Systematics as a Tool of Agronomy

1.1. Let Us Recall the Key Concepts of the Course

Before moving on to practical examples, it is necessary to clearly fix the terminology that we have used throughout the entire course. As Pandey (2021) notes, systematics is the science of the diversity of organisms, including the discovery, description, and interpretation of biological diversity, as well as its use in the form of predictive classification systems. Taxonomy, in turn, is the branch of systematics that deals with the principles and practice of classification, including identification, description, classification, and naming of taxa (Pandey, 2021).

A taxon is a group of organisms that has been assigned a certain rank in a hierarchical classification. A taxon can be of any level: species, genus, family, order. For example, the species Solanum tuberosum L. (potato) is a taxon of species rank, while the genus Solanum is a taxon of genus rank (Caliskan et al., 2023).

A clade is a group consisting of a common ancestor and all of its descendants. In phylogenetic systematics, only clades are recognized as natural groups. Judd et al. (2018) emphasize that a monophyletic group (clade) can be removed from a phylogenetic tree by a single “cut.” This is a key concept that distinguishes modern systematics from traditional systematics, in which paraphyletic groups, such as “dicots,” were often recognized (Judd et al., 2018).

Phylogeny is the evolutionary history of a group of organisms, which is reconstructed on the basis of the analysis of characters: morphological, molecular, and biochemical. A phylogenetic tree is a diagram reflecting kinship relationships between ancestors and descendants (Judd et al., 2018).

Nomenclature is the formal naming of taxa in accordance with established rules. For plants, algae, and fungi, the International Code of Nomenclature for algae, fungi, and plants (ICNafp) applies. Nomenclature ensures the universality and stability of scientific names, which is critically important for communication (Pandey, 2021).

Identification is the process of establishing that an unknown specimen belongs to a known taxon. This is a practical skill that requires knowledge of diagnostic characters and the ability to use identification keys (Pandey, 2021).

All these concepts are interconnected. Systematics provides the language (nomenclature) and the map (phylogeny), while identification is the practical skill of orienting oneself on that map.

1.2. Systematics as Language

Imagine the following situation: an agronomist in Russia discovers symptoms of a disease on tomatoes that he calls “brown spot.” His colleague in Spain sees the same symptoms and calls them “mancha parda.” And a farmer in China uses a completely different name. How can they understand each other? The answer is simple: use the scientific name of the pathogen.

The scientific name Alternaria tomatophila E.G. Simmons (synonym Alternaria solani Sorauer) unambiguously identifies the causal agent of tomato Alternaria leaf spot throughout the world (Blancard, 2012). It is nomenclature that ensures that very universal communication without which neither international trade, nor exchange of scientific information, nor quarantine measures are possible.

Pandey (2021) emphasizes that nomenclature is not simply the assigning of names, but a strict system of rules that guarantees that each name is tied to a certain taxon and cannot be used arbitrarily. For example, when we speak of Fusarium oxysporum f. sp. lycopersici (the specialized form affecting tomatoes), we know precisely which pathogen is meant, even if it is called differently in different countries (Blancard, 2012).

Moreover, nomenclature ensures the continuity of knowledge. If a taxonomic revision has split one species into several, the old names are preserved as synonyms so that information in older publications can still be found. This is especially important in agronomy, where data on pathogens and pests accumulate over decades.

1.3. Systematics as Map

Phylogeny is a map of evolutionary relationships. And like any map, it allows not only orientation but also prediction. If we know that two species are close relatives, we can assume that they possess similar characters: resistance to certain pathogens, biochemical composition, and ecological preferences.

Judd et al. (2018) give a classic example: the search for medicinal compounds in plants. Having discovered cortisone precursors in some species of the genus Dioscorea (yam), researchers began to search for them in closely related species and found higher concentrations. The same principle works in agronomy.

Moreover, phylogeny makes it possible to predict where to look for donors of economically valuable traits. As Biancardi et al. (2012) note, the wild relative of cultivated beet Beta maritima is a valuable source of resistance to Cercospora leaf spot, rhizomania, nematodes, and other pathogens. Knowledge of the phylogenetic relationships between B. maritima and cultivated forms of beet allowed these genes to be purposefully transferred into modern cultivars (Biancardi et al., 2012).

Caliskan et al. (2023) emphasize that the phylogeny of the genus Solanum (section Petota) serves as the basis for searching for sources of resistance to late blight, viruses, nematodes, and insects among wild potato species. Without an understanding of kinship relationships, the breeder does not know with which species cultivated potato can be crossed and what traits can be expected in the progeny.

Thus, phylogeny is not merely a theoretical scheme but a practical tool that directs the search for genetic resources and helps predict the results of crosses.

1.4. Systematics in Action: Several Examples

To avoid being unfounded, let us consider several concrete situations in which systematics directly influences the decisions of an agronomist.

Example 1. Fungi and oomycetes: why does this matter?

For a long time, the causal agents of late blight and downy mildews were classified as fungi. However, as Agrios (2005) explains, oomycetes (Oomycota) have cell walls consisting of glucans and a small amount of cellulose, but without chitin, whereas true fungi contain chitin. This is not merely an academic difference. It determines the choice of fungicide: many systemic fungicides effective against true fungi do not act on oomycetes, and vice versa. For example, metalaxyl is effective against Phytophthora infestans (the causal agent of potato and tomato late blight), but useless against Alternaria tomatophila (Blancard, 2012; Agrios, 2005).

This example shows that the taxonomic affiliation of a pathogen directly determines the strategy of chemical protection.

Example 2. Pathogen races and the choice of a resistant cultivar

Blancard (2012) describes three races of Fusarium oxysporum f. sp. lycopersici — the causal agent of Fusarium wilt of tomato. Tomato cultivars may be resistant to one, two, or three races depending on the presence of resistance genes (I, I-2, I-3). To choose a cultivar correctly, the agronomist must know which races of the pathogen are present in a specific field. And for this, accurate identification is needed — morphological or molecular. Without systematic knowledge, this choice becomes random.

Example 3. Quarantine objects

EPPO (2025) publishes lists A1 and A2 of quarantine pests recommended for regulation. These lists contain hundreds of species: bacteria, fungi, viruses, insects, nematodes. For example, Ralstonia solanacearum (bacterial wilt) and Globodera rostochiensis (golden potato cyst nematode) are included in list A2. For quarantine service inspectors, it is critically important to be able to identify these objects and distinguish them from closely related but non-quarantine species. Systematics provides tools for such identification: morphological keys, molecular tests, and reference collections (EPPO, 2025).

Example 4. Biological control

Fujino et al. (2025) discuss the role of predatory protists in suppressing pathogens. For example, Colpoda sp. is capable of directly feeding on Ralstonia solanacearum, reducing tomato disease incidence. However, for successful use of biological control, it is necessary to know precisely the species identity of both the agent and the target. An error in identification can lead to undesirable effects: the agent may attack beneficial species or prove ineffective against the target pathogen. Here systematics is the basis of safety and effectiveness.

Example 5. Breeding and genetic resources

Haverkort and Anisimov (2007) describe the work of the All-Russian Institute of Plant Genetic Resources (VIR) on the conservation and use of potato genetic resources. The VIR collection includes about 9,000 accessions, including 3,000 accessions of wild species. These resources are used to create cultivars resistant to late blight, viruses, and nematodes. But to use this diversity effectively, a system is needed: phylogenetic classification, data on ploidy, crossability, and ecological preferences. Systematics provides this system.

