Managing plant disease in a changing climate
Goals
Plants have to defend themselves against various stresses such as attacks by animals and diseases. Moreover, they must deal with environmental stresses that impact their immunity. Whilst experiencing external threats, plants steer the production of hormones, genes and specific defense processes. The team examines how plants recognise stresses. It studies the role of metabolites and genes in defense signaling. This enables pinpointing key genes and processes involved in a plant’s defense against various stresses. This knowledge is crucial. If plants activate their defense system at the right moment, the dependency on pesticides can be reduced. Ultimately the knowledge gained should lead to breeding crop plants that can better handle environmental stress.
Approach
The team analyses how the model plant Arabidopsis thaliana (thale cress) defends itself when it is exposed to one or a combination of stresses, including elevated temperature. Furthermore, it examines what external stress means for the defense metabolite production of the plant. The team develops a Gene Regulatory Networks Model (GRN) using ‘deep learning’, a machine learning technique. The model should predict which genes are triggered and expressed when a plant is exposed to multiple stresses. Next, the team connects this model to a Metabolic Network Model (MNM). This is a model that reflects the metabolite production of a plant when it is exposed to temperature extremes and pathogen (diseases) attacks. It then integrates the various models into one model.
Visualisation of the approach. Created by Xenja Ploeger.
Activities
The team collects RNA to investigate gene expression under various stresses such as pathogen attacks and elevated temperature. Moreover, it analyses the accumulation of defense metabolites and hormones over time. With this information, the team constructs models that predict which genes are important for the plant under stress. Furthermore, the model conveys information about the regulation of defense molecule production. By examining how defense processes and metabolic networks function, the team aims to gain fundamental insights into a plant’s stress response. This knowledge can be utilized in the eventual breeding process when selecting the most resilient plant.
Team
Work package leader Petra Bleeker, Associate Professor Plant Physiology, UvA
Aalt-Jan van Dijk, Professor Biosystems Data Analysis, UvA
Anna Neefjes, PhD candidate, UvA
Guido van den Ackerveken, Professor of Translation Plant Biology and Scientific Director CropXR, UU
Huub Hoefsloot, Associate Professor Biosystems Data Analysis, UvA
Jordan Earle, PhD candidate, UvA
Jordi Alonso Esteve, PhD candidate, UvA
Julia Ruiz Capella, PhD candidate, UU
Niels Aerts, Postdoc Researcher, UU
Robert Schuurink, Professor of Plant Specialized Metabolism and Defence in Plant Physiology, UvA
Samara Almeida Landman, PhD candidate, UU
Saskia van Wees, Professor in Hormonal Regulation of Plant Defence, UU
Xenja Ploeger, Technician, UvA