Each year, crop diseases cause devastating losses in agricultural production, threatening food security and the livelihoods of millions of farmers. In the heart of Alentejo, an innovative project is harnessing 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 in wheat and olive quick decline syndrome are real scourges for farmers,” explains Rute Rego, a researcher at AlViGen. “These diseases can decimate entire harvests, leading to severe economic losses and compromising food quality.”
But AlViGen is not limited to 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 circulating in the air,” Rute continues. “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 the DNA from the spores and performs advanced genomic analyses, using powerful DNA sequencing technology based on the metabarcoding method, carried out with cutting-edge technology like the portable Nanopore sequencer.
Rute Rego, a researcher at InnovPlantProtect, analyzes samples of the fungus causing olive quick decline syndrome as part of the AlViGen project.
Unraveling the Genetic Code of Fungi
To better explain what metabarcoding is and its advantage in 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 grains - rice, beans, corn - being analyzed by the reader. “Metabarcoding is like placing a unique label (a ‘barcode’) on each type of grain. Then, you can mix all the grains in a single sample, and by reading the labels, you can identify the quantity of each type of grain present.'”
In the case of AlViGen, this technique allows for the analysis of multiple fungal species simultaneously (in multiple samples), each with its own genetic ‘barcode,’ and to ‘identify exactly which fungi are present, even in small quantities,'” the researcher explains.
And what is the practical impact of this method for monitoring and predicting disease? The AlViGen project researcher can identify, with high precision, the moment when the pathogenic agent begins to appear in the field, which makes it possible to alert farmers in real-time about the risk of disease. Producers can adopt preventative measures and apply the necessary products to avoid infection, contributing to a rapid and effective response in disease prevention.
The Timeline of Fungal Evolution
AlViGen's research is not limited to identifying the microorganisms harmful to crops; it also seeks to understand their evolution and diversity. João Bilro, another researcher on the project, is dedicated to studying the phylogeny of the Colletotrichum fungus, a microorganism responsible for causing olive anthracnose or blight, a disease that affects olive groves in Portugal. This disease mainly affects the olives, which compromises the quality of the olive oil.
“Phylogeny is crucial for understanding how the different strains of Colletotrichum Just as a family tree traces the history of a family, showing how 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 are genetically closer or more distant, and thus infer characteristics such as virulence or resistance to fungicides,” he reveals.
This knowledge allows researchers to identify patterns of dissemination and adaptation of the fungus, which is fundamental for 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.”
Left photo: João Bilro, a bioinformatician at InnovPlantProtect, studying the phylogeny of the Colletotrichum fungus within the scope of the AlViGen project; Right photo: 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 Alentejo, a region with a strong agricultural tradition. By providing farmers with early detection tools and precise information about the microorganisms that cause crop diseases, the project intends to aid in decision-making, allowing 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,” states Rute. “We believe that genomic surveillance is a key tool for the future of crop protection.”
João Bilro agrees and adds, “Continuous research is fundamental to keep up with the evolution of harmful microorganisms and to develop new, consistently effective control strategies. In the future, we hope to expand the scope of AlViGen to include other microorganisms and crops, and to 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-world problems and transform agriculture. By unraveling the genetic secrets of crop microorganisms, Rute Rego and João Bilro are paving the way for a 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.
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.
On May 13th, the project team AI4Leafhopper presented the new application iCountPests, an innovative solution that uses Artificial Intelligence (AI) to detect and count green leafhoppers in chromotropic traps - quickly, accurately and in real time.
Developed as an intuitive mobile application, the iCountPests was designed to facilitate the monitoring of various agricultural pests. With a simple and accessible interface, it allows users to record the evolution of pests in their crops by submitting photographs of the traps installed in the field.
The application uses advanced computer vision models to automatically detect and count insects, delivering results in around a minute - a much faster and more practical process than traditional manual counting.
In its first version, the app already has a model for detecting the green leafhopper (Jacobiasca lybica), achieving an average accuracy of approximately 90%. Functionalities will soon be added to identify other relevant pests, such as curl moth (Cryptoblabes gnidiella) and grape moth (Lobesia botrana).
In addition to automatic counting, the iCountPests makes it possible to monitor the evolution of pest populations over time, making it easier to identify trends and plan more effective interventions.
