Chilean plant pathology is experiencing a particularly intense period, with agriculture under pressure from climate change, emerging diseases, and a strong need for collaboration among scientists, businesses, and the public sector. In Chile, studying plant diseases is no longer just the domain of agronomists: today, traditional field techniques are combined with molecular tools, web platforms, and artificial intelligence to better understand what is happening in crops.
In this context, key players such as the Chilean Society of Phytopathology (SOCHIFIT) and the Chilean Collection of Microbial Genetic Resources (CChRGM) of INIA are driving the development of the discipline from various angles: scientific conferences, historical databases, public collections of phytopathogenic strains, and a collaborative network that strives to anticipate problems in the field. All of this constitutes a Chilean phytopathological ecosystem that, although small and highly specialized, is crucial for the sustainability of the forestry and agricultural sector.
Phytopathology in Chile: a field that has modernized at full speed
In recent decades, Chilean phytopathology has undergone a tremendous technological leap . What was once resolved primarily through field observation, microscopy, and classical biological methods now relies systematically on genomics, DNA analysis, and digital tools that allow for the tracking, comparison, and classification of information on a massive scale. This transition has not been merely a change of "laboratory toys," but a genuine transformation in the way science is conducted.
As evidenced at the congresses of the Chilean Society of Phytopathology (SOCHIFIT), the scientific community has moved from working with slower and less sensitive identification methods to a scenario where it is possible to detect minute quantities of a pathogen's genetic material in a plant sample. This ability to locate "even the smallest DNA molecule" has significantly increased the accuracy of disease detection and has made it possible to address phytosanitary problems that were previously vague or poorly characterized.
This modernization is also reflected in how information generated by Chilean researchers themselves is organized and analyzed. A prime example is the work led by Nicolás Quiroga, president of SOCHIFIT , who spearheaded a comprehensive taxonomic and scientific classification of the abstracts presented at one of the Society's congresses. Building on this initial effort, an artificial intelligence was trained to replicate the classification process for all congresses held over the past 30 years.
Thanks to this project, a platform was created to consult a historical database that allows users to search for papers by pathogen, crop, region, or other relevant categories. The system identifies presentations associated with the search and facilitates access to the abstracts. For the Chilean phytopathology community, this tool represents a kind of living record of three decades of research, where trends, shifts in focus, and the evolution of health problems in Chilean agriculture can be detected.
SOCHIFIT: a small society, but very connected to the countryside
SOCHIFIT has established itself as the leading scientific organization in Chilean phytopathology, serving as a meeting place for researchers, students, and industry professionals. Despite its relatively small membership, its influence is significant because it brings together a large number of specialists working on plant diseases in Chile.
One of SOCHIFIT's defining characteristics is its strong collaborative nature. As its president emphasizes, the willingness to share data, experiences, and results is practically a hallmark of the organization: when faced with phytosanitary problems affecting many producers simultaneously, keeping the information to oneself doesn't make much sense. On the contrary, sharing it allows for faster progress in developing practical solutions for the sector.
This collaborative approach is also reflected in the relationship with the agricultural industry and the agronomic advisor in plant health . SOCHIFIT encourages companies to openly present their problems to the scientific community, so that laboratories and universities can incorporate these real needs into their lines of work.
This collaborative approach is also reflected in the relationship with the agricultural industry. SOCHIFIT encourages companies to openly discuss their problems with the scientific community, so that laboratories and universities can incorporate these real needs into their work. The idea is that academia should not remain isolated, but rather become part of the production system, providing concrete solutions to the country's phytosanitary challenges.
In recent congresses, this connection has resulted in high attendance and a diverse range of participants . The last three editions have exceeded 200 attendees, with approximately 30% being students, underscoring the Society's educational role. Furthermore, SOCHIFIT publicly recognizes the work of its members through the "SOCHIFIT Spirit" award and the SOCHIFIT Lifetime Achievement Award, reinforcing the culture of community and recognition of individual contributions.
Society has also been progressively opening up to professions beyond agronomy . Although its roots are agronomic, the incorporation of molecular techniques and advanced analysis has necessitated the participation of biochemists, biotechnologists, biologists, engineers, and other technical professionals. This mix of disciplines enriches the types of studies conducted and expands the range of tools available to address phytopathological problems.
Cutting-edge technology and academic inbreeding: lights and shadows
The modernization of Chilean phytopathology is not without its nuances. On the one hand, technological advancements have enabled a profound renewal in the way science is conducted , with the massive use of genomic data, web platforms, and information systems that facilitate large-scale analysis. On the other hand, the very structure of the scientific community generates particular internal dynamics, such as what is known as academic inbreeding.
