During the conference team members will present insights of their research. Join this session and start the conversation!
Poster session Thursday October 17, 17:15 – 18:30
How do we model gene regulatory networks when there are too many genes?
By Ben Noordijk, Marcel Reinders, Aalt D.J. van Dijk, Dick de Ridder
Plants are resilient to different stresses through a number of biological processes. To understand how these processes interact, it is essential to unravel the underlying gene regulatory networks. Typically, these networks are studied using ordinary differential equation (ODE) models, but these models cannot be built for large gene networks (>100 genes). Here, we tackle this problem by reducing the dimensionality of gene networks into gene modules, which are groups of co-expressed and/or co-regulated genes. We demonstrate a method of ODE modelling gene modules and show that it allows prediction of module dynamics under stress.
Work package C1
Integration of drought and heat responses in Arabidopsis thaliana seedlings
By Francesca Giaume, Pinelopi Kokkinopoulou, Jelle Keijzer, Martijn van Zanten, Christa Testerink
In recent years, the challenge of food security has intensified. Developing climate-resilient crops able to succeed in abiotic stress conditions, including heat and drought, as well as their combinations, has become necessary. Furthermore, predicting plant responses to combined stresses is deeply demanding, as demonstrated by the significant differences observed in the transcriptomic and phenomic responses of plants treated with both drought and heat stress compared to single stress conditions.
To this aim, CropXR is exploiting advanced technologies and data-driven approaches to develop highly resilient and productive plants and crop varieties by integrating genomics, phenomics and machine learning. In the framework of the CropXR project, my research focuses on identifying genes involved in the resilience response to drought and temperature stresses, leveraging transcriptomic and phenomic data retrieved from Arabidopsis seedlings grown in soil and exposed to a matrix of different severe isolated and combined stresses.
Work package C1
Assessing natural variation in Arabidopsis thaliana acclimation strategies to combined high temperature and drought conditions
By Jelle Keijzer, Francesca Giaume, Christa Testerink, Bram van Eijnatten, Basten L. Snoek, Martijn van Zanten
In nature multiple stresses often co-occur, with high temperature and drought being two prominent factors. Although these stresses frequently occur together, they can elicit antagonistic and agonistic responses, depending on sequentially, timing, tissue and stress severity, during seedling development. This makes studying their interactions particularly relevant in the context of climate change adaptation of crops. Given that different climates exert varying levels of these stresses, it’s likely that natural genetic variation exists among natural Arabidopsis accessions obtained from diverse environments world-wide, that evolved distinct strategies to cope with these suboptimal conditions.
Our goal is to assess genetic regulatory networks underlying plants adaption to (combined) high temperature and drought. To this aim, we will quantify responses of a core set of natural Arabidopsis accessions from the 1001 Genomes Project on agar plates to elucidate variation in acclimation strategies in both root and shoot. By applying a stress matrix that ranges from no stress to severe levels of both temperature and drought, we aim to identify accessions with diverse response strategies. To select a manageable subset of the 1001 Genomes we created an environmentally diverse EcoCore set, containing around 300 accessions based on climate variables from the AraClim and WorldClim datasets. By screening the phenotypes of this EcoCore set, we aim to identify promising accessions and strategies, which will subsequently be explored in molecular detail and by high-resolution phenotyping at NPEC Utrecht, HADES.
Work package C1
Mechanistic modelling of Arabidopsis responses to mild drought and suboptimal high temperatures
By Thijs van Loo, Monica L Garcia-Gomez, Kirsten ten Tusscher
Plants respond to temperature and water availability changes by modifying their growth and development. These modifications result from coordinated responses in different organs through complex gene regulatory networks, hormonal regulators enabling long-range shoot to root communication, and physiological responses. Here we aim to understand this regulation using a mechanistic modelling approach to integrate prior evidence and experimental data into ordinary differential equations. Using the model, we aim to explain how single and combined temperature and water conditions affect plant growth, development, and ultimately resilience. Collaboration with experimental, bioinformatics, and ML experts will be essential for model development and completeness.
