Disentangling the genetic basis of rhizosphere microbiome assembly in tomato

TY - JOUR

T1 - Disentangling the genetic basis of rhizosphere microbiome assembly in tomato

AU - Oyserman, Ben O.

AU - Flores, Stalin Sarango

AU - Griffioen, Thom

AU - Pan, Xinya

AU - van der Wijk, Elmar

AU - Pronk, Lotte

AU - Lokhorst, Wouter

AU - Nurfikari, Azkia

AU - Paulson, Joseph N.

AU - Movassagh, Mercedeh

AU - Stopnisek, Nejc

AU - Kupczok, Anne

AU - Cordovez, Viviane

AU - Carrion, Victor J.

AU - Ligterink, Wilco

AU - Snoek, Basten L.

AU - Medema, Marnix H.

AU - Raaijmakers, Jos M.

N1 - 7458, ME; Data archiving: ENA

PY - 2022/6/16

Y1 - 2022/6/16

N2 - 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.

AB - 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.

UR - https://www.ebi.ac.uk/ena/browser/view/PRJNA789467

UR - https://www.ebi.ac.uk/ena/browser/view/PRJNA787039

U2 - 10.1038/s41467-022-30849-9

DO - 10.1038/s41467-022-30849-9

M3 - Article

C2 - 35710629

SN - 2041-1723

VL - 13

JO - Nature Communications

JF - Nature Communications

IS - 1

M1 - 3228

ER -