Every year, crop diseases cause devastating losses in agricultural production, threatening the food security and livelihoods of millions of farmers. In the heart of the Alentejo, an innovative project is using the power of genomics to help combat these invisible threats. The AlViGen Project, with the participation of InnovPlantProtect researchers Rute Rego and João Bilro, is paving the way for a new era of crop surveillance and protection.
The Problem and the Solution
“Yellow rust on wheat and gafa in olive groves are real scourges for farmers,” explains Rute Rego, a researcher at AlViGen. “These diseases can wipe out entire harvests, leading to severe economic losses and compromising food quality.”
But AlViGen isn't just observing the problem. The team is using cutting-edge technology to detect and identify the strains of fungi that cause these diseases, long before the symptoms become visible.
“We use traps to collect spores that circulate in the air,” continues Rute. “These traps allow us to monitor the presence of fungi in real time, which gives us an important advantage in preventing infections.”
But the magic happens in the laboratory, where the team extracts DNA from the spores and carries out advanced genomic analysis using powerful DNA sequencing technology based on the metabarcoding, The Nanopore portable sequencer is a state-of-the-art technology.
Rute Rego, InnovPlantProtect researcher, analyzes samples of the fungus that causes gafa, as part of the AlViGen project.
Unlocking the genetic code of fungi
To explain more about metabarcoding and its advantage for detecting the presence of species or strains of fungi that cause diseases in crops, the researcher gives the example of a bag full of different types of grain: rice, beans, corn, which is being analyzed by the reader. “Metabarcoding is like putting a unique label (a ‘barcode’) on each type of grain. You can then mix all the grains into a single sample and, by reading the labels, you can identify the amount of each type of grain present.”
In the case of AlViGen, this technique makes it possible to analyze multiple species of fungi at the same time (in multiple samples), each with its own genetic ‘barcode’ and “identify exactly which fungi are present, even in small quantities”, explains the researcher.
And what is the practical impact of this method for monitoring and predicting the disease? The researcher of the AlViGen project is able to identify, with high precision, the moment when the pathogen begins to appear in the field, which makes it possible to alert farmers in real time to the risk of the disease. Producers can adopt preventive measures and apply the necessary products to avoid infection, contributing to a rapid and effective response to disease prevention.
The Timeline of Fungal Evolution
AlViGen's research is not limited to identifying microorganisms that damage crops; it also seeks to understand their evolution and diversity. João Bilro, another researcher on the project, is studying the phylogeny of the fungus Colletotrichum, This is a microorganism responsible for causing gafa or anthracnose, a disease that affects olive groves in Portugal. This disease mainly affects the olives, which compromises the quality of the oil.
“Phylogeny is crucial to understanding how the different strains of Colletotrichum are related and how they have evolved over time,” explains João. “Just as a family tree traces the history of a family, showing how the members are related to each other, phylogenetic trees reveal the evolutionary relationships between the different strains of this fungus. Each branch of the tree represents an evolutionary lineage, and the nodes indicate common ancestors. By comparing the DNA sequences of these strains, we can reconstruct their evolutionary history, identifying which ones are closer or more genetically distant, and thus infer characteristics such as virulence or resistance to fungicides,” he reveals.
This knowledge allows researchers to identify patterns of spread and adaptation of the fungus, which is fundamental to developing more effective strategies to contain and/or reduce the damage this fungus causes to Portuguese olive groves.
“One of the challenges of our research is the great genetic diversity of the Colletotrichum,” admits João. “However, by uncovering their evolutionary secrets, we are paving the way for the development of more precise and targeted detection and control methods.”
Photo from left: João Bilro, InnovPlantProtect bioinformatician, studying the phylogeny of the fungus Colletotrichum as part of the AlViGen project; Photo right: Rute Rego and João Bilro discuss ideas about the AlViGen project
The Future of Agriculture Starts Here
The AlViGen Project aims to have a significant impact on the agricultural landscape, especially in the Alentejo, a region with a strong agricultural tradition. By providing farmers with early detection tools and accurate information on the microorganisms that cause crop diseases, the project aims to help with decision-making, enabling farmers to protect their crops and reduce production losses.
“Our ultimate goal is to empower farmers with the knowledge and tools they need to protect their crops sustainably,” says Rute. “We believe that genomic surveillance is a key tool for the future of crop protection.”
João Bilro agrees and adds: “Continuous research is essential to monitor the evolution of harmful microorganisms and develop new control strategies that are always effective. In the future, we hope to expand the scope of AlViGen to include other microorganisms and crops, and make genomic surveillance an accessible tool for all farmers.”
Science at the Service of Agriculture
The AlViGen Project, supported by the Promove Program of the “la Caixa” Foundation, in partnership with Banco BPI and the Foundation for Science and Technology (FCT), is an inspiring example of how science and technology can be applied to solve real problems and transform agriculture. By unlocking the genetic secrets of crop microorganisms, Rute Rego and João Bilro are paving the way for safer, more sustainable and resilient agriculture.
The fight against crop diseases continues, but with AlViGen, farmers can finally see the enemy before it becomes visible.
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