In this study, we chose 17 worldwide sheep populations of eight breeds, which were intensively selected for different purposes (meat, milk, or wool), or locally-adapted breeds, in order to identify and characterize factors impacting the detection of runs of homozygosity (ROH) and heterozygosity-rich regions (HRRs) in sheep. We also applied a business intelligence (BI) tool to integrate and visualize outputs from complementary analyses. We observed a prevalence of short ROH, and a clear distinction between the ROH profiles across populations. The visualizations showed a fragmentation of medium and long ROH segments. Furthermore, we tested different scenarios for the detection of HRR and evaluated the impact of the detection parameters used. Our findings suggest that HRRs are small and frequent in the sheep genome; however, further studies with higher density SNP chips and different detection methods are suggested for future research. We also defined ROH and HRR islands and identified common regions across the populations, where genes related to a variety of traits were reported, such as body size, muscle development, and brain functions. These results indicate that such regions are associated with many traits, and thus were under selective pressure in sheep breeds raised for different purposes. Interestingly, many candidate genes detected within the HRR islands were associated with brain integrity. We also observed a strong association of high linkage disequilibrium pattern with ROH compared with HRR, despite the fact that many regions in linkage disequilibrium were not located in ROH regions.

Structural variants (SVs) contribute more nucleotide divergence between mammalian genomes than single nucleotide polymorphisms, yet no population‐scale, long‐read‐validated SV catalog has been available for Bos indicus cattle. Nelore, the most numerically important indicine breed worldwide, diverges substantially from the taurine‐derived reference genome used for most bovine SV discovery, leaving its structural variation largely uncharacterized. Long‐read sequencing of 20 Nelore bulls with two complementary callers (Sniffles2, SVIM) yielded 82 581 dual‐caller concordant SVs, of which 74 222 insertions and deletions passed independent read‐based validation. Ensembl VEP annotation identified 561 HIGH‐impact variants (0.75% of the catalog) across 7040 protein‐coding genes. Only 22 894 SVs (30.7%), including 147 of 561 HIGH‐impact variants (26.2%), could be tagged by an existing BovineHD SNP ( r ² ≥ 0.8), showing that routine array genotyping captures a minority of this variation. Intersection with an indicine‐ancestry SNP map identified 6114 SVs (8.2%) enriched in Bos indicus , including 61 HIGH‐impact variants overlapping genes with plausible roles in immune/inflammatory defense and oxidative‐stress response, providing a resource and candidate variant set for genomic selection and tropical‐adaptation studies in indicine cattle.