1.5. Connection of All Course Modules

Our course consisted of several modules: fundamental concepts of systematics, nomenclature, identification methods, phylogenetic analysis, genetic resources, quarantine, biological control. Each of these modules is a separate tool. But only together do they form a coherent picture.

• Fundamental concepts (taxon, clade, phylogeny) provide the theoretical basis.
• Nomenclature ensures stability and universality of communication.
• Identification is a practical skill that allows one to “recognize” objects in the field.
• Phylogeny provides an evolutionary perspective and predictive power.
• Genetic resources (CWR, gene pools) are the material basis for breeding.
• Quarantine is a regulatory function based on systematic data.
• Biological control is the application of systematic knowledge to manage agrocenoses.
• Biodiversity conservation is an ethical and ecological task that also relies on systematics.

All these modules are interconnected. For example, to choose a biological control agent, one needs to know its phylogenetic relationships with other species (to avoid non-target effects), its nomenclature (to identify it correctly), and its ecological preferences (to create conditions for survival). To include a quarantine object in a list, one needs to know its taxonomy, distribution, and harmfulness. To find a source of resistance, one needs to know the phylogeny of the cultivated species and its wild relatives.

1.6. Systematics as the Basis of Professionalism

In conclusion to this chapter, let us emphasize: systematics is not a dogma but a developing field of knowledge. Taxonomic revisions occur constantly: species are renamed, genera are reorganized, phylogenetic trees are refined. A modern agronomist must be prepared for the fact that the names he learned at university may change. But this is not a reason to ignore systematics — on the contrary, it is a reason to follow updates and use modern tools.

Pandey (2021) notes that systematics is the basis for all biology, since organisms cannot be discussed scientifically until a classification is achieved that allows them to be recognized and named. In agronomy this is especially important, because errors in identification can lead to significant economic losses and ecological consequences.

An agronomist who has mastered systematics makes more precise and well-founded decisions. He knows which pathogen is in front of him, how to control it, where to look for resistant cultivars, which quarantine measures to apply, and which biological agents to use. He understands that an agrocenosis is part of the biosphere, and that managing it requires a systems approach.

In the following chapters, we will consider concrete applications of systematics in the diagnosis of diseases and pests, in breeding and genetic resources, in plant quarantine, in biological control, and in biodiversity conservation. We will see how theoretical knowledge turns into practical solutions, and how systematics becomes an indispensable tool of sustainable agriculture.

2.1. Why Is Accurate Identification Critically Important?

Imagine a situation: spots have appeared on tomato leaves in a field. The agronomist may assume several causes: Alternaria leaf spot, Septoria leaf spot, bacterial spot, or even a physiological disorder. If he makes a mistake and applies a fungicide against a fungal infection, when the true cause is a bacterium, the treatment will not only fail to help but may also harm beneficial microflora and the environment. Moreover, as we will see below, even within one group of pathogens, different taxa require different active ingredients.

Blancard (2012), in his guide to tomato diseases, emphasizes that many symptoms caused by different pathogens can be very similar. For example, spots caused by Alternaria tomatophila, Stemphylium spp., and some bacteria may look almost identical to an inexperienced eye. However, accurate diagnosis requires not only visual inspection but also an understanding of the biology of the causal agent, its taxonomic affiliation, and its life cycle. Only on this basis can the correct protection strategy be chosen.

2.2. Fungi and Oomycetes: Why Is This Not Merely an Academic Difference?

One of the clearest examples in which systematics directly influences the choice of control method is the difference between true fungi (Fungi) and oomycetes (Oomycota). For a long time, oomycetes such as Phytophthora infestans (the causal agent of potato and tomato late blight) and Pythium spp. were considered fungi. However, as Agrios (2005) explains, modern systematics places them in a separate kingdom, Chromista (or Stramenopila), because their cell walls contain cellulose and glucans but do not contain chitin, which is characteristic of true fungi. Moreover, oomycetes are diploid in the vegetative phase, whereas most fungi are haploid.

This difference is of enormous practical importance. Many fungicides effective against true fungi do not act on oomycetes, and vice versa. For example, as Blancard (2012) notes, metalaxyl (Ridomil) is highly effective against Phytophthora infestans and other oomycetes, but useless against Alternaria tomatophila or Botrytis cinerea. Conversely, strobilurins (azoxystrobin) act on a broad spectrum of fungi, but their effectiveness against oomycetes may be limited. Without knowledge of the taxonomic affiliation of the pathogen, the agronomist risks applying the wrong product, losing the crop, and causing environmental damage.

Moreover, Agrios (2005) emphasizes that oomycetes such as Pythium and Phytophthora require free water for the formation and movement of zoospores. This also determines cultural control measures: drainage, avoiding waterlogging, and proper irrigation. Whereas many true fungi, for example powdery mildews, can develop at high air humidity but without free water on leaves. Thus, systematics provides the key to understanding the ecology of the pathogen, and ecology determines the protection strategy.

2.3. Races and Strains: Why Is One Species Name Not Enough?

The next level of complexity is intraspecific differentiation. Many pathogens exist as specialized forms (formae speciales), races, or strains that differ in virulence to certain cultivars. Blancard (2012) gives the example of Fusarium oxysporum f. sp. lycopersici — the causal agent of Fusarium wilt of tomato. This fungus exists as three races: race 0 (sometimes called race 1), race 1 (race 2), and race 2 (race 3). Tomato cultivars may be resistant to one, two, or three races depending on the presence of resistance genes (I, I-2, I-3). To choose a cultivar correctly, the agronomist must know which races of the pathogen are present in a particular field. And for this, accurate identification is needed — morphological or molecular.

A similar situation exists with Phytophthora infestans. Agrios (2005) describes that until the 1980s, only one mating type (A1) predominated in Europe and other regions, and the pathogen reproduced asexually. However, after the introduction of the second type (A2) from Mexico, sexual reproduction with the formation of oospores, which can survive in soil for years, became possible. This led to the appearance of new, more aggressive strains resistant to certain fungicides (for example, to metalaxyl). For the agronomist, this means that old protection schemes may no longer work, and constant diagnosis and monitoring of the racial composition of the pathogen are needed.

Caliskan et al. (2023), in the chapter on potato taxonomy, also emphasize that knowledge of races and strains is critically important for breeding for resistance. For example, resistance to Globodera rostochiensis (golden potato cyst nematode) is determined by the genes H1, H2, and others, which are effective against certain pathotypes (Ro1, Ro2, etc.). Without identification of the pathotype, it is impossible to select a resistant cultivar correctly.

2.4. Diagnostic Methods: From Morphology to Molecules

How can an agronomist or phytopathologist accurately identify a pathogen? Systematics offers a whole arsenal of methods that can be divided into several groups.

Morphological methods remain the basis of diagnosis. Agrios (2005) describes that the most significant characters for identifying fungi are spores and sporulating structures, as well as characteristics of the mycelium. For example, Alternaria tomatophila forms multicellular club-shaped conidia with a long thread-like appendage, whereas Stemphylium spp. form multicellular spores with a warty surface and a pointed end (Blancard, 2012). These characters can be observed under a microscope after isolating the pathogen on a nutrient medium or directly from affected tissues.

