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Genomewide association study of reproductive efficiency in female cattle

T. G. McDaneld, L. A. Kuehn, M. G. Thomas, W. M. Snelling, T. P. L. Smith, E. J. Pollak, J. B. Cole, J. W. Keele
Journal of animal science 2014 v.92 no.5 pp. 1945-1957
DNA, autosomes, beef cattle, breeds, calves, cattle production, cows, daughters, early selection, genetic markers, genome, genotyping, phenotype, pregnancy, ranching, reproductive efficiency, single nucleotide polymorphism, sires, zebu, United States
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 genomewide association study (GWAS) approach based on the >700,000 SNP marker assay, using a procedure based on genotyping multianimal 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 U.S. Meat Animal Research Center, 2 large commercial ranch populations, and a number of smaller populations (<100 head) across the United States. We detected 2 SNP with significant genomewide association (P ≤ 1.49 × 10–7), on BTA21 and BTA29, 3 SNP with suggestive associations (P ≤ 2.91 × 10–6) on BTA5, and 1 SNP with suggestive association each on BTA1 and BTA25. In addition to our novel findings, we confirmed previously published associations for SNP on BTA-X and all autosomes except 3 (BTA21, BTA22, and BTA28) 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 in cattle.