Genetic analysis of blood traits and stress resistance in Kirghiz sheep

The Kirghiz (KIR) sheep is a native sheep breed adapted to the extreme ecological environment of the Pamir Plateau. To explore the genetic mechanisms underlying its environmental adaptability, we collected whole-genome resequencing data from 100 KIR sheep and high-density genomic chip data from 509 individuals across 12 breeds. The genetic diversity of the population was evaluated through the inbreeding coefficient (F), nucleotide diversity (π), and linkage disequilibrium (LD). Subsequently, we performed genome-wide association studies (GWAS) on 13 blood traits in KIR populations and identified key environmentally adaptive genes through selective sweeps. The results indicate that while the KIR population exhibits high genetic diversity, its inbreeding coefficient is increasing, reflecting a lack of systematic breeding and improvement. GWAS identified 21 key genes (e.g., IL11, TRPC6, CASP9) significantly associated with blood traits for the first time. Selective sweep analysis identified multiple candidate genes (e.g., THSR, NF1, and MITF) involved in regulating environmental adaptability. Enrichment analysis and functional annotation further elucidated the potential mechanisms of these candidate genes in environmental adaptation. Our study provides a crucial scientific foundation for conserving genetic resources and implementing adaptive breeding strategies for this valuable local breed.