This project is the result of a multidisciplinary team combining skills in ecology, entomology, artificial intelligence, computer vision, remote sensing and software development, with the aim of making pest monitoring simpler, more accurate and more accessible.
During the presentation session, it was possible to hear the opinions and suggestions of future users of the application. These contributions are essential if we are to continue to improve the tool and ensure that it responds in a practical way to the real needs of farmers and technicians in the sector. We want to develop solutions that evolve with agriculture!
Innovation is at the heart of everything we do and our motto is clear: “Innovate together, protect better.”
If you want to know more about iCountPests, contact us by email: 📩 apps@iplantprotect.pt
“InnovPlantProtect (InPP) uses state-of-the-art biological and digital knowledge to work together with producers, plant protection and seed companies, research institutions and local authorities to solve the problems posed to Mediterranean agriculture by climate change, the reduced availability of active ingredients for crop protection and the emergence of new pests and diseases for which there are no prevention and combat solutions,” says Pedro Fevereiro, InPP's executive director, in a press conference. Voz do Campo magazine.
InPP is featured in the February edition of Voz do Campo magazine and its online edition, with an opinion article entitled “InnovPlantProtect: 5 years of a Collaborative Laboratory for the protection of Mediterranean crops”, which includes an “x-ray” of the 5 years of existence of the collaborative laboratory (CoLAB) carried out by InPP's executive director.
And as far as the future is concerned, Pedro Fevereiro has some clues: “We will continue to invest in the development of innovation for crop protection using biological compounds or living organisms from different sources and types, with a view to the circular economy and sustainability, adding value to products through their industrial protection and subsequent sale.”.
This Wednesday, February 7, we had the pleasure of welcoming a delegation of members of the Angolan Embassy to the InnovPlantProtect (InPP) facilities, accompanied by the Mayor of Elvas, José Rondão Almeida.
During the visit, the ambassador of the Republic of Angola, Maria de Jesus Ferreira, as well as 1st secretary Analberto Guilherme and 3rd secretary Maria da Conceição Pimenta, had the opportunity to get to know the collaborative laboratory (CoLAB), the laboratories and find out a little more about the work and the different areas of activity being explored by the five departments of CoLAB.
This was a great opportunity to identify and discuss future opportunities for new partnerships, collaborations and projects.
I would like to thank the delegation from the Angolan embassy for their visit.
InnovPlantProtect (InPP) celebrated its fifth anniversary this Wednesday, January 24th, at 2pm, in the building of the National Institute for Agricultural and Veterinary Research (INIAV) - Elvas Pole, in Elvas, with the presence of 120 guests. The commemorative event, which brought together InPP members, different representatives of the innovation ecosystem, representatives of other collaborative laboratories (CoLAB) in the agri-food sector, producer associations, farmers and policy makers, aimed to take stock of the 5 years of CoLAB activity and explore prospects for the future.
The afternoon began with the opening session, which was attended by Margarida Oliveira, chairman of the InPP Board of Directors, who warned of the need for more sustainable crop protection solutions than the current ones, reducing the negative impacts on food safety and agrosystems, adding that the new export markets have tighter certification processes, in which there is greater control, and therefore the new solutions should focus on crops that can be grown in the region, i.e. Mediterranean crops.
InPP, an initiative of the New University of Lisbon (UNL) led by the Green-it research center of the Institute of Chemical and Biological Technology (in Oeiras), in cooperation with other UNL scientific units, “is one of the 41 approved CoLABs that make up the existing CoLAB network in Portugal, and one of the 7 that is based in regions of low population density and the only one whose area of activity is the protection of agricultural crops,” said the Chairman of the Board of Directors.
The 14 members that currently make up CoLAB were also highlighted. In 2023, the Polytechnic Institute of Portalegre and Lusosem joined the 12 members that make up InPP, such as the Municipality of Elvas, universities, R&D centers, agricultural companies and producers“ associations. ”However, we intend to increase this number and include all the educational and research institutions in the Alentejo and also increase the number of associated agricultural companies," said Margarida Oliveira.
