Projects / Programmes
Visualisation and interpretation of gene expression data in potato-virus interaction
| Code |
Science |
Field |
Subfield |
| 4.06.00 |
Biotechnical sciences |
Biotechnology |
|
| Code |
Science |
Field |
| T490 |
Technological sciences |
Biotechnology |
plant, potato, virus, biotic interactions, microarray, data analysis, data visualisation
Researchers (1)
| no. |
Code |
Name and surname |
Research area |
Role |
Period |
No. of publicationsNo. of publications |
| 1. |
19116 |
PhD Špela Baebler |
Biotechnology |
Head |
2007 - 2008 |
313 |
Organisations (1)
| no. |
Code |
Research organisation |
City |
Registration number |
No. of publicationsNo. of publications |
| 1. |
0105 |
National Institute of Biology |
Ljubljana |
5055784 |
13,296 |
Abstract
Understanding of the plant-pathogen interaction enables selection of efficient strategies for plant protection therefore several studies have been carried out regarding this matter. Microarrays are an efficient tool for probing plant-pathogen interactions. Nevertheless data analysis and biological interpretation can be problematic due to the huge amount of obtained data. Tools for visualization of gene expression data in the context of biological processes and metabolic pathways can improve biological interpretation of research results substantially.
In the framework of the proposed project, quality control of microarray data, its submission to public databases, following the MIAME standards, and integration of publicly available data with our experimental data will be established. Microarray data of previously performed experiments on the influence of PVYNTN virus infection on gene expression in potato will be analyzed using statistical models. Thus genes that express differentially in the time course following infection or in differentially sensitive cultivars will be identified.
MapMan tool for gene expression visualization will be conversed to visualize »TIGR potato 10k array« data. In the next stage, we will focus on the processes involved in plant response to biotic stress. Firstly, genes will be classified according to the process of involvement, then, using publicly available and our experimental data, gene expression under different experimental conditions will be compared. In this manner virus infection – specific markers will be identified and validated by real-time PCR.
Significance for science
A robust scheme of microarray data analysis was developed in the framework of the project (Rotter et al, 2008) and was used in potato as well as other transcriptomic projects.
A great deal of plant transcriptomic data is derived from a model plant, Arabidopsis thaliana. However in some cases, model plant data cannot be directly implemented in crop species. Potato is fourth most important food crop; therefore its research has important implications in agronomy. Moreover potato virus Y is the most detrimental potato viral pathogen. Adaptation of gene expression data visualisation in the context of biological pathways greatly improved transtriptomic data of the interaction.
The adaptation of visualization of potato cDNA microarrays data, published as an Open Acess paper (Rotter et al, 2007) as well as on MapMan webpage http://www.gabipd.org/projects/MapMan/ received great response in the international scientific community. In a year after its publication, the paper was cited several times and the use of mapping or new scheme of biotic stress response was reported (e.g. Reiwe et al, 2007; Uppalapati et al, 2009). Therefore, we expect that the mapping for new potato oligonucleotide arrays (Agilent POCI array) will receive same if not greater response.
Improved data analysis with efficient data interpretation enabled a thorough analysis of potato-virus interaction microarray data and its publishing in one of the top Plant Science journals (Baebler et al., 2009).
Moreover, interaction marker genes and candidate genes for functional analyses were identified as a result of the research in the framework of the postdoctoral project.
References:
Baebler Š et al (2009) PVYNTN elicits a diverse gene expression response in different potato genotypes in the first 12 h after inoculation. Mol Plant Pathol 10 (2):263-275
Riewe D et al (2008) The Potato-Specific Apyrase Is Apoplastically Localized and Has Influence on Gene Expression, Growth, and Development. Plant Physiol. 147 (3):1092-1109.
Rotter A et al (2007) Adaptation of the MapMan ontology to biotic stress responses: application in solanaceous species. Plant Methods 3 (1):10.
Rotter A et al (2008) Finding differentially expressed genes in two-channel DNA microarray datasets: how to increase reliability of data preprocessing. OMICS. 12 (3):171-182.
Uppalapati SR et al (2009) Global Gene Expression Profiling During Medicago truncatula-Phymatotrichopsis omnivora Interaction Reveals a Role for Jasmonic Acid, Ethylene, and the Flavonoid Pathway in Disease Development. MPMI 22 (1):7.
Significance for the country
Despite a high potential of microarray analysis, not only in plant science but also in microbiology, medicine and pharmacy, their use is often limited to rare research institutions. The reason lies in the complexity of microarray labelling and hybridization and especially data analysis and interpretation.
Slovenian pharmaceutical industry (especially Lek d.d.) has shown its interest in the technology by joining the Consortium for biochip preparation and analysis equipment in the framework of the Centre of Functional Genomics and Biochips.
The results of our research were directly connected in our collaboration with Lek. In the time of the duration of the projects, we had three projects, all connected with the use of microarrays in drug production and development. The results of our collaboration have therefore contributed to economical growth and competitive position of Slovenia.
The project results were presented as papers in international journals and at several international scientific meetings and therefore increased international recognition of Slovenia.
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