Genetic traceability, conservation effectiveness, and selection signatures analysis based on ancestral information: a case study of Beijing-You chicken.

BACKGROUND: Genetic resources are essential components of biodiversity. As national strategy, the conservation of genetic resources is crucial not only for biodiversity but also for sustainable agriculture and cultural heritage. However, the exact origin of most local breeds remains unclear at the genomic level. The conservation efforts are becoming more challenging as local breeds are currently experiencing genetic drift and admixture, which may be further complicated by historical hybridizations. A typical example is the Beijing-You chicken, a local breed renowned for its excellent meat flavor and unique appearance. With a relatively recent history (~ 300 years), it displays mixed phenotypes which may have resulted from genomic admixture, with its exact origin yet to be determined.

RESULTS: Through comprehensive genomic similarity analysis, we identified 12 genetic donor breeds for the Beijing-You chicken and quantified their genetic contributions, with the highest ancestry proportion coming from Henan chickens. The local ancestry components and genomic structure analyses of the Beijing-You chicken suggest recent hybridization in the formation of this breed. Furthermore, we innovatively used ancestry components as new material for genetic evaluation and selection signature detection, demonstrating that conservation efforts over the past decade have been effective. Analysis of selection signatures revealed genes and regions associated with polydactyly, egg production, intramuscular fat, and spermatogenesis.

CONCLUSIONS: By integrating various analytical strategies, we developed a novel framework for genetic traceability and evaluation. Our results highlight the effectiveness of ancestry components in genetic assessment and offer valuable insights for the conservation, improvement, and sustainable utilization of local breeds.