Extent and Consistency Across Generations of Linkage Disequilibrium in Commercial Layer Chicken Breeding Populations

• Published in: Genetics (Austin) Vol. 171; no. 3; pp. 1173 - 1181
• Main Authors: Heifetz, E. M, Fulton, J. E, O'Sullivan, N, Zhao, H, Dekkers, J. C. M, Soller, M
• Format: Journal Article
• Language: English
• Published: United States Genetics Soc America 01.11.2005; Genetics Society of America; Copyright © 2005 by the Genetics Society of America
• Subjects: Animal populations; Animals; Chi-Square Distribution; Chickens - genetics; Gallus gallus; Genetic Markers; Genetics; Genetics, Population; Genomics; Genotype & phenotype; Investigations; Linkage Disequilibrium; Male; Molecular biology; Population Dynamics; Quantitative Trait Loci; Regression analysis; Ruminantia; Studies; Synteny
• ISSN: 0016-6731; 1943-2631; 1943-2631
• DOI: 10.1534/genetics.105.040782

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 (chi(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.