Comparative genomic studies of Tomtom and Nuaimi sheep breeds of Bahrain, and Asian and European sheep breeds revealed selection signatures

Abstract

Abstract The segments of the genome harboring genes subject to past selection because of their biological relevance can be identified due to their lower genetic divergence and distinctive regional linkage disequilibrium (LD) patterns. The origins of the sheep breeds known as Tomtom and Nuaimi in Bahrain are unknown, as are the special genetic variants that they carried throughout their evolution and presumably differ from ancient breeds native to Europe and Asian. We pinpointed signals of selection in sheep breeds by comparing the regional genomic (50k SNp chip) differences in LD variation between the Tomtom and Nuaimi sheep breeds with the Afshari, European Mouflon, Asian Mouflon, and Zel breeds. The autosomal genome's LD variation among breeds was compared using the VarLD approach. The NCBI assembly was used to assess the genomic regions bearing the top 0.01 and 0.1 percentiles of signals, determine the genes in those regions, and compare those regions with previously published selection signatures. The wild Mouflon (Asian and European) and Tomtom breeds were divided into three separate components by the PCA, whereas Nuaimi, Zel, and Afshari were grouped inside a single quartile and given special distinction because their individuals looked to be close to one another (genetically related). A total of 59 genes were found to be close to the selection signatures (94 selection signatures) detected on various ovine chromosomes, and many were crucial for reproductive and productive attributes that were influenced by selection as the Tomtom and Nuaimi sheep breeds evolved. According to the genome scan, the Tomtom sheep breed is genetically distant as it was isolated in a separate quartile, far from the Nuaimi, Zel, and Al-Afshari on the one hand, and Asian and European Mouflon on the other. The differences found between the studied breeds combinations may have resulted from special genomic selection signals (94) detected on different chromosomes. The results obtained for the Bahraini local sheep breeds are critical for the future genetic selection plan, as they will serve as a foundation for comparison with any future evolution.