NIB

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The central theme of my research is understanding how plant cells function at the molecular level and based on that, to understand the functioning of whole organism. This requires interdisciplinary research, linking life sciences with computer sciences and mathematics. Our experimental model is the potato (Solanum tuberosum L.) and how it responds to different environmental cues. We focus mainly on potato virus Y (PVY) and the Colorado potato beetle, both of which cause significant economic damage.  Lately, we also explore the interaction of potato with its microbiota. We also study response of potato to abiotic stresses such as drought, heat, and flooding, as well as combinations of these. Our main goal is to identify the key components of plant immunity/stress responses that determine whether the outcome of an encounter will be susceptibility, disease, tolerance, or resistance. In our work, we use advanced methods such as analysis of responses over time and space (single-cell and spatial transcriptomics). We combine transcriptomic, metabolomic, hormonomic, proteomic approaches and integrate phenotypic data with various tools, such as integration with knowledge networks (skm.nib.si), which allows us to visualise metabolic and signalling pathways.

Figure 1: experimental system potato, virus PVY, Colorado potato beetle, epi/endophytes



To facilitate the interpretation of biological data, we have developed several tools:

• SKM: resource integrating knowledge on molecular interactions in plants, specifically protein–protein interactions, protein–promoter interactions, catalysis, transport, post-translational modifications, miRNA–mRNA interactions, and transport
• BoolDog: semiquantitative modelling environment
• DiNAR: allows for visualisation of multiconditional omics data
• Unitato: all annotations of the potato DM genome merged
• QuantGenius: http://quantgenius.nib.si/user/login - a tool for reliable quantification with qPCR, including Fluidigm HT qPCR
• GoMapMan: multispecies visualisation of MapMan gene function ontology

Link SKM >>	Link BoolDoG >>
Link Unitato >>	Link DiNAR >>

Link GoMapMan >>

 

potatoGEM, is a computational model of the entire metabolic system of the potato. It enables simulations of metabolic changes under different environmental conditions or during attacks by diseases and pests. With this model, it is possible to predict which enzymes and pathways are crucial for resistance or higher yield, thereby guiding the development of new, sustainably cultivated varieties.

Together, the Stress Knowledge Map and potatoGEM form a powerful research platform: the first offers a comprehensive overview of signalling pathways and interactions, while the second enables in-depth simulation of metabolic responses. Combined they allow us to understand plant responses from the moment a threat is perceived to the metabolic reaction, accelerating the development of more resistant plants and sustainable agricultural solutions.

Bleker, C., Ramšak, Ž., Bittner, A., Podpečan, V., Zagorščak, M., Wurzinger, B., Baebler, Š., Petek, M., Križnik, M., van Dieren, A., Gruber, J., Afjehi-Sadat, L., Weckwerth, W., Županič, A., Teige, M., Vothknecht, U. C., & Gruden, K. (2024). Stress knowledge map: a knowledge graph resource for systems biology analysis of plant stress responses. Plant communications, 6(100920), 1–15. https://doi.org/10.1016/j.xplc.2024.100920

Zrimec, J., Correo, S., Zagorščak, M., Petek, M., Bleker, C., Stare, K., Schuy, C., Sonnewald, S., Gruden, K., & Nikoloski, Z. (2025). Evaluating plant growth–defense trade-offs by modeling the interaction between primary and secondary metabolism. Proceedings of the National Academy of Sciences of the United States of America, 122(32, [ ] 2502160122), 1–11. https://doi.org/10.1073/pnas.2502160122

Zagorščak, M., Abdelhakim, L., Rodriguez-Granados, N. Y., Bleker, C., Blejec, A., Zrimec, J., Baebler, Š., Županič, A., Pompe Novak, M., & Gruden, K. (2025). Integration of multi-omics data and deep phenotyping provides insights into responses to single and combined abiotic stress in potato. Plant physiology, 197(4, [ ] 126), 1–42.  https://doi.org/10.1093/plphys/kiaf126

 

We discovered that plants regulate their immune response to viral infections with remarkable precision – both spatially and temporally. Using spatial transcriptomics, we could see exactly how genes in infected tissue and its immediate surroundings are expressed in characteristic patterns. Particularly important is the NADPH oxidase RBOHD, which forms a clear boundary between infected and healthy tissue and enables the correct distribution of salicylic acid to keep the virus contained.
 

 


Figure 3: 3D representation of spatial responses to viral infection

Observations of changes in chloroplast redox state revealed that during the hypersensitive response signals spread not only in the cells that die, but also in distant “signalling” cells. These signals are part of the systemic defence network that enables the plant to mount a rapid and coordinated response, with salicylic acid remaining crucial for maintaining the signalling chain.