Within- and between-Breed Selection Signatures in the Original and Improved Valachian Sheep

SIMPLE SUMMARY: Each country has their own national breeds that are well adapted to the local climate and other conditions. Our study examines two national sheep breeds from Slovakia, the Original and the Improved Valachian sheep. The main goal of the study was to identify parts of their genome which contain genes enabling such adaptations. These are the so called selection signatures. Within the breed we look for genomic regions that were remarkably similar among a large proportion of genotyped individuals. The results point towards adaptation to high altitude pastures and resistance to parasites. The signatures of selection between the Original and Improved Valachian sheep focus on regions with striking difference in the same region of the genome between the two breeds. These results highlighted genes that improve the milk, meat and wool production, and their quality characteristics. ABSTRACT: This study explored the genomic diversity and selection signatures in two Slovakian national breeds, the Original Valachian and the Improved Valachian sheep. As they are an important animal genetic resource within the country, but with decreasing population size, our aim is to identify potentially valuable genomic regions. A total of 97 sheep (18 male and 79 female) from the Original Valachian, and 69 sheep (25 male and 44 female) from the Improved Valachian populations were genotyped using the GeneSeek GGP Ovine 50 K chip. The inbreeding levels were assessed with runs of homozygosity (ROH). The selection signatures within breeds were identified based on the top 1% of most homozygous regions within the breed, the so-called ROH islands. The selection signatures between breeds were assessed based on variance in linkage disequilibrium. Overall, we have identified selection signatures with quantitative trait loci (QTL) and genes pointing towards all three production purposes of the Valachian sheep, milk, meat, and wool, including their quality characteristics. Another group with apparent large importance was the various traits related to health and resistance to parasites, which is well in line with the sturdy nature of this breed.