Detection of homozygosity and heterozygosity regions in mediterranean sheep breeds revealed by high-density SNP array

Abstract

Genome-wide studies in livestock have become essential tools for investigating genetic diversity, population structure, and adaptive evolution. By leveraging high-density single nucleotide polymorphism (SNP) arrays, researchers can identify genomic regions under selection and trace the demographic history of breeds. Among the most informative genomic features are Runs of Homozygosity (ROH), which reflect inbreeding levels and historical population dynamics, and Heterozygosity-Rich Regions (HRR), which may indicate loci under balancing selection and contribute to important functional traits. In this study, we investigated the ROH and HRR patterns in four different Mediterranean sheep breeds (Barbaresca—BAR, n=48; Noticiana—NOT, n=48; Valle del Belice—VDB, n=142; and Sarda—SAR, n=144) genotyped using the Illumina Ovine SNP600K array. The population structure analysis revealed a distinct separation among the four breeds, likely due to differences in breeding areas or management. Clear differences in ROH and HRR patterns were also observed. The endangered breeds (NOT and BAR) showed a higher mean number of ROH per individual (92.38 and 83.71, respectively) compared to SAR (60.38) and VDB (58.49). A total of 12 ROH islands, ranged from 0.13 to 2.83Mb, have been detected. These genomic regions mapped genes associated with economically important traits, such as reproduction (ZDHHC21), milk (HERC3 and HERC6) and meat (ABCG2, PKD2, LAP3, NCAPG, and SPP1) production, and body size (LCORL). Regarding the HRR, the mean number of segments for individuals ranged from 4.65 (BAR) to 6.50 (VDB), and over 52% of these were shorter than 150kb. The 16 HRR islands mapped genes related to reproduction (CAPSPERB and TC2N) and climate adaptation (VPS13B). Our results showed the usefulness of ROH and HRR for investigating genomic regions harboring genes associated with important traits that are consistent with the phenotypic characteristics of the investigated breeds, which present differences in both morphology and production traits and show excellent adaptability to the local environments. These findings may help in designing effective breeding or conservation programs for these sheep breeds.