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

Abstract 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 EEF1A2 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.