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United States Department of Agriculture

Agricultural Research Service

Research Project: ENHANCING GENETIC MERIT OF DAIRY CATTLE THROUGH GENOME SELECTION AND ANALYSIS Title: Genomic and functional characteristics of copy number variations in Angus cattle selected for resistance or susceptibility to gastrointestinal nematodes

Authors
item Hou, Yali -
item Liu, Ge
item Bickhart, Derek
item Matukumalli, L.K. -
item Song, Jiuzhou -
item Gasbarre, Louis -
item Van Tassell, Curtis
item Sonstegard, Tad

Submitted to: BARC Poster Day
Publication Type: Abstract Only
Publication Acceptance Date: March 8, 2011
Publication Date: April 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.

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.

Last Modified: 4/20/2014