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

## TL;DR

This study uses whole-genome sequencing to explore the genetic diversity and structure of red-feathered chickens in Taiwan, revealing distinct farm-based genetic patterns.

## Contribution

The study provides the first comprehensive genomic overview of Taiwan’s commercial red-feathered country chickens.

## Key findings

- Chickens from different farms formed distinct genetic clusters.
- Genetic diversity was uniformly low across all farms.
- Farm-specific differences in recent inbreeding patterns were identified.

## Abstract

Red-feathered country chickens are an important food source in Taiwan and are widely appreciated for their meat quality. Understanding their genetic makeup is important because it helps farmers improve breeding programs. In this study, we examined chickens from four major breeding farms in Taiwan. We used whole-genome sequencing to learn how the chickens from different farms are related to one another. Our results showed that chickens formed distinct groups by farm, reflecting each farm’s unique breeding line and practices over time. The findings provide a foundation for future efforts to improve breeding, protect genetic diversity, and support the long-term development of high-quality poultry production in Taiwan.

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.