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Projects / Programmes source: ARIS

FUNCTIONAL GENOMICS OF POTATO – PVY INTERACTION

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Research activity

Code Science Field Subfield
1.03.04  Natural sciences and mathematics  Biology  Plant physiology 

Code Science Field
B310  Biomedical sciences  Physiology of vascular plants 

Code Science Field
1.06  Natural Sciences  Biological sciences 
Keywords
potato, Solanum tuberosum, potato virus Y, plant transformation, small RNAs, bioinformatics, plant defense, functional analysis
Evaluation (rules)
source: COBISS
Citations Citations for bibliographic records in COBIB.SI that are linked to records in citation databases
source: WoS source: Scopus source: COBISS
Researchers (18)
no. Code Name and surname Research area Role Period No. of publications
1.  19116  PhD Špela Baebler  Biotechnology  Researcher  2011 - 2014  302 
2.  14360  PhD Mojca Benčina  Biotechnology  Researcher  2011 - 2014  382 
3.  34130  PhD Anna Coll Rius  Biochemistry and molecular biology  Researcher  2012 - 2014  150 
4.  16324  PhD Janez Demšar  Computer science and informatics  Researcher  2011 - 2014  340 
5.  19994  MSc Tina Demšar  Biotechnology  Researcher  2011 - 2014  168 
6.  29616  PhD David Dobnik  Biotechnology  Researcher  2011 - 2014  284 
7.  12688  PhD Kristina Gruden  Biotechnology  Researcher  2011 - 2014  957 
8.  06628  PhD Roman Jerala  Biochemistry and molecular biology  Researcher  2011 - 2014  1,155 
9.  33225  PhD Ana Lazar  Plant production  Junior researcher  2011 - 2014  29 
10.  19119  PhD Mojca Milavec  Biotechnology  Researcher  2011 - 2014  291 
11.  29178  PhD Dany Morisset  Biotechnology  Researcher  2011 - 2013  121 
12.  36139  Adviti Naik  Computer science and informatics  Researcher  2013  0 
13.  17280  Darija Oven    Technical associate  2011 - 2014  4 
14.  31175  Gregor Rot  Computer science and informatics  Researcher  2011 - 2013  45 
15.  24821  Dejan Štebih  Biochemistry and molecular biology  Researcher  2011  147 
16.  30142  PhD Marko Toplak  Computer science and informatics  Researcher  2011 - 2014  27 
17.  12536  PhD Blaž Zupan  Computer science and informatics  Researcher  2011 - 2014  524 
18.  03765  PhD Jana Žel  Biotechnology  Head  2011 - 2014  613 
Organisations (3)
no. Code Research organisation City Registration number No. of publications
1.  0104  National Institute of Chemistry  Ljubljana  5051592000  21,015 
2.  0105  National Institute of Biology  Ljubljana  5055784  13,114 
3.  1539  University of Ljubljana, Faculty of Computer and Information Science  Ljubljana  1627023  14,821 
Abstract
In nature plants must face numerous environmental factors, including attacks of viruses, bacteria, fungi and other pathogens. Understanding of the plant-pathogen interaction enables selection of efficient strategies for plant protection therefore several studies have been carried out in this direction, most of them in model plant Arabidopsis thaliana. Potato virus YNTN (PVYNTN), causing tuber ring necrosis disease of potato (Solanum tuberosum), 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. Although it has been shown that different potato cultivars are differentially susceptible to the virus, the mechanisms underlying this difference has not been explicitly explained. Our previous research was aimed to find differences in gene expression between differentially sensitive cultivars response to PVY attack. Several genes that might be involved in resistance were identified. These are part of carbohydrates and secondary metabolism, signalization and degradation of proteins and cell wall components. In the framework of our proposed project first goal will be to apply functional genomics approach to get the novel informations on the roles of selected genes in defence response of potato plants following PVYNTN infection. Stable or transient transformation of differently sensitive potato cultivars will be used to silence the expression of the selected genes or over-expressing them. Genes or promoters fused to fluorescent reporter will be used for following host spatio-temporal gene expression. Besides newly transformed plants the experiments will also include pre-existing mutants and/or transformants with changes of the selected genes, which were yet not validated in virus interactions. Part of the project will focus on development of high-throughput transient transformation approaches, which would enable faster evaluation of wider sets of genes in the potato-virus interaction. Second goal of the project will be to address the topic of potato – PVY interaction from the perspective of small RNAs (sRNA). The presence of individual sRNAs will be determined by high-throughput cloning, next generation sequencing approaches and with other appropriate techniques. Specialized data analysis tools for the identification, annotation and quantification of novel sRNA sequences will be developed and additionally several bioinformatics tools already developed will be used. We will integrate the knowledge