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

Southwestern local chicken breeds in China have long been recognized for their strong adaptability and disease resistance, shaped by unique selective pressures during domestication. In this study, we combined Fst and π ratio analyses to detect selection signatures from RAD-seq data of four southwestern local breeds, Red Junglefowl, and 17 other Chinese local breeds. We identified 460 candidate genes under strong selection potentially associated with domestication, affecting behaviors, physiology, reproduction, immunity, and adaptability. Importantly, 34 genes showed strong and unique selection signals when comparing southwestern breeds with other local breeds. Among these, CCR6, CD40LG, and CSF3R represent candidate genes that have been previously associated with immune processes, while MAPK10, FGFR4, and STAT3 represent candidate genes potentially related to disease resistance. Furthermore, HTR1B, HSPB9, and RYR2 represent candidate genes potentially associated with environmental adaptability. Notably, ALX1, the only gene detected across all comparison groups, may reflect morphological adaptation related to feeding efficiency. Our findings provide valuable insights into the genetic basis of unique adaptations in southwestern local chicken breeds and highlight potential targets for breeding and conservation.