title: Evolutionary and Functional Features of Copy Number Variation in the Cattle Genome.
abstract: Genomic structural variations are an important source of genetic diversity. Copy number variations (CNVs), gains and losses of large regions of genomic sequence between individuals of a species, have been associated with a wide variety of phenotypic traits. However, in cattle, as well as many other species, relatively little is understood about CNV, including frequency of CNVs in the genome, sizes, and locations, chromosomal properties, and evolutionary processes acting to shape CNV. In this work, we focused on copy number variation in the bovine genome, with the aim to detect CNVs inBos tauruscoding sequence and explore potential evolutionary mechanisms shaping these CNV. We identified and characterized CNV regions by utilizing exome sequence from 175 influential sires used in the Germplasm Evaluation project, representing 10 breeds. We examined various evolutionary and functional aspects of these CNVs, including selective constraint on CNV-overlapped genes, centrality of CNV genes in protein-protein interaction networks, and tissue-specific expression of CNV genes. Patterns of CNV in theBos taurusgenome reveal that reduced functional constraint and mutational bias may play a prominent role in shaping this type of structural variation.
authors.affiliation: Agricultural Research Service (USDA), Meat Animal Research Center Clay Center, NE, USA.
authors.forename: Brittney N
authors.initials: BN
authors.lastname: Keel
authors.affiliation: Agricultural Research Service (USDA), Meat Animal Research Center Clay Center, NE, USA.
authors.forename: Amanda K
authors.initials: AK
authors.lastname: Lindholm-Perry
authors.affiliation: Agricultural Research Service (USDA), Meat Animal Research Center Clay Center, NE, USA.
authors.forename: Warren M
authors.initials: WM
authors.lastname: Snelling
keywords: cattle genome; copy number variation; deletion; duplication; gene expression; network centrality; next-generation sequencing; selective constraint