Integrated Genomic and Transcriptomic Analysis of Polydactyly in Chickens Reveals Novel Insights into Extra-Toe Formation

Scientists from the Institute of Animal Husbandry and Veterinary Medicine in Guizhou, China have conducted a comprehensive study on polydactyly, a heritable limb anomaly observed in several chicken breeds. The research aimed to elucidate the genomic variants and gene expression changes underlying this trait in the Puan Panjiang black-bone chicken, which uniquely exhibits both four- and five-toed phenotypes. By leveraging whole-genome resequencing, RNA sequencing, and bioinformatics tools, the researchers identified key genes and pathways involved in extra-toe formation, providing a critical window for selective breeding in poultry.

Key Takeaways:

• The study utilized whole-genome resequencing (WGS) on 43 Puan Panjiang chickens (22 four-toed, 21 five-toed) and integrated publicly available data from 17 red junglefowl (RJF).
• The researchers identified 1,339 and 1,035 positively selected genes in five-toed and four-toed chickens, respectively, with 335 shared loci relative to RJF.
• Top candidate genes for polydactylous birds included AUH, SEMA4D, and ROR2, while four-toed birds showed strong signals at RYR2, KITLG, and PGR.
• Transcriptome profiling demonstrated that the greatest transcriptional divergence between phenotypes occurred at embryonic Days 8-9, pinpointing a critical window for extra-digit differentiation.
• The integrated analysis pinpointed MAPK pathway genes and lipid-vascular interactions as central to extra-toe formation, with the Days 8-9 embryonic window being pivotal.

Statistics:

• 43 Puan Panjiang chickens (22 four-toed, 21 five-toed) were used in the whole-genome resequencing (WGS) analysis.
• 1,339 and 1,035 positively selected genes were identified in five-toed and four-toed chickens, respectively.
• 335 shared loci were identified relative to red junglefowl (RJF).
• 24 four-toed and 24 five-toed samples were used for RNA sequencing and transcript level quantification.
• Genomic scans revealed significant signals at 335 shared loci across five-toed and four-toed chickens relative to RJF.

Sources:

• Institute of Animal Husbandry and Veterinary Medicine Reports Findings in Veterinary Science (Integrated genomic and transcriptomic analysis of polydactyly in chickens). Veterinary Week. June 16, 2025; p 39.
• Frontiers in Veterinary Science, 2025;12:1592068. Frontiers in Veterinary Science can be contacted at: Frontiers Media Sa, Avenue Du Tribunal Federal 34, Lausanne, Ch-1015, Switzerland.
• Xiaomeng Miao, Institute of Animal Husbandry and Veterinary Medicine, Guizhou Academy of Agricultural Sciences (CAAS), Guiyang, Guizhou, People's Republic of China.