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The genetic basis of rapid plant pathogen evolution

English title The genetic basis of rapid plant pathogen evolution
Applicant Croll Daniel
Number 173265
Funding scheme Project funding (Div. I-III)
Research institution Institut de Biologie Université de Neuchâtel
Institution of higher education University of Neuchatel - NE
Main discipline Genetics
Start/End 01.08.2017 - 30.04.2021
Approved amount 549'680.00
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All Disciplines (4)

Discipline
Genetics
Botany
Agricultural and Forestry Sciences
Ecology

Keywords (6)

Genome-wide association mapping; Zymoseptoria tritici; Selection scans; Population genomics; Plant pathogens; Fungi

Lay Summary (German)

Lead
Pflanzenkrankheiten stellen eine ernsthafte Bedrohung der weltweiten Nahrungssicherheit dar. Die Züchtung von natürlichen Resistenzen gegen Pathogene hat in vielen Nutzpflanzen zu beachtlichen Erfolgen geführt. Gewisse Pathogene zeigen jedoch ein bedrohliches Potential, innerhalb kurzer Zeit Resistenzmechanismen zu überwinden. Unser Forschungsprojekt wird die Prozesse studieren, die zu schneller Anpassung von Pathogenen führen und nach Mechanismen suchen, die solche Anpassungsprozesse eindämmen können.
Lay summary

Inhalt und Ziele des Forschungsprojekts 

Wir haben in den letzten Jahren Methoden entwickelt, die uns erlauben Anpassungsprozesse in Pathogenen präzise nachzuvollziehen. Zu diesen Methoden gehören die Analyse einer grossen Anzahl vollständig sequenzierter Erbgüter (Genomen) von Pathogenpopulationen.

In diesem Projekt werden wir den Erreger erforschen, der für die Septoria-Blattdürre, die wichtigste Krankheit von Weizen, verantwortlich ist. Der erste Teil des Projekts wird aufzeigen, welche Gene im Pathogen so mutiert haben, dass sie bestimmte Resistenzen im Weizen überwinden können. Diese Analysen werden anhand von genomweiten Assoziationsstudien (GWAS) durchgeführt. Der zweite Teil des Projekts wird aufzeigen, welche Regionen im Genom der Pathogene für den Befall eines Weizenfelds verantwortlich sind. Unser besonderes Interesse gilt den Faktoren, welche die Anpassung beschleunigen oder Verlangsamen können.

Wissenschaftlicher und gesellschaftlicher Kontext des Forschungsprojekts 

Die Bekämpfung von Pflanzenkrankheiten ist eine weltweit prioritäre Aufgabe sowohl auf der ökonomischen wie auch auf der ökologischen Ebene. Das Projekt beschäftigt sich mit Anpassungsprozessen in Pathogenen, die bei Getreide zu grossen Ernteverlusten führen können. Die präzise Charakterisierung von Anpassungsprozessen wird erlauben, dauerhafte Strategien zur Krankheitseindämmung zu entwickeln. 

 
Direct link to Lay Summary Last update: 21.04.2017

Responsible applicant and co-applicants

Employees

Project partner

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
Zymoseptoria tritici community meeting Poster The genetic basis of host-­‐pathogen interactions 05.09.2017 Kiel, Germany Singh Nikhil Kumar;
Zymoseptoria tritici community meeting Talk given at a conference How variation in the genome speeds up the evolution of Zymoseptoria tritici 05.09.2017 Kiel, Germany Croll Daniel;
The Sainsbury Laboratory Summer School 2017 Talk given at a conference Retracing pathogen genome evolution during rapid disease emergence 07.08.2017 Norwich, Great Britain and Northern Ireland Croll Daniel;


Self-organised

Title Date Place
Host-Microbes Genomics Meeting 2017 08.09.2017 Neuchâtel, Switzerland

Communication with the public

Communication Title Media Place Year
Media relations: radio, television CQFD RTS1 Western Switzerland 2017

Associated projects

Number Title Start Funding scheme
183365 Ultra High Performance Liquid Chromatography-High Resolution Tandem Mass Spectrometry (UHPLC-HRMS/MS) for metabolomics and identification of bioactive molecules 01.10.2019 R'EQUIP

Abstract

Plants and pathogens are locked in arms races to detect invasion and to disable host resistance, respectively. A key evolutionary step for pathogens is to evolve effectors, which are small proteins that specifically target and disable the plant immune system. The effector content is a major determinant of the pathogen's host range and evolutionary potential. The ability of hosts to detect specific pathogen effectors is expected to lead to strong directional selection on pathogen populations. However, for most plant pathogenic fungi, the content in effector genes and their evolutionary trajectory are poorly known. Plants in agricultural ecosystems are attacked by a multitude of microbial pathogens. Rapid evolution in pathogens poses a significant threat to food security. What enables pathogens to overcome disease resistance of crops and cause damage is poorly understood. In this project, we will use the highly polymorphic pathogen of wheat Zymoseptoria tritici as a model. The wheat genome encodes a large number of uncharacterized resistance factors against the pathogen. The very large population sizes of the pathogen enabled the rapid evolution of fungicide resistance and virulence on previously resistant wheat cultivars. However, it is largely unknown what loci in the pathogen genome contribute to virulence on wheat. We also lack an understanding how selection, imposed by the host’s ability to detect the pathogen, impacts the evolutionary trajectory of pathogen populations. The major goal of the proposed research is to establish a comprehensive understanding of the loci in the pathogen genome that contribute to virulence evolution. The first set of experiments will map phenotypic traits of the pathogen to loci in the genome using genome-wide association studies (GWAS). For this, we will create a highly diverse mapping population from an experimental wheat field site. We will measure the ability of fungal strains to cause disease on a series of different wheat cultivars in greenhouse experiments. We will also assay the mapping population for the ability to tolerate abiotic stress factors and quantify the secretion of secondary metabolites, which likely play a role in ecological interactions during infection. Whole genome sequencing will provide a highly dense set of genetic markers for association mapping. The second set of experiments takes a “reverse ecology” approach to identify targets of selection in pathogen populations. For this, we will collect pathogen strains in replicated plots of multiple wheat cultivars grown at the same experimental wheat field site. Pathogen genotypes better adapted to cause disease on a specific wheat cultivar are expected to accumulate over the growing season. We will perform a large-scale sequencing study to detect responses to selection in pathogen populations by identifying consistent allele frequency changes over time. Finally, we will combine knowledge gained from the first and second part of this project. Importantly, we will be able to disentangle loci segregating adaptive genetic variation to cause disease from loci responding to selection pressure to colonize the same host. In principle, pathogen loci contributing to virulence on a specific host (identified by GWAS) should match the targets of selection on the same host in the field experiments. However, mismatches in the identity of loci recovered by the two approaches will provide important insights into how ecological factors impact the evolution of host specialization. This project will identify key mechanisms driving rapid plant pathogen evolution. Knowledge generated in this project will advance the functional understanding of fungal pathogenesis and inform sustainable strategies to manage disease in agricultural ecosystems.
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