Work package C1
Untangling gene regulation through Deep Learning
By Jordi Alonso Esteve, Dick de Ridder, Aalt D.J van Dijk
Understanding the gene regulatory mechanisms underlying plant responses to stress is crucial for advancing agricultural resilience. We aim to infer the Gene Regulatory Network involved in the transcriptional response of A. thaliana to combinations of abiotic and biotic stress. Our approach focuses on leveraging the information contained in gene promoter regions for this inference. By studying gene-transcription factor interactions at the DNA level, we seek to improve the inference process, extrapolate these relationships to modified promoters, and deepen our understanding of how promoters drive specific transcriptional responses.
Work package C2
Reprogramming of defense-related plant hormone networks under temperature stress
By Julia Ruiz Capella, Niels Aerts, Saskia van Wees
Plant diseases caused by pests and pathogens represent a major constraint for agriculture worldwide. These problems are aggravated by a changing climate, particularly harsh conditions such as drought, flooding, and high temperatures. These abiotic factors negatively impact plant performance, not only by affecting growth and yield, but also by influencing plant immunity levels, thus potentially making the plants more vulnerable to pathogens and insects. Plant performance under various stress conditions relies on precise and timely activation and repression of different hormone-inducible gene regulatory networks (GRNs). While the role of individual hormone GRNs in controlling plant resistance to single stresses is well studied, much less is known about the interaction between these hormone GRNs when plants experience multiple stresses at the same time, a situation that occurs frequently in nature and agriculture. Deciphering the key regulators involved in the immunity-high temperature interaction would bring the scientific community closer to the growth of crops resilient to the challenges associated to climate change.
This project aims to study the effect of elevated temperature on plant immune responses by identifying which sectors within the hormone GRNs are differentially engaged under dual stress conditions and pinpoint key genes in early signaling that can be used to improve resilience. To this end, data from existing
RNA-seq time series of plants treated with plant hormones (methyl jasmonate (MeJA), salicylic acid (SA), abscisic acid (ABA), MeJA+SA, MeJA+ABA) together with two additional generated treatments from the same time series (ethylene (ET) and ET+MeJA) will be combined with an elevated temperature treatment at a limited number of time points. Reference leaf samples from the previously treated plants with ET and ET+MeJA were sent for RNA-seq to ensure proper comparison of the newly generated data with the old data of the time series. Good quality of the RNA and sequencing results were obtained. RNA isolation and sequencing of the remaining samples is therefore planned soon. Additionally, different regimes of elevated temperature are being tested on plants exposed to biotrophic and necrotrophic pathogens attacks. Expression levels of stress-responsive marker genes are being analyzed to potentially identify main regulators of the immune response towards the exposure of the dual stress and response differences among the different applied regimes. These results will be used as input to define which temperature regime will be used for the treatment with plant hormones.
Work package C2
Metabolic modeling of glucosinolates in stressed conditions
By Jordan Earle, Huub Hoefsloot, Petra Bleeker
Modelling the metabolic pathways of glucosinolates in Arabidopsis thaliana to determine how temperature effects the plants response to pests and pathogens. Initially, we have been investigating known metabolic pathways and recreating two existing models. The next step is to investigate response metabolic pathways.
This project is a joint project with other researchers, who are measuring the response of the plant to different changes in conditions and who are modeling the changes in gene expression levels due to environmental changes. Using these we will predict how the glucosinolate levels of interest respond to these changes.
Work package C2
Proteomic analysis of growth-stress interaction
By Linfei Guo, Mark Roosjen, Dolf Weijers
Plants, as sessile organisms, integrate various internal and environmental signals, such as hormones, light, and temperature, through intracellular networks that regulate growth and defense. This project aims to elucidate the role of key protein complexes, specifically BAP-D and COP1/SPA, in modulating these processes. By focusing on the composition and post-translational modifications of these complexes in response to growth cues and stress, we aim to understand how they mediate signal integration. Using protein proximity labeling, we will map interactions and modifications to uncover the regulatory mechanisms that govern plant growth under stress conditions.
Work package C4
Regulations for just transitions: shaping relations of exchange
By E.A.W. (Elsenoor) Wijlhuizen, Prof. Dr. E.H.M. (Ellen) Moors, K. (Koen) Beumer,
J. (Julia) Tschersich
Access to a wide variety of genetic resources is crucial in developing new, resilient crops for sustainable agriculture. Currently, the access to those resources is regulated via Access and Benefit Sharing (ABS)-mechanisms. These regulations state that benefits arising from the utilization of genetic resource material should be shared “fair” and “equitably”. This raises questions of justice: what do we mean by sharing benefits “equitably”? When do we consider it “fair”? This research takes on a relational justice approach, studying the way ABS-mechanisms shape relations between different actors involved and whether we can consider those relations “fair” and “equitable”.
