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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: Whole genome linkage disequilibrium maps in cattle

Authors
item Mckay, Stephanie -
item Schnabel, Robert -
item Murdoch, Brenda -
item Matukumalli, Lakshmi -
item Aerts, Jan -
item Coppieters, Wouter -
item Crews, Denny -
item Neto, Emmanuel -
item Gill, Clare -
item Gao, Chuan -
item Mannen, Hideyuki -
item Stothard, Paul -
item Wang, Zhiquan -
item Van Tassell, Curtis
item Williams, John -
item Taylor, Jeremy -
item Moore, Stephen -

Submitted to: Journal of Animal Breeding and Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: October 25, 2007
Publication Date: October 25, 2007
Citation: Mckay, S.D., Schnabel, R.D., Murdoch, B.M., Matukumalli, L.K., Aerts, J., Coppieters, W., Crews, D., Neto, E.D., Gill, C.A., Gao, C., Mannen, H., Stothard, P., Wang, Z., Van Tassell, C.P., Williams, J.L., Taylor, J.F., Moore, S.S. 2007. Whole genome linkage disequilibrium maps in cattle. Journal of Animal Breeding and Genetics. 25(8):74.

Interpretive Summary: For the purposes of extensive selection of specific functional characteristics or production traits such as milk/beef cattle are segregated into different breeds. Sequencing of the cattle genome, polymorphism discovery and advances in genotyping technology have allowed us to rapidly genotype thousands of markers in hundreds of animals. In this study we have identified 8 breeds of diverse cattle representing both Bos indicus and Bos Taurus genera. The breeds represented are from Angus, Brahman, Charolais, Dutch Black and White Dairy, Holstein, Japanese Black, Limousin and Nelore. This is the first study to use large-scale SNP data revealing the linkage disequilibrium in cattle breeds across the world. This study revealed that r2 is a better estimator than D’ for LD and the prior estimates of LD in cattle were inflated.

Technical Abstract: Bovine whole genome linkage disequilibrium maps were constructed for eight breeds of cattle. These data provide fundamental information concerning bovine genome organization which will allow the design of studies to associate genetic variation with economically important traits and also provides background information concerning the extent of long range linkage disequilibrium in cattle. Linkage disequilibrium was assessed using r2 among all pairs of syntenic markers within eight breeds of cattle from the Bos taurus and Bos indicus subspecies. Bos taurus breeds included Angus, Charolais, Dutch Black and White Dairy, Holstein, Japanese Black and Limousin while Bos indicus breeds included Brahman and Nelore. Approximately 2670 markers spanning the entire bovine autosomal genome were used to estimate pairwise r2 values. We found that the extent of linkage disequilibrium is no more than 0.5 Mb in these eight breeds of cattle. Linkage disequilibrium in cattle has previously been reported to extend several tens of centimorgans. Our results, based on a much larger sample of marker loci and across eight breeds of cattle indicate that in cattle linkage disequilibrium persists over much more limited distances. Our findings suggest that 30,000–50,000 loci will be needed to conduct whole genome association studies in cattle.

Last Modified: 8/21/2014
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