However, morphological identification has limitations. As Blancard (2012) notes, some pathogens, for example Fusarium oxysporum f. sp. lycopersici, do not always form characteristic spores in culture, and their identification requires additional methods. In addition, many species are morphologically indistinguishable but differ in pathogenicity and require different control measures.

Molecular methods have revolutionized diagnosis. Agrios (2005) points out that polymerase chain reaction (PCR) and DNA sequencing make it possible to detect a pathogen in plant tissues at early stages of infection, when its presence is minimal. This is especially important for quarantine objects and for seed material. For example, to detect Clavibacter michiganensis subsp. michiganensis (the causal agent of bacterial canker of tomato) in seeds, DNA primers specific to the internal transcribed spacers of ribosomal DNA are used (Blancard, 2012). This allows infected seeds to be identified before sowing and prevents the spread of the disease.

Molecular methods also make it possible to identify races and strains. For example, for Fusarium oxysporum f. sp. lycopersici, primers have been developed that distinguish race 1, race 2, and race 3 (Blancard, 2012). This makes it possible not only to diagnose the disease but also to predict which cultivar will be resistant.

Serological methods, such as ELISA, are widely used for mass testing of seeds and plants for viruses. Blancard (2012) notes that ELISA is used to detect tomato mosaic virus (ToMV), tomato spotted wilt virus (TSWV), and many others. These methods are rapid, relatively inexpensive, and suitable for analyzing large samples.

Collections and databases play an important role in diagnosis. Haverkort and Anisimov (2007) describe the collection of the All-Russian Institute of Plant Genetic Resources (VIR), which includes thousands of accessions of potato and its wild relatives. Such collections serve as references for comparison and identification. In addition, international databases such as the EPPO Global Database contain information on quarantine organisms, their distribution, and methods of detection and identification (EPPO, 2025).

2.5. Quarantine Objects: Diagnosis in the Service of Security

A special place in diagnosis is occupied by quarantine objects. EPPO (2025) publishes lists A1 and A2 of pests recommended for regulation in member countries of the EPPO region. List A1 includes organisms absent from the region but representing a potential threat, for example Ralstonia solanacearum (bacterial wilt) and Globodera rostochiensis (golden potato cyst nematode). List A2 includes organisms present in the region but not widely distributed, for example Clavibacter michiganensis (bacterial canker) and Synchytrium endobioticum (potato wart).

For quarantine service inspectors, it is critically important to be able to identify these objects and distinguish them from closely related but non-quarantine species. Systematics provides tools for such identification: morphological keys, molecular tests, and reference collections. For example, to detect Synchytrium endobioticum in soil, biological tests with susceptible potato cultivars are used, as well as microscopy of resting spores (EPPO, 2025). For Ralstonia solanacearum, serological and molecular methods, including PCR, are used.

Moreover, quarantine lists are constantly updated. For example, in 2025, Tomato brown rugose fruit virus (ToBRFV) was added to list A2 — a new virus causing serious losses in tomatoes (EPPO, 2025). This means that agronomists and phytopathologists must be aware of taxonomic changes and new threats. Here systematics acts as the basis for monitoring and early warning.

2.6. Practical Examples: Potato and Tomato

Let us consider several concrete examples to illustrate how systematics works in diagnosis.

Late blight of potato and tomato. The causal agent is Phytophthora infestans, an oomycete. As we have already said, its taxonomic affiliation determines the choice of fungicides (metalaxyl, mancozeb) and cultural measures (avoiding waterlogging). In addition, identification of the mating type (A1 or A2) is important for predicting the appearance of oospores and new aggressive strains (Agrios, 2005).

Fusarium wilt of tomato. The causal agent is Fusarium oxysporum f. sp. lycopersici. Identification of the race (1, 2, or 3) determines the choice of a resistant cultivar. Morphologically the races are indistinguishable, so molecular methods or tests on differential cultivars are necessary (Blancard, 2012).

Bacterial canker of tomato. The causal agent is Clavibacter michiganensis subsp. michiganensis. This is a gram-positive bacterium that can be transmitted with seeds. For diagnosis, serological and molecular methods are used, as well as isolation on selective media (Blancard, 2012). Here systematics helps distinguish this species from other phytopathogenic corynebacteria.

Septoria leaf spot of tomato. The causal agent is Septoria lycopersici. Morphologically it forms pycnidia with thread-like multicellular conidia. However, the symptoms may resemble Alternaria leaf spot. Accurate identification requires microscopy and, in some cases, isolation in pure culture (Blancard, 2012).

Potato cyst nematode. The causal agents are Globodera rostochiensis and G. pallida. Identification of species and pathotypes is critically important for choosing a resistant cultivar. For diagnosis, morphometry of cysts and molecular methods are used (Caliskan et al., 2023). In addition, as Haverkort and Anisimov (2007) note, pathotype Ro1 predominates in Russia, but there is a risk of introduction of other pathotypes (Ro2, Ro3, Ro4, Ro5), so constant diagnosis is necessary.

2.7. The Role of Systematics in Pest Diagnosis

Although we have mainly spoken about pathogens, systematics is no less important for the diagnosis of pests — insects, mites, and nematodes. For example, identification of the aphid Myzus persicae (green peach aphid) is important because it is an efficient vector of many viruses, including potato virus Y (PVY) and cucumber mosaic virus (CMV). Other aphid species may not be vectors or may transmit different viruses (Blancard, 2012). An error in identification can lead to an incorrect vector control strategy.

Systematics is also important for identifying entomophages and antagonists used in biological control. Fujino et al. (2025) describe the use of predatory protists, such as Colpoda sp., to suppress Ralstonia solanacearum. To use this method successfully, it is necessary to know precisely the species identity of both the agent and the target. An error can lead to undesirable effects: the agent may attack beneficial species or prove ineffective against the target pathogen.

3.1. Phylogeny as the Basis for Searching for Wild Relatives

The key idea that we already discussed in the first chapter is that phylogeny is a map of evolutionary relationships that makes it possible to predict where to look for economically valuable traits. If we know that two species are close relatives, we can assume that they possess similar characters: resistance to certain pathogens, biochemical composition, and ecological preferences (Judd et al., 2018).

Biancardi et al. (2012), in the book on Beta maritima — the wild relative of cultivated beet — emphasize that the evolutionary proximity between wild beet and cultivated forms facilitates accidental crosses. Important disease resistance traits that are now present in cultivated cultivars were isolated from wild material. According to several authors, B. maritima is also an important means of increasing the genetic diversity of cultivated forms, which is currently rather narrow because of the domestication bottleneck and continuous selection for improved productivity and quality (Biancardi et al., 2012).

Caliskan et al. (2023), in the chapter on potato taxonomy, note that wild relatives and landraces of potato are distributed across a wide range of geographical habitats, representing great genetic diversity in the Petota gene pool with respect to variation in moisture, temperature, soil conditions, and biotic stresses. Many studies have examined the genetic diversity of wild relatives and landraces of potato in terms of agromorphological, molecular, and biochemical responses under various environmental conditions. Thus, they have been used as donors to broaden the genetic base of European and North American gene pools (Caliskan et al., 2023).

