The chicken pan-genome reveals gene content variation and a promoter region deletion in IGF2BP1 affecting body size

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.Funding provided by: National Natural Science Foundation of ChinaCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100001809Award Number: 31902144Funding provided by: Program for Innovation Research Team of the Ministry of Education*Crossref Funder Registry ID: Award Number: IRT16R23Funding provided by: The Scientific Studio of Zhongyuan Scholars*Crossref Funder Registry ID: Award Number: 30601985Funding provided by: Program for Innovation Research Team of the Ministry of EducationCrossref Funder Registry ID: Award Number: IRT16R23Funding provided by: The Scientific Studio of Zhongyuan ScholarsCrossref Funder Registry ID: Award Number: 3060198