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Initial analysis of copy number variations in cattle selected for resistance or susceptibility to intestinal nematodes

Liu, George E., Brown, Twain, Hebert, Deborah A., Cardone, Maria Francesca, Hou, Yali, Choudhary, Ratan K., Shaffer, Jessica, Amazu, Chinwendu, Connor, Erin E., Ventura, Mario, Gasbarre, Louis C.
Mammalian genome 2011 v.22 no.1-2 pp. 111
Angus, Nematoda, artificial selection, binding sites, cattle, chromosomes, digestive system diseases, disease resistance, fecal egg count, fluorescence in situ hybridization, gene dosage, genes, genetic resistance, genetic variation, immunity, microarray technology, nematode infections, nucleic acid hybridization, parasites, pepsinogen, phenotype, polymerase chain reaction, promoter regions, quantitative analysis, receptors, resistance mechanisms, signal transduction, transcription (genetics), transcription factors
Genomic structural variation is an important and abundant source of genetic and phenotypic variation. We report an initial analysis of copy number variations (CNVs) in cattle selected for resistance or susceptibility to intestinal nematodes. We performed three array comparative genomic hybridization (CGH) experiments to compare Angus cattle with extreme phenotypes for fecal egg count and serum pepsinogen level. We identified 20 CNVs in total, of which 12 were within known chromosomes harboring or adjacent to gains or losses. About 85% of the CNV identified (17/20) overlapped with cattle CNV regions that were reported recently. Selected CNVs were further validated by independent methods using quantitative PCR (qPCR) and FISH. Pathway analyses indicated that annotated cattle genes within these variable regions are particularly enriched for immune function affecting receptor activities, signal transduction, and transcription. Analysis of transcription factor binding sites (TFBS) within the promoter regions of differentially expressed genes suggested that common transcription factors are probably involved in parasite resistance. These results provide valuable hypotheses for the future study of cattle CNVs underlying economically important health and production traits.