3.2. Centers of Origin and Diversity (Vavilov’s Concept)

Nikolai Vavilov, an outstanding Russian geneticist and plant scientist, formulated the concept of centers of origin of cultivated plants. According to Vavilov, each cultivated species has a center of origin where the maximum genetic diversity of its wild relatives and primitive forms is concentrated (Caliskan et al., 2023).

For potato, this center is the Andes in South America. Caliskan et al. (2023) describe two main hypotheses of the origin of cultivated potato. The first, supported by Russian scientists (Bukasov, Juzepczuk, Vavilov), assumes multiple origins of potato from the Peruvian-Bolivian Plateau and southern Chile. According to Vavilov’s classification, the Andes are the center of origin and distribution of potato. Wild tuber-bearing Solanum species are distributed over a vast geographical territory from the southwestern United States to central Argentina and adjacent Chile, with a wide diversity of adaptive ranges, including high-altitude Andean regions from 3,500 to 4,500 m (Caliskan et al., 2023).

The second hypothesis, advanced by English scientists (Salaman, Simmonds, Hawkes), is known as the “restricted origin hypothesis.” According to it, South America, specifically southern Peru and adjacent northern Bolivia, is considered the original center of cultivated potato. Molecular studies using AFLP markers supported the monophyletic (single) origin of potato from southern Peru (Caliskan et al., 2023).

Radiocarbon dating showed that potato tuber remains found by Engel are 7,000 years old. This indicates that potato was domesticated in ancient times (Caliskan et al., 2023).

Knowledge of centers of origin has direct practical significance for breeding. It is precisely in these regions that maximum genetic diversity is concentrated, and it is there that the breeder can find sources of resistance to diseases, pests, and abiotic stresses. Biancardi et al. (2012) note that B. maritima is distributed along the coasts of the Mediterranean and North Seas, and it was there that sources of resistance to Cercospora leaf spot, rhizomania, and nematodes were found.

3.3. Gene Pools: GP1, GP2, GP3

The concept of gene pools was proposed by Harlan and de Wet (1971) and developed in works on the systematics of cultivated plants. It classifies wild relatives of cultivated species according to the ease with which genes can be transferred into the cultivated species (Biancardi et al., 2012).

The primary gene pool (GP-1) includes cultivated forms (GP-1A) and wild or weedy forms of the same species (GP-1B). Crossing between representatives of the primary gene pool usually does not encounter serious barriers, and genes are transmitted easily. For beet, GP-1 includes cultivated beet (Beta vulgaris subsp. vulgaris) and wild beet (B. vulgaris subsp. maritima). Biancardi et al. (2012) note that, unlike other species of the genus Beta, the evolutionary proximity between B. maritima and cultivated forms facilitates accidental crosses.

The secondary gene pool (GP-2) includes species less closely related to the cultivated species, from which gene transfer is difficult but possible using traditional breeding methods. For beet, GP-2 includes species that cross with cultivated forms with difficulty but still produce viable progeny (Biancardi et al., 2012).

The tertiary gene pool (GP-3) includes species from which gene transfer into the cultivated species is impossible or requires complex biotechnological methods (Biancardi et al., 2012).

Caliskan et al. (2023) apply this concept to potato. They note that section Petota of the genus Solanum contains about 200 species, including wild species, landraces, and modern cultivars, distributed from the southwestern United States to central Argentina. Potato genetic resources are divided into four main categories: wild relatives, local landraces, modern cultivars, and research material (Caliskan et al., 2023).

Understanding gene pools is critically important for the breeder. It determines the strategy of crosses: if a resistance gene is in GP-1, it can be transferred relatively easily; if in GP-2, special methods will be required (for example, embryo culture); if in GP-3, genetic transformation may be required (Biancardi et al., 2012).

3.4. Examples of Successful Use of Wild Relatives

The history of breeding knows many examples in which wild relatives of cultivated plants saved entire industries from catastrophic losses. Let us consider several of the most striking.

Wheat resistance to rust. Agrios (2005) describes that wheat stem rust, caused by Puccinia graminis f. sp. tritici, was for centuries one of the most destructive diseases. The use of resistant cultivars became the main control method. Resistance genes were found in wild relatives of wheat, and their transfer into cultivated cultivars made it possible to significantly reduce losses. For example, the genes Sr31 and Sr38 were transferred from wild wheat species and provided resistance to a number of pathogen races (Agrios, 2005).

Tomato resistance to diseases. Blancard (2012) describes that many tomato resistance genes were transferred from wild Lycopersicon species. For example, the gene Mi from L. peruvianum provides resistance to root-knot nematodes Meloidogyne spp. The gene Sw-5 from L. peruvianum provides resistance to tomato spotted wilt virus (TSWV). The genes Cf-2, Cf-4, Cf-5, Cf-6, and Cf-9 from L. pimpinellifolium and L. hirsutum provide resistance to Mycovellosiella fulva (the causal agent of leaf mold) (Blancard, 2012).

Agrios (2005) also notes that the use of wild tomato relatives made it possible to improve fruit taste. The botanist Hugh Iltis collected samples in the Peruvian Andes of a new species, Solanum chmielewskii, which was crossed with cultivated tomato and transferred genes that significantly improved taste (Judd et al., 2018).

Potato resistance to nematodes. Caliskan et al. (2023) describe that resistance to the golden potato cyst nematode (Globodera rostochiensis) was found in wild Solanum species. The gene H1 from S. tuberosum group Andigena provides resistance to pathotypes Ro1 and Ro4. The genes Gpa2, Gpa5, Gpa1, H2, and H3 from S. vernei and other species provide resistance to G. pallida (Caliskan et al., 2023).

Haverkort and Anisimov (2007) describe the work of the All-Russian Institute of Plant Genetic Resources (VIR) on creating potato cultivars resistant to nematodes. On the basis of wild species S. chacoense and S. vernei, the cultivars “Bryanskii delikates” and “Nakra” were created, resistant to pathotype Ro1. At present, specially created parental lines, backcrosses 88.16/20 and 88.34/14, possessing high fertility, resistance to PVY, and moderate resistance to P. infestans, are used in breeding (Haverkort and Anisimov, 2007).

Beet resistance to Cercospora leaf spot and rhizomania. Biancardi et al. (2012) describe in detail the history of the use of B. maritima in beet breeding. The first documented case of successful transfer of disease resistance from wild beet to cultivated beet was carried out by Munerati, who used B. maritima from the Po Delta as a source of resistance to Cercospora leaf spot. Subsequently, other European researchers also began to work with B. maritima as a source of disease resistance (Biancardi et al., 2012).

Resistance to rhizomania (caused by BNYVV virus) was found in B. maritima and transferred into cultivated cultivars. The gene Rz1, providing qualitative resistance, was identified in the cultivar “Rizor,” created in Italy. The gene Rz2 was found in accession WB42 from Denmark and provides a higher level of resistance than Rz1. The genes Rz3, Rz4, and Rz5 were also identified in various accessions of B. maritima (Biancardi et al., 2012).

