Measuring the extent of linkage disequilibrium in commercial pig populations

Summary To evaluate the extent of linkage disequilibrium in domestic pigs, we genotyped 33 and 44 unrelated individuals from two commercial populations for 29 and five microsatellite markers located on chromosomes 15 and 2 respectively. A high proportion of marker pairs up to 40 cM apart exhibited significant linkage disequilibrium in both populations. Pair-wise r2 values averaged between 0.15 and 0.50 (depending on chromosome and population) for markers <1 cM apart and declined to values of 0.05 for more distant syntenic markers. Our results suggest that both populations underwent a bottleneck approximately 20 generations ago, which reduced the effective population size from thousands to <200 animals.