Abstract: 【Objective】 Dolang sheep,Luobu sheep,Altay sheep,Bashibai sheep,and Turpan Black sheep are representative local sheep breeds in Xinjiang.This study focused on five major local sheep breeds in Xinjiang,aiming to characterize their genetic features and develop a rapid identification strategy,thereby providing a scientific basis for precise breed identification and the conservation of genetic resources.【Method】 This study focused on the analysis of population structure and breed identification of local sheep breeds in Xinjiang.A total of 206 samples from 27 representative sheep populations were selected,encompassing five major local breeds (Luobu sheep,Altay sheep,Bashibai sheep,Dolang sheep,and Turpan Black sheep),as well as several cultivated and introduced breeds.The sample design considered geographic distribution,breeding background,and economic type,providing a comprehensive reflection of the current genetic structure of sheep resources.Whole-genome single nucleotide polymorphism (SNP) variation detection and population genetic analysis were performed to assess the genetic independence of Xinjiang local sheep breeds.Using a case-control approach,the fixation index (Fst) and allele frequency difference (ΔAF) were calculated to preliminarily screen for breed-specific variants.A random forest (RF) algorithm was subsequently employed to identify the optimal set of breed-specific SNP markers for the five local sheep breeds.Principal component analysis (PCA) and Neighbor-Joining (NJ) phylogenetic tree construction were used to validate the accuracy of the identification results.【Result】 This study conducted a targeted selection of specific markers for five indigenous sheep breeds in Xinjiang.By integrating Fst,ΔAF,and RF algorithms for comprehensive screening and optimization,and validating the selected markers through PCA and NJ phylogenetic tree construction,a set of highly discriminative SNP was successfully identified.Specifically,30 SNPs were selected for Dolang sheep,47 SNPs for Bashibai sheep,46 SNPs for Luobu sheep,50 SNPs for Altay sheep,and 46 SNPs for Turpan Black sheep.All selected SNPs met stringent selection criteria,achieving an identification accuracy of approximately 98%,and demonstrated strong capability for efficient and precise breed differentiation.【Conclusion】 Leveraging whole-genome data,this study developed a SNP-based breed-specific genetic labeling system for five indigenous sheep breeds in Xinjiang.This system enabled rapid and accurate molecular-level identification,providing a robust theoretical basis for the future development of breed-specific molecular diagnostic kits.The approach offered an effective tool for the precise identification of local sheep breeds in Xinjiang,thereby supporting genetic resource management and advancing precision breeding initiatives.

Key words: sheep; whole-genome resequencing; single nucleotide polymorphism (SNP); breed identification