3.5. Polyploidy, EBN, and Hybridization in Breeding

One of the key problems in using wild relatives is incompatibility associated with different ploidy levels and the Endosperm Balance Number (EBN). This problem is especially acute for potato, where cultivated cultivars are tetraploid (2n = 4x = 48), while many wild species are diploid (2n = 2x = 24) or have other ploidy levels.

Caliskan et al. (2023) explain that the basic chromosome number of all Petota species is x = 12. There are four ploidy levels: diploid (2n = 2x = 24), triploid (2n = 3x = 36), tetraploid (2n = 4x = 48), and pentaploid (2n = 5x = 60). Wild relatives also include hexaploids (2n = 6x = 72) (Caliskan et al., 2023).

However, ploidy is not the only barrier. The concept of EBN (Endosperm Balance Number) was proposed by Johnston and Hanneman (1980) to explain the success or failure of interspecific crosses. EBN is the effective ploidy in the endosperm, which must be in a ratio of 2 maternal : 1 paternal for normal endosperm development (Ortiz and Mihovilovich, 2020).

Caliskan et al. (2023) explain that each Solanum species has a specific EBN, determined experimentally. For example, S. commersonii (1EBN) and S. berthaultii (2EBN) are diploid species, but crossing between them fails because of the difference in EBN. At the same time, S. chacoense (2EBN) and S. tuberosum subsp. andigena (2EBN) cross successfully because they have the same EBN (Caliskan et al., 2023).

Ortiz and Mihovilovich (2020) add that EBN does not always reflect the actual ploidy of a species. For example, there are 2x (1EBN), 2x (2EBN), 3x (2EBN), 4x (2EBN), 4x (4EBN), 5x (4EBN), and 6x (4EBN) Solanum species. This means that for successful crossing it is necessary to know not only the chromosome number but also the EBN.

To overcome incompatibility barriers, breeders use several approaches:

Haploids. Ortiz and Mihovilovich (2020) describe that haploids (2n = 2x = 24) obtained from tetraploid S. tuberosum make it possible to simplify genetic analysis and facilitate crossing with wild diploid species. Haploids are obtained by gynogenesis using special inducers — clones of S. tuberosum group Phureja, such as “IVP 35,” “IVP 101,” and “PL-4.” These inducers promote the development of haploid embryos from the egg cells of the maternal plant (Ortiz and Mihovilovich, 2020).

2n gametes. Caliskan et al. (2023) explain that 2n gametes are gametes with the somatic chromosome number. They are formed as a result of meiotic disturbances (FDR — first division restitution, SDR — second division restitution). Heterozygous 2x parents transmit 80% (FDR) or 40% (SDR) of their heterozygosity to 4x hybrid progeny after sexual polyploidization. The use of 2n gametes makes it possible to overcome ploidy barriers and transfer valuable genes from diploid species into tetraploid cultivars (Caliskan et al., 2023).

Bridge crosses. Ortiz and Mihovilovich (2020) describe the use of S. verrucosum (2x, 2EBN) as a “bridge species” for transferring genes from 1EBN diploid species, such as S. bulbocastanum, S. pinnatisectum, and S. polyadenium, into cultivated potato. The absence of S-RNase in the pistils of self-fertile S. verrucosum plants allows pollen tubes of these 1EBN species to grow and fertilize egg cells (Ortiz and Mihovilovich, 2020).

Somatic hybridization. Caliskan et al. (2023) note that somatic hybridization has been used to overcome sexual incompatibility between diploid species (1EBN and 2EBN) and cultivated potato of the Tuberosum group (4EBN). Somatic synthesis has been used for introgression of resistance traits from wild relatives (soft rot and early blight from S. brevidens, late blight from S. bulbocastanum) into cultivated potato (Caliskan et al., 2023).

3.6. Ex Situ and In Situ Conservation of Genetic Resources

Conservation of genetic resources is the basis of breeding. Without collections of wild relatives and landraces, the breeder has no material for work. There are two main approaches to conservation: ex situ and in situ.

Ex situ conservation is the conservation of plant material outside its natural habitat. This is the most widespread method, including the creation of gene banks where seeds, tubers, DNA, and pollen are stored, as well as in vitro collections and cryopreservation (Caliskan et al., 2023).

Haverkort and Anisimov (2007) describe the collection of the All-Russian Institute of Plant Genetic Resources (VIR), which is one of the largest in the world. It contains about 9,000 accessions, including 3,000 accessions of wild species, 3,500 accessions of cultivated species, 2,100 cultivars, and 400 interspecific hybrids and dihaploids. About 300 old cultivars created 60 or more years ago are unique because they are preserved only in the VIR gene bank (Haverkort and Anisimov, 2007).

Caliskan et al. (2023) provide data on the largest potato gene banks: the International Potato Center (CIP) in Peru (4,727 accessions of cultivated potato and 4,052 accessions of wild potato), the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) in Germany (6,200 accessions), the U.S. Potato Gene Bank (5,700 accessions), the All-Russian Institute of Plant Genetic Resources (VIR) (about 10,000 accessions), and others.

In vitro collections play a special role for potato, since it propagates vegetatively and its tubers cannot be stored for long periods. Haverkort and Anisimov (2007) note that the VIR in vitro collection contains about 300 accessions and was created as a duplicate collection of virus-free plants representing unique and most valuable material. Accessions are maintained under minimal growth conditions at +20 °C as microtubers and stored from 1 to 3 years without transfer to fresh nutrient medium (Haverkort and Anisimov, 2007).

Cryopreservation is the most promising method of long-term storage. Caliskan et al. (2023) explain that cryopreservation involves the preservation of organs, tissues, and organisms at ultra-low temperatures (usually in liquid nitrogen at -196 °C). At such a temperature, all metabolic processes stop, and material can be stored indefinitely. For potato, vitrification methods (PVS2 droplet-vitrification) have been developed, allowing high survival rates after cryopreservation (Caliskan et al., 2023).

In situ conservation is the conservation of populations in their natural habitat. This method makes it possible to preserve evolutionary processes and ecological interactions. Caliskan et al. (2023) note that in situ conservation is especially important for wild relatives of cultivated plants (CWR), since it allows genetic diversity and the adaptive potential of populations to be preserved. However, this method is vulnerable to natural disasters, anthropogenic impact, and climate change (Caliskan et al., 2023).

Biancardi et al. (2012) emphasize the importance of in situ conservation of B. maritima, since many populations of this species are threatened with extinction due to habitat destruction. They note that it is necessary to identify not only the species subject to protection in the relevant areas but also to determine measures for their in situ and ex situ conservation (Biancardi et al., 2012).

3.7. Molecular Markers and Genomic Tools in Breeding

Modern breeding is unimaginable without molecular markers. They make it possible to accelerate selection, increase its accuracy, and reduce costs. Caliskan et al. (2023) describe various types of markers used to characterize potato germplasm: RAPD, AFLP, SSR, ISSR, IRAP, and SNP.

SSR (microsatellites) are short tandem DNA repeats that possess high polymorphism, codominance, and reproducibility. They are widely used for genotyping cultivars, assessing genetic diversity, identifying duplicates in collections, and analyzing population structure. Ghislain et al. (2004) developed a set of 18 SSR markers (Potato Genetic Identification kit), which are used to characterize 931 potato accessions from eight different cultivar groups (Caliskan et al., 2023).

