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Title:   Author  item
                                            HOU, YALI - University Of Marylanditem
                                            Liu, Ge

                                                         - *George*item
                                            Bickhart, Derekitem
                                            MATUKUMALLI, L.K. - George Mason Universityitem
                                            SONG, JIUZHOU - University Of Marylanditem
                                            GASBARRE, LOUIS - Retired ARS Employeeitem
                                            Van Tassell, Curtis

                                                         - *Curt*item
                                            Sonstegard, Tad
  Submitted to: BARC Poster Day
                                    Publication Type: Abstract Only
                                    Publication Acceptance Date: 3/8/2011
                                    Publication  Date: 4/27/2011
                                    Citation: Hou, Y., Liu, G., Bickhart, D.M., Matukumalli, L., Song, J., Gasbarre, L., Van Tassell, C.P., Sonstegard, T.S. 2011. Genomic and functional characteristics of copy number variations in Angus cattle selected for resistance or susceptibility to gastrointestinal nematodes [abstract].  BARC Poster Day. No. 17.Interpretive Summary:
                                Technical Abstract: Genomic structural variation is an important and abundant source of genetic and phenotypic variation. We previously reported an initial analysis of copy number variations (CNVs) in Angus cattle selected for resistance or susceptibility to intestinal nematodes. In this study, we performed a large scale analysis of CNVs using SNP genotyping data from 472 animals of the same population. We detected 811 candidate CNV regions, which represent 141.8 Mb (~4.7%) of the genome. To investigate the functional impacts of CNVs, we created two groups of individual animals with extreme low or high estimated breeding values (EBVs) of eggs per gram of feces (EPG), and referred to these groups as parasite resistant (PR) or susceptible (PS), respectively. We identified 195 (~32 Mb) from PR and 182 (~30 Mb) CNV regions from PS groups, and about two third of the CNV regions were specific to each group. Selected PR or PS-specific CNVs and associated genes were further experimentally validated by quantitative PCR (qPCR). A total of 97 PR-specific CNV regions overlapped with 234 ensembl genes over represented in immunity and defense, like WC1 a gene uniquely expressed on gamma/delta T cells in cattle. Pathway analyses indicated that these PR genes were predominantly involved in inflammatory response, cell-to-cell signaling and interaction, tissue development and immunological disease. In contrast, 95 PS-specific CNV regions contained 280 genes which are enriched in environmental interactions, such as lymphocyte-specific protein 1 (LSP1). Pathway analyses indicated that the PS genes are also particularly enriched for cell death, DNA repair, drug metabolism, glutathione depletion in liver and gastrointestinal disease. These results provide valuable foundation for the future study of cattle CNVs underling economically important health and production traits.


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