Dorper sheep (DOR) are a commercially important mutton breed renowned for their high growth rate, favorable carcass composition, environmental adaptability, and natural wool shedding. In China, they are widely utilized as terminal sires to enhance growth and carcass yield in local breeds. To elucidate the genetic basis of these traits, we sequenced the genomes of 20 DOR and integrated the data with whole-genome sequences from 73 individuals representing four Chinese indigenous breeds. Analyses of genetic diversity, inbreeding coefficients, and population structure revealed reduced genomic diversity, elevated inbreeding levels, and clear genetic separation for DOR from other indigenous breeds. Selective sweep scans using F_ST, pi, and XP-EHH identified candidate genes involved in five major trait categories: growth performance and development (COL2A1, DAB2IP, EPYC, TSPAN18, WNT1, CTPS1, FBXW7, INSR, S100A6, SOCS2), energy metabolism (ACSS3, ADGRE3, CPT2, GCGR, PRKAA1), fat deposition and adipocyte differentiation (EHBP1, FOXP1, KLF12, PDGFD, RALGAPA2), immune response (CXCR6, IL17RB, NFKBIZ, TMEM154), and wool traits (CERS4, MITF). These results will provide novel insights into the genomic architecture of economically important traits in DOR and support their genetic improvement through informed crossbreeding with Chinese local breeds.

The Wadi sheep (WAD) is a unique Chinese indigenous breed previously reported to show adaptation to humid and saline–alkali lowlands, disease resistance, high fecundity, and favorable meat quality. However, the recent widespread introduction of commercial sheep breeds has led to a sharp decline in the purebred WAD population, posing serious threats to the preservation of its unique genetic resources. Therefore, there is an urgent need to assess the current population structure and genetic diversity of WAD to support its conservation and sustainable utilization. In this study, we systematically analyzed genomic variation, population structure, and selection signatures using whole-genome resequencing data from 30 WAD sheep and 80 publicly available genomes representing five other breeds obtained from the NCBI database. Population genomic analyses revealed that WAD retains substantial genetic diversity and exhibits a distinct population structure, shaped by its unique breeding history. Selection signature analyses using F_ST, π ratio, and XP-EHH identified 457 candidate genes under positive selection, which are associated with key biological processes including environmental adaptation, immune defense, muscle traits, growth, and reproduction. These findings identify genomic regions potentially related to reported WAD traits and provide a theoretical basis for its conservation, molecular breeding, and sustainable utilization in lowland environments.