Comparison of Genomic Variation and Population Structure of Latvian Dark-Head with Other Breeds in Latvia Using Single-Nucleotide Polymorphisms

The Latvian Dark-head (Latvijas tumšgalve; LT) is the only sheep breed developed in Latvia. It is fully adapted to the country’s climatic conditions. As the sole national breed, it holds notable cultural importance by supporting traditional husbandry practices, landscape preservation, and regional identity. However, the dominance of commercial breeds threatens local genetic resources. Small-scale farms, where the LT population is concentrated, are especially vulnerable to population decline and possible extinction. This study assesses the genetic diversity within the LT breed and compares it with that of other major sheep breeds in Latvia. For the first time, lambs from sire rams of major breeds in Latvia underwent genotyping using the Illumina Ovine SNP50 BeadChip® (San Diego, CA, USA). Genetic diversity was assessed with minor allele frequency (MAF) analysis. Breed-specific markers were identified by detecting fixed SNPs (MAF = 0) unique to each breed. In total, 27,561 highly polymorphic SNPs (MAF 0.3–0.5) were identified in the LT breed. This indicates substantial genetic differentiation from other sheep breeds raised in Latvia. Among the analyzed SNPs, 2668 (5.45%) were fixed in the LT breed. Of these, 55–131 were unique compared with other breeds. The OvineSNP50 panel is an effective tool for characterizing the genetic structure of the LT breed. It enables the detection of distinct genetic traits and interbreed differences. These results establish a genomic basis for targeted conservation and selective breeding strategies. Such strategies maintain the genetic integrity and competitiveness of the Latvian Dark-head.