SNP (single nucleotide polymorphisms) are the most common type of genetic variation. Caliskan et al. (2023) note that SNPs exist as biallelic markers with wide distribution in noncoding regions of the genome. In potato, from 3.8 million SNPs in diploids to 12.9 million SNPs in pentaploids have been identified. The SolCAP Infinium platform (8K, 12K, 20K, 69K arrays) allows high-throughput genotyping and is used for analyzing population structure, QTL mapping, and GWAS (Caliskan et al., 2023).

QTL mapping makes it possible to identify loci controlling quantitative traits, such as disease resistance, yield, and tuber quality. Caliskan et al. (2023) describe the mapping of QTL for resistance to late blight, potato virus Y (PVY), nematodes, and other pathogens. For example, the gene Ryadg from S. tuberosum group Andigena and the gene Rysto from S. stoloniferum have been mapped on chromosomes 11 and 12, respectively, and provide resistance to PVY (Caliskan et al., 2023).

GWAS (genome-wide association study) is a method that uses historical recombinations in existing natural populations to identify genes associated with phenotypic traits. Caliskan et al. (2023) give an example of a GWAS study of 330 potato genotypes in which the gene Sen1, providing resistance to potato wart, associated with the SNP marker PotVar0067008, was identified. Another study using the 12K SolCAP array identified SNP markers associated with resistance to common scab (Yuan et al., 2019, cited in Caliskan et al., 2023).

Haverkort and Anisimov (2007) note that in recent years molecular genetic methods, including PCR analysis, have been used in potato breeding for genotyping cultivars, studying the variability of meristem lines, identifying mutations, detecting viruses and viroids, and also for studying breeding material using DNA markers of resistance genes to various pathogens (Haverkort and Anisimov, 2007).

4.1. Why Is Plant Quarantine So Important?

Agrios (2005) provides convincing historical examples of the catastrophic consequences of introducing pathogens into new regions. When a pathogen enters an area where its hosts have developed in its absence, the consequences can be far more destructive than those of endemic pathogens. Plants that developed without contact with the pathogen have no opportunity to select resistance factors specific against it, and therefore prove unprotected and extremely vulnerable. In addition, in a new region, microorganisms that are antagonists or competitors of the pathogen are usually absent, while the pathogen itself finds an enormous amount of available susceptible tissue on which it can reproduce unhindered (Agrios, 2005).

Some of the most destructive epidemics of plant diseases were caused by pathogens introduced from abroad. Agrios (2005) lists such examples: grape downy mildew in Europe, citrus bacterial canker, chestnut blight, Dutch elm disease, and soybean cyst nematode in the United States. All these diseases were introduced from other regions and caused enormous damage. It has been estimated that if soybean rust were introduced into the United States, losses to consumers and other sectors of the economy would amount to several billion dollars per year (Agrios, 2005).

That is why in 1912 the United States adopted the Plant Quarantine Act, which prohibits or restricts the importation into the country of plants, plant products, soil, and other materials that may carry pathogens not established in the country. Similar quarantine rules exist in most other countries (Agrios, 2005).

4.2. Systematics as the Basis of Quarantine Lists

Quarantine lists are lists of pests recommended for regulation. EPPO (2025) publishes lists A1 and A2, which are the basis for national quarantine legislation in member countries of the European and Mediterranean Plant Protection Organization.

List A1 includes pests absent from the EPPO region but representing a potential threat. List A2 includes pests present in the EPPO region but not widely distributed (EPPO, 2025).

These lists are constructed on a systematic basis. Each organism is identified by its scientific name, which ensures universal communication. For example, in list A1 we find Ralstonia solanacearum (bacterial wilt), Globodera rostochiensis (golden potato cyst nematode), Synchytrium endobioticum (potato wart), Tomato brown rugose fruit virus (ToBRFV), and many others (EPPO, 2025).

Systematics determines not only names but also taxonomic affiliation, which is critically important for understanding the biology of the pathogen and developing control measures. For example, Ralstonia solanacearum is a gram-negative bacterium that can be transmitted with seeds, soil, plant residues, and water. Knowledge of its taxonomy makes it possible to develop specific diagnostic methods and quarantine measures (EPPO, 2025).

Moreover, quarantine lists are constantly updated. EPPO (2025) describes the procedure for adding and removing pests from the lists. The addition of an organism to list A1 or A2 is based on a proposal by a member country, which provides a pest risk analysis (PRA) corresponding to EPPO standard PM 5/3. Since 2006, special Expert Working Groups for PRA have conducted PRA on the basis of ISPM 11 and EPPO standards (EPPO, 2025).

This means that systematics does not stand still — it develops, and quarantine lists reflect these changes. For example, in 2025, Tomato brown rugose fruit virus (ToBRFV) was added to list A2 — a new virus causing serious losses in tomatoes (EPPO, 2025). This means that agronomists and phytopathologists must be aware of taxonomic changes and new threats.

4.3. Identification of Quarantine Objects: Morphology and Molecules

The quarantine service is an area where the accuracy of identification is of critical importance. An error can lead to a dangerous pathogen being missed at the border or, conversely, to a healthy consignment being destroyed. Therefore, quarantine diagnostics uses the entire arsenal of methods available to systematics.

Morphological methods remain the basis of quarantine diagnostics. Agrios (2005) describes that for identifying fungi, spores and sporulating structures are used; for nematodes, morphometric characters (size, shape, arrangement of organs); for insects, external morphological characters. For example, to identify Globodera rostochiensis and G. pallida, morphometric characters of cysts and larvae are used (EPPO, 2025).

However, morphological identification has limitations. Many species are morphologically indistinguishable but differ in pathogenicity and require different quarantine measures. In addition, morphological identification requires high qualification of the specialist and often takes a long time.

Molecular methods have revolutionized quarantine diagnostics. Agrios (2005) points out that polymerase chain reaction (PCR) and DNA sequencing make it possible to detect a pathogen in plant tissues at early stages of infection, when its presence is minimal. This is especially important for quarantine objects, which may be present in seeds or planting material at low concentrations.

Blancard (2012) describes the use of molecular methods for detecting Clavibacter michiganensis subsp. michiganensis (the causal agent of bacterial canker of tomato) in seeds. For this, DNA primers specific to the internal transcribed spacers of ribosomal DNA are used. This makes it possible to identify infected seeds before sowing and prevent the spread of the disease (Blancard, 2012).

EPPO (2025) notes that various molecular methods are used to detect quarantine objects, including PCR, real-time PCR, LAMP, and sequencing. For example, to detect Ralstonia solanacearum in soil and water, PCR tests are used, and to identify races and strains, multiplex PCR is used.

Serological methods, such as ELISA, are widely used for mass testing of seeds and plants for viruses. Blancard (2012) notes that ELISA is used to detect tomato mosaic virus (ToMV), tomato spotted wilt virus (TSWV), and many others. These methods are rapid, relatively inexpensive, and suitable for analyzing large samples.

Collections and databases play an important role in quarantine diagnostics. Haverkort and Anisimov (2007) describe the collection of the All-Russian Institute of Plant Genetic Resources (VIR), which includes thousands of accessions of potato and its wild relatives. Such collections serve as references for comparison and identification. In addition, international databases such as the EPPO Global Database contain information on quarantine organisms, their distribution, and methods of detection and identification (EPPO, 2025).

