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Originally published as Genetics Published Articles Ahead of Print on October 18, 2007.
Genetics, Vol. 177, 2161-2169, December 2007, Copyright © 2007
doi:10.1534/genetics.107.082206
Linkage Disequilibrium in Related Breeding Lines of Chickens
Cristina Andreescu*,
Santiago Avendano
,
Stewart R. Brown,
Abebe Hassen*,
Susan J. Lamont* and
Jack C. M. Dekkers*,1
* Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Ames, Iowa 50010 and Aviagen, Newbridge, Edinburgh EH28 8SZ, United Kingdom
1 Corresponding author: Department of Animal Science, 239D Kildee Hall, Iowa State University, Ames, IA 50011-3150.
E-mail: jdekkers{at}iastate.edu
High-density genotyping of single-nucleotide polymorphisms (SNPs) enables detection of quantitative trait loci (QTL) by linkage disequilibrium (LD) mapping using LD between markers and QTL and the subsequent use of this information for marker-assisted selection (MAS). The success of LD mapping and MAS depends on the extent of LD in the populations of interest and the use of associations across populations requires LD between loci to be consistent across populations. To assess the extent and consistency of LD in commercial broiler breeding populations, we used genotype data for 959 and 398 SNPs on chromosomes 1 and 4 on 179–244 individuals from each of nine commercial broiler chicken breeding lines. Results show that LD measured by r2 extends over shorter distances than reported previously in other livestock breeding populations. The LD at short distance (within 1 cM) tended to be consistent across related populations; correlations of LD measured by r for pairs of lines ranged from 0.17 to 0.94 and closely matched the line relationships based on marker allele frequencies. In conclusion, LD-based correlations are good estimates of line relationships and the relationship between a pair of lines a good predictor of LD consistency between the lines.
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