Genetic Diversity and Population Structure of Four Korean Native Chicken Lines using SNP Chip Data

This study evaluated the genetic diversity and population structure of four Korean native chicken lines using 30K SNP chip data. A total of 192 birds from the four lines were analyzed to assess heterozygosity, inbreeding coefficients, linkage disequilibrium (LD), effective population size (Ne), and inter-line relationships. All lines exhibited similar levels of genetic diversity, with slightly negative inbreeding coefficient values indicating minimal inbreeding. LD decay patterns were comparable across lines, and Ne values suggested stable long-term genetic variability. Principle component analysis, population structure analysis, and phylogenetic analyses consistently showed clear separation among the four lines, with the Ogye line most distinct and the grey-brown and white line pair genetically closest. Overall, these results demonstrate that the current breeding and mating scheme effectively maintains within-line genetic diversity while preserving distinct line identities.