ArticleBMC genomics2024
Genome-wide detections for runs of homozygosity and selective signatures reveal novel candidate genes under domestication in chickens.
Article in BMC genomics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Multi-omics integration and artificial intelligence for the conservation and utilization of local chicken genetic resources.Poultry science · 2026Review
- Selection Signatures from RAD-Seq Reveal Candidate Genomic Regions Potentially Underlying Immune and Adaptive Traits in Southwest Chinese Local Chickens.Animals : an open access journal from MDPI · 2026Article
- Low-pass whole-genome sequencing reveals genomic diversity and ecotype-specific adaptation in indigenous Tigrayan chickens.Scientific reports · 2026Article
- Genomic diversity, population structure and runs of homozygosity in Spanish native chicken breeds assessed with high-density SNP data.Poultry science · 2026Article
- Genome-wide analysis of inbreeding patterns and candidate genes for adaptation in indigenous chickens of Botswana.Poultry science · 2026Article
- Kinglet in the Poultry Court of Russia: Whole-Genome Insights into Ancestry, Genetic Variability, Selection Footprints and Candidate Genes in a Unique Local Chicken Breed Relative to Other Bantam/Dwarf Breeds.Animals : an open access journal from MDPI · 2026Article
- Whole-Genome Sequencing Reveals Genetic Diversity and Structure of Taiwan Commercial Red-Feathered Country Chickens.Animals : an open access journal from MDPI · 2026Article
- Article
- Comparative Analysis of Runs of Homozygosity Islands in Indigenous and Commercial Chickens Revealed Candidate Loci for Disease Resistance and Production Traits.Veterinary medicine and science · 2025Article
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Authors and funding
14 authors.
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Abstract
backgroundIndigenous chickens were developed through a combination of natural and artificial selection; essentially, changes in genomes led to the formation of these modern breeds via admixture events. However, their confusing genetic backgrounds include a genomic footprint regulating complex traits, which is not conducive to modern animal breeding.
resultsTo better evaluate the candidate regions under domestication in indigenous chickens, we considered both runs of homozygosity (ROHs) and selective signatures in 13 indigenous chickens. The genomes of Silkie feather chickens presented the highest heterozygosity, whereas the highest inbreeding status and ROH number were found in Luhua chickens. Short ROH (< 1 Mb), were the principal type in all chickens. A total of 291 ROH islands were detected, and QTLdb mapping results indicated that body weight and carcass traits were the most important traits. An ROH on chromosome 2 covering VSTM2A gene was detected in 12 populations. Combined analysis with the Tajima's D index revealed that 18 genes (e.g., VSTM2A, BBOX1, and RYR2) were under selection and covered by ROH islands. Transcriptional analysis results showed that RYR2 and BBOX1 were specifically expressed in the heart and muscle tissue, respectively.
conclusionBased on genome-wide scanning for ROH and selective signatures, we evaluated the genomic characteristics and detected significant candidate genes covered by ROH islands and selective signatures. The findings in this study facilitated the understanding of genetic diversity and provided valuable insights for chicken breeding and conservation strategies.
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