Genomic origin and consequence of captive red junglefowl in zoological parks

Abstract

Understanding the genetic status of captive animal populations is essential for their long-term conservation and effective management. In this study, we investigated the genetic origin, admixture patterns, and genomic health of red junglefowls (Gallus gallus; RJFs) maintained in zoological parks (zooRJFs). We conducted whole-genome sequencing of 27 zooRJFs and performed comparative population genomic analyses with wild RJFs and domesticated chicken breeds. Our analyses revealed that zooRJFs originated from Gallus gallus spadiceus. We also found that zooRJFs have undergone severe population bottlenecks, resulting in reduced genetic diversity and extremely long runs of homozygosity. These results highlight the value of genomic approaches for tracing ancestry and assessing genetic health in zoo-managed populations and provide insights into genome-informed breeding strategies for conserving captive animals. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-025-12366-3.