Genetic diversity, selection signatures, and breed-specific SNP marker identification in Baerchuke sheep

Indigenous sheep genetic resources are important for breeding improvement and germplasm conservation. Baerchuke (BECK) sheep, an indigenous breed from Xinjiang, China, is valued for its meat quality and environmental adaptability, but its genomic characteristics remain poorly understood. Here, 343 BECK sheep were genotyped using a 50 K SNP chip and integrated with genomic data from six indigenous Xinjiang sheep populations. Population genetic analyses revealed moderate genetic diversity and close genetic affinity between BECK and Bayinbuluke sheep. Selection signature analyses identified 26 candidate genes, including ZNF385B, TSHZ2, and FCHSD2, with potential roles in growth and muscle-related biological processes. In addition, the HITSNP approach identified 343 breed-informative SNP markers with high informativeness and low redundancy that effectively differentiated BECK from the other populations examined. This study provides the first systematic genome-wide characterization of BECK sheep and provides genomic resources for germplasm conservation, breed identification, and future marker-assisted breeding.