ArticleGenome biology and evolution2013
Genome-wide patterns of genetic variation in two domestic chickens.
Article in Genome biology and evolution, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed.
- Transcriptomic Landscape of Gut Microbiota-Host Interactions Reveals Domestication-Related Changes in the Pearl OysterAnimals : an open access journal from MDPI · 2026Article
- Whole-genome sequencing identifies genetic diversity and adaptive signatures of hypoxia and ultraviolet radiation in Chinese chickens.Journal of advanced research · 2026Article
- Whole-Genome Sequencing Reveals Genetic Diversity and Structure of Taiwan Commercial Red-Feathered Country Chickens.Animals : an open access journal from MDPI · 2026Article
- Population genomic analysis identifies the complex structural variation at the fibromelanosis (FM) locus in chicken.Scientific reports · 2025Article
- Omics in mini-livestock: a genomic perspective on the future of sustainable food systems.Frontiers in genetics · 2025Review
- Genetic diversity, demographic history, and selective signatures of Silkie chicken.BMC genomics · 2024Article
- The main genetic locus associated with the evolution of gamecocks is centered on ISPD.G3 (Bethesda, Md.) · 2024Article
- Whole-genome sequencing and genomic analysis of Norduz goat (Capra hircus).Mammalian genome : official journal of the International Mammalian Genome Society · 2023Article
- Whole genome analyses reveal novel genes associated with chicken adaptation to tropical and frigid environments.Journal of advanced research · 2023Article
- Decoding the fibromelanosis locus complex chromosomal rearrangement of black-bone chicken: genetic differentiation, selective sweeps and protein-coding changes in Kadaknath chicken.Frontiers in genetics · 2023Article
- Genome Assembly and Evolutionary Analysis of the Mandarin Duck Aix galericulata Reveal Strong Genome Conservation among Ducks.Genome biology and evolution · 2022Article
- Assessment of linkage disequilibrium patterns between structural variants and single nucleotide polymorphisms in three commercial chicken populations.BMC genomics · 2022Article
- Genomic Analyses for Selective Signatures and Genes Involved in Hot Adaptation Among Indigenous Chickens From Different Tropical Climate Regions.Frontiers in genetics · 2022Article
- The Chicken Pan-Genome Reveals Gene Content Variation and a Promoter Region Deletion in IGF2BP1 Affecting Body Size.Molecular biology and evolution · 2021Article
- Integrating Genomic and Transcriptomic Data to Reveal Genetic Mechanisms Underlying Piao Chicken Rumpless Trait.Genomics, proteomics & bioinformatics · 2021Article
- Article
- The evolutionary genetics of paternal care: How good genes and extrapair copulation affect the trade-off between paternal care and mating success.Ecology and evolution · 2021Article
- 863 genomes reveal the origin and domestication of chicken.Cell research · 2020Article
- Genome-wide analysis reveals molecular convergence underlying domestication in 7 bird and mammals.BMC genomics · 2020Article
- Accumulation of genetic variants associated with immunity in the selective breeding of broilers.BMC genetics · 2020Article
Corrections and comments
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Authors and funding
14 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Domestic chickens are excellent models for investigating the genetic basis of phenotypic diversity, as numerous phenotypic changes in physiology, morphology, and behavior in chickens have been artificially selected. Genomic study is required to study genome-wide patterns of DNA variation for dissecting the genetic basis of phenotypic traits. We sequenced the genomes of the Silkie and the Taiwanese native chicken L2 at ∼23- and 25-fold average coverage depth, respectively, using Illumina sequencing. The reads were mapped onto the chicken reference genome (including 5.1% Ns) to 92.32% genome coverage for the two breeds. Using a stringent filter, we identified ∼7.6 million single-nucleotide polymorphisms (SNPs) and 8,839 copy number variations (CNVs) in the mapped regions; 42% of the SNPs have not found in other chickens before. Among the 68,906 SNPs annotated in the chicken sequence assembly, 27,852 were nonsynonymous SNPs located in 13,537 genes. We also identified hundreds of shared and divergent structural and copy number variants in intronic and intergenic regions and in coding regions in the two breeds. Functional enrichments of identified genetic variants were discussed. Radical nsSNP-containing immunity genes were enriched in the QTL regions associated with some economic traits for both breeds. Moreover, genetic changes involved in selective sweeps were detected. From the selective sweeps identified in our two breeds, several genes associated with growth, appetite, and metabolic regulation were identified. Our study provides a framework for genetic and genomic research of domestic chickens and facilitates the domestic chicken as an avian model for genomic, biomedical, and evolutionary studies.
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