Linkage Disequilibrium, Haplotype Sharing And Prospects For Hapmapping The Chicken Genome

A total of eight 1cM regions located on two macro and two micro chromosomes (GGA1, GGA2, GGA26 and GGA27) were genotyped at high SNP density (1 SNP / 2kb) in a wide variety of chicken populations: two female and one male broiler parent line, a brown layer line, a white layer line, two traditional Dutch breeds, and a wild chicken population. The white layer had the highest extent of LD, while the wild chicken had the lowest. Of domesticated chicken populations, broiler lines displayed the lowest extend of LD. While LD in micro chromosomes extends less far than in macro chromosomes, the differences are not significant. In contrast to the small differences in LD, there is a very marked reduction in haplotype sharing on the micro compared to macro chromosomes. A difference in haplotype sharing as well as LD was expected based on the higher recombination rates in the micro chromosomes. Haplotype sharing between breeds was not common. The resulting haplotype map showed very small haploblocks with no or very limited overlap between lines, even between the two broiler lines. This results shows that with the low levels of both LD and haplotype sharing it will be necessary to perform haplotype-mapping at a very high density of SNP markers