Crops such as cucumber, watermelon, squash and cantaloupe are affected by the fungi Pseudoperonospora humuli and Pseudoperonospora cubensis, both which produce the downy mildew disease. In response, bioinformatics technology is being used, for the first time, to allow to for the identification of genes of these pathogens, in order to define the ideal treatment to attack back.
With over two years of research, the purpose is to understand at a genomic level the differences between these fungi. If expressed genes are identified in a fungus but not in another, they serve as markers that will allow to apply the appropriate treatment in these crops, says Dr. Elsa Gongora Castillo, plant biotechnologist who works at North Carolina State University.
There she works in computer analysis for the study of identifying fungi that affect the plant family Cucurbitaceae (cucumber, pumpkin, cantaloupe, watermelon) in order to understand them.
"It's a bit like human disease but in plants, to understand the pathogen and its interaction with the plant allows to develop a functional cure to treat the affected plants" emphasizes the specialist in plant genomics.
The researcher explains that she seeks to define alternative systems beyond conventional fungicides to be applied in cucumber, pumpkin, cantaloupe and watermelon.
The downy mildew disease affecting these plants is caused by a fungal infection; therefore research aims to analyze their differences. First, samples of leaves from these plants are collected for in vitro cultures to isolate the fungi; then the DNA and RNA of fungi are extracted to sequence them and, through bioinformatic analysis, the researcher can determine the expression, the presence or absence of genes in the genomes of a species against each other.
"Here comes my computer analysis. With thesequences of pathogens, I identify the genes and their expression level; in other words, to study genes, I compare two of them, in this case genes from 'Pseudoperonospora cubensis' against 'Pseudoperonospora humuli', I see how many sequences there are for a given gene of P. cubensis and how many are there for the same gene P . humuli; if there is a difference in the number of sequences, we say that this gene is expressed or repressed; or if the gene is present or not in the genome " explained doctor Gongora.
Currently laboratory results obtained from computer analysis are being corroborated and the research team seeks to benefit American farmers and their crops. This analysis will provide help in creating study models with which to understand other large-scale phenomena.
"Our model can be replicated elsewhere, in Mexico for example. But I think it takes a lot of investment in science, to turn heads and, above all, a strong link between industry and science," concluded Dr. Elsa Gongora Castillo.
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