Extent and consistency across generations of linkage disequilibrium in commercial layer chicken breeding populations

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 (χ^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.