Application of genomic big data to analyze the genetic diversity and population structure of Korean domestic chickens

Eunjin Cho1, Minjun Kim2, Jae-Hwan Kim3, Hee-Jong Roh3, Seung Chang Kim3, Dae-Hyeok Jin3, Dae Cheol Kim4, Jun Heon Lee1,2,*
Author Information & Copyright
1Department of Bio-AI Convergence, Chungnam National University, Daejeon 34134, Korea.
2Division of Animal & Dairy Science, Chungnam National University, Daejeon 34134, Korea.
3Animal Genetic Resources Research Center, National Institute of Animal Science, Rural Development Administration, Hamyang 50000, Korea.
4Jeju Special Self-Governing Province Livestock Promotion Agency, Jeju 63078, Korea.
*Corresponding Author: Jun Heon Lee, Department of Bio-AI Convergence, Chungnam National University, Daejeon 34134, Korea, Republic of. Division of Animal & Dairy Science, Chungnam National University, Daejeon 34134, Korea, Republic of. E-mail:

© Copyright 2023 Korean Society of Animal Science and Technology. This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.


Genetic diversity analysis is crucial for maintaining and managing genetic resources. Several studies have examined the genetic diversity of Korean domestic chicken (KDC) populations using microsatellite markers, but it is difficult to capture the characteristics of the whole genome in this manner. Hence, this study analyzed the genetic diversity of several KDC populations using high-density single nucleotide polymorphism (SNP) genotype data. We examined 935 birds from 21 KDC populations, including indigenous and adapted Korean native chicken (KNC), Hyunin and Jeju KDC, and Hanhyup commercial KDC populations. A total of 212,420 SNPs of 21 KDC populations were used for calculating genetic distances and fixation index, and for ADMIXTURE analysis. As a result of the analysis, the indigenous KNC groups were genetically closer and more fixed than the other groups. Furthermore, Hyunin and Jeju KDC were similar to the indigenous KNC. In comparison, adapted KNC and Hanhyup KDC populations derived from the same original species were genetically close to each other, but had different genetic structures from the others. In conclusion, this study suggests that continuous evaluation and management are required to prevent a loss of genetic diversity in each group. Basic genetic information is provided that can be used to improve breeds quickly by utilizing the various characteristics of native chickens.

Keywords: Genetic diversity; Population structure; Korean domestic chicken; Single nucleotide polymorphism