Genomic characterization and diversity of indigenous goat breeds from Croatia

Goats have been undervalued and marginalized in the past despite their high productivity compared to other ruminants. Today, many goat breeds encounter the threat of extinction due to factors such as small population size, geographic isolation, lack of economic competition, and declining interest in breeding. In order to determine the population structure and level of diversity of Croatian goats, we conducted population-level SNP genotyping. The aim of our study was to evaluate the genetic relatedness between Croatian breeds and other European goat breeds. We genotyped a total of 44 animals representing native Croatian goat breeds, including the Croatian Colored Goat (CCG) and the Istrian Goat (CIG), with the Illumina Goat_IGGC_65K_v2. We also included publicly available goat breeds from Europe, mainly from the Mediterranean region. The two indigenous Croatian goat breeds differ in morphological and productive traits, which is reflected in their genetic diversity and breed segregation. While CCG showed clear breed separation and genetic similarity to Balkan breeds, CIG showed higher heterogeneity with genetic closenes to Austrian Alpine breeds. PCA, Admixture and TreeMix analyses did not detect any genetic influence of Boer goat on Croatian goat breeds. Despite the small effective population size of the Istrian Goat (N-e = 27), both breeds show a high degree of genetic variability with low inbreeding (F-ROH>2Mb = 0.054 and F-ROH>2Mb = 0.059, for CCG and CIG, respectively). However, the Istrian Goat requires careful conservation planning due to the small number of individuals and limited breeding area. Our results could be valuable for future conservation and breeding programmes aimed at conserving and sustainably using these important genetic resources.