Comparison of linkage disequilibrium and haplotype diversity on macro- and microchromosomes in chicken

Megens, H-K.; Crooijmans, R.; Bastiaansen, J.; Kerstens, H.; Coster, A.; Jalving, R.; Vereijken, A.; Silva, P.; Muir, W.; Cheng, H.; Hanotte, O.; Groenen, M. 2009. Comparison of linkage disequilibrium and haplotype diversity on macro and microchromosomes in chicken. BMC Genetics 10:86.

The chicken (Gallus gallus), like most avian species, has a very distinct karyotype consisting of many micro- and a few macrochromosomes. While it is known that recombination frequencies are much higher for micro- as compared to macrochromosomes, there is limited information on differences in linkage disequilibrium (LD) and haplotype diversity between these two classes of chromosomes. In this study, LD and haplotype diversity were systematically characterized in 371 birds from eight chicken populations (commercial lines, fancy breeds, and red jungle fowl) across macro- and microchromosomes. To this end we sampled four regions of ~1 cM each on macrochromosomes (GGA1 and GGA2), and four 1.5 -2 cM regions on microchromosomes (GGA26 and GGA27) at a high density of 1 SNP every 2 kb (total of 889 SNPs).