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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: Copy number variation detection in cattle reveals potential breed specific differences

Authors
item Bickhart, Derek
item Hou, Yali -
item Schroeder, Steven
item Alkan, Can -
item Cardone, Maria Francesca -
item Matukumalli, Lakshmi -
item Song, Jizhou -
item Schnabel, Robert -
item Ventura, Mario -
item Taylor, Jeremy -
item Garcia, Jose Fernando -
item Van Tassell, Curtis
item Sonstegard, Tad
item Eichler, Evan -
item Liu, Ge

Submitted to: BARC Poster Day
Publication Type: Abstract Only
Publication Acceptance Date: April 16, 2012
Publication Date: April 19, 2012
Citation: Bickhart, D.M., Hou, Y., Schroeder, S.G., Alkan, C., Cardone, M., Matukumalli, L.K., Song, J., Schnabel, R.D., Ventura, M., Taylor, J., Garcia, J., Van Tassell, C.P., Sonstegard, T.S., Eichler, E.E., Liu, G. 2012. Copy number variation detection in cattle reveals potential breed specific differences. BARC Poster Day. p. 13

Technical Abstract: Copy Number Variations (CNVs) are large, common deletions or duplications of genome sequence among individuals of a species that have been linked to diseases and phenotypic traits. For example, a CNV-generating, translocation mechanism encompassing the KIT gene is responsible for color sidedness in cattle. CNVs represent an important type of genetic variation among cattle breeds and even individual animals; however, a large percentage of CNVs cannot be easily linked to the SNP markers commonly used to genotype cattle. Using a read depth approach based on next-generation sequencing, we examined genome-wide copy number differences among five taurine (three Angus, one Holstein and one Hereford) and one indicine (Nelore) cattle. Within mapped chromosomal sequence, we identified 1,265 CNV regions -- 476 of which (~38%) had not been previously reported -- comprising approximately 2% of the cattle genome sequence. We validated this sequence-based CNV call set with aCGH, qPCR and FISH data, achieving a validation rate of 82% and a false positive rate of 8%. CNVs were identified within 414 annotated genes in the cattle genome, allowing us to look at the potential functional impacts of CNVs on animal fitness and traits. We identified genes related to pathogen- and parasite-resistance, such as CATHL4 and ULBP17, that were highly duplicated in the Nelore individual relative to the taurine cattle. The Nelore breed is well-known for its tick and parasite-resistance, so the selection of specific gene duplicates of this type may infer increased resistance in taurine breeds of cattle. Genes involved in lipid transport and metabolism, including APOL3 and FABP2, were found to be highly duplicated in the beef breeds. Given the importance of intra-muscular fat deposition and feed efficiency in the beef industry, genotyping these CNVs within the beef cattle populations may increase the efficiency and quality of meat production through selective breeding. By providing the first individualized cattle CNV and segmental duplication maps and genome-wide gene copy number estimates, we enable future research into CNV influenced traits that may be targeted for selection by cattle breeders.

Last Modified: 10/23/2014
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