A telomere-to-telomere pangenome reveals structural variations as key drivers of complex traits in chickens

Chicken is one of the most popular animal protein sources for humans and serves as an excellent model for genetics and evolutionary research. However, the contribution of structural variations (SVs) to complex trait genetics remains underexplored. Here, we generated eight new telomere-to-telomere (T2T) chicken genome assemblies, including wild, indigenous, broiler, and layer breeds, which resolved 39.23–83.93 Mb of previously unresolved regions (PURs) per breed. By integrating these with five existing references, we constructed a T2T pangenome graph and genotyped 72,147 SVs in 2,021 whole-genome resequenced chickens, with 29.89% of SVs anchored in PURs. Crucially, beyond SNPs/InDels, SVs captured 14.88 Mb of 59.78 Mb (24.89%) selective sweep regions, explained 43,330 of 156,039 (27.76%) gene expression quantitative trait loci (eQTL), and uncovered 37 of 124 (29.84%) complex-trait QTLs. Remarkably, PUR-located SVs contributed 27.02% SV-trait QTL, while 50.99% SV-eQTL localized on the previously unresolved dot chromosomes. In summary, we provide a comprehensive T2T pangenome resource and demonstrate the significant potential of SVs for dissecting complex traits (e.g., production, adaptation) in chickens.