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Inference of Polyploid Origin and Inheritance Mode from Population Genomic Data

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Polyploidy

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

Abstract

Whole-genome duplications yield varied chromosomal pairing patterns, ranging from strictly bivalent to multivalent, resulting in disomic and polysomic inheritance modes. In the bivalent case, homeologous chromosomes form pairs, where in a multivalent pattern all copies are homologous and are therefore free to pair and recombine. As sufficient sequencing data is more readily available than high-quality cytological assessments of meiotic behavior or population genetic assessment of allelic segregation, especially for non-model organisms, bioinformatics approaches to infer origins and inheritance modes of polyploids using short-read sequencing data are attractive. Here we describe two such approaches, where the first is based on distributions of allelic read depth at heterozygous sites within an individual, as the expectations of such distributions are different for disomic and polysomic inheritance modes. The second approach is more laborious and based on a phylogenetic assessment of partially phased haplotypes of a polyploid in comparison to the closest diploid relatives. We discuss the sources of deviations from expected inheritance patterns, advantages and pitfalls of both methods, effects of mating types on the performance of the methods, and possible future developments.

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Acknowledgments

We thank Robin Burns, Filip Kolář, Matt Johnson, and Arthur Zwaenepoel for their insights and advice during the preparation of this chapter.

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Authors and Affiliations

  1. Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany

    Alison Dawn Scott, Jozefien D. Van de Velde & Polina Yu Novikova

Authors
  1. Alison Dawn Scott
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  2. Jozefien D. Van de Velde
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  3. Polina Yu Novikova
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Corresponding author

Correspondence to Polina Yu Novikova .

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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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Scott, A.D., Van de Velde, J.D., Novikova, P.Y. (2023). Inference of Polyploid Origin and Inheritance Mode from Population Genomic Data. 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_15

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  • DOI: https://doi.org/10.1007/978-1-0716-2561-3_15

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2560-6

  • Online ISBN: 978-1-0716-2561-3

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