Characterisation of runs of homozygosity and inbreeding coefficients in the red-brown Korean native chickens

Macharia, John Kariuki; Kim, Jaewon; Kim, Minjun; Cho, Eunjin; Munyaneza, Jean Pierre; Lee, Jun Heon

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Anim Biosci > Accepted Articles

Article

https://doi.org/10.5713/ab.23.0514 [Accepted] Published online April 25, 2024.

Characterisation of runs of homozygosity and inbreeding coefficients in the red-brown Korean native chickens

John Kariuki Macharia¹

, Jaewon Kim¹

, Minjun Kim¹

, Eunjin Cho²

, Jean Pierre Munyaneza¹, Jun Heon Lee^1,2,*

¹Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea
²Department of Bio-AI Convergence, Chungnam National University, Daejeon 34134, Korea

Correspondence: Jun Heon Lee, Tel: +82-42-821-5779, Fax: +82-42-825-9754, Email: junheon@cnu.ac.kr

Received: 10 December 2023 • Revised: 5 February 2024 • Accepted: 27 February 2024

Abstract

Objective
The analysis of runs of homozygosity (ROH) has been applied to assess the level of inbreeding and identify selection signatures in various livestock species. The objectives of this study were to characterize the ROH pattern, estimate the rate of inbreeding, and identify signatures of selection in the red-brown Korean native chickens.
Methods
The Illumina 60K SNP chip data of 651 chickens was used in the analysis. Runs of homozygosity were analysed using the PLINK v1.9 software. Inbreeding coefficients were estimated using the GCTA software and their correlations were examined. Genomic regions with high levels of ROH were explored to identify selection signatures.
Results
A total of 32,176 ROH segments were detected in this study. The majority of the ROH segments were shorter than 4 Mb. The average ROH inbreeding coefficients (FROH) varied with the length of ROH segments. The means of inbreeding coefficients calculated from different methods were also variable. The correlations between different inbreeding coefficients were positive and highly variable (r = 0.18 –1). Five ROH islands harbouring important Quantitative trait loci were identified.
Conclusion
This study assessed the level of inbreeding and patterns of homozygosity in Red-brown native Korean chickens. The results of this study suggest that the level of recent inbreeding is low which indicates substantial progress in the conservation of red-brown Korean native chickens. Additionally, Candidate genomic regions associated with important production traits were detected in homozygous regions.

Keywords: Inbreeding Coefficient; Run of Homozygosity; ROH Island; Selection Signatures