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.