Skip to main content
ARS Home » Research » Publications at this Location » Publication #243126

Title: Whole genome linkage disequilibrium maps in cattle

item MCKAY, STEPHANIE - University Of Alberta
item SCHNABEL, ROBERT - University Of Missouri
item MURDOCH, BRENDA - University Of Alberta
item MATUKUMALLI, LAKSHMI - George Mason University
item AERTS, JAN - Roslin Institute
item COPPIETERS, WOUTER - University Of Liege
item CREWS, DENNY - University Of Alberta
item NETO, EMMANUEL - Universidad De Sao Paulo
item GILL, CLARE - Texas A&M University
item GAO, CHUAN - Texas A&M University
item MANNEN, HIDEYUKI - Kobe University
item STOTHARD, PAUL - University Of Alberta
item WANG, ZHIQUAN - University Of Alberta
item Van Tassell, Curtis - Curt
item WILLIAMS, JOHN - Parco Tecnologico Padano
item TAYLOR, JEREMY - University Of Missouri
item MOORE, STEPHEN - University Of Alberta

Submitted to: Journal of Animal Breeding and Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/25/2007
Publication Date: 10/25/2007
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.