Work package C7
What is resilience? Societal aspects of CropXR
By Aisha So, Koen Beumer, Ellen Moors
The CropXR institute is developing technologies and strategies for increasing agricultural resilience. But what is resilience? Stakeholders can interpret the meaning of agricultural resilience in diverging ways, and they can have contrasting preferences, expectations, and concerns regarding potential strategies and technologies to increase resilience. In this PhD project, we aim to investigate how different stakeholders understand the concept of resilience. To enhance resilience in a desirable way, it is important that we consider and accommodate possibly diverse understandings of resilience. During this conference, I would like to talk with scientists and other stakeholders about their understanding of resilience.
Work package C7
Towards a constructive concept of responsiveness for responsible innovation practices
By Víctor Betriu Yáñez, Prof. Dr. Vincent Blok, Dr. Koen Beumer, Dr. Hao Wang
The development of AI-enabled plant breeding tools for achieving crop resilience under the threat of climate change presents itself as an innovation with a societal and environmental motivation, insofar as it is addressed to make agriculture more sustainable and strives towards food security. Does this good intention suffice to call such an innovation “responsible” (i.e., legitimate, ethically defendable and socially praiseworthy)? From the perspective of Responsible Research and Innovation (RRI), an innovation is not responsible if it is not responsive—if it is not concerned about identifying the foreseeable and unforeseeable societal issues that the innovation might unleash in different contexts, and if it is not ready to act in every here and now to address the ethical demand of those affected. This is so that no philanthropic, economic or scientific interest ever justifies a harm. However, while RRI scholars see the notion of responsiveness as a praiseworthy ideal, there is a lack of understanding about what the term actually means. Indicative of this is not only the large number of approaches trying to put responsiveness into practice and the simultaneous lack of conceptual work on the meaning of such a term, but also the fact that RRI appears to be frustrated when put into practice. If we are then truly committed to the responsible development of science and innovation, we must philosophically inquire into the meaning of responsiveness in order to construct a notion that can be explicit and successfully operationalized in responsible innovation practices. Taking CropXR as its central case study, this PhD project thus aims to answer the following research question: how could a philosophical concept of responsiveness inform responsible innovation practices? This poster sketches three ways that contribute to answer this question: (1) a critical hermeneutics on the implicit and explicit understandings of responsiveness in the RRI literature; (2) an philosophical construction of the notion of responsiveness; (3) an interdisciplinary collaboration with plant physiologists to explore whether the operative and unproblematic biological notion of ‘plant responsiveness’ could inform the philosophical concept and/or its operationalization.
Work package C7
Who does what? Understanding potential roles of different stakeholders in smart-breeding innovation development processes
By Eva Marina Valencia Leñero
Smart-breeding innovations aim at increasing the quality and quantity of data to improve breeding
processes with digital tools. Even as niche innovations, they already engage multiple stakeholders in their
data management processes. Innovation and transition literature describe some stakeholders engagement
requirements useful for smart-breeding innovation development processes, but it does not show their changing character. Thus, we aim to understand the multistakeholder role dynamics to understand how they could contribute to smart-breeding development process, building from their related data creation and diffusion capacities. The methodology learns from relevant stakeholders in smart-breeding data management processes, learning from their past, present and future knowledge and expertise.
Work package C7
Physiology-informed data-supported modelling of potato crop resilience
By C. Verburg, A. Heinlein, F.A. van Eeuwijk, N.V. Budko
A novel physiology-informed data-supported modelling approach is proposed to assess potato crop
resilience by incorporating the inherent variability in crop traits. The model integrates mechanistic crop
models with stochasticity using the Probability Density Evolution Method (PDEM), enabling a more
accurate representation of the distribution of crop traits rather than relying on single-value averages.
Preliminary results demonstrate the potential of this approach. Future research will focus on expanding
the range of rate/response functions, applying the model to diverse datasets, comparing its performance
to other modelling methodologies, and evaluating its generalizability across different crop species and environmental conditions.
Work package S1