ArticleAnimal bioscience2024
Runs of homozygosity analysis for selection signatures in the Yellow Korean native chicken.
Article in Animal bioscience, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- KhufuEnv, an auxiliary toolkit for building computational pipelines for plant and animal breeding.BMC bioinformatics · 2026Article
- Genome-wide analysis of inbreeding patterns and candidate genes for adaptation in indigenous chickens of Botswana.Poultry science · 2026Article
- Development and validation of a dual-purpose 60K single nucleotide polymorphism chip for simultaneous genotyping of chicken and duck.Animal bioscience · 2026Article
- Genomic Evaluation of the Genetic Structure and Analysis of Selective Evolutionary Signatures of Xupu Goose.Biology · 2026Article
- Whole-Genome Sequencing Reveals Genetic Diversity and Structure of Taiwan Commercial Red-Feathered Country Chickens.Animals : an open access journal from MDPI · 2026Article
- Pathogen purification and genetic characterization of SPF BWEL chicken population.Poultry science · 2025Article
- Whole-genome resequencing reveals genetic differentiation and selection signatures among wild, local and commercial duck populations.Animal bioscience · 2025Article
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Authors and funding
7 authors.
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Abstract
objectiveYellow 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.
methodsA 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.
resultsIn 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.
conclusionThis 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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