CoLAB's first five years were about “setting up the conditions, getting the project off the ground, starting to show results (...) and demonstrating credibility in the field. This is extremely important in order to move on to the next phase because you can't win competitive projects with a team that isn't recognized as having quality,” he explained.
According to the chairwoman of the Board of Directors, for the next phase “we need to find someone to promote the products that are coming out of the InPP team's work and someone to obtain contracts that will ensure InPP's viability when public funds reduce” due to the institution's coming of age.
Currently, InPP develops innovative bio-inspired and digital solutions to protect crops, develops services according to users' needs, promotes more sustainable agriculture, adaptable to climate change and in solidarity with the environment, and takes on board the European Union's environmental, climate and digital transition directives.
Margarida Oliveira ended her speech by pointing out that “maintaining a CoLAB like the InPP is something critical for the country and something we not only need, but have a duty to invest in”.
The Secretary of State for Regional Development, Isabel Ferreira, began her speech by recalling the network of collaborative laboratories, initially designed by Manuel Reitor, Portugal's former Minister of Science, Technology and Higher Education, who prioritized inland regions as places to set up CoLABs.
“Collaborative laboratories are still very young, but today we can be proud to have a network of CoLABs spread throughout the country (...) and also in different themes (...) that result from what is most important for the territory where they are located. In the case of InPP (...) it is undoubtedly today an essential driving force for the development of the Alentejo region (...) which is the interface between the Academy and the socio-economic/productive fabric, the companies,” said the Secretary of State.
Isabel Ferreira congratulated the work carried out by the entire team that makes up the InPP, “especially on issues that are so relevant to what is the country's strategy for 2030 (...), aligned with the European context and which is of enormous importance for the European Union's environmental, climate and digital transition directives”.
The InPP's “obvious” contribution to mitigating the impact of climate change on crops was also highlighted by the Secretary of State, “who knows that today [crops] face such important challenges that require increasingly focused research and an increasingly rapid response, and only by working in a network, in partnership, can this be achieved.”
When asked about the ease of attracting highly qualified human resources to the interior territories, particularly to Elvas, the Secretary of State's answer left no room for doubt: “They will never have any difficulties because the project is attractive, the job they are offering is a highly qualified, motivating job and, therefore, people come and stay. And this is a very powerful weapon for territorial cohesion and the development of the interior.”.
Isabel Ferreira ended her speech by saying that it has been a “real privilege” to witness the growth of CoLAB, which has gone through a process with different stages, from signing, recovering facilities and obtaining state-of-the-art equipment and technologies, and which has culminated in the evolution of these structures with “competence and quality”.
At 3:15 p.m., the session “What innovation is produced at InPP?” took place, in which the five department directors Cristina Azevedo, Sandra Correia, David Learmonth (three photos above, from left to right), Ricardo Ramiro and iLaria Marengo (two photos below, from left to right), presented their teams and the work they have been able to develop, as well as the new technologies, products and services that have been produced in the various areas of CoLAB's activity.
“We want to create value through the management of living organisms in the farmer's field. This is the purpose of the InPP”. These were the words chosen by InPP's executive director, Pedro Fevereiro, to kick off the closing session, which took place from 4pm.
The executive director considers the InnovPlantProtect brand to already be a recognized reference throughout the country, particularly in the agricultural sector, and emphasized the four patents already produced by CoLAB to protect crops against various diseases that affect them at regional and national level and the more than 2 million euros raised in 8 innovation and development projects that are currently active, one of which is the first CoLAB project funded by the international Horizon Europe program.
One of CoLAB's latest innovations - the InPP app store, which is in the final stages of development and will soon be available to farmers - was also highlighted. The app aims to give users access to six applications that the team has been developing.
What about the future? Pedro Fevereiro believes that if the “good pace” of innovation production and patent creation continues, and if the ability to attract contracts with companies and producers who want to see their problems solved and who turn to InPP increases, CoLAB will be able to complete the 1/3 of funding from its own revenues that is required of CoLABs.
For InPP, the executive director aims to increase interaction with the regional network through projects and partnerships, participate in the training of young people at various levels of schooling, extend the international network, ensure budgetary sustainability and guarantee jobs.
