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 (r2 ≥ 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.