In very specific areas of phytopathology, such as the study of wood-decay fungi , the number of active research groups in Chile is small: in some cases, there are only two or three teams at most. This naturally leads them to cite each other in their publications and conference papers. This is not so much a scientific vice as a direct consequence of the size of the community, which concentrates knowledge in a few specialized centers.
In parallel, two major approaches coexist within phytopathological practice in Chile : the more traditional approach, based on direct observation of symptoms, pathogenicity tests, and field management, and the molecular approach, which focuses on the study of DNA, mutations, and pathogen resistance mechanisms. Far from competing for prominence, both approaches complement each other. Molecular work may not offer immediate solutions to an urgent field problem, but it provides long-term insights, for example, into why a fungicide has become ineffective due to a mutation in the target fungus.
This combination of perspectives makes it possible to address long-standing problems with modern techniques . Diseases that have affected a specific crop for years can now be reinterpreted thanks to DNA sequencing, comparative genomics, and bioinformatics. In this way, processes that were previously only partially explained can be described in greater detail, opening the door to developing more refined and specific management strategies.
At the same time, the discipline has been forced to adapt to an extremely changing agricultural environment, where markets and the expansion of certain crops end up shaping much of the research agenda. This was clearly seen in the case of kiwifruit, when its expansion in Chile was accompanied by a notable increase in scientific studies on its diseases, and it was repeated with cherryfruit from the 2010s onwards, as its planted area grew and new phytopathological problems emerged.
Climate change and crop migration: a scenario of emerging diseases
The global forestry and agricultural sector faces enormous challenges in meeting the growing demand for food , while governments try to mitigate the effects of climate change. Chile is no exception: rising temperatures, altered rainfall patterns, and extreme weather events are forcing many commercial crops to relocate south in search of more favorable conditions.
This shift in the agricultural frontier has had a clear consequence: the emergence of new plant diseases in areas where they were previously absent. New pathogens find suitable hosts in newly cultivated areas, or pathogens already present are expressed more strongly due to the stress associated with climate change. The result is a constantly reshaping plant health map, much more dynamic and difficult to predict.
By the end of 2024, more than 323 causal agents of diseases in commercial crops had been identified in Chile . The vast majority are fungi (around 90%), followed by oomycetes (8%) and bacteria (2%). Between 2013 and 2023, more than 60 first reports of diseases were documented in key fruit crops for the country, such as cherry, blueberry, hazelnut, grape, walnut, and avocado. These crops together represent more than 60% of the national fruit-growing area, which gives an idea of the magnitude of the challenge.
These figures highlight that emerging diseases have become a growing problem for Chilean agriculture. This is compounded by the intensified use of agrochemicals, which not only generates resistance pressures in pathogens but also has negative impacts on ecosystems, biodiversity, and soil health . In this scenario, it is not enough for agriculture to adapt; scientific research must also keep pace, developing more refined detection methods and integrated management strategies that reduce dependence on short-term chemical solutions.
The combination of climate change, crop shifts, and intensive input use has made crop health planning in Chile much more complex . Researchers no longer work solely with the historical problems of each region, but must anticipate those that might arise as environmental conditions and production systems change. This requires continuous monitoring, effective monitoring networks, and a fluid flow of information between the field and the laboratory.
The strategic importance of conserving and sharing phytopathogenic strains
To respond scientifically to the challenges described, it is critical to have correctly isolated, identified, and preserved phytopathogenic microorganisms . Without reliable access to the strains that cause diseases, it is impossible to validate diagnostic methods, evaluate new biocontrol products or agrochemicals, or develop plant breeding programs that incorporate resistance to specific pathogens.
In Chile, one of the main bottlenecks has been the historical absence of a public repository of phytopathogenic strains . This deficiency limits the R&D system's capacity to conduct comparable, reproducible, and reference-based trials. Furthermore, it complicates collaboration between institutions, as each laboratory may end up working with its own fragmented collections with varying levels of characterization.
Adding to this structural problem is the role of the Agricultural and Livestock Service (SAG), whose mission is to protect the country's phytosanitary status . To achieve this objective, the SAG maintains very strict restrictions on the importation of phytopathogenic microorganisms from abroad. Strains that manage to enter the country are subject to quarantine and can only be handled in specially equipped facilities designed for safe handling, with stringent biosafety protocols.
While these measures are logical from a national biosecurity standpoint, they create an additional challenge for research that needs to work with globally relevant pathogens or standardized materials for comparison with international studies. Without well-maintained collections within the country, and with restricted access to external material, the capacity to design comprehensive disease detection and management strategies is severely limited.
In this context, the development of high-quality national culture collections becomes essential , guaranteeing long-term conservation, well-documented species-level identification, and the possibility of safe distribution to third parties (whether companies, universities, or public and private research centers). Having a robust reference bank is, in practice, a basic requirement for Chilean phytopathology to keep pace with current challenges.
