Abstract
As the first sequenced non-mammalian amniote, the chicken (Gallus gallus) has served as a major source of cost-effective and protein-enriched foods since domestication. However, how structural variations (SVs) affect 3D genome reorganization to influence domestication and production traits remains unclear in chickens. Here, fifteen de novo chromosome-level genome assemblies are newly generated, along with high-throughput chromosome conformation capture (Hi-C), ATAC and RNA sequencing data. By integrating 13 published assemblies, the first pan-3D genome resource is constructed, spanning genes, SVs, and chromatin architectures, to investigate the dynamic characteristics of the 3D genome at different levels and the roles of SVs in the conservation and reorganization of chromatin architectures. Furthermore, candidate SVs and their linked genes are identified for domestication and production traits based on 1,735 resequencing accessions. Notably, the 240-bp and 81-bp SVs in the TSHR and DIO2 genes are considered the key targets in artificial selection for seasonal reproduction, and a 266-bp deletion upstream of the KLF3 gene affects carcass performance by rewriting the chromatin loop interaction network. Finally, SVs significantly improve the predictive accuracy in genomic selection models. Collectively, this study presents a comprehensive pan-3D resource to advance functional genomic research and breeding practice for the community.