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Title:   Author  item
                                            XU, LINGYANG - University Of Marylanditem
                                            HOU, YALI - Chinese Academy Of Sciencesitem
                                            Bickhart, Derekitem
                                            ZHOU, YANG - Northwest Agricultural & Forestry Universityitem
                                            Hay, El Hamidiitem
                                            SONG, JIUZHOU - University Of Marylanditem
                                            SONSTEGARD, TAD - Former ARS Employeeitem
                                            Van Tassell, Curtis

                                                         - *Curt*item
                                            Liu, Ge

                                                         - *George*
  Submitted to: Scientific Reports
                                    Publication Type: Peer Reviewed Journal
                                    Publication Acceptance Date: 2/25/2016
                                    Publication  Date: 3/23/2016
                                    Citation: Xu, L., Hou, Y., Bickhart, D.M., Zhou, Y., Hay, E.A., Song, J., Sonstegard, T., Van Tassell, C.P., Liu, G. 2016. Population-genetic properties of differentiated copy number variations in cattle. Scientific Reports. 6:23161.Interpretive Summary: Copy number variations (CNVs) comprise large insertions, deletions, and duplications of genomic regions, which contribute to variations in traits among individuals. The differentiation, selection and population genetic properties of CNVs are not well investigated across diverse cattle populations. We performed a population genetics survey based on CNVs derived from the BovineHD SNP array data of eight distinct cattle breeds. These CNV results provide a new glimpse of diverse selections during cattle speciation, domestication, breed formation, and recent genetic improvement. Farmers, scientist, and policy planners who need to improve animal health and production based on genome-enable animal selection will benefit from this manuscript.
                                Technical Abstract: Besides single nucleotide polymorphism (SNP), copy number variation (CNV) which comprise insertions, deletions and duplications of genomic sequence, is a new informative type of genetic variations. CNVs have been shown to be both common in mammals and important for understanding 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. We further identified 78 unique CNV regions under diverse selection across three pairwise comparisons among European taurine, African taurine, and indicine groups. These CNV regions overlapped with some genes, which are involved in traits related to parasite resistance, immune response, body size, fertility, and milk production. Our results revealed the overall CNV diversity among cattle populations and provided evidence for divergent selection for lineage-specific CNVs.


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