4.4. Risks of Introduction: New Pathogens, Pests, Weeds

Plant quarantine is not only the control of already known pathogens but also the prevention of the introduction of new, still unknown threats. Agrios (2005) emphasizes that pathogens can be introduced in the form of spores or eggs on unsuspected carriers, and latent infections of seeds and other reproductive organs can persist even after treatment.

Modern globalization of trade and tourism increases the risk of introducing new pathogens. EPPO (2025) notes that the increasing globalization of markets and the expansion of human travel around the world have led to an increase in the intensity and frequency of introduction of invasive organisms into various countries. Therefore, suitable and effective management strategies are needed for these invasive pests and pathogens.

Caliskan et al. (2023) give an example with potato. They note that pathotype Ro1 of the golden potato cyst nematode (Globodera rostochiensis) predominates in Russia, but other pathotypes (Ro2, Ro3, Ro4, Ro5) are widespread in Europe, and there is a possibility of their introduction into Russia. Therefore, Russian breeders must work not only on resistance to pathotype Ro1 but also begin to use source material possessing resistance to various pathotypes of G. rostochiensis and other species — G. pallida (Pa1, Pa2, Pa3) (Caliskan et al., 2023).

Another example is Tomato brown rugose fruit virus (ToBRFV). This virus was first described in 2014 in Israel and has since spread to Europe, America, and Asia. It causes serious losses in tomatoes and has been included in EPPO list A2 (EPPO, 2025). This shows that quarantine lists must be constantly updated to reflect new threats.

Weeds are also objects of quarantine. EPPO (2025) includes in list A2 such invasive species as Ambrosia artemisiifolia (common ragweed), Heracleum sosnowskyi (Sosnowsky’s hogweed), Solidago canadensis (Canada goldenrod), and many others. These plants cause damage to agriculture by competing with cultivated plants for light, water, and nutrients, and some of them are toxic to humans and animals.

4.5. International Cooperation: EPPO, FAO, IPPC

Plant quarantine is an area in which international cooperation is critically important. Pathogens do not recognize borders, and the efforts of one country may be nullified if neighboring countries do not take similar measures.

IPPC (International Plant Protection Convention) is an international treaty aimed at protecting plants and plant products from pests. IPPC was adopted in 1951 under the auspices of FAO (Food and Agriculture Organization of the United Nations) and currently has more than 180 member countries. IPPC develops international standards for phytosanitary measures (ISPM), which are the basis for national quarantine legislation (IPPC, 1997).

EPPO (European and Mediterranean Plant Protection Organization) is a regional plant protection and quarantine organization that unites 52 member countries. EPPO develops standards, conducts pest risk analysis, publishes lists A1 and A2, and coordinates the efforts of member countries in controlling quarantine organisms (EPPO, 2025).

EPPO (2025) describes the procedure for developing standards. EPPO standards are developed by working groups and panels of experts, approved by the EPPO Council, and published in the EPPO Bulletin. The standards cover a wide range of issues: from pest risk analysis to diagnostic protocols and control measures.

FAO (Food and Agriculture Organization) plays a key role in coordinating international efforts in plant quarantine. FAO provides the secretariat for IPPC and supports the development of international standards. In addition, FAO publishes guidelines and recommendations on plant quarantine (FAO, 2013).

Agrios (2005) notes that in the United States there is the National Plant Germplasm Quarantine Center in Glenn Dale, Maryland, where all introduced plants are held and tested for certain pathogens for 1–4 years before release. This is an example of how systematics and quarantine work together to protect the country from the introduction of dangerous pathogens (Agrios, 2005).

4.6. The Role of Collections and Databases in Quarantine

Collections and databases are the infrastructure of plant quarantine. Without reference specimens, it is impossible to identify a pathogen accurately. Without databases, it is impossible to quickly obtain information on the distribution, biology, and control methods of a quarantine object.

Haverkort and Anisimov (2007) describe the collection of the All-Russian Institute of Plant Genetic Resources (VIR), which includes about 9,000 accessions of potato and its wild relatives. This collection serves as a reference for identifying pathogens and for breeding for resistance. In addition, VIR conducts comprehensive evaluation of accessions for resistance to diseases and pests, including quarantine objects (Haverkort and Anisimov, 2007).

EPPO (2025) maintains the EPPO Global Database — an online database that contains information on quarantine organisms, their distribution, and methods of detection and identification. The database includes more than 90,000 records on pests and their hosts. It is available to plant quarantine specialists worldwide (EPPO, 2025).

Caliskan et al. (2023) describe potato germplasm databases, including the CIP (International Potato Center) database in Peru, which contains information on 4,727 accessions of cultivated potato and 4,052 accessions of wild potato. These databases are used to search for sources of resistance to diseases and pests, including quarantine objects (Caliskan et al., 2023).

4.7. Examples of Quarantine Objects

Let us consider several concrete examples of quarantine objects to illustrate how systematics works in quarantine.

Ralstonia solanacearum (bacterial wilt). EPPO (2025) includes this species in list A2. It is a gram-negative bacterium that affects more than 200 plant species, including potato, tomato, eggplant, pepper, and many others. The bacterium can be transmitted with seeds, soil, plant residues, and water. For diagnosis, serological and molecular methods, including PCR, are used. Quarantine measures include prohibiting the import of infected planting material, disinfection of soil, and destruction of infected plants (EPPO, 2025).

Globodera rostochiensis (golden potato cyst nematode). EPPO (2025) includes this species in list A2. It is a cyst-forming nematode that affects potato, tomato, eggplant, and other solanaceous crops. Cysts can survive in soil for more than 30 years. For diagnosis, morphometric characters of cysts and larvae, as well as molecular methods, are used. Quarantine measures include prohibiting the import of infected planting material, disinfection of soil, and crop rotation with non-host crops (EPPO, 2025).

Synchytrium endobioticum (potato wart). EPPO (2025) includes this species in list A2. It is an obligate parasite that affects potato and causes galls on tubers. The pathogen can survive in soil for more than 40 years in the form of resting spores. For diagnosis, biological tests with susceptible potato cultivars, as well as microscopy of resting spores, are used. Quarantine measures include prohibiting the import of infected planting material, disinfection of soil, and the use of resistant cultivars (EPPO, 2025).

Tomato brown rugose fruit virus (ToBRFV). EPPO (2025) includes this virus in list A2. It is a tobamovirus that affects tomato and pepper and causes serious yield losses. The virus can be transmitted with seeds, by contact, and through infected plants. For diagnosis, molecular methods, including RT-PCR, are used. Quarantine measures include prohibiting the import of infected seeds and plants, as well as destruction of infected consignments (EPPO, 2025).

5.1. Systematics as the Basis for Choosing a Biocontrol Agent

The first thing to do when developing a biocontrol strategy is to identify the target. As we already said in chapter 2, accurate diagnosis of the pathogen or pest is the first step toward successful protection. But it is no less important to identify the biocontrol agent itself. An error in identification can lead to the agent proving ineffective against the target species or, even worse, beginning to attack beneficial organisms.

