Whole genome linkage disequilibrium maps in cattle.
BACKGROUND
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.


RESULTS
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.


CONCLUSIONS
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.
McKay
Stephanie D
SD
Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada. Stephen.Moore@afhe.ualberta.ca
Schnabel
Robert D
RD
Murdoch
Brenda M
BM
Matukumalli
Lakshmi K
LK
Aerts
Jan
J
Coppieters
Wouter
W
Crews
Denny
D
Dias Neto
Emmanuel
E
Gill
Clare A
CA
Gao
Chuan
C
Mannen
Hideyuki
H
Stothard
Paul
P
Wang
Zhiquan
Z
Van Tassell
Curt P
CP
Williams
John L
JL
Taylor
Jeremy F
JF
Moore
Stephen S
SS
D000818:Animals; D002417:Cattle / Q000235:genetics*; D002874:Chromosome Mapping / Q000379:methods*; D005787:Gene Frequency; D005819:Genetic Markers; D016678:Genome; D006239:Haplotypes; D015810:Linkage Disequilibrium; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci
D005819:Genetic Markers