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Open Access Research

Linkage disequilibrium on chromosome 6 in Australian Holstein-Friesian cattle

Mehar S Khatkar*, Peter C Thomson, Imke Tammen, Julie AL Cavanagh, Frank W Nicholas and Herman W Raadsma

Author Affiliations

Centre for Advanced Technologies in Animal Genetics and Reproduction (ReproGen), and Co-operative Research Centre for Innovative Dairy Products, Faculty of Veterinary Science, University of Sydney PMB 3, Camden NSW 2570, Australia

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Genetics Selection Evolution 2006, 38:463-477  doi:10.1186/1297-9686-38-5-463

The electronic version of this article is the complete one and can be found online at:

Received:17 June 2005
Accepted:20 April 2006
Published:6 September 2006

© 2006 INRA, EDP Sciences


We analysed linkage disequilibrium (LD) in Australian Holstein-Friesian cattle by genotyping a sample of 45 bulls for 15 closely-spaced microsatellites on two regions of BTA6 reported to carry important QTL for dairy traits. The order and distance of markers were based on the USDA-MARC linkage map. Frequencies of haplotypes were estimated using the E-M approach and a more computationally-intensive Bayesian approach as implemented in PHASE. LD was then estimated using the Hedrick multiallelic extension of Lewontin normalised coefficient D'. Estimates of D' from the two approaches were in close agreement (r = 0.91). The mean estimates of D' for marker pairs with an inter-marker distance of less than 5 cM (n = 13) are 0.57 and 0.51, and for distances more than 20 cM (n = 44) are 0.29 and 0.17, estimated from the E-M and Bayesian approaches, respectively. The Malecot model was fitted for the exponential decline of LD with map distance between markers. The swept radii (the distance at which LD has declined to 1/e (~37%) of its initial value) are 11.6 and 13.7 cM for the above two methods, respectively. The Malecot model was also fitted using map distance in Mb from the bovine integrated map (bovine location database, bLDB) in addition to cM from the MARC map. Overall, the results indicate a high level of LD on chromosome 6 in Australian dairy cattle.

linkage disequilibrium; dairy cattle; markers; chromosome 6


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