Estimation of linkage disequilibrium and effective population size in Korean native chicken

The linkage disequilibrium (LD) is an important indicator for population genetic parameters such as inbreeding rate and effective population size. The extent of LD also provides information about historical events of population such as past effective population size (Ne), and it allows inferences on the genetic diversity of chicken lines. The objective of this study was to estimate the LD and Ne in Korean purebred native chicken (NR and NY) and commercial native chicken (CL1-CL8), which are maintained for commercial purposes by commercial company. In this study, eight types of commercial native chicken lines that are derived from two types of Korean purebred native chicken lines were used. As the results of LD analysis, commercial native chicken lines have lower LD than Korean purebred native chicken lines, and we can estimate that they have different ancestors in two of the populations. In addition, purebred native chickens could estimate higher inbreeding level than commercial native chickens, and commercial native chickens have higher effective population size compared with purebred native chickens. The population structure was depicted in a multidimensional scaled plot. In MDS plot, Korean purebred native chicken were positioned in close proximity to each other, far from the other eight commercial chicken breeds. These results can provide useful information for estimation of effective population size and LD structure between the markers in native chicken population. In conclusion, the differences in LD and Ne for each breeds reflect historical events and recent selection through the breeding program. The LD and Ne values would be useful for sustainable breeding program in commercial native chicken lines, and efforts are needed to maintain genetic diversity for sustainability.