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Multi-GBS: A massively multiplexed GBS-based protocol optimized for large, repetitive conifer genomes

Miguel Vallebueno-Estrada, Sonja Steindl, Vasilina Akulova, Julia Riefler, Lucyna Slusarz, Alexis Arizpe, View ORCID ProfileKelly Swarts
doi: https://doi.org/10.1101/2022.01.10.475685
Miguel Vallebueno-Estrada
1Gregor Mendel Institute, Austrian Academy of Sciences, Dr. Bohr-Gasse 3, 1030, Vienna, Austria
2Vienna International Postdoctoral Program, Campus-Vienna-Biocenter 1, 1030, Vienna, Austria
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  • For correspondence: kelly.swarts@gmi.oeaw.ac.at
Sonja Steindl
1Gregor Mendel Institute, Austrian Academy of Sciences, Dr. Bohr-Gasse 3, 1030, Vienna, Austria
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Vasilina Akulova
1Gregor Mendel Institute, Austrian Academy of Sciences, Dr. Bohr-Gasse 3, 1030, Vienna, Austria
3Vienna BioCenter PhD Program, Campus-Vienna-Biocenter 1, 1030, Vienna, Austria
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Julia Riefler
1Gregor Mendel Institute, Austrian Academy of Sciences, Dr. Bohr-Gasse 3, 1030, Vienna, Austria
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Lucyna Slusarz
1Gregor Mendel Institute, Austrian Academy of Sciences, Dr. Bohr-Gasse 3, 1030, Vienna, Austria
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Alexis Arizpe
1Gregor Mendel Institute, Austrian Academy of Sciences, Dr. Bohr-Gasse 3, 1030, Vienna, Austria
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Kelly Swarts
1Gregor Mendel Institute, Austrian Academy of Sciences, Dr. Bohr-Gasse 3, 1030, Vienna, Austria
4Max Perutz Labs, Department of Structural and Computational Biology, University of Vienna, Campus-Vienna-Biocenter 5, 1030, Vienna, Austria
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  • ORCID record for Kelly Swarts
  • For correspondence: kelly.swarts@gmi.oeaw.ac.at
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Abstract

Reduced representation library approaches are still a valuable tool for breeding and population and ecological genomics, even with impressive increases in sequencing capacity in recent years. Unfortunately, current approaches only allow for multiplexing up to 384 samples. To take advantage of increased sequencing capacity, we present Multi-GBS, a massively multiplexable extension to Genotyping-by-Sequencing that is also optimized for large conifer genomes. In Norway Spruce, a highly repetitive 20Gbp diploid genome with high population genetic variation, we call over a million variants in 32 genotypes from three populations, two natural forest in the Alps and Bohemian Alps, and a managed population from southeastern Austria using the existing TASSEL GBSv2 pipeline. Metric MDS analysis of replicated genotypes shows that technical bias in resulting genotype calling is minimal and that populations cluster in biologically meaningful ways.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted January 11, 2022.
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Multi-GBS: A massively multiplexed GBS-based protocol optimized for large, repetitive conifer genomes
Miguel Vallebueno-Estrada, Sonja Steindl, Vasilina Akulova, Julia Riefler, Lucyna Slusarz, Alexis Arizpe, Kelly Swarts
bioRxiv 2022.01.10.475685; doi: https://doi.org/10.1101/2022.01.10.475685
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Multi-GBS: A massively multiplexed GBS-based protocol optimized for large, repetitive conifer genomes
Miguel Vallebueno-Estrada, Sonja Steindl, Vasilina Akulova, Julia Riefler, Lucyna Slusarz, Alexis Arizpe, Kelly Swarts
bioRxiv 2022.01.10.475685; doi: https://doi.org/10.1101/2022.01.10.475685

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