GCRP: Integrated Global Chicken Reference Panel from 11,951 Chicken Genomes
Chickens are a crucial source of protein for humans and a popular model animal for bird research. Despite the emergence of imputation as a reliable genotyping strategy for large populations, the lack of a high-quality chicken reference panel has hindered progress in chicken genome research. To address this, here we introduce the first phase of the 100K Global Chicken Reference Panel (100K GCRP). Currently, two panels are available: a comprehensive mix panel (CMP) for domestication diversity research and a commercial breed panel (CBP) for breeding broilers specifically. Evaluation of genotype imputation quality showed that CMP had the highest imputation accuracy compared to imputation using existing chicken panels in Animal-SNPAtlas and Animal Genotype Imputation Database (AGIDB), whereas CBP performed stably in the imputation of commercial populations. Additionally, we found that genome-wide association studies using GCRP-imputed data, whether on simulated or real phenotypes, exhibited greater statistical power. In conclusion, our study indicates that the GCRP effectively fills the gap in high-quality reference panels for chickens, providing an effective imputation platform for future genetic and breeding research. The project includes 11,951 samples and provides services for various applications on its website at http://farmrefpanel.com/GCRP/#/.
Authors
- Yiqiang Zhao (ORCID: https://orcid.org/0000-0002-0076-3476)
- Lingzhao Fang (ORCID: https://orcid.org/0000-0003-1103-3679)
- Zheya Sheng (ORCID: https://orcid.org/0000-0002-4487-2682)
- Yuzhan Wang (ORCID: https://orcid.org/0000-0003-4463-4075)
- Dingming Shu (ORCID: https://orcid.org/0000-0001-6054-9378)
- Xiaoxiang Hu (ORCID: https://orcid.org/0000-0001-7045-0283)
- Qinghua Nie (ORCID: https://orcid.org/0000-0003-3934-3820)
- Zi-Qin Jiang
- Hui Li (ORCID: https://orcid.org/0000-0001-6282-5559)
- Hui Zhang (ORCID: https://orcid.org/0000-0002-0708-8848)
- Di Zhu (ORCID: https://orcid.org/0000-0002-9362-3834)
- Hao Qu (ORCID: https://orcid.org/0000-0001-6561-4271)
- Dexiang Zhang (ORCID: https://orcid.org/0009-0008-7144-3761)
- Yuzhe Wang (ORCID: https://orcid.org/0000-0003-3474-7957)
- Zhenqiang Xu (ORCID: https://orcid.org/0000-0002-3328-9547)
- Suqiao Chu
- Yunliang Jiang (ORCID: https://orcid.org/0000-0002-2914-6818)
- Chugang Feng
Institutions
- South China Agricultural University (CN)
- Nanjing Agricultural University (CN)
- Northeast Agricultural University (CN)
- Aarhus University (DK)
- Huazhong Agricultural University (CN)
- Animal Husbandry & Veterinary (IN)
- Guangdong Academy of Agricultural Sciences (CN)
- Wen's Food Group (China) (CN)
- China Agricultural University (CN)
- Shandong Agricultural University (CN)
Publication Details
- Journal
- Genomics Proteomics & Bioinformatics
- Published
- 2025-04-15
- DOI
- https://doi.org/10.1093/gpbjnl/qzaf032
- Citations
- 5
- Primary Topic
- Livestock and Poultry Management
- Type
- article
- Field-Weighted Citation Impact
- 5.97