A Nelore Cattle Structural Variant Catalog

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.