New insights into genetic architecture of Guangxi indigenous chickens using whole-genome sequencing

Guangxi indigenous chickens represent valuable genetic resources characterized by diverse phenotypic features, disease resistance, and superior meat quality, making them ideal breeding materials for modern breeding systems. Elucidating the genetic basis underlying these traits in Guangxi indigenous chickens is crucial for further advancements in breeding programs. In the current study, using whole-genome sequencing, we performed comprehensive genomic analyses to characterize the genetic diversity, population structure, demographic history and selection signatures for seven Guangxi indigenous chicken breeds and two commercial breeds. The results of genetic diversity indices and effective population size demonstrated Guangxi indigenous chicken breeds maintain significantly higher genetic diversity and have undergone less intensive artificial selection than commercial breeds. Population genetic analyses revealed obvious geographic stratification, dividing Guangxi chicken breeds into southern and northern clusters. Southern populations showed closer genetic affinity to red junglefowl (Gallus gallus spadiceus) than northern populations, suggesting differential selection patterns. Genome-wide selection scans identified strong signals between southern and northern populations, uncovering genes associated with pigmentation (BCO2, SOX10, GRM5, MC1R, MITF, EDN3), body size (IGF1, POU1F1, CDH12) and egg production (AKT3, WDR25). Additionally, comparative genomic analysis with commercial breeds identified divergent selection at loci governing genes related to growth, reproduction, disease resistance and environmental adaptability, such as IGF1, LRP1B, GLI3, CDH7, KIF18A, ROBO2, EVA1A, IKZF1, GRID2, and EPHA7. These selection patterns likely reflect the unique genomic features of Guangxi indigenous chickens, shaped by ecological adaptations, traditional husbandry practices, and consumer preferences. Our findings offer new perspectives on the genetic architecture of Guangxi indigenous chickens, facilitating their conservation and utilization in modern breeding programs.