An analysis of genomic variation and population structure through single-nucleotide polymorphisms of the Latvian dark-headed breed in comparison to other breeds in Latvia

The Latvian Dark-head (Latvijas tumšgalve; LT) is the sole species developed in Latvia, having fully acclimatised to the local climatic circumstances. It is the only national breed, possessing cultural importance and contributing to traditional lifestyles, landscape conservation, and regional identity. As commercially desirable sheep breeds prevail, indigenous genetic resources, especially in small agricultural communities, are at heightened risk of extinction.

This study assesses the genetic diversity of the LT breed and compares it with other prevalent sheep breeds in Latvia. For the first time, lambs from sire rams of prominent breeds in Latvia were genotyped using the Illumina Ovine SNP50 BeadChip®. The analysis of genetic diversity encompassed evaluations of minor allele frequency (MAF), and distinct breed markers were identified by ascertaining fixed SNPs (MAF = 0) that are exclusive to each breed.

This research identified 27,561 highly polymorphic SNPs (MAF 0.3–0.5) in LT breed samples, demonstrating considerable genetic differences from other breeds. Of the identified SNPs, 2,668 (5.45%) were fixed in the LT breed, with 55 to 131 SNPs being exclusive to it in comparison to other breeds. The OvineSNP50 panel is a crucial tool for elucidating the genetic architecture of the LT breed, facilitating the identification of unique genetic characteristics and differences from other breeds.

The results provide an additional understanding of the genetic background of the Latvian national sheep breed, creating new opportunities for genetic research and the development of genetic selection in the Latvian sheep population.

Acknowledgements: This study received support from the Latvian Council of Science, specifically through projects LZP-2021/1-0489 and LZP-2024/1-0092.