Genome-wide comparison of traditional and commercial Mehraban sheep populations reveals differences in genetic structure, linkage disequilibrium, and inbreeding patterns

Understanding the genetic architecture of sheep under different breeding systems is crucial for enhancing productivity and maintaining adaptive capacity. We analyzed 145 Mehraban sheep from commercial ( n = 97) and traditional ( n = 48) populations utilizing the OvineSNP50 BeadChip array. The analysis revealed that the linkage disequilibrium (LD) was numerically higher on average in the traditional population at both short and long distances (mean r² = 0.249 at < 10 kb; 0.037 at 5 Mb) in comparison to the commercial population (mean r² = 0.220 and 0.027, respectively), suggesting a smaller historical effective population size (Ne). Principal component and admixture analyses validated strong genetic difference, with the commercial population showing moderate admixture from traditional lines. Principal component and admixture analysis confirmed significant genetic difference, with the commercial population exhibiting considerable admixture from traditional lines. Analysis of runs of homozygosity (ROH) revealed more numerous and longer ROH segments in commercial animals (total ROH ~ 43,768 Mb, F ROH = 0.183 ± 0.052) compared to traditional population (11,741 Mb, F ROH = 0.139 ± 0.066), potentially indicating a potential increase in inbreeding and prolonged artificial selection. ROH islands contained 1,586 genes in commercial population and 797 genes in traditional population, with quantitative trait loci (QTL) for muscle development, carcass yield, and milk production enriched in commercial population, whereas traditional population harbored QTL for fertility, immune response, and wool characteristics. Functional analysis further identified Hippo signaling, TCA cycle, and growth-related pathways in commercial population, as well as immune (IL-17, TNF), reproductive, and DNA repair pathways in traditional population. These findings demonstrate how breeding systems shape genome-wide diversity, inbreeding, and functionally relevant loci, highlighting the importance of traditional populations as reservoirs of adaptive alleles for sustainable improvement of commercial flocks.