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Originally published as Genetics Published Articles Ahead of Print on August 22, 2005.
Genetics, Vol. 171, 1173-1181, November 2005, Copyright © 2005
doi:10.1534/genetics.105.040782
Extent and Consistency Across Generations of Linkage Disequilibrium in Commercial Layer Chicken Breeding Populations
E. M. Heifetz*,
,1,
J. E. Fulton
,
N. O'Sullivan,
H. Zhao,
J. C. M. Dekkers and
M. Soller*,2
* Department of Genetics, Hebrew University, 91904 Jerusalem, Israel, Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Ames, Iowa 50011 and Hy-Line International, Dallas Center, Iowa 50063
2 Corresponding author: Department of Genetics, Hebrew University, 91904 Jerusalem, Israel.
E-mail: soller{at}vms.huji.ac.il
Recent studies report a surprisingly high degree of marker-to-marker linkage disequilibrium (LD) in ruminant livestock populations. This has important implications for QTL mapping and marker-assisted selection. This study evaluated LD between microsatellite markers in a number of breeding populations of layer chickens using the standardized chi-square (
2') measure. The results show appreciable LD among markers separated by up to 5 cM, decreasing rapidly with increased separation between markers. The LD within 5 cM was strongly conserved across generations and differed among chromosomal regions. Using marker-to-marker LD as an indication for marker-QTL LD, a genome scan of markers spaced 2 cM apart at moderate power would have good chances of uncovering most QTL segregating in these populations. However, of markers showing significant trait associations, only 57% are expected to be within 5 cM of the responsible QTL, and the remainder will be up to 20 cM away. Thus, high-resolution LD mapping of QTL will require dense marker genotyping across the region of interest to allow for interval mapping of the QTL.
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