Optical mapping compendium of structural variants across global cattle breeds

Abstract

Structural variants (SV) have been linked to several important bovine disease phenotypes, but due to the difficulty of their accurate detection with standard sequencing approaches, their role in shaping economically important traits across global cattle breeds is largely unexplored. Optical mapping is an alternative approach for mapping SVs that has been shown to have higher sensitivity than DNA sequencing approaches. The aim of this project was to use optical mapping to develop a high quality database of structural variation across cattle breeds from different geographical regions and origins, to enable further studies of the important roles of SV in cattle. To do this we generated 100X Bionano optical mapping data for 18 cattle of nine different ancestries, three continents and covering both major cattle lineages. In total we identified 13,457 SVs, of which 1,200 putatively overlap a coding region. This resource therefore provides a high-quality set of optical mapping-based SV calls that can be used across studies, from validating DNA sequencing based SV calls to prioritising candidate functional variants in genetic association studies and expanding our understanding of the role of SVs in the evolution of cattle.

Graph construction method impacts variation representation and analyses in a bovine super-pangenome

“…We used optical mapping from two unrelated Hereford and two unrelated Nellore samples [16] to further validate SV consensus in the pangenomes. The overlap is expected to be low due to the unrelated origin of samples, only covering two of the twelve breeds, and the different variant sizes accessible with optical mapping and sequencing reads.…”

“…We used optical mapping from two unrelated Hereford and two unrelated Nellore samples [16] 6). Out of the pangenomes, minigraph also had the most private variants validated (58), compared to cactus (48) and pggb (36).…”

“…While all tools recovered more insertions than deletions, minigraph contained proportionally less insertions than pggb and cactus (Figure 2d,e). We used optical mapping from two unrelated Hereford and two unrelated Nellore samples [16] to further validate SV consensus in the pangenomes. The overlap is expected to be low due to the unrelated origin of samples, only covering two of the twelve breeds, and the different variant sizes accessible with optical mapping.…”

Optical mapping compendium of structural variants across global cattle breeds

“…The output of the Solve workflows can be downloaded from Zenodo (https://doi.org/10.5281/zenodo.6516993 36 and https://doi.org/10.5281/ zenodo.6517172 37 ). The raw and filtered VCF files, converted using smap_2_vcf_v2.py, can be found on Zenodo with https://doi.org/10.5281/zenodo.6854879 38 . genome 39 , expanded with the BTau5 Y chromosome generated by the 1000 bulls genome project, using Bionano Solve (v3.3 and 3.5) to assemble the genome maps and call SVs.…”