Animal Bioscience

Asian Australasian Association of Animal Production Societies (아세아태평양축산학회)
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Runs of homozygosity analysis for selection signatures in the Yellow Korean native chicken

  • Jaewon Kim (Division of Animal and Dairy Science, Chungnam National University) ;
  • John Kariuki Macharia (Division of Animal and Dairy Science, Chungnam National University) ;
  • Minjun Kim (Division of Animal and Dairy Science, Chungnam National University) ;
  • Jung Min Heo (Division of Animal and Dairy Science, Chungnam National University) ;
  • Myunghwan Yu (Division of Animal and Dairy Science, Chungnam National University) ;
  • Hyo Jun Choo (Poultry Research Institute, National Institute of Animal Science, Rural Development Administration) ;
  • Jun Heon Lee (Division of Animal and Dairy Science, Chungnam National University)
  • Received : 2024.02.14
  • Accepted : 2024.04.29
  • Published : 2024.10.01
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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 111 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 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.

Keywords

Acknowledgement

This research study was funded by the project (RS-2021-RD009516) of the Rural Development Administration, Republic of Korea.

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