Selection Signatures from RAD-Seq Reveal Candidate Genomic Regions Potentially Underlying Immune and Adaptive Traits in Southwest Chinese Local Chickens

Abstract

Simple Summary Local chicken breeds in Southwest China are highly valued for their remarkable ability to survive variable ecological environments and resist diseases, yet the genes responsible for these traits remain largely unknown. In this study, we analyzed DNA from four southwestern local chicken breeds and compared them with wild red junglefowl and other Chinese breeds. We discovered a number of genes that have been changed through domestication, many of which are candidate genes potentially involved in metabolism, behavior, growth, reproduction, and immunity. Thirty-four of these genes showed especially strong and unique changes in the southwestern breeds. Some of these genes have been reported to be associated with immune responses, while others are candidate genes potentially linked to environmental adaptation. One gene, called ALX1, which influences beak shape, was found in all comparisons, suggesting that changes in how chickens eat may have been important during domestication. These findings provide genetic evidence that may help explain why southwestern local chickens are so well adapted to their environments and provide breeders with valuable information to help preserve these unique genetic resources and improve chicken farming for the future.