Genomic Data Reveals Key Candidate Genes Underlying Chicken Comb Morphology.
- 1Fujian Key Laboratory of Animal Genetics and Breeding, Institute of Animal Husbandry and Veterinary Medicine Fujian Academy of Agricultural Sciences Fuzhou China.
- 2College of Life Sciences Jiangxi Science and Technology Normal University Nanchang PR China.
Abstract
Comb morphology is a salient chicken trait of biological and breeding interest. We analyzed whole-genome data from 228 birds representing 10 breeds, including Hetian (HTC) and Xiangdong (XDC)-the only two Chinese breeds with carnation combs-to investigate population structure, diversity, and genomic correlates of comb type. Population analyses revealed clear breed stratification, with clustering that partly tracked comb type; breeds subjected to strong artificial selection or bottlenecks showed reduced genetic diversity. The integrated fixation index (F ST) and genome-wide association study (GWAS) approach highlighted multiple regions differentiating carnation- from non-carnation-comb birds, with the strongest, most consistent signal at HSF5. Additional associated loci included EDN3, ITGB8, PDE4B, SDK1, MC1R, CDKL5, NRXN1, and STAG3. Gene-set enrichment pointed to pathways involved in vascular development and embryogenesis, processes plausibly contributing to comb morphogenesis. Notably, while HTC and XDC maintained distinct global genomic backgrounds, they exhibited high similarity within the major candidate genes influencing the carnation comb phenotype, suggesting that independent breed differentiation occurred alongside a shared genetic basis for this trait. While causative variants were not established, these results nominate tractable candidates and pathways for functional validation and inform marker development for conservation and selection in indigenous breeds.
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BibTeX
@article{miao2026genomic,
title = {{Genomic Data Reveals Key Candidate Genes Underlying Chicken Comb Morphology.}},
author = {Junjie Miao and Hao Chen and Guowen Song and Zhongwei Miao and Lili Zhang and Qingwu Xin and Li Li and Xiaopan Liu and Liang Huang and Qinlou Huang and Xueming Yan and Nenzhu Zheng and Zhiming Zhu},
journal = {Evolutionary applications},
year = {2026},
month = oct,
doi = {10.1111/eva.70345},
url = {https://europepmc.org/article/MED/42926913},
note = {CC BY},
}
RIS
TY - JOUR
TI - Genomic Data Reveals Key Candidate Genes Underlying Chicken Comb Morphology.
AU - Junjie Miao
AU - Hao Chen
AU - Guowen Song
AU - Zhongwei Miao
AU - Lili Zhang
AU - Qingwu Xin
AU - Li Li
AU - Xiaopan Liu
AU - Liang Huang
AU - Qinlou Huang
AU - Xueming Yan
AU - Nenzhu Zheng
AU - Zhiming Zhu
PY - 2026
DA - 2026/10/24
JO - Evolutionary applications
DO - 10.1111/eva.70345
UR - https://europepmc.org/article/MED/42926913
AB - Comb morphology is a salient chicken trait of biological and breeding interest. We analyzed whole-genome data from 228 birds representing 10 breeds, including Hetian (HTC) and Xiangdong (XDC)-the only two Chinese breeds with carnation combs-to investigate population structure, diversity, and genomic correlates of comb type. Population analyses revealed clear breed stratification, with clustering that partly tracked comb type; breeds subjected to strong artificial selection or bottlenecks showed reduced genetic diversity. The integrated fixation index (F ST) and genome-wide association study (GWAS) approach highlighted multiple regions differentiating carnation- from non-carnation-comb birds, with the strongest, most consistent signal at HSF5. Additional associated loci included EDN3, ITGB8, PDE4B, SDK1, MC1R, CDKL5, NRXN1, and STAG3. Gene-set enrichment pointed to pathways involved in vascular development and embryogenesis, processes plausibly contributing to comb morphogenesis. Notably, while HTC and XDC maintained distinct global genomic backgrounds, they exhibited high similarity within the major candidate genes influencing the carnation comb phenotype, suggesting that independent breed differentiation occurred alongside a shared genetic basis for this trait. While causative variants were not established, these results nominate tractable candidates and pathways for functional validation and inform marker development for conservation and selection in indigenous breeds.
SN - 1752-4571
ER -