Over the past 15 years, thirty different sheep breeds have been raised in Latvia, yet only one, the Latvian Dark-head sheep (Latvijas tumšgalve; LT), is a nationally developed breed. With the growing dominance of commercially attractive breeds, there is an increasing risk of losing local genetic resources, especially in small farming communities. The LT breed fully adapts to local environmental conditions and holds cultural significance, contributing to traditional lifestyles, landscape preservation, and regional identity. Therefore, genetic studies on LT are essential to preserve its diversity and inform future breeding programs.

This study aimed to evaluate the genetic diversity within the LT breed and compare it to other commonly raised sheep breeds in Latvia. For the first time, lambs from sire rams representing major breeds in Latvia were genotyped using the Illumina Ovine SNP50 BeadChip®. Genetic diversity was assessed by minor allele frequency (MAF) analysis, and breed-specific markers were identified by locating fixed SNPs (MAF = 0 or 1) unique to each breed.

We identified 47,139 highly polymorphic (MAF 0.3 – 0.5) SNPs in LT breed samples, observing a large genetic differentiation (FST > 0.15) from other breeds. Among all analysed SNPs, 2735 (1540 (3.00%) MAF = 0 and 1195 (2.33%) MAF = 1) were found to be fixed SNPs in the LT breed, while from 55 to 296 SNPs were unique to the LT breed compared to other frequently raised breeds in Latvia.

The OvineSNP50 panel provides a sufficiently informative set of molecular markers for distinguishing the LT breed and monitoring its genetic diversity. Given the high level of polymorphism, the data also holds potential for future studies in genetic selection and breed improvement.

Acknowledgements: This study was supported by the Latvian Council of Science, Latvia, projects LZP-2021/1-0489 and LZP-2024/1-0092.