Genetic diversity and selection signatures in related Mediterranean breeds: Sarda, Pag, and Istrian sheep

Local sheep breeds in southern Europe are highly adapted to their environments, often characterized by hot climate and poor pasture availability, where other types of agriculture would not be possible. In order to better exploit these livestock resources, genomic regions associated with adaptation could be identified. The objective of this work was to use population genetic and genomic approaches to identify shared and private signatures of selection between an Italian breed, Sarda (SAR); and two Croatian breeds, Pag (PAG) and Istrian (IST) sheep. Common genomic regions will give insights into Mediterranean climate adaptations and past crossbreeding, while differences will provide information on specific environmental adaptations and selection pressures. A total of 4,791 (825 SAR, 2,683 PAG, 1,283 IST) sheep were SNP genotyped (40,995 SNP after quality control). Population structure was studied through linkage disequilibrium and admixture. To identify signatures of selection, we used four approaches, runs of homozygosity (ROH), Wright’s fixation index (FST), cross population extended haplotype homozygosity (XP-EEH), and ratio of extended haplotype homozygosity between populations (Rsb). According to FST results, SAR and IST were the most divergent breeds. The latter breed showed the largest ROH-based inbreeding. A large selection signature on chromosome 6 (33.26- 46,31 Mb) was found by all involved approaches as associated with IST. The results of the present study enabled the identification of common and private regions among three Mediterranean sheep breeds raised under similar environmental conditions.