Systematics provides tools for such identification. Morphological characters, molecular markers, and serological tests all make it possible to determine precisely the species identity of both the target and the agent. But systematics is not limited to identification. It provides an understanding of phylogenetic relationships that make it possible to predict the specificity of the agent.

Fujino et al. (2025), in their review on the role of predatory protists in suppressing pathogens, emphasize that accurate identification of the biocontrol agent is critically important, since different species may have different specificity. For example, Colpoda sp. is capable of directly feeding on Ralstonia solanacearum, reducing tomato disease incidence. However, other protist species may not be effective against this pathogen or, conversely, may attack beneficial bacteria. Without systematic knowledge, it is impossible to predict which species will be effective and safe.

Hasanuzzaman (2019), in the chapter on integrated plant protection, notes that biocontrol is not simply replacing one chemical product with another. It is a strategy that requires a deep understanding of ecological interactions. Systematics here serves as the basis for such understanding, since it makes it possible to establish which organisms are natural enemies of pests, which are antagonists of pathogens, and which are neutral or beneficial.

5.2. Main Groups of Biocontrol Agents

Biocontrol agents can be divided into several groups depending on their taxonomic affiliation and mechanism of action. Let us consider the main ones.

Entomophages and acariphages are predatory and parasitic insects and mites that feed on pests. These include, for example, Trichogramma (Trichogramma spp.), Phytoseiulus (Phytoseiulus persimilis), Encarsia (Encarsia formosa), and Macrolophus (Macrolophus caliginosus). Hasanuzzaman (2019) describes the use of Trichogramma for controlling sugarcane stem borer and other lepidopteran pests, and Phytoseiulus for controlling spider mites. These agents possess high specificity, and their effectiveness depends on the precise correspondence of the agent species to the target species.

Antagonistic microorganisms are bacteria and fungi that suppress pathogens through competition, antibiosis, parasitism, or induction of plant defense reactions. These include, for example, Trichoderma spp., Bacillus subtilis, Pseudomonas fluorescens, and Gliocladium virens. Agrios (2005) describes the use of Trichoderma harzianum for controlling Rhizoctonia solani, Pythium spp., and Sclerotium rolfsii. Blancard (2012) notes that Trichoderma is also effective against Botrytis cinerea on tomatoes.

Entomopathogens are microorganisms that cause diseases in insects. The best known is Bacillus thuringiensis (Bt), which produces toxins specific to larvae of Lepidoptera, Diptera, and Coleoptera. Hasanuzzaman (2019) describes the use of Bt for controlling many pests, including cutworms and borers. Other entomopathogens include the fungi Beauveria bassiana, Metarhizium anisopliae, and viruses such as baculoviruses.

Predatory protists are a relatively new group of biocontrol agents. Fujino et al. (2025) describe how predatory protists such as Cercomonas spp., Acanthamoeba spp., Leptomyxa spp., and Colpoda sp. can directly feed on pathogenic fungi and bacteria. For example, Colpoda sp. was isolated from the tomato rhizosphere and showed the ability to directly consume Ralstonia solanacearum in greenhouse experiments. This opens new possibilities for biocontrol, since protists can act both directly (by eating pathogens) and indirectly (by stimulating the activity of antagonistic bacteria).

5.3. Systematics and Specificity: How to Avoid Undesirable Effects

One of the main problems of biocontrol is undesirable effects on non-target organisms. If a biocontrol agent has broad specificity, it may attack beneficial species, disrupting ecological balance. Systematics helps predict such risks, since it makes it possible to assess the phylogenetic proximity between the target and non-target species.

Fujino et al. (2025) warn that, although most studies report a positive effect of predatory protists, protists may potentially transport, protect, and enhance the survival of pathogenic microorganisms. For example, some bacteria can survive and multiply inside the digestive vacuole of protists and even avoid the effects of disinfectants. Although such cases have not yet been described in soil ecosystems, the possibility that protists may be vectors of pathogens must be thoroughly investigated before they are used as biocontrol agents (Fujino et al., 2025).

Hasanuzzaman (2019) emphasizes that the use of biocontrol agents may have negative consequences. For example, bacterial agents producing chitinase or toxins may harm non-target fungi, nematodes, and earthworms. Therefore, before releasing an agent, a thorough assessment of its specificity is necessary, including tests on closely related species. Systematics provides the basis for such assessment: knowing phylogenetic relationships, one can predict which species may be affected.

Agrios (2005) also notes that some antagonists may be effective in the laboratory but not in the field, since they cannot compete with the existing microflora. Systematics helps understand the ecological niches of the agent and the target, which makes it possible to predict its survival and activity under specific conditions.

5.4. Examples of Successful Biocontrol Application

Let us consider several concrete examples to illustrate how systematics works in biocontrol.

Trichogramma (Trichogramma spp.). This is a genus of parasitoid wasps that lay eggs in the eggs of lepidopteran pests. Hasanuzzaman (2019) describes the use of Trichogramma chilonis for controlling the sugarcane stem borer. The systematics of Trichogramma is complex: there are many species that differ in host specificity. For successful use, it is necessary to identify precisely the Trichogramma species and the pest species. An error can lead to the parasitoid not finding a host or attacking non-target species. Molecular methods, such as PCR and sequencing, make it possible to distinguish closely related Trichogramma species (Hasanuzzaman, 2019).

Phytoseiulus (Phytoseiulus persimilis). This is a predatory mite that feeds on spider mites. Hasanuzzaman (2019) notes that Phytoseiulus is an effective biocontrol agent in greenhouses. The systematics of mites is crucial: it is necessary to identify precisely both the predator and the prey. Some spider mite species may be resistant to Phytoseiulus, or Phytoseiulus itself may be sensitive to certain conditions. Understanding the phylogenetic relationships between mite species makes it possible to predict which predator-prey pairs will be effective (Hasanuzzaman, 2019).

Bacillus thuringiensis (Bt). This is an entomopathogenic bacterium that produces crystalline toxins (Cry proteins) specific to certain groups of insects. Hasanuzzaman (2019) describes the use of Bt for pest control. The systematics of Bt includes many strains that differ in their spectrum of action. For example, Bt subsp. kurstaki is effective against Lepidoptera, Bt subsp. israelensis against Diptera, and Bt subsp. tenebrionis against Coleoptera. For successful use, it is necessary to identify precisely the strain and its toxins, as well as the pest species. The systematics of insects and the systematics of bacteria work together to ensure effectiveness and safety (Hasanuzzaman, 2019).

Trichoderma spp. This is a genus of fungi that are antagonists of many soilborne pathogens. Agrios (2005) describes the use of Trichoderma harzianum for controlling Rhizoctonia solani, Pythium spp., and Sclerotium rolfsii. Blancard (2012) notes that Trichoderma is also effective against Botrytis cinerea on tomatoes. The systematics of Trichoderma is complex: there are many species that differ in mechanisms of action and specificity. Molecular methods, such as sequencing of ITS regions, make it possible to identify species accurately. Understanding the phylogeny of Trichoderma helps select the most effective strain for a particular pathogen (Agrios, 2005; Blancard, 2012).

Predatory protists. Fujino et al. (2025) describe the use of Colpoda sp. for controlling Ralstonia solanacearum on tomatoes. In greenhouse experiments, Colpoda sp. directly consumed R. solanacearum, reducing disease incidence. