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 SNP۵۰ BeadChip genotypes, the distribution of ROH across the nine different sheep populations (Soay n= ۱۱۰, Australian Poll Dorset n=۱۰۸, Australian Suffolk, n=۱۰۹, Finn sheep, n= ۹۹ , Scottish Texel, n= ۸۰ , Scottish Blackface, n= ۵۶ , Galway, n= ۴۹ , Border Leicester, n= ۴۸ , German Texel, n=۴۶) from Europe were investigated. ROHs were detected by used PLINK v۱.۰۹ with the minimal number of SNPs in ROH was set to ۴۰; the maximal gap between the adjacent SNPs was set۱ to Mb; the minimum SNP density per ROH was set to ۱/۱۰۰ kb and no heterozygote allowed less than ۱۶ Mb. The detected ROHs were specified based on length to four categories: ۱–۴ Mb, ۴–۸ Mb, ۸–۱۶ Mb and above ۱۶ Mb. A total of ۲۲,۲۰۴ ROHs were identified, in which ~ ۹۲ – ۹۸ % of them were less than ۱۶ Mb in length, which covered ۴.۶% to ۱۲.۹% of the entire genome. The inbreeding coefficient based on ROH (FROH) varied among populations (ranging from ۰.۰۵ to ۰.۱۴). The highest inbreeding rate was found in Border Leicester and Soay breeds. In addition, we detected ۹۰ 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.

کلیدواژه ها:

autozygosity ، genomic inbreeding ، runs of homozygosity ، roh Islands ، sheep