Pedro Fevereiro thanked the Minister for Territorial Cohesion for all the support and funding that her Ministry has made available to CoLAB whenever difficulties have arisen, the Municipality of Elvas, NOVA University, INIAV, the National Innovation Agency (ANI), InPP's associates and the human resources that make up the InPP team.
“InPP is about people. (...) Everything else is just talk. If we don't have these people with us, we don't have patents, we don't have InPP, we don't have anything. We owe this to them,” he concluded.
The second speaker at the closing session was Hermenegildo Rodrigues, a councillor from Elvas Municipal Council (CM), who was present on behalf of José Rondão Almeida, president of Elvas Municipal Council, and who began by highlighting the work carried out by the InPP over the last five years and identifying the “added value it brings to the municipality, the region and the world of science, and, at the same time, its proactivity with the farming and school community, both through contracts and partnerships, protocols that have raised awareness, changed habits and added knowledge”.
The Elvas city councilor continued his speech with the topic of CoLAB's internationalization, saying that “it is to the credit of all the professionals who work here, for the way they have integrated, dignified and interacted with Elvish society, and for the work they have done, and for fostering collaboration between the various players”.
The municipality's support for InPP was reinforced in the words of Hermenegildo Rodrigues: “It's up to us, the local authorities, to keep the door open, your door. We will, as always, be available to walk side by side in the search for solutions that make strategies and objectives viable. (...) From us to you, thank you very much,” he concluded.
The closing session continued with Gonçalo Rodrigues, Secretary of State for Agriculture, representing the Minister for Agriculture and Food, Maria do Céu Antunes, who highlighted the role of the country's inland regions for agricultural activity.
“This CoLAB is about bringing the countryside, which is often “ostracized and forgotten” (in the words of Hérman José, quoted by the Secretary of State), but which is actually at the heart of it all. This is where agriculture is. The urban environment, unfortunately, continues to create a gap with the rural world. But we also have to bring in this experience, bring in academia, bring in scientists, to feel the land, to feel the countryside, and then somehow produce what are the necessary tools for the development of this basic economic activity, (...) without which we wouldn't have quality, safe food on our shelves,” recalled the Secretary of State for Agriculture.
In his speech, Gonçalo Rodrigues stressed the importance of the InPP in making the agricultural sector more sustainable, innovative and competitive: “This is a demonstration of what a collaborative laboratory should be. (...) I would venture to say that few or perhaps very few have had or have the success that we find here at the InPP. It must also serve as a flagship for what is done well in our country and try to transfer this capacity to others, materializing it in our sector. This is what our agriculture needs,” he concluded.
The session ended with a speech by the Minister for Territorial Cohesion, Ana Abrunhosa, who thanked the municipality and the Alentejo Regional Coordination and Development Commission (CCDR Alentejo) for their support for the InPP, which, according to the minister, she hopes will continue to be given to this project.
For Ana Abrunhosa, “[the InPP] has helped us a lot to get across the idea that quality research can and should be done anywhere, as long as the essential conditions are met”.
“It's a benchmark project, which carries out scientific research at the highest level, attracts talent (...) from different geographical origins, some of whom have had the opportunity to return to our country after their world experience, through this project. What's very important about these projects is that they guarantee fair pay, with excellent working qualities. And if we add to all this that this project is located in this beautiful city in the countryside, (...) the quality of life is exceptional,” he said.
The Minister for Territorial Cohesion continued her speech by reiterating the government's support for CoLABs, because according to her “there is no better use for European funds than projects like this”. Government support for the CoLAB network began in 2020, with the Portugal 2020 program, and will continue until 2030, with the current Portugal 2030 program.
“We spend our lives trying to invent the wheel. This is an example [of a project, the InPP] that we can give and that we would very much like to multiply throughout the rest of our country and, above all, it's important that those who have responsibility do so,” he concluded.
From 4.45 p.m. guests gathered for a drink and to sing happy birthday to InPP with birthday cake.
The balance of the commemorative event was positive, having been able to attract the Elven community, representatives of various companies and agricultural producers, and the academic community.
After five years, InPP promotes the transfer of knowledge, reinforces its position as a CoLAB capable of fostering the development of new technologies, products and services with a strong technological and innovation component, and strengthens its commitment to promoting solutions that make a difference in tackling the various challenges of agricultural crop protection.
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