Article
Analysis of runs of homozygosity in Yeonsan Ogye chickens using 600K SNP arrays
Jaewon Kim1, Minjun Kim1,*, Eunjin Cho2,**, Seung-sook Lee3, Seungchang Kim4,***, Daehyeok Jin4,****, Jun Heon Lee1,2,*****
1Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea.
2Department of Bio-AI Convergence, Chungnam National University, Daejeon 34134, Korea.
3Yeonsan Ogye Foundation, Nonsan 32910, Korea.
4Animal Genetic Resources Research Center, National Institute of Animal Science, Rural Development Administration, Hamyang 50000, Korea.
*Corresponding Author: Minjun Kim, Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea, Republic of. E-mail:
kimmin6023@gmail.com.
**Corresponding Author: Eunjin Cho, Department of Bio-AI Convergence, Chungnam National University, Daejeon 34134, Korea, Republic of. E-mail:
eunjjinie@gmail.com.
***Corresponding Author: Seungchang Kim, Animal Genetic Resources Research Center, National Institute of Animal Science, Rural Development Administration, Hamyang 50000, Korea, Republic of. E-mail:
kisc@korea.kr.
****Corresponding Author: Daehyeok Jin, Animal Genetic Resources Research Center, National Institute of Animal Science, Rural Development Administration, Hamyang 50000, Korea, Republic of. E-mail:
jdh1662@korea.kr.
*****Corresponding Author: Jun Heon Lee, Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea, Republic of. Department of Bio-AI Convergence, Chungnam National University, Daejeon 34134, Korea, Republic of. Phone: +82-42-821-7031. E-mail:
junheon@cnu.ac.kr.
© Copyright 2024 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 (http://creativecommons.org/licenses/by-nc/4.0/) which permits
unrestricted non-commercial use, distribution, and reproduction in any
medium, provided the original work is properly cited.
Received: Sep 04, 2023; Revised: Nov 24, 2023; Accepted: Jan 29, 2024
Published Online: Feb 01, 2024
Abstract
Runs of homozygosity (ROHs) are caused by identical haplotypes inherited from ancestors. ROHs provide useful information regarding the inbreeding rate, demographics, and selection history. The Yeonsan Ogye (YO) breed is an indigenous chicken in Korea that is characterized by a completely black body. In this study, we investigated ROH in the YO genome to determine ROH-based inbreeding coefficients and their correlations with other inbreeding estimators, then analyzed their genetic characteristics. Using 600K single nucleotide polymorphism (SNP) chip information for 189 chickens, we found 20,339 ROHs in the YO population. The average number of ROHs was 107, the total average ROH length was 165 Mb, and the average ROH length was 1.542 Mb. Most ROHs were short (< 8 Mb), suggesting a past population bottleneck. The average inbreeding coefficient (<strong><italic>F<sub>ROH</sub></italic></strong>) calculated based on ROHs was 0.184 and this was correlated with other inbreeding coefficients estimated using allele frequencies. 17 ROH islands were detected and these regions exceeded the threshold of the top 1% of SNPs among SNPs present in ROHs. In the ROH islands, 152 genes were annotated, some of which were genes associated with meat production traits and hyperpigmentation in chickens. A comparison of overlapping regions between ROH islands and quantitative trait loci (QTLs) indicated that most QTLs were related to color traits. These results will help to optimize conservation strategies for the YO breed.
Keywords: Local chicken breed; Yeonsan Ogye; Runs of homozygosity; Genomic inbreeding coefficient; ROH islands; Conservation