Extent of linkage disequilibrium in wild and domestic chicken populations

Linkage disequilibrium (LD) analyses play a fundamental role in gene mapping, both as a tool for fine mapping of complex trait gene and in genome-wide association studies. The use of LD analyses in practice depends crucially on the understanding of the patterns of LD in the genome. In the present study, a total of 36 SNP were selected initially in a region (200 kb) of Contig.060226.1 on GGA1 based on the average physical distance. After verifying their level of polymorphism, 21 SNP were selected finally to genotype one wild and two domestic chicken populations, Red Jungle Fowl (RJF), Taihe Silkie chicken (TS) and White Recessive Rock chicken (WRR). Two distinct measures of linkage disequilibrium, D' and r(2), between marker pairs were used. The D'map of RJF is spurious. Many marker pairs showed complete LD. TS and WRR showed distinct characteristic of decreasing D' value over increasing physical distance. The r(2) showed much less inflation than did D' in RJF population, and also showed a characteristic decreasing value over increasing physical distance. In TS and WRR populations, although the two measures differed in scale, their decay profiles were similar. The data in the present study suggested that the extent of LD in this region is about 150 kb, corresponding to 0.4 cM. Our results imply that a very dense map of SNP markers will be required for LD mapping methods. Thus, association studies based on polymorphisms within all known genes, and candidate QTL mapping, may ultimately prove to be a more effective strategy.