Projects / Programmes source: ARIS

Growth and defense trade-offs in multitrophic interaction between potato and its two major pests

Research activity

Code Science Field Subfield
4.06.05  Biotechnical sciences  Biotechnology  Plant biotechnology 

Code Science Field
T490  Technological sciences  Biotechnology 

Code Science Field
1.06  Natural Sciences  Biological sciences 
potato, Solanum tuberosum, potato virus Y, Colorado potato beetle, Leptinotarsa decemlineata, multitrophic interactions, omic technologies, bioinformatics, plant defense, insect adaptation
Evaluation (rules)
source: COBISS
Researchers (20)
no. Code Name and surname Research area Role Period No. of publicationsNo. of publications
1.  19116  PhD Špela Baebler  Biotechnology  Researcher  2011 - 2014  313 
2.  06989  PhD Andrej Blejec  Mathematics  Researcher  2011 - 2014  287 
3.  34130  PhD Anna Coll Rius  Biochemistry and molecular biology  Researcher  2012 - 2014  163 
4.  23399  PhD Tomaž Curk  Computer science and informatics  Researcher  2014  253 
5.  12688  PhD Kristina Gruden  Biotechnology  Head  2011 - 2014  985 
6.  28291  PhD Petra Kralj Novak  Computer science and informatics  Researcher  2011 - 2014  130 
7.  08949  PhD Nada Lavrač  Computer science and informatics  Researcher  2011 - 2014  867 
8.  03323  PhD Igor Mozetič  Computer science and informatics  Researcher  2011 - 2014  184 
9.  29617  PhD Marko Petek  Biotechnology  Researcher  2011 - 2014  168 
10.  18467  PhD Maruša Pompe Novak  Biotechnology  Researcher  2011 - 2014  291 
11.  05229  PhD Maja Ravnikar  Biotechnology  Researcher  2011 - 2014  1,369 
12.  31175  Gregor Rot  Computer science and informatics  Researcher  2011 - 2013  45 
13.  27503  PhD Ana Rotter  Biotechnology  Researcher  2011 - 2014  328 
14.  32253  PhD Borut Sluban  Computer science and informatics  Researcher  2011 - 2014  41 
15.  29635  Katja Stare  Biology  Researcher  2011 - 2013  86 
16.  32092  PhD Tjaša Stare  Biochemistry and molecular biology  Junior researcher  2011 - 2014  69 
17.  30142  PhD Marko Toplak  Computer science and informatics  Researcher  2011 - 2014  27 
18.  34129  Neža Turnšek    Technical associate  2012 - 2013  35 
19.  12536  PhD Blaž Zupan  Computer science and informatics  Researcher  2011 - 2014  531 
20.  03765  PhD Jana Žel  Biotechnology  Researcher  2011 - 2014  619 
Organisations (3)
no. Code Research organisation City Registration number No. of publicationsNo. of publications
1.  0105  National Institute of Biology  Ljubljana  5055784  13,236 
2.  0106  Jožef Stefan Institute  Ljubljana  5051606000  90,590 
3.  1539  University of Ljubljana, Faculty of Computer and Information Science  Ljubljana  1627023  16,224 
Plant pathogens and pests are the cause of substantial crop yield loss throughout the world. Damage caused by pests is estimated to be app. 100 billions USD per year despite the intensive use of pesticides. Understanding the principles of plant-pathogen and plant-herbivore interactions is necessary for establishment of effective systems for plant protection. Substantial knowledge has been gathered during past decades on the mechanisms of attack/defence in one-to-one interaction studies in lab conditions. In the field, however, plants are not exposed to one type of stress only. Normally plants have to face a combination of different stresses, like drought and several types of pathogens and pests in parallel. Newly emerging tools in molecular biology and functional genomics now enable higher analytical throughput and thus more complex and realistic experimental setups. Within the proposed project we would like to investigate a system of tritrophic interaction of potato with viral pathogen and insect pest. Potato virus YNTN (PVYNTN), causing tuber ring necrosis disease of potato (Solanum tuberosum L.), is spread all over Europe, North America and even in some parts of Asia. Since it is causing symptoms on plantlets as well as on tubers, it diminishes the crop yield and significantly lowers its quality. On the other hand, Colorado potato beetle is a major pest of potato in Europe and North America. Potato plants will be first exposed to infection with virus PVY and subsequently to larvae of Colorado potato beetle and, in parallel, to individual pathogen/pest only. Besides wild type potato plants, selected transgenic lines with perturbed major signalling pathways or with modified activitiy of critical defence components will be included. Potato plants will be allowed to communicate via volatiles emission in this experimental setup. Ongoing processes in both direct interaction tissues (potato leaves and larval guts), will be studied on different levels using state of the art methodological approaches. Gene expression will be measured using next generation sequencing approach and DNA microarrays while for more detailed studies and confirmatiory analysis quantitative PCR will be applied. The knowledge obtained on the transcriptome level will be complemented with proteomics experiments. 2D-PAGE system is already set for both analysis of potato leaves and beetle guts in our laboratory, which we will complement with target oriented mass spectroscopy based approach Multiple Selection Monitoring. With the first draft of the potato genome available and substantial sequence information available at the cDNA level we will try different approaches for shot-gun proteomics of potato leaves. 2D-nanochromatography of different preparations of leaf protein extract will be combined with tandem mass spectroscopy to provide us both with qualitative sequence data and with the information on protein quantity. The emission of volatile organic compounds is an important signal in indirect plant defence to attract predators or parasitoids of feeding herbivores. Furthermore, data will be integrated with public knowledge using bioinformatics tools to prepare improved models/hypothesis on the studied system. Knowledge of plant-pathogen/pest interactions will be, through the results of this study brought into new perspective, as multitrophic interaction systems are ecologically more relevant. Potential paradigm shift in further research within this area and development of potential biotechnological applications is thus expected.