already available together with all data obtained from new experiments. For better interpretation and evaluation of integrated results, different visualization approaches (e.g. MapMan, SolCyc) will be used. A complex and systemic approach will enable us to achieve the ultimate goal of deeper insight in the knowledge of potato-virus interaction and resistance responses between an important crop plant and its significant pathogen. Moreover, results of the project will give us the basis for identification of possible strategies for plant protection needed to breed virus resistant potato plants. Understanding of interaction will be potentially transferrable to other agriculturally important plants and will support novel strategies for protection of plants against pathogens. Project is very interdisciplinary, partners being three Slovenian institutions and three international ones with different fields of knowledge.
Significance for science
Functional analyses of genes involved in the interaction of plants and their pathogens have been so far mostly performed in the model plant Arabidopsis thaliana. The results of these studies, however, cannot be directly transferred to the crops. Potato is the world's fourth most important crop used for food, thus the research of this kind is essential. On top of it, the interactions of plants and viruses are the least known among all the interactions of plants and pathogens. The results of the functional analyses of genes involved in the interaction of potato-virus, which were obtained in this project, will have a significant impact on the international understanding of the interactions between plants and pests. The results will also facilitate in identification of possible strategies for plant protection, important for breeding of virus-resistant potato plants and potentially even other important crops. The knowledge of the interaction was taken to a new level of understanding with inclusion of studies of small RNAs. In this way, the research was taken to a new level, increasing the range of options to improve agronomically important properties of potatoes. The acquired knowledge will be important in other areas, such as the production of proteins in plants. This is a new rapidly growing area, as more and more complex proteins are produced in plants. Knowledge gained in the project helped to apply for a patent for an improved production of proteins in plants. Manufacturers of heterologous proteins in plants thus got the opportunity to improve production systems, while this knowledge can also be the basis for possible new improvements. Overall, the results of the project lead to important discoveries, new knowledge, and high-quality publications in scientific journals and patent, with which we undoubtedly contributed to the development of science, as well as the potential practical applications.
Significance for the country
Within the project we have cooperated with many European institutions from Slovenia and abroad (Faculty of Computer and Information Science, University of Ljubljana (Slovenia), Institute of Chemistry (Slovenia), Leibniz Institute of Plant Biochemistry (Germany), Institute of Biochemistry and Biophysics (Poland) Wageningen University and Research Centre (Netherlands)). Participation in this project has strengthened the position of Slovenian institutes and also increased the possibilities for future cooperation within the framework of the European projects. Furthermore, the results of the project were presented at various international meetings and in the form of scientific publications and patents, which helped to promote Slovenian science. The acquired knowledge has been and will continue to be presented to the general public through publications in newspapers, popular magazines and through lectures. Within the project two young researchers were educated. The acquired knowledge was and will be passed on to undergraduate and graduate students through lectures and practical work with graduates and masters graduates. New knowledge will also improve the quality of the lectures, which are held at various universities by the members of the Department of Biotechnology and Systems Biology. Also important are the newly established approaches for studies of functional analysis of genes by transformation systems and also by analysis of small RNAs. Based on the acquired knowledge also other topics relevant to the Slovenia can be examined. Knowledge gained in the field of transgenic plants is also important for risk assessment applications for work and marketing of genetically modified organisms (GMOs). Some members of the project group (Žel, Gruden) are also members of the Scientific Committees related to GMOs in the Ministry of the Environment and Spatial Planning. National Institute of Biology is also the National Reference Laboratory for GMO detection. Even with this diagnostic work, the basic knowledge of GMOs, to which also helped this project, is important.
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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