu et al, 2010;Seroussi et al, 2010;Hou et al, 2011Hou et al, , 2012aJiang et al, 2012Jiang et al, , 2013Cicconardi et al, 2013), horses (Doan et al, 2012), pigs (Wang et al, , 2013, sheep , chickens (Crooijmans et al, 2013), rabbits (Fontanesi et al, 2012), and dogs (Alvarez and Akey, 2012). There are several methods to identify CNVs genome-wide: comparative genomic hybridization arrays (aCGH); single nucleotide polymorphism (SNP) genotyping arrays; and high-throughput (next-generation) sequencing (Wang et al, 2013).…”

Identification of CNVs in the Nelore genome and its association with meat tenderness

“…The detected CNVRs (UMD_3.1 genomic coordinates, ZIMIN et al, 2009) were compared to CNVRs from 14 previous cattle studies (BAE et al, 2010;BICKHART et al, 2012;CHOI et al, 2013;CICCONARDI et al, 2013;HOU et al, 2011HOU et al, , 2012aHOU et al, , 2012bHOU et al, , 2012cKIJAS et al, 2011;LIU et al, 2010;STOTHARD et al, 2011;ZHAN et al, 2011) and structural variation data for bovine from Ensembl . From those, eleven were Btau_4.0 -> UMD_3.1 liftOver converted [https://genome.ucsc.edu/cgibin/hgLiftOver].…”

“…Most of cattle CNV studies use copy number variation regions (CNVRs) to arrange individual CNVs in a given population (BAE et al, 2010;CICCONARDI et al, 2013;HOU et al, 2011HOU et al, , 2012bHOU et al, , 2012cHOU et al, , 2012a This variation can be due to the technical or biological sources (CAHAN et al, 2009;. The use of CNVRs, to group animals with the same structural event, can result in a non-normal structural state (gain or loss)…”

“…Frequently observed is copy number variation (CNV) and is, thus, increasingly researched in cattle (BAE et al, 2010;CICCONARDI et al, 2013;HOU et al, 2011HOU et al, , 2012bHOU et al, , 2012cHOU et al, , 2012aMATUKUMALLI et al, 2009;. CNVs are defined as large genomic regions (conventionally >1 kb) with deviation from the normal diploid state due to duplication or deletion events (LIU; BICKHART, 2012).…”

“…CNVs from SNP-chip data with subsequent validation of selected regions by quantitative polymerase chain reaction (qPCR) (BAE et al, 2010;CICCONARDI et al, 2013;HOU et al, 2011HOU et al, , 2012bHOU et al, , 2012cHOU et al, , 2012aMATUKUMALLI et al, 2009;.…”