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Runs of homozygosity analysis for selection signatures in the Yellow Korean native chicken |
Jaewon Kim1 
, John Kariuki Macharia1
, Minjun Kim1
, Jung Min Heo1
, Myunghwan Yu1
, Hyo Jun Choo2,*
, Jun Heon Lee1,*
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1Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea
2Poultry Research Institute, National Institute of Animal Science, Rural Development Administration, Pyeongchang 25342, Korea |
Correspondence:
Hyo Jun Choo,Email: hyojy@korea.kr
Jun Heon Lee, Tel: +82-42-821-5779, Fax: +82-42-825-9754, Email: junheon@cnu.ac.kr
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Received: 14 February 2024 • Revised: 15 April 2024 • Accepted: 29 April 2024 |
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| Abstract |
Objective
Yellow Korean native chicken (KNC-Y) is one of the five pure Korean indigenous chicken breeds that were restored through a government project in 1992. KNC-Y is recognized for its superior egg production performance compared to other KNC lines. In this study, we performed runs of homozygosity (ROH) analysis to discover selection signatures associated with egg production traits in the KNC-Y population.
Methods
A total of 675 DNA samples from KNC-Y were genotyped to generate single nucleotide polymorphism (SNP) data using custom 60K Affymetrix SNP chips. ROH analysis was performed using PLINK software, with predefined parameters set for the analysis. The threshold of ROH island was defined as the top 1% frequency of SNPs withing the ROH among the population.
Results
In the KNC-Y population, a total of 29,958 runs of homozygosity (ROH) fragments were identified. The average total length of ROH was 120.84 Mb, with each ROH fragment having an average length of 2.71 Mb. The calculated ROH-based inbreeding coefficient (FROH) was 0.13. Furthermore, we revealed the presence of ROH islands on chromosomes 1, 2, 4, 5, 7, 8, and 11. Within the identified regions, a total of 113 genes were annotated, and among them were genes related to economic traits, including PRMT3, ANO5, HDAC4, LSS, PLA2G4A, and PTGS2. Most of the overlapping quantitative trait locus (QTL) regions with ROH islands were found to be associated with production traits.
Conclusion
This study conducted a comprehensive analysis of ROH in the KNC-Y population. Notably, among the findings, the PTGS2 gene is believed to play a crucial role in influencing the laying performance of KNC-Y.
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| Keywords:
Local Chicken Breed; ROH Island; Runs of Homozygosity; Selection Signature Analysis; Yellow Korean Native Chicken |
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