A Nelore Cattle Structural Variant Catalog.
7 affiliations
- 1Department of Animal Nutrition & Production, School of Veterinary Medicine and Animal Science, University of São Paulo, Pirassununga, Brazil.
- 2Animal Genomics, ETH Zürich, Zürich, Switzerland.
- 3Instituto de Ganadería de Montaña, CSIC - Universidad de León, Grulleros, León, Spain.
- 4GenSys Consultores Associados, Jaboticabal, Brazil.
- 5Department of Animal Science, Universidade Estadual Vale Do Acaraú, Sobral, Brazil.
- 6Department of Animal Science, School of Agricultural and Veterinarian Sciences, São Paulo State University, Jaboticabal, Brazil.
- 7Commonwealth Scientific and Industrial Research Organization, Hobart, Tasmania, Australia.
Abstract
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.
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BibTeX
@article{silva2026nelore,
title = {{A Nelore Cattle Structural Variant Catalog.}},
author = {Thales de Lima Silva and Alexander S Leonard and Pablo Augusto de Souza Fonseca and Haroldo Henrique de R Neves and Alexandre M Ruiz and Lucas Tassoni Andrietta and Gerardo A Fernandes Júnior and Júlio Cesar de C Balieiro and Hubert Pausch and Roberto Carvalheiro and Ricardo Vieira Ventura},
journal = {Animal genetics},
year = {2026},
month = oct,
doi = {10.1002/age.70225},
url = {https://europepmc.org/article/MED/42893698},
note = {CC BY},
}
RIS
TY - JOUR
TI - A Nelore Cattle Structural Variant Catalog.
AU - Thales de Lima Silva
AU - Alexander S Leonard
AU - Pablo Augusto de Souza Fonseca
AU - Haroldo Henrique de R Neves
AU - Alexandre M Ruiz
AU - Lucas Tassoni Andrietta
AU - Gerardo A Fernandes Júnior
AU - Júlio Cesar de C Balieiro
AU - Hubert Pausch
AU - Roberto Carvalheiro
AU - Ricardo Vieira Ventura
PY - 2026
DA - 2026/10/01
JO - Animal genetics
DO - 10.1002/age.70225
UR - https://europepmc.org/article/MED/42893698
AB - 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.
SN - 0268-9146
SN - 1365-2052
ER -