Originally published as Genetics Published Articles Ahead of Print on July 2, 2006.

Genetics, Vol. 174, 79-85, September 2006, Copyright © 2006
doi:10.1534/genetics.106.060418

A First-Generation Metric Linkage Disequilibrium Map of Bovine Chromosome 6

Mehar S. Khatkar*,1, Andrew Collins{dagger}, Julie A. L. Cavanagh*, Rachel J. Hawken{ddagger}, Matthew Hobbs*, Kyall R. Zenger*, Wes Barris{ddagger}, Alexander E. McClintock*, Peter C. Thomson*, Frank W. Nicholas* and Herman W. Raadsma*

* Centre for Advanced Technologies in Animal Genetics and Reproduction (ReproGen), University of Sydney and CRC for Innovative Dairy Products, Camden NSW 2570, Australia, {dagger} Human Genetics Division, University of Southampton, Southampton General Hospital, Southampton SO16 6YD, United Kingdom and {ddagger} CSIRO Livestock Industries, St. Lucia QLD 4067, Australia

1 Corresponding author: Centre for Advanced Technologies in Animal Genetics and Reproduction (ReproGen), University of Sydney, 425 Werombi Rd., Camden NSW 2570, Australia.
E-mail: mehark{at}camden.usyd.edu.au

We constructed a metric linkage disequilibrium (LD) map of bovine chromosome 6 (BTA6) on the basis of data from 220 SNPs genotyped on 433 Australian dairy bulls. This metric LD map has distances in LD units (LDUs) that are analogous to centimorgans in linkage maps. The LD map of BTA6 has a total length of 8.9 LDUs. Within the LD map, regions of high LD (represented as blocks) and regions of low LD (steps) are observed, when plotted against the integrated map in kilobases. At the most stringent block definition, namely a set of loci with zero LDU increase over the span of these markers, BTA6 comprises 40 blocks, accounting for 41% of the chromosome. At a slightly lower stringency of block definition (a set of loci covering a maximum of 0.2 LDUs on the LD map), up to 81% of BTA6 is spanned by 46 blocks and with 13 steps that are likely to reflect recombination hot spots. The mean swept radius (the distance over which LD is likely to be useful for mapping) is 13.3 Mb, confirming extensive LD in Holstein–Friesian dairy cattle, which makes such populations ideal for whole-genome association studies.




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