title: Massive screening of copy number population-scale variation in Bos taurus genome.
abstract: BACKGROUND
  Copy 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.
  
  
  RESULTS
  Here 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).
  
  
  CONCLUSIONS
  This 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.
authors: Department for innovation in biological, agro-food and forest systems, University of Tuscia, via de Lellis, Viterbo 01100, Italy. francicco@gmail.com
authors: Francesco
authors: F
authors: Cicconardi
authors: Giovanni
authors: G
authors: Chillemi
authors: Anna
authors: A
authors: Tramontano
authors: Cinzia
authors: C
authors: Marchitelli
authors: Alessio
authors: A
authors: Valentini
authors: Paolo
authors: P
authors: Ajmone-Marsan
authors: Alessandro
authors: A
authors: Nardone
mesh_terms: D000465:Algorithms; D000818:Animals; D002417:Cattle; D055028:Comparative Genomic Hybridization; D019295:Computational Biology; D056915:DNA Copy Number Variations; D016678:Genome; D005838:Genotype; D020641:Polymorphism, Single Nucleotide; D056916:Segmental Duplications, Genomic; D017422:Sequence Analysis, DNA