Scientists at the Institution of Plant Protection Biology within the Swedish University of Agricultural Sciences, have been researching into how to reduce the dependence on chemical fungicides in farming.
The goal of the researchers has been to understand plant defense mechanisms and so produce plants that are more resistant to disease, which will lessen pesticide use, and ultimately benefit the environment, and have been using Qlucore Omics Explorer to aid their research.
The research is focused on how plants defend themselves against oomycetes and fungi. Oomycetes, also known as "water molds", are a group of several hundred organisms that include some of the most devastating plant pathogens. The diseases they cause include seedling blights, damping-off, root rots, foliar blights and downy mildews. Some notable diseases are the late blight of potato, downy mildew of grape vine, sudden oak death, and root and stem rot of soybean. The team of 16 at the Institution of Plant Protection Biology have been studying biochemical components of plant defense and the interactions with pathogens and trying to identify resistance factors that can be used in future breeding for disease resistance crops, and in developing methods for induced resistance by applying non-toxic inducing agents. The goal is to reduce the dependence on chemical fungicides.
The simple potato comes under particular scrutiny. Potato late blight, caused by Phytophthora infestans, is one of the most devastating pathogens worldwide. In Swedish agriculture almost half of all fungicides are used against this pathogen. To reduce the dependence on fungicides there is a great need for novel resistance, and several projects involve work with resistance against this disease, and also breeding of potatoes. The resistance mechanisms are ilucidated by identification of proteins involved in the interaction between this oomycete and the plant (proteomics and phosphoproteomics) and by studies of the infection process with microscopical and molecular methods.
In the past, one of the major problems facing the scientists was how to handle the increasingly vast amounts of data that was being produced from their research.
"Seeing structures in the data and finding meaningful biology in them has been a problem," commented Dr Erik Alexandersson, Assistant professor at SLU Alnarp, Institution of Plant Protection Biology. "We started using Qlucore Omics Explorer in 2009 for studies in, Proteomics, Evolutionary biology, Phylogenetics and Microarray analysis. Using Qlucore Omics Explorer has overcome these failings to a large extent through its dynamic visualization tool".
By the active use of Visualisation techniques important structures and patterns can be identified quickly, with the user getting instant feedback. Qlucore Omics Explorer allows 3D modeling and the ability to change parameters quickly and easily which has speeded up the whole process of analysis, and can be done by biologists and researchers with no specialist knowledge of mathematics.
"We have used Qlucore both for gene expression and quantitative proteomics data," continued Dr Erik Alexandersson . "Some of the sampling is done in the field in order to obtain molecular data in a realistic setting as it would be out in the farm avoiding laboratory artifacts. We see clear differences in the mechanisms at play in these two settings. Qlucore has turned out to be very powerful in handling noisy data and quickly assessing underlying structures not relevant to the research question. We were recently able to "save" a noisy dataset by taking the set-up time into account and use the function "eliminate factor" in Qlucore."
In other studies Qlucore has helped the researchers to identify transcript and proteins associated to resistance against Phytopthora by comparing the expression status under various conditions of potato lines with varying levels of resistance. These candidates are currently being confirmed by genetic transformations in the laboratory as part of the SSF grant "Resistance to late blight in potato".
The discoveries being made are now being tried out in wet lab studies.