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Population Genomic Analysis of Diploid-Autopolyploid Species

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Polyploidy

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2545))

Abstract

This chapter outlines an empirical analysis of genome-wide single-nucleotide polymorphism (SNP) variation and its underlying drivers among multiple natural populations within a diploid-autopolyploid species. The aim is to reconstruct the genetic structure among natural populations of varying ploidy and infer footprints of selection in these populations, framed around specific questions that are typically encountered when analyzing a mixed-ploidy data set,e.g., addressing the relevance of natural whole-genome duplication for speciation and adaptation. We briefly review the options for the analysis of polyploid population genomic data involving variant calling, population structure, demographic history inference, and selection scanning approaches. Further, we provide suggestions for methods and associated software, possible caveats, and examples of their application to mixed-ploidy and autopolyploid data sets.

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Acknowledgments

We are grateful to Arthur Zwaenepoel, Patrick Meirmans, Josselin Clo, Nélida Padilla García, and Polina Novikova for very useful comments on an earlier version of this chapter. We thank Veronika Konečná, Nélida Padilla García, and Gabriela Šrámková for help with running particular analyses of the example data set and Doubravka Požárová for photos of alpine plants. This work was supported by the Czech Science Foundation (project 20-22783S to FK) and the long-term research development project no. RVO 67985939 of the Czech Academy of Sciences. Access to computing and storage facilities has been provided by the National Grid Infrastructure MetaCentrum provided under the program “Projects of Large Research, Development, and Innovations Infrastructures” (CESNET LM2015042).

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Authors and Affiliations

  1. Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic

    Magdalena Bohutínská, Jakub Vlček & Filip Kolář

  2. Institute of Botany of the Czech Academy of Sciences, Průhonice, Czech Republic

    Magdalena Bohutínská & Filip Kolář

  3. Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA

    Patrick Monnahan

Authors
  1. Magdalena Bohutínská
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  2. Jakub Vlček
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  3. Patrick Monnahan
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  4. Filip Kolář
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Correspondence to Filip Kolář .

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Editors and Affiliations

  1. Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium

    Yves Van de Peer

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Bohutínská, M., Vlček, J., Monnahan, P., Kolář, F. (2023). Population Genomic Analysis of Diploid-Autopolyploid Species. In: Van de Peer, Y. (eds) Polyploidy. Methods in Molecular Biology, vol 2545. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2561-3_16

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  • DOI: https://doi.org/10.1007/978-1-0716-2561-3_16

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  • Publisher Name: Humana, New York, NY

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