Disentangling the genetic basis of rhizosphere microbiome assembly in tomato

Ben O. Oyserman* (Corresponding author), Stalin Sarango Flores, Thom Griffioen, Xinya Pan, Elmar van der Wijk, Lotte Pronk, Wouter Lokhorst, Azkia Nurfikari, Joseph N. Paulson, Mercedeh Movassagh, Nejc Stopnisek, Anne Kupczok, Viviane Cordovez, Victor J. Carrion, Wilco Ligterink, Basten L. Snoek, Marnix H. Medema, Jos M. Raaijmakers* (Corresponding author)

*Corresponding author for this work

Research output: Contribution to journal/periodicalArticleScientificpeer-review

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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, we map the molecular features of the rhizosphere microbiome as quantitative traits of a diverse hybrid population of wild and domesticated tomato. Gene content analysis of prioritized tomato quantitative trait loci suggests 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 water channel aquaporin SlTIP2.3. Within metagenome-assembled genomes of root-associated Streptomyces and Cellvibrio, we identify bacterial genes involved in metabolism of plant polysaccharides, iron, sulfur, trehalose, and vitamins, whose genetic variation associates with specific tomato QTLs. By integrating ‘microbiomics’ and quantitative plant genetics, we pinpoint putative plant and reciprocal rhizobacterial traits underlying microbiome assembly, thereby providing a first step towards plant-microbiome breeding programs.
Original languageEnglish
Article number3228
Number of pages16
JournalNature Communications
Volume13
DOIs
Publication statusPublished - 16 Jun 2022

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