Originally published as Genetics Published Articles Ahead of Print on July 13, 2008.

Genetics, Vol. 179, 1503-1512, July 2008, Copyright © 2008
doi:10.1534/genetics.107.084301

Linkage Disequilibrium and Persistence of Phase in Holstein–Friesian, Jersey and Angus Cattle

A. P. W. de Roos*,1, B. J. Hayes{dagger}, R. J. Spelman{ddagger} and M. E. Goddard{dagger},§

* CRV, 6800 AL Arnhem, The Netherlands, {dagger} Animal Genetics and Genomics, Primary Industries Research Victoria, Attwood 3049, Australia, {ddagger} Livestock Improvement Corporation, Hamilton, New Zealand and § Faculty of Land and Food Resources, University of Melbourne, Parkville 3052, Australia

1 Corresponding author: CRV, P.O. Box 454, 6800 AL Arnhem, The Netherlands.
E-mail: roos.s{at}hg.nl

When a genetic marker and a quantitative trait locus (QTL) are in linkage disequilibrium (LD) in one population, they may not be in LD in another population or their LD phase may be reversed. The objectives of this study were to compare the extent of LD and the persistence of LD phase across multiple cattle populations. LD measures r and r2 were calculated for syntenic marker pairs using genomewide single-nucleotide polymorphisms (SNP) that were genotyped in Dutch and Australian Holstein–Friesian (HF) bulls, Australian Angus cattle, and New Zealand Friesian and Jersey cows. Average r2 was ~0.35, 0.25, 0.22, 0.14, and 0.06 at marker distances 10, 20, 40, 100, and 1000 kb, respectively, which indicates that genomic selection within cattle breeds with r2 ≥ 0.20 between adjacent markers would require ~50,000 SNPs. The correlation of r values between populations for the same marker pairs was close to 1 for pairs of very close markers (<10 kb) and decreased with increasing marker distance and the extent of divergence between the populations. To find markers that are in LD with QTL across diverged breeds, such as HF, Jersey, and Angus, would require ~300,000 markers.