Journal article
The chicken pan-genome reveals gene content variation and a promoter region deletion in IGF2BP1 affecting body size
Molecular Biology and Evolution, Vol.38(11), pp.5066-5081
2021
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 ∼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 level 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 GWAS 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 QTL 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.
Details
- Title
- The chicken pan-genome reveals gene content variation and a promoter region deletion in IGF2BP1 affecting body size
- Authors/Creators
- K. Wang (Author/Creator) - Henan Agricultural UniversityH. Hu (Author/Creator) - The University of Western AustraliaY. Tian (Author/Creator) - Henan Agricultural UniversityJ. Li (Author/Creator) - Huazhong Agricultural UniversityA. Scheben (Author/Creator) - Cold Spring Harbor LaboratoryC. Zhang (Author/Creator) - Henan Agricultural UniversityY. Li (Author/Creator) - Henan Agricultural UniversityJ. Wu (Author/Creator) - Henan Agricultural UniversityL. Yang (Author/Creator) - Henan Agricultural UniversityX. Fan (Author/Creator) - Henan Agricultural UniversityG. Sun (Author/Creator) - Henan Agricultural UniversityD. Li (Author/Creator) - Henan Agricultural UniversityY. Zhang (Author/Creator) - Henan Agricultural UniversityR. Han (Author/Creator) - Henan Agricultural UniversityR. Jiang (Author/Creator)H. Huang (Author/Creator) - Henan Agricultural UniversityF. Yan (Author/Creator)Y. Wang (Author/Creator) - Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, ChinaZ. Li (Author/Creator) - Henan Agricultural UniversityG. Li (Author/Creator) - Henan Agricultural UniversityX. Liu (Author/Creator) - Henan Agricultural UniversityW. Li (Author/Creator) - Henan Agricultural UniversityD. Edwards (Author/Creator) - The University of Western AustraliaX. Kang (Author/Creator) - Henan Agricultural UniversityP. Wittkopp (Author/Creator)
- Publication Details
- Molecular Biology and Evolution, Vol.38(11), pp.5066-5081
- Publisher
- Oxford University Press on behalf of the Society for Molecular Biology and Evolution
- Identifiers
- 991005541833907891
- Copyright
- © The Author(s) 2021
- Murdoch Affiliation
- Murdoch University
- Language
- English
- Resource Type
- Journal article
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- Domestic collaboration
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- Citation topics
- 1 Clinical & Life Sciences
- 1.189 Genome Studies
- 1.189.310 Population Genetics
- Web Of Science research areas
- Biochemistry & Molecular Biology
- Evolutionary Biology
- Genetics & Heredity
- ESI research areas
- Molecular Biology & Genetics