The Chilean Collection of Microbial Genetic Resources (CChRGM) as a pillar of the system
The Chilean Collection of Microbial Genetic Resources (CChRGM), part of the INIA Microbial Bank, has established itself as an internationally recognized collection of cultures , with the infrastructure and know-how necessary to characterize and conserve microorganisms over long periods. Its expertise in both conservation and phytopathology makes it a key player in promoting a public repository of plant pathogens in Chile.
Within the framework of a project supported by the Foundation for Agricultural Innovation (FIA), the CChRGM is working, in partnership with various institutions, to create a public collection of phytopathogenic microorganisms identified to the species level, conserved long-term, and available for distribution to third parties. This effort aims to reduce the gap in the availability of reference strains and facilitate access to quality material for research, development, and innovation for the scientific and agricultural communities.
The CChRGM guarantees the purity and viability of the strains through two key techniques: cryopreservation and lyophilization. Both allow microorganisms to be preserved for years, and even decades, from the moment they are isolated. For shipping, the collection offers two formats: glass ampoules with lyophilized material and live cultures, which facilitates transport logistics to any region of the country.
The freeze-dried glass ampoule format is particularly innovative in the Chilean context, as no other culture collection distributes material in this way. This method offers clear advantages over shipping live cultures: it ensures sterility, provides greater physical protection against shocks, and offers superior durability, since it can be stored at 4°C in the receiving laboratory. Furthermore, it does not require a continuous power supply, a valuable feature in a country where earthquakes and other natural disasters can disrupt access to electricity.
Before the project, supported by FIA, the CChRGM already had 125 phytopathogenic strains in its online catalog ready for distribution. With the implementation of this initiative, the number of identified plant pathogen strains is projected to increase by 160, and approximately 30 new species are expected to be added thanks to donations from collaborating entities such as SAG, the Chilean Agricultural Laboratory (LAGRIC), and BIOFOREST.
The ultimate goal is to create a public catalog of 315 well-characterized phytopathogenic strains, accompanied by key information: host plant, observed symptoms, collection site, isolation date, DNA sequences, and other data essential for researchers. By the end of 2024, the project had reached 24% completion, resulting in 69 new phytopathogenic strains characterized to the species level.
A diverse catalog of phytopathogenic genera and their impact on research
Thanks to the work carried out, the Chilean Collection of Microbial Genetic Resources has assembled a broad set of phytopathogenic genera relevant to the country's agriculture and forestry resources. These include fungi and bacteria belonging to Alternaria, Arambarria, Botrytis, Bjerkandera, Chondrostereum, Colletotrichum, Corinectria, Cytospora, Diaporthe, Diplodia, Fusarium, Gaeumannomyces, Gnomoniopsis, Lasiodiplodia, Neofusicoccum, Neopestalotiopsis, Ophiostoma, Phacidium, Phytophthora, Pseudomonas, Rhizobium, Schizophyllum, Sclerotinia, Thyronectria, and Xanthomonas, among other relevant groups.
Having this range of pathogens in an accessible public collection has significant implications. For bio-input and agrochemical companies, it provides reference pathogens with which to test the efficacy of new products. For genetic improvement programs, it enables the evaluation of crop varieties against specific strains and the selection of more resistant materials. For diagnostic laboratories, it offers control materials with which to validate and standardize molecular or serological detection methods.
Furthermore, the existence of a detailed catalog, with data on geographic origin, host plant, and symptoms , allows for a better understanding of the distribution and relative importance of each pathogen within the country. This can help design more targeted surveillance strategies, focusing resources on the species that pose the greatest risk to certain crops or regions.
As the collection grows and new strains are added, the catalog aims to become a reference platform for the Chilean phytopathology community , offering not only biological material but also valuable associated information. In an environment of emerging diseases and climate change, having this data in an organized and updatable format is a strategic resource of paramount importance.
The work behind the CChRGM and the phytopathogen collection involves specialists such as Matías Guerra P. , technical manager of the Microbial Genetic Resources Bank at INIA, and Jean Franco Castro F. , curator of the Chilean Collection of Microbial Genetic Resources itself. Their technical work and coordination with other institutions are fundamental to maintaining the quality, traceability, and safety of the preserved material.
Looking at the whole picture, Chilean phytopathology is at a turning point : on the one hand, it faces a growing number of emerging diseases associated with climate change, crop migration, and intensified production; on the other, it is building scientific infrastructures and collaborative networks that allow it to respond more effectively. The combination of active scientific societies like SOCHIFIT, historical databases supported by artificial intelligence, and national strain collections like the CChRGM is laying the foundation for a more resilient system, better prepared for what lies ahead, even though it remains a small discipline with limitations inherent to its context.
