Estimation of runs of homozygosity reveals moderate autozygosity in North European sheep breeds

Runs of homozygosity (ROH) stretches are continuous homozygous fragments of the genome, which are more suitable for calculating genomic inbreeding, identifying footprints involved in economic traits and understanding population history in livestock species. In this study, using a dataset of Ovine SNP50 BeadChip genotypes, the distribution of ROH across the nine different sheep populations (Soay n= 110, Australian Poll Dorset n=108, Australian Suffolk, n=109, Finn sheep, n= 99 , Scottish Texel, n= 80 , Scottish Blackface, n= 56 , Galway, n= 49 , Border Leicester, n= 48 , German Texel, n=46) from Europe were investigated. ROHs were detected by used PLINK v1.09 with the minimal number of SNPs in ROH was set to 40; the maximal gap between the adjacent SNPs was set1 to Mb; the minimum SNP density per ROH was set to 1/100 kb and no heterozygote allowed less than 16 Mb. The detected ROHs were specified based on length to four categories: 1–4 Mb, 4–8 Mb, 8–16 Mb and above 16 Mb. A total of 22,204 ROHs were identified, in which ~ 92 – 98 % of them were less than 16 Mb in length, which covered 4.6% to 12.9% of the entire genome. The inbreeding coefficient based on ROH (FROH) varied among populations (ranging from 0.05 to 0.14). The highest inbreeding rate was found in Border Leicester and Soay breeds. In addition, we detected 90 possible ROH Islands that were overlapped with candidate genes associated with different economic traits such as; body weight, meat production, fat deposition, horn-less, and coat color in sheep. Our results suggest that although genetic selection for meat and wool traits in these breeds have been extensively carried out for the last decades, the autozygotic proportion of their genome is still considerably low, and it could lead an acceptable response to selection in breeding schemes.