Disentangling the genetic basis of rhizosphere microbiome assembly in tomato
Oyserman, Ben O; Flores, Stalin Sarango; Griffioen, Thom; Pan, Xinya; van der Wijk, Elmar; Pronk, Lotte; Lokhorst, Wouter; Nurfikari, Azkia; Paulson, Joseph N; Movassagh, Mercedeh; Stopnisek, Nejc; Kupczok, Anne; Cordovez, Viviane; Carrión, Víctor J; Ligterink, Wilco; Snoek, Basten L; Medema, Marnix H; Raaijmakers, Jos M
(2022) Nature Communications, volume 13, issue 1, pp. 1 - 16
(Article)
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
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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.
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Keywords: Iron/metabolism, Lycopersicon esculentum/metabolism, Microbiota/genetics, Plant Breeding, Plants/metabolism, Rhizosphere
ISSN: 2041-1723
Publisher: Nature Publishing Group
Note: Funding Information: The project was financially supported, in part, by the NWO-TTW Perspective program BackToRoots (TTW-project 14218 to J.M.R., V.J.C., V.C., and B.O.O.), by the NWO-Gravitation program MICRop (to J.M.R., M.H.M.), a National Institutes of Health (NIH) Genome to Natural Products Network supplementary award (no. U01GM110706 to M.H.M.), a ZonMW Enabling Technologies Hotel project (no. 40-43500-98-210 to M.H.M.), a Senescyt fellowship awarded to S.S.F., and by internal funding from the Netherlands Institute of Ecology. Publisher Copyright: © 2022, The Author(s).
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