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ARS Home » Research » Publications at this Location » Publication #254940
Title: Initial analysis of copy number variations in cattle selected for resistance or susceptibility to intestinal nematodes

Author
item Liu, Ge - George
item Brown, Twain
item Hebert, Deborah - Van Hook
item CARDONE, MARIA - University Of Bari
item HOU, YALI - University Of Maryland
item CHOUDHARY, RATAN - University Of Maryland
item Shaffer, Jessica
item AMAZU, CHINWENDU - Eleanor Roosevelt High School
item Connor, Erin
item VENTURA, MARIO - University Of Bari
item GASBARRE, LOUIS - Retired ARS Employee

Submitted to: Mammalian Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/11/2010
Publication Date: 12/3/2010
Citation: Liu, G., Brown, T.E., Hebert, D.A., Cardone, M.F., Hou, Y., Choudhary, R.K., Shaffer, J.F., Amazu, C., Connor, E.E., Ventura, M., Gasbarre, L.C. 2010. Initial analysis of copy number variations in cattle selected for resistance or susceptibility to intestinal nematodes. Mammalian Genome. 22:111-121.

Interpretive Summary: In this study, we employed an integrated approach combining array CGH screens, PCR confirmations and FISH verifications to study the CNVs associated with parasite resistance. We describe an initial genome-wide analysis of CNVs in the 2 Angus populations selected for selected for either resistance or susceptibility to intestinal nematodes. We identified 25 CNVRs covering about 3.8 mega bases. Selected CNVs were further validated by independent methods using quantitative PCR and FISH. Pathway analyses indicated that annotated cattle genes within these variable regions are particularly enriched for immune function by regulating receptor activities, signal transduction, and transcription. Analysis of TFBS within the promoter regions of differentially-expressed genes suggested that common transcription factors are probably involved in parasite resistance. Results of this study provide valuable hypotheses for the future study of cattle CNVs underling economically-important health and production traits. This work is an important first step for studying the functional impacts of CNVs. It provides the foundation for correlating structural variation in the genome with the genetic basis of host responses.

Technical Abstract: 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 4 array comparative genomic hybridization (CGH) experiments to compare 6 Angus cattle with extreme phenotypes for fecal egg count and serum pepsinogen level. We identified 25 candidate CNVs in total, of which 13 were within known chromosomes harboring or adjacent to gains or losses. Over 90% of the CNV identified (23/25) overlapped with cattle CNV regions that were reported recently. Selected CNVs were further validated by independent methods using quantitative PCR (qPCR) and FISH. Pathway analysis indicated that annotated cattle genes within these variable regions are particularly enriched for immune function by regulating receptor activities, signal transduction, and transcription. Analysis of 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 underling economically-important health and production traits.