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Title:   Author  item
                                            ZHOU, YANG - Northwest Agricultural & Forestry Universityitem
                                            UTSUNOMIYA, YURI - Collaboratoritem
                                            XU, LINGYANG - University Of Marylanditem
                                            HAY, EL HAMIDI - Collaboratoritem
                                            Bickhart, Derekitem
                                            CARVALHEIRO, ROBERTO - Collaboratoritem
                                            NEVES, HAROLDO - Collaboratoritem
                                            Van Tassell, Curtis

                                                         - *Curt*item
                                            SONSTEGARD, TAD - Former ARS Employeeitem
                                            GARCIA, JOSE FERNANDO - Collaboratoritem
                                            Liu, Ge

                                                         - *George*
  Submitted to: Scientific Reports
                                    Publication Type: Peer Reviewed Journal
                                    Publication Acceptance Date: 6/14/2016
                                    Publication  Date: 7/6/2016
                                    Citation: Zhou, Y., Utsunomiya, Y.T., Xu, L., Hay, E.A., Bickhart, D.M., Carvalheiro, R., Neves, H.H., Van Tassell, C.P., Sonstegard, T.S., Garcia, J., Liu, G. 2016. Comparative analyses across cattle breeds reveal the pitfalls caused by artificial and lineage-differential copy number variations. Scientific Reports. 6:29219.Interpretive Summary: Genome assembly is the cornerstone for genome-enable animal selection. To avoid the pitfalls caused by assembly errors and differentiated regions between diverse breeds, we identified dozens of artificial and lineage-differential copy number variations through comparative analyses. We then evaluated their adverse effects on the association study and concluded that they should be carefully removed to reduce false-positive calls. Farmers, scientist, and policy planners who need to improve animal health and production based on genome-enable animal selection will benefit from this chapter.
                                Technical Abstract: Copy number variations (CNV) are well known genomic variants, which often complicate structural and functional genomics studies. Here, we integrated the CNV region (CNVR) result detected from 1,682 Nellore cattle with the equivalent result derived from the Bovine HapMap samples. Through comparing CNV segment frequencies between different genders, we found 9 artificial CNVRs with a length of 0.8 Mb caused by assembly errors and evaluated their effects of causing false positive results in the association analyses. The effects of the artificial CNVRs were also detected when we compared Nellore to non-Nellore cattle at CNV segment level. Between these two populations, we found one 54 kb deletion on chr5 drastically enriched in Nellore cattle, though only weak evidence was seen for the lineage differential CNVRs. Through overlapping with genes, we found differences between Nellore and non-Nellore cattle were mainly attributed to sequences similar to OR and ABC genes, while MHC genes were commonly variable among them. In summary, our study detected artificial CNVRs caused by assembly errors and evaluated the separation of Nellore cattle from others at the CNV level, which will remind animal scientists to avoid the pitfalls caused by the assembly errors and differentiated regions between diverse breeds.


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