Significance for science
Substantial knowledge has been gathered during past decades on the mechanisms underlying plant-pathogen and plant-pest interactions in one-to-one interaction studies in lab conditions. In the field, however, plants are not exposed to one type of stress only. Normally plants have to face a combination of different stresses, like drought and several types of pathogens and pests in parallel. We have indeed shown that combined action of different stressors cannot be predicted from single one-to-one stressor studies. Within this project we have thus paved the way for relevant agrobiotech research for other crop species also, at the same time promoting the understanding of the complex interaction network of a single cell, in whole plant tissue or among different species of the ecosystem. Such complex studies can however only be performed with the advance of molecular biology and bioinformatics methodologies linked with a systems biology approach. Due to the high interconnectedness between components of the chosen system (cell, plant, ecosystem), it is increasingly obvious that a stand-alone approach will not bring satisfactory results for the goals of system understanding. Therefore a number of tools and applications were developed, that support analysis and consequent integration of experimental data. For example, a de-novo workflow for quantitative analysis of GC-MS data in potato was developed. The cutting edge methodology for integration of multilevel omics data and prior knowedge using semantic knowledge discovery approaches (Segmine and Biomine) will be relevant and beneficial also in other areas of biotech and medical research. And finally, GoMapMan application is of great interest for plant science community in general as already shown by numerous accessions, contributions to manual annotations and its registry in Elixir Tools and Data Services Registry (https://elixir-registry.cbs.dtu.dk/#/) and in Ontologies BioPortal (http://bioportal.bioontology.org/).
Significance for the country
Efficiency of crop production is in Slovenia in stagnation if not even decreasing. As a result Slovenia is performing worst in terms of food self-sustainability among EU countries. In Slovenia potato production represents the second most important segment of agriculture, right after the cereals. The yields and quality of production in Slovenia is however not reaching the levels typical for Western Europe. Potato production is extremely susceptible to stress thus breeding of stress resilient varieties based on our novel knowledge would be really beneficial for Slovenian as well as European agriculture. An additional aspect of the proposed research is development of new technologies for unrevealing complex biological pathways. The methodological principles established within the project can be easily adapted to investigations of other biological systems, for example the ones important for interested industrial partners in pharmacy or biotech. Such transfer of knowledge has been proven very successful in previous year when the project team was successfully solving problems in pharmaceutical industry. To ensure better flow of information we have organised a workshop on importance of systems biology in society. The workshop was very successful with more than 100 participants including different profile from students, high school teachers to researchers from biotech industry and researchers in social sciences. The project engaged also several PhD students from all three Slovenian participants building their research scientific profiles. As planned the collaboration with our international partners was enhanced through short time exchange of early stage researchers. This also ensured easy transfer of knowledge between the groups. These project activities were enhanced as the project was incorporated into several COST actions, most intensively in FA0804 ‘Plant virus control employing RNA-based vaccines: A novel non-transgenic strategy’, BM1006 ‘Next Generation Sequencing Data Analysis Network’ in FA 1106 ‘An integrated systems approach to determine the developmental mechanisms controlling fleshy fruit quality in tomato and grapevine’. We were additionally tightly involved also in the setup of European infrastructure for systems biology ISBE. Results of the project were published in high ranking peer-reviewed scientific publications and at several international conferences which increases recognition of Slovenian research excellence worldwide. Additionally, for more general audience, a workshop on systems biology and its application was organised by NIB, targeting industrial partners, high school teachers and undergraduate students as well as members of several ministries and researchers engaged in other scientific fields.
Most important scientific results Annual report 2011, 2012, 2013, final report, complete report on dLib.si
Most important socioeconomically and culturally relevant results Annual report 2011, 2012, 2013, final report, complete report on dLib.si
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