High-density genomic characterization of native Croatian sheep breeds

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.