Conservation & local programs

Insights into the genetic diversity and population structure of Thuringian and other European goat breeds using SNP chip data

---

Abstract

The Thuringian goat is an endangered German dairy breed, developed in the early 20th century through crossbreeding between local goats in Thuringia and the Swiss Toggenburg. It is valued for milk production and is the only indigenous German goat breed not crossed with other German or foreign breeds. This study aimed to identify breeds that are genetically closely related to Thuringian goat, especially in relationship to its historical connection to Toggenburg goat. An additional objective was the characterization of the genetic diversity within Thuringian goat and the identification of genomic regions under positive selection. Genomic variation was assessed using SNP chip data from 87 Thuringian goats genotyped with the Axiom Caprine 60K SNP Chip, and from an additional 1,600 goats representing 46 goat populations across 38 European breeds genotyped with Illumina Goat SNP50 BeadChip. After quality control, 47,670 SNPs remained for downstream analyses. Thuringian goat showed moderate genetic relatedness to all investigated European breeds, with FST values ranging from 0.107 (Alpine, Italy) to 0.165 (Maltese, Italy) including Toggenburg goats with FST of 0.132 and 0.141 for Swiss and Tanzanian Toggenburg populations, respectively. In a Principle Component Analysis, Thuringian goat clustered closely with Swiss Toggenburg and Italian Saanen, whereas Toggenburg goat from Tanzania shows greater divergence. ADMIXTURE analysis at K=4 revealed Thuringian (Germany), Landrace (Denmark), Alpine (Italy), and Maltese (Spain) as the four primary ancestral breeds, which were genetically most distinct. Tanzanian Toggenburg shared about 10% ancestry with Thuringian, Landrace, and Alpine breeds. The examined Thuringian goat population showed the lowest genetic diversity across all breeds with the lowest heterozygosity (36.3%), the lowest nucleotide diversity (6.48 x 10-06), and the high inbreeding level (FHom = 18.2%). Runs of homozygosity (RoH) showed high homozygosity for regions shorter than 1 Mb (FRoH = 5.94 %) and low homozygosity for region longer than >4 Mb (FRoH = 3.89%). These values suggest historical inbreeding in Thuringian goats, while recent conservation efforts seem to mitigate inbreeding. Within RoH islands, genes like FITM2 (lipid metabolism and milk production) and C5 (immune function) reside. Given the Thuringian goat's unique genetic profile, limited diversity, and moderate relatedness to other European breeds, including its historical ancestor, Toggenburg, we recommend strengthening breeders networks, expanding the genetic base, and implementing rigorous conservation strategies to minimise inbreeding. These efforts are essential to maintain the long-term viability, productivity, and genetic integrity of this endangered breed.

Keywords: 2026

How to Cite:

Omar, A., Korkuč, P., Strucken, E., Neumann, G., Arends, D., Conington, J., Reissmann, M., Martínez, A., Carolan, S., Lenstra, J., Brockmann, G. & Rahmatalla, S., (2026) “Insights into the genetic diversity and population structure of Thuringian and other European goat breeds using SNP chip data”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286771. doi: https://doi.org/10.31274/wcgalp.24115

Rights: 1