Genomic assessment of population structure, admixture and conservation status of two Croatian goat breeds

The aim of this study was to determine the position of two Croatian goats in the global context using genome-wide SNP data, while assessing population structure, admixture, and conservation status. All analyses were performed on the genotypes of 11 Istrian and 33 Croatian coloured goats and a sample of 2255 goats from 66 global goat breeds. Neighbor net and admixture results show that two breeds have high genetic diversity, with much of the historical admixture due to an extensive produc tion system. Principal component analysis (PCA) showed clear clustering between the two breeds, while some Istrian goats showed clear clustering with the Saanen breed. The Croatian Coloured goat was most similar to the Greek goats. The results obtained with the Treemix software confirmed these findings and showed gene flow from the Croatian Coloured goat to the Istrian goat. Despite the low Ne for the Istrian goat, both breeds showed a low degree of inbreeding (FROH~0.05). Consider ing these results, the Istrian goat is at high risk of extinction and should be carefully monitored.