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Genetic mapping of genotype-by-ploidy effects in Arabidopsis thaliana

Cris L. Wijnen, Frank F.M. Becker, Andries A. Okkersen, C. Bastiaan de Snoo, Martin P. Boer, Fred A. van Eeuwijk, View ORCID ProfileErik Wijnker, View ORCID ProfileJoost J.B. Keurentjes
doi: https://doi.org/10.1101/2021.11.19.469311
Cris L. Wijnen
1Laboratory of Genetics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
2Biometris, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
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Frank F.M. Becker
1Laboratory of Genetics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
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Andries A. Okkersen
1Laboratory of Genetics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
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C. Bastiaan de Snoo
3Rijk Zwaan R&D Fijnaart, Eerste kruisweg 9, 4793 RS Fijnaart, The Netherlands
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Martin P. Boer
2Biometris, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
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Fred A. van Eeuwijk
2Biometris, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
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Erik Wijnker
1Laboratory of Genetics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
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  • ORCID record for Erik Wijnker
Joost J.B. Keurentjes
1Laboratory of Genetics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
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  • ORCID record for Joost J.B. Keurentjes
  • For correspondence: joost.keurentjes@wur.nl
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Abstract

Plants can express different phenotypic responses following polyploidization, but ploidy-dependent phenotypic variation has so far not been assigned to specific genetic factors. To map such effects, segregating populations at different ploidy levels are required. The availability of an efficient haploid-inducer line in Arabidopsis thaliana allows for the rapid development of large populations of segregating haploid offspring. Because Arabidopsis haploids can be self-fertilised to give rise to homozygous doubled haploids, the same genotypes can be phenotyped at both the haploid and diploid ploidy level. Here, we compared the phenotypes of recombinant haploid and diploid offspring derived from a cross between two late flowering accessions to map genotype x ploidy (GxP) interactions. Ploidy-specific quantitative trait loci (QTLs) were detected at both ploidy levels. This implies that mapping power will increase when phenotypic measurements of monoploids are included in QTL analyses. A multi-trait analysis further revealed pleiotropic effects for a number of the ploidy specific QTLs as well as opposite effects at different ploidy levels for general QTLs. Taken together, we provide evidence of genetic variation between different Arabidopsis accessions being causal for dissimilarities in phenotypic responses to altered ploidy levels, revealing a GxP effect. Additionally, by investigating a population derived from late flowering accessions we revealed a major vernalisation specific QTL for variation in flowering time, countering the historical bias of research in early flowering accessions.

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Posted November 20, 2021.
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Genetic mapping of genotype-by-ploidy effects in Arabidopsis thaliana
Cris L. Wijnen, Frank F.M. Becker, Andries A. Okkersen, C. Bastiaan de Snoo, Martin P. Boer, Fred A. van Eeuwijk, Erik Wijnker, Joost J.B. Keurentjes
bioRxiv 2021.11.19.469311; doi: https://doi.org/10.1101/2021.11.19.469311
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Genetic mapping of genotype-by-ploidy effects in Arabidopsis thaliana
Cris L. Wijnen, Frank F.M. Becker, Andries A. Okkersen, C. Bastiaan de Snoo, Martin P. Boer, Fred A. van Eeuwijk, Erik Wijnker, Joost J.B. Keurentjes
bioRxiv 2021.11.19.469311; doi: https://doi.org/10.1101/2021.11.19.469311

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