A recent comprehensive genomic analysis based on 50K SNP profiles has shown that the regional Balkan sheep populations have considerable genetic overlap but are distinctly different from surrounding breeds. All eight Croatian sheep breeds were represented by a small number of individuals per breed. Here, we genotyped 220 individuals representing the native Croatian sheep breeds (Istrian Sheep, Krk Island Sheep, Cres Island Sheep, Rab Island Sheep, Lika Pramenka, Pag Island Sheep, Dalmatian Pramenka, Dubrovnik Sheep) and mouflon using the Ovine Infinium® HD SNP BeadChip (606,006 SNPs). In addition, we included publicly available Balkan Pramenka and other Mediterranean sheep breeds. Our analyses revealed the complex population structure of Croatian sheep breeds and their origin and geographic barriers (island versus mainland). Migration patterns confirmed the historical establishment of breeds and the pathways of gene flow. Inbreeding coefficients (FROH>2 Mb) between sheep populations ranged from 0.025 to 0.070, with lower inbreeding coefficients observed in Dalmatian Pramenka and Pag Island Sheep and higher inbreeding in Dubrovnik sheep. The estimated effective population size ranged from 61 to 1039 for Krk Island Sheep and Dalmatian Pramenka, respectively. Higher inbreeding levels and lower effective population size indicate the need for improved conservation management to maintain genetic diversity in some breeds. Our results will contribute to breeding and conservation strategies of native Croatian sheep breeds.

Montenegro has a great diversity of indigenous and locally developed sheep breeds, adapted to different regions and climates. However, the current trend of the steady decline in sheep populations means that some of them are threatened with extinction. The aim of this study was the investigation of the genetic diversity and population structure of five Montenegrin sheep populations, using the OvineSNP50K BeadChip. Data from the studied sheep were supplemented with publicly available genotypes of worldwide breeds to determine admixture contributions and genetic relationships. Higher genetic diversity and low inbreeding were observed in Pivska Pramenka and Sjenicka sheep, with Ho = 0.411, He = 0.423, and FROH>2Mb = 0.056 and Ho = 0.421, He = 0.421, and FROH>2Mb = 0.041, respectively. Zetska Zuja had much lower FIS (0.001) and high FROH inbreeding (0.090), indicating a small population size and genetic drift. An analysis of the genetic population structure showed that Montenegrin sheep populations are genetically distinct populations. This analysis revealed the presence of admixture in most sheep populations (high heterogeneity), while genetic purity was observed in Zetska Zuja. The obtained results will help in the conservation management of endangered Montenegrin sheep populations.

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Licensed under a Creative Commons Attribution 4.0 International License Lipizzan horse breed was founded in 1580 in Lipica and introduced to Croatia in 1800 by earl Andrija Jankovich-Bésán. Earl Jankovich founded stallion bloodline Tulip and mare families Czirka, Ercel, Traviata, Margit, Manczi and 502 Moszgo Perla. Herd books showed that South African Lipizzan population is based on Czirka and Ercel mare families that are originally Croatian thus provided potential genetic enrichment of Croatian Lipizzan gene pool. In this study a 648 bp mitochondrial DNA fragment from 50 South African Republic Lipizzan horses was analysed and 249 sequences from Čačić doctoral thesis was retrieved. Mitochondrial DNA analysis of South African Lipizzan horses and their comparison with Croatian Lipizzan horses present that South African Lipizzan horses have five unique haplotypes but still maintain connection with Croatian Lipizzan by sharing a haplotype. Future analysis with high throughput genetic marker such as SNP or WGS will surely provide interesting results.