Haplotype‐resolved genome and pan‐genome graphs reveal the impacts of structural variation on functional genome and feather colors in chickens

Structural variation (SV) refers to a wide range of genetic variations that significantly affect genome biology and complex phenotypes. However, the population-level SV landscape and its functional impacts on chickens are largely unknown. Here, we generated haplotype-resolved genome assemblies for the Chinese Wenchang chicken and then integrated them with another 29 assemblies and 354 genome resequencing data to construct a pan-genome graph for SV genotyping. We detected 185,205 high-confidence SVs and found that one-third of them were derived from homology-based and transposable element (TE) insertion-based mutational mechanisms. By examining the ChickenGTEx resource, we discovered 1728 SVs associated with molecular phenotypes (e.g., gene expression and alternative splicing), including a 2.7-kb insertion in the exon of the <i>EEF1A2</i> gene related to egg-laying rates, which showed a significant difference in frequency between broilers and layers. Additionally, we identified a lncRNA gene with a Variable Number of Tandem Repeats (VNTR)-mediated SV influencing white feathers in Wenchang chicken due to gene flow from white layers. Overall, our study provides a valuable resource for chicken genetics and genomics and sheds light on the SV landscape in chickens as well as its potential contributions to genome structure, gene regulation, and complex traits.