title: Population-genetic properties of differentiated copy number variations in cattle.
abstract: While single nucleotide polymorphism (SNP) is typically the variant of choice for population genetics, copy number variation (CNV) which comprises insertion, deletion and duplication of genomic sequence, is an informative type of genetic variation. CNVs have been shown to be both common in mammals and important for understanding the relationship between genotype and phenotype. However, CNV differentiation, selection and its population genetic properties are not well understood across diverse populations. We performed a population genetics survey based on CNVs derived from the BovineHD SNP array data of eight distinct cattle breeds. We generated high resolution results that show geographical patterns of variations and genome-wide admixture proportions within and among breeds. Similar to the previous SNP-based studies, our CNV-based results displayed a strong correlation of population structure and geographical location. By conducting three pairwise comparisons among European taurine, African taurine, and indicine groups, we further identified 78 unique CNV regions that were highly differentiated, some of which might be due to selection. These CNV regions overlapped with genes involved in traits related to parasite resistance, immunity response, body size, fertility, and milk production. Our results characterize CNV diversity among cattle populations and provide a list of lineage-differentiated CNVs.
authors.affiliation: Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, Maryland 20705, USA.|Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland 20742, USA.
authors.forename: Lingyang
authors.initials: L
authors.lastname: Xu
authors.affiliation: Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
authors.forename: Yali
authors.initials: Y
authors.lastname: Hou
authors.affiliation: Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, Maryland 20705, USA.
authors.forename: Derek M
authors.initials: DM
authors.lastname: Bickhart
authors.affiliation: Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, Maryland 20705, USA.|College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Agricultural Molecular Biology, Yangling, Shaanxi, 712100, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Zhou
authors.affiliation: Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, Maryland 20705, USA.
authors.forename: El Hamidi Abdel
authors.initials: el HA
authors.lastname: Hay
authors.affiliation: Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland 20742, USA.
authors.forename: Jiuzhou
authors.initials: J
authors.lastname: Song
authors.affiliation: Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, Maryland 20705, USA.
authors.forename: Tad S
authors.initials: TS
authors.lastname: Sonstegard
authors.affiliation: Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, Maryland 20705, USA.
authors.forename: Curtis P
authors.initials: CP
authors.lastname: Van Tassell
authors.affiliation: Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, Maryland 20705, USA.
authors.forename: George E
authors.initials: GE
authors.lastname: Liu
mesh_terms: D000818:Animals; D001947:Breeding; D002417:Cattle; D016000:Cluster Analysis; D056915:DNA Copy Number Variations; D005828:Genetics, Population; D060005:Genotyping Techniques / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D058974:Phylogeography; D020641:Polymorphism, Single Nucleotide; D011157:Population Dynamics; D040641:Quantitative Trait Loci