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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Genetics and Animal Breeding » Research » Publications at this Location » Publication #295244
Title: Genomewide association study of reproductive efficiency in female cattle

Author
item McDaneld, Tara
item Kuehn, Larry
item THOMAS, MILT - Colorado State University
item Snelling, Warren
item Smith, Timothy - Tim
item Pollak, Emil
item Cole, John
item Keele, John

Submitted to: Journal of Animal Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/3/2014
Publication Date: 5/1/2014
Publication URL: http://handle.nal.usda.gov/10113/58870
Citation: McDaneld, T.G., Kuehn, L.A., Thomas, M.G., Snelling, W.M., Smith, T.P.L., Pollak, E.J., Cole, J.B., Keele, J.W. 2014. Genomewide association study of reproductive efficiency in female cattle. Journal of Animal Science. 92(5):1945-1957.

Interpretive Summary: Reproductive efficiency is of economic importance in commercial beef cattle production, as failure to achieve pregnancy reduces the number of calves marketed per cow exposed. Identification of genetic markers associated with reproductive success would facilitate early selection of sires with daughters having improved reproductive rate. To identify regions of the genome harboring variation affecting reproductive success, we applied a genome wide association study approach based on the 700,000 genetic marker assay and DNA pooling to increase the number of animals that could be genotyped with available resources. Cows from several populations were classified according to reproductive efficiency, and DNA was pooled within population and phenotype prior to genotyping. We detected 1 genetic marker with significant association on chromosome 29, 3 genetic markers with suggestive associations on chromosome 5, and 1 genetic marker with suggestive association each on chromosomes 1, 21 and 25. The study identified regions of the genome associated with reproductive efficiency, which are being targeted for further analysis to develop robust marker systems, and demonstrated that DNA pooling can be used to substantially reduce the cost of genome wide association studies in cattle.

Technical Abstract: Reproductive efficiency is of economic importance in commercial beef cattle production, as failure to achieve pregnancy reduces the number of calves marketed per cow exposed. Identification of genetic markers with predictive merit for reproductive success would facilitate early selection of sires with daughters having improved reproductive rate without increasing generation intervals. To identify regions of the genome harboring variation affecting reproductive success, we applied a genome wide association study (GWAS) approach based on the >700,000 SNP marker assay, using a procedure based on genotyping multi-animal pools of DNA to increase the number of animals that could be genotyped with available resources. Cows from several populations were classified according to reproductive efficiency, and DNA was pooled within population and phenotype prior to genotyping. Populations evaluated included a research population at the US Meat Animal Research Center (USMARC), 2 large commercial ranch populations, and a number of smaller populations (<100 head) across the US. We detected 1 SNP with significant genome-wide association (P = (0.05 / 770,775 SNP)) on BTA29, 3 SNP with suggestive associations (P = (1 / 770,775 SNP)) on BTA5, and 1 SNP with suggestive association each on BTA1, 21 and 25. In addition to our novel findings, we confirmed previously published associations for SNP on BTA X and all autosomes except 3 (BTA21, 22 and 28) encompassing substantial breed diversity including Bos indicus and Bos taurus breeds. The study identified regions of the genome associated with reproductive efficiency, which are being targeted for further analysis to develop robust marker systems, and demonstrated that DNA pooling can be used to substantially reduce the cost of GWAS studies in cattle.