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.

[Comparative study of SNP diversity and calculation of the effective size of population in chicken].

A region (200 kb) of Contig. 060226.1 on GGA1 was selected to study the average diversity of Red Jungle Fowl (RJF), Taihe Silk chicken (TS), and White Recessive Rock (WRR), and estimate the effective population size (Ne) of chicken. The mean heterozygosities of RJF, TS and WRR were 0.28533+/-0.034747, 0.32926+/-0.039191 and 0.30168+/-0.040382, respectively. Significant test indicted that there is not significant difference between them (P=0.2368>0.05). The initial chicken effective population size was estimated to be about 20 000-150 000. Chicken has undergone serious population bottleneck effect during the first stage of domestication. However, this bottleneck effect did not result in a substantial loss of diversity as revealed by SNP. The possible explanations for similar SNP diversity between domesticated chicken and Red Jungle Fowl might due to many factors, such as a big Ne in earlier phase of domestication, population expending in breed differentiation, abroad crossing between breeds (especially crossing with RJF), together with high recombination rate in chicken genome.