ArticleMolecular biology and evolution2021
The Chicken Pan-Genome Reveals Gene Content Variation and a Promoter Region Deletion in IGF2BP1 Affecting Body Size.
Article in Molecular biology and evolution, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 88 papers.
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Who cites it
88 citing papers in PubMed.
- IGF2BP1 regulates chicken skeletal muscle development through an m6A-dependent inter-organ regulatory axis.Poultry science · 2026Article
- Multi-omics integration and artificial intelligence for the conservation and utilization of local chicken genetic resources.Poultry science · 2026Review
- Revealing the Shared Genetic Basis of Thermal Adaptation and Abdominal Adiposity in Wenchang Chicken Using Whole-Genome Structural Variation Analysis.Animals : an open access journal from MDPI · 2026Article
- Identification of candidate genes and regulatory mechanisms for thick shank phenotype of Dong Tao chickens.Poultry science · 2026Article
- Integrated Analysis of SNPs and Structural Variations via High-depth Whole-genome Sequencing Reveals the Genetic Architecture and Optimizes Genomic Prediction in Chickens.Poultry science · 2026Article
- The Pan-Genome of 1107 Spotted Sea Bass Accessions Reveals Gene Evolution Patterns During Domestication Selection.Molecular ecology resources · 2026Article
- Applicability and performance evaluation of the Shennong 1 chicken 40 K liquid chip in commercial chicken populations.Poultry science · 2026Article
- Bayesian fine-mapping pinpoints candidate genes and pleiotropic loci of production traits from a chicken backcrossing scheme.BMC genomics · 2026Article
- Integrated genomic, transcriptomic, and metabolomic profile analysis reveals molecular mechanism underlying meat quality traits in Chinese Kangle chickens.Food chemistry. Molecular sciences · 2026Article
- Integrative analysis of CUT&Tag-seq and RNA-seq reveals widespread H3K27ac upregulation associated with the activation of muscle-growth-related transcriptional programs in broiler breast muscle.Poultry science · 2026Article
- Pangenomics for Agricultural Breeding: Construction Strategies, Evidence Integration, and Translational Constraints.Biology · 2026Review
- Mining of important genetic loci and evaluation of genetic effects for growth traits in Baicheng You Chicken.Poultry science · 2026Article
- Pan-3D Genome Analysis Reveals the Roles of Structural Variation in Chicken Chromatin Architectures, Domestication and Production Traits.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Genomic Signatures Underlying Environmental Adaptation and Reproductive Traits in the Tibetan Pig.Animals : an open access journal from MDPI · 2026Article
- Article
- Pangenomic and machine learning approaches to divergent pathogenic strategies in avianFrontiers in microbiology · 2026Review
- Egg-laying ChickenGTEx resource deciphers context-specific regulatory effects on fertility traits.Nature communications · 2025Article
- Detection of differentially expressed genes in bantam chickens providing insights into chicken dwarfism.BMC genomic data · 2025Article
- Current State of Fish Reference Genome and Pangenome: Methodologies, Sampling Strategies, Quality Assessment and Future Perspectives to Aquaculture Breeding.Marine biotechnology (New York, N.Y.) · 2025Review
- RepeatOBserver: Tandem Repeat Visualisation and Putative Centromere Detection.Molecular ecology resources · 2025Article
28 more citing papers are in PubMed but not listed here.
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24 authors.
Funding
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Abstract
Domestication and breeding have reshaped the genomic architecture of chicken, but the retention and loss of genomic elements during these evolutionary processes remain unclear. We present the first chicken pan-genome constructed using 664 individuals, which identified an additional approximately 66.5-Mb sequences that are absent from the reference genome (GRCg6a). The constructed pan-genome encoded 20,491 predicated protein-coding genes, of which higher expression levels are observed in conserved genes relative to dispensable genes. Presence/absence variation (PAV) analyses demonstrated that gene PAV in chicken was shaped by selection, genetic drift, and hybridization. PAV-based genome-wide association studies identified numerous candidate mutations related to growth, carcass composition, meat quality, or physiological traits. Among them, a deletion in the promoter region of IGF2BP1 affecting chicken body size is reported, which is supported by functional studies and extra samples. This is the first time to report the causal variant of chicken body size quantitative trait locus located at chromosome 27 which was repeatedly reported. Therefore, the chicken pan-genome is a useful resource for biological discovery and breeding. It improves our understanding of chicken genome diversity and provides materials to unveil the evolution history of chicken domestication.
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