Genome- Wide Scans of ROH Islands and Related Genes in the World's Sheep Populations

Run of homozygosity (ROH) was used to detecting the genomic inbreeding in sheep. The locations of ROHs which are under positive selection, or laboring favorable allele in population, tend to be fixed in the genome and formation of ROH Island during long times. As detecting the ROH Islands, the genomic regions containe economic traits could be detectable.

In this study in order to identify the ROH Islands associated with the genes under selection, the 50k BeadChip genotyped data of 2536 sheep from 68 different breeds from all over the world were used. After quality control, ROHs were identified using Plink v1.09 software. One percent of SNP with the highest frequency in ROH were considered as ROH Islands.

A total of 465 ROH Islands (length: 27.43 Kb to 17 Mb) were identified, which covering less than 1% of the sheep genome. The ROH Islands was not distributed across the genome uniform and varied among breeds, but some common were identified. The highest and largest ROH islands were observed in European breeds. In contrast, the lowest and shortest were detected in African and American breeds, respectively. In this study, 256 genes were identified in 111 ROH Islands from total of 465 ROH Islands. of A quarter of the total reference genes identified in the sheep genome, were detected within the ROH islands. Totally 103 QTLs associated with milk, carcass, body weight, and wool traits were identified in these regions.

The results of this study revealed that, the formation of sheep breeds and selection for economic traits during several years, has led to the formation of many ROH islands in sheep genome, therefore scanning these regions at the genome can be an alternative strategy to identify genes and associated loci with economic traits.