Projects / Programmes
Metabolome analysis of the potato infected with mild and aggressive Potato virus Y isolates for better understanding of the disease
| Code |
Science |
Field |
Subfield |
| 1.03.04 |
Natural sciences and mathematics |
Biology |
Plant physiology |
| Code |
Science |
Field |
| B191 |
Biomedical sciences |
Plant biochemistry |
| Code |
Science |
Field |
| 1.06 |
Natural Sciences |
Biological sciences |
Solanum tuberosum; potato virus Y-NTN; plant – pathogen interaction; metabolomics; transcriptomics
Researchers (1)
| no. |
Code |
Name and surname |
Research area |
Role |
Period |
No. of publicationsNo. of publications |
| 1. |
25523 |
PhD Polona Kogovšek |
Biology |
Head |
2011 - 2013 |
216 |
Organisations (1)
Abstract
Potato (Solanum tuberosum) is one of the most important species in Slovenia and in the world. However, potato growing and producing is facing with new challenges. Potato diseases represent a major problem in the production of both seed and edible potato. Great impact on potato production and its quality has Potato virus Y (PVY), which can reduce up to 100-percent crop yields. PVY isolate, PVYNTN, is causing extremely severe symptoms in susceptible potato cultivars. On potato tubers it causes the formation of necrotic rings. However, some PVY isolates, as PVYN, do not cause such devastating effects on crops.
Understanding of the plant response to virus infection and the course of symptom development is extremely important in the breeding of new resistant potato cultivars. Only by knowing the metabolic pathways that lead to disease development, we will be able to grow planting material, which will provide an abundant and healthy crops. Response of the potato plant to infection with the virus PVY has already been studied in transcriptomic level. However, data on the modified gene expression is not sufficient for reliable interpretation of changes in plant cell. To supplement the gap between transcriptomic and final state of metabolites in the cell, a potato metabolome analysis is required. Metabolomics is recognized as a technology that offers the widest and non-targeted access to the rich variety of small molecules found in plants.
Within the proposed postdoctoral project we will analyse the metabolom of the potato after infection with two differently aggressive PVY isolates using GC-MS/MS. By analyzing the metabolom we will make a step closer to the understanding of the plant response to each virus isolate and the symptom development. At the same time we will analyze healthy potato plant metabolom, which will contribute to better knowledge of plant metabolites. For now, only a small proportion of metabolites is known, but it is estimated to be between 100.000 and 200.000 metabolites in plant kingdom (Hall, 2006).
Furthermore, we will examin the expression of genes that encode key enzymes in the metabolism of metabolites, which will prove important in plant response to infection. Integrating the results of different omics approaches is one of the tasks of systems biology, thus giving a comprehensive insight into the plant metabolism. By combining the results of the transcriptomics and metabolomics we will also critically evaluate our previous results of the transcriptomics and facilitate their interpretation.
The results of the two levels of study will be statistically evaluated and visualized in the program MapMan. In this way we will be able to observe the lists of metabolites and genes, of which amount will be significantly changes, within the schemes representing metabolic pathways. If necessary, we will improve and adapt the program for the analysis and presentation of our biological system. With the creation of schemes of individual metabolic pathways, which are the basic building blocks of the entire metabolic network of plants, will contribute to the understanding of the general metabolism of plants, not only changes in metabolism after viral infection. Metabolomics and transcriptomics results will be integrated in a public database.
We expect that the findings of our research will fill the gaps in understanding the interactions between plant and pathogens. We also expect that our results will contribute significantly to a better understanding of plant metabolism and indirectly influenced the development of biotechnological applications.
Significance for science
Understanding of the interactions between plant and pathogens got to a new extension, since the metabolom changes in plants after infection are at least surveyed, yet highly significant level of interaction between plant and pathogens. In the last two decades there has been considerable knowledge gained on the changes in transcriptomic and proteomic level in plants after infection, contributing to a better understanding of the mechanism of interaction between plant and pathogens. However, knowledge about changes in the level of gene expression and protein synthesis does not explain fully the final state in the plant cell, as the quantity of metabolites is not necessarily proportional to the level of gene expression and protein quantity. By analyzing the metabolom we significantly contributed to filling the gaps in knowledge about the interaction between plant and pathogens. Metabolomic results were upgraded by analysis of the expression of genes for key enzymes by real-time PCR. In this way, we also evaluated the correlation between gene expression and its final product. The latter is of great importance for the biological interpretation of the results, which still represents a major challenge for the researchers. We assume that the findings of our research significantly contributed to the understanding of interactions between plant and pathogens and will in future influence the development of biotechnological applications. Metabolomic results were used in the formulation of schemes for individual metabolic pathways, which will form the basic building blocks for the entire metabolic network of plants. The latter will contribute to the understanding of the general metabolism of plants, not only changes in metabolism after viral infection. At the same time we established an experimental system that covers all steps of the analysis; from the material preparation, through the realization of laboratory work, to data analysis, visualization and data integration. The system is easily transferable to other combinations of plants and pathogens, and application of an existing experimental system allows us and other researchers to facilitate the planning and realisation of the experiments.
Significance for the country
Regarding the production, the potato is the world's fourth major crops intended for food, after rice, wheat and maize (http://faostat.fao.org/). In 2008, several international organizations emphasized the importance of potato for the global food production, since it is exceptional in that their production is cheap and plentiful and that it is capable to grow at very different climates and locations. Therefore, the United Nations has proclaimed year 2008 as international year of the potato and stress the importance of potato for developing countries (http://www.potato2008.org/en/world/index.html). Research of the potato - PVYNTN virus interaction has a major socio-economic importance for Slovenia, Europe and world. In the last decade of the twentieth century PVYNTN virus epidemically spread across Europe and world. Scientists report of PTNRD disease outbreaks also in North America, Asia and Africa. Moreover, new and more aggressive PVY virus isolates are emerging which additionally hinder production of a healthy crop. Potato growers grow more resistant varieties, which are very few. Knowledge of the disease and the response of plants to PVY infection will contribute to more effective breeding of new resistant varieties. The most effective protection against epidemic diseases, in addition to cultivation of resistant cultivars, is application of insecticides to suppress leaf aphids that transmit the virus. Knowledge of the disease will also contribute to a more rational and economically efficient farming and to reduction of the use of expensive and also environmentally harmful plant protection products. One of the possibilities is use of endophytic bacteria and/or fungi, which can protect plants against pathogenic microorganisms and in meantime offer better use of minerals and other nutrients.
Most important scientific results
Annual report
2011,
2012,
final report,
complete report on dLib.si
Most important socioeconomically and culturally relevant results
Annual report
2011,
2012,
final report,
complete report on dLib.si
