Sequencing & Pangenomes

Application of an indicine cattle multi-assembly graph to discover structural variants associated with adaptability to harsh environments

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Abstract

The field of bovine genomics has been limited by the reliance on a single linear reference genome, which makes it difficult to detect genetic variations, particularly structural variants that are large ( >50 bp) and complex. This limitation compromises the studies since the genetic sequences absent from the reference genome (ARS-UCD2.0) are simply ignored, potentially missing important sources of phenotypic variation. By constructing a pangenome from multiple indicine cattle breeds, we hope to reveal novel and functionally relevant structural variants associated with adaptation traits to harsh environments. We utilized 13 high-quality de novo assemblies from five indicine cattle breeds (Nelore, Guzerat, Gyr, Tabapua and Sindi), that are widely established and adapted to the tropical environment in Brazil, to identify structural variants unique to each breed while determining which variants are conserved across the indicine breeds examined. The genomes were generated using Oxford Nanopore Technologies long-read sequencing, assembled with Hifiasm, and polished using Medaka. The pangenome graph was constructed using Minigraph with ARS-UCD2.0 as the backbone, and structural variants were subsequently called using vg deconstruct. The resulting pangenome contained approximately 84.7 Mb of novel DNA sequences that are not present in the reference genome. We identified 285,331 structural variants, of which 155,290 are shared across all five zebu breeds examined. This study provides a genomic resource of structural variants and novel sequences for the five most widely exploited indicine cattle breeds in Brazil. The pangenome approach proved essential for capturing indicine genetic diversity by incorporating complex structural variants and novel sequences absent from the linear Bos taurus reference. We revealed functional structural variants and millions of previously undescribed bases that represent potential sources of phenotypic variation and candidate genes involved in the adaptation of indicine cattle breeds to tropical environments.

Keywords: 2026

How to Cite:

Silva, T., Leonard, A., van Elst, T., Milia, S., Neves, H., Balieiro, J., Carvalheiro, R., Pausch, H. & Ventura, R., (2026) “Application of an indicine cattle multi-assembly graph to discover structural variants associated with adaptability to harsh environments”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2285389. doi: https://doi.org/10.31274/wcgalp.23676

Rights: 1