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Disentangling the genetic basis of rhizosphere microbiome assembly in tomato

View ORCID ProfileBen O Oyserman, View ORCID ProfileStalin Sarango Flores, View ORCID ProfileThom Griffioen, Xinya Pan, View ORCID ProfileElmar van der Wijk, View ORCID ProfileLotte Pronk, View ORCID ProfileWouter Lokhorst, View ORCID ProfileAzkia Nurfikari, View ORCID ProfileNejc Stopnisek, View ORCID ProfileAnne Kupczok, View ORCID ProfileViviane Cordovez, View ORCID ProfileVíctor J Carrión, View ORCID ProfileWilco Ligterink, View ORCID ProfileBasten L Snoek, View ORCID ProfileMarnix H Medema, View ORCID ProfileJos M Raaijmakers
doi: https://doi.org/10.1101/2021.12.20.473370
Ben O Oyserman
1Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
2Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
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  • For correspondence: benoyserman@gmail.com j.raaijmakers@nioo.knaw.nl
Stalin Sarango Flores
1Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
3Institute of Biology, Leiden University, Leiden, The Netherlands
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Thom Griffioen
1Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
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  • ORCID record for Thom Griffioen
Xinya Pan
1Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
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Elmar van der Wijk
2Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
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  • ORCID record for Elmar van der Wijk
Lotte Pronk
2Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
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Wouter Lokhorst
1Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
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  • ORCID record for Wouter Lokhorst
Azkia Nurfikari
1Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
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  • ORCID record for Azkia Nurfikari
Nejc Stopnisek
1Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
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Anne Kupczok
2Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
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Viviane Cordovez
1Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
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  • ORCID record for Viviane Cordovez
Víctor J Carrión
1Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
3Institute of Biology, Leiden University, Leiden, The Netherlands
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Wilco Ligterink
4Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Wageningen, the Netherlands
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Basten L Snoek
5Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
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Marnix H Medema
2Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
3Institute of Biology, Leiden University, Leiden, The Netherlands
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Jos M Raaijmakers
1Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
3Institute of Biology, Leiden University, Leiden, The Netherlands
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  • ORCID record for Jos M Raaijmakers
  • For correspondence: benoyserman@gmail.com j.raaijmakers@nioo.knaw.nl
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Abstract

Microbiomes play a pivotal role in plant growth and health, but the genetic factors involved in microbiome assembly remain largely elusive. Here, 16S amplicon and metagenomic features of the rhizosphere microbiome were mapped as quantitative traits of a recombinant inbred line population of a cross between wild and domesticated tomato. Gene content analysis of prioritized tomato QTLs suggested a genetic basis for differential recruitment of various rhizobacterial lineages, including a Streptomyces-associated 6.31-Mbp region harboring tomato domestication sweeps and encoding, among others, the iron regulator FIT and the aquaporin SlTIP2.3. Within metagenome-assembled genomes of the rhizobacterial lineages Streptomyces and Cellvibrio, we identified microbial genes involved in metabolism of plant polysaccharides, iron, sulfur, trehalose, and vitamins, whose genetic variation associated with either modern or wild tomato QTLs. Integrating ‘microbiomics’ and quantitative plant genetics pinpointed putative plant and reciprocal microbial traits underlying microbiome assembly, thereby providing the first step towards plant-microbiome breeding programs.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://osf.io/f45ek/

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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 December 21, 2021.
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Disentangling the genetic basis of rhizosphere microbiome assembly in tomato
Ben O Oyserman, Stalin Sarango Flores, Thom Griffioen, Xinya Pan, Elmar van der Wijk, Lotte Pronk, Wouter Lokhorst, Azkia Nurfikari, Nejc Stopnisek, Anne Kupczok, Viviane Cordovez, Víctor J Carrión, Wilco Ligterink, Basten L Snoek, Marnix H Medema, Jos M Raaijmakers
bioRxiv 2021.12.20.473370; doi: https://doi.org/10.1101/2021.12.20.473370
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Disentangling the genetic basis of rhizosphere microbiome assembly in tomato
Ben O Oyserman, Stalin Sarango Flores, Thom Griffioen, Xinya Pan, Elmar van der Wijk, Lotte Pronk, Wouter Lokhorst, Azkia Nurfikari, Nejc Stopnisek, Anne Kupczok, Viviane Cordovez, Víctor J Carrión, Wilco Ligterink, Basten L Snoek, Marnix H Medema, Jos M Raaijmakers
bioRxiv 2021.12.20.473370; doi: https://doi.org/10.1101/2021.12.20.473370

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