Skip to main content
ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #415957
Research Project: Accelerating Genetic Improvement of Ruminants Through Enhanced Genome Assembly, Annotation, and Selection

Location: Animal Genomics and Improvement Laboratory

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

Author
item GU, LIHONG - Collaborator
item PENG, CHEN - Zhejiang University
item CHEN, ANHONG - Collaborator
item CHEN, KAIYU - Zhejiang University
item ZHENG, XINLI - Collaborator
item YU, DONGYOU - Zhejiang University
item WANG, ZHENGGUANG - Zhejiang University
item FANG, LINGZHAO - Aarhus University
item Liu, Ge
item ZHAO, PENGJU - Zhejiang University

Submitted to: iMeta
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/12/2025
Publication Date: 5/24/2025
Citation: Gu, L., Peng, C., Chen, A., Chen, K., Zheng, X., Yu, D., Wang, Z., Fang, L., Liu, G., Zhao, P. 2025. Haplotype-resolved genome and pan-genome graphs reveal the impacts of structural variation on functional genome and feather colors in chickens. iMetaOmics. https://doi.org/10.1002/imo2.70027.
DOI: https://doi.org/10.1002/imo2.70027

Interpretive Summary: Studying structural variations (SVs), which are genome alterations involving DNA segments over 50 base pairs, is essential. We generated a high-quality genome assembly for the Wenchang breed, constructed a pan-genome graph, and examined SV impacts on the functional genome. We detected two SV events related to egg laying rates and feather colors in chickens. Farmers, scientists, and policy planners who need to improve animal health and production based on genome-enabled animal selection will benefit from this study.

Technical 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 chicken 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 1,728 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 VNTR (variable number of tandem repeats)-mediated SV influencing white feathers in Wenchang chicken due to the gene flow from the white layers. Overall, our study provides a valuable resource for chicken genetics and genomics and shine lights the SV landscape in chickens as well as its potential contributions to genome structure, gene regulation, and complex traits.