Whole-Genome Sequencing Reveals Genetic Diversity and Structure of Taiwan Commercial Red-Feathered Country Chickens

Whole-genome sequencing is a powerful approach for exploring genomic diversity in livestock species. Chickens (Gallus gallus) are an important food source worldwide, and in Taiwan, poultry production contributes substantially to the livestock industry. Taiwan's commercial red- and black-feathered country chickens dominate this category and play a crucial role in local poultry production. However, fundamental genomic information on their population structure remains limited. To address this gap, this study generated whole-genome sequencing data from red-feathered country chickens originating from four major breeding farms. Genetic diversity analyses revealed uniformly low genetic diversity across all farms. Runs of homozygosity (ROH) analyses indicated predominantly historical inbreeding, with farm-specific differences in recent inbreeding patterns. Population structure analyses revealed clear clustering of individuals according to farm origin, indicating distinct line structures among breeding farms. These results provide the first comprehensive genomic overview of Taiwan's commercial red-feather country chickens and offer valuable reference information for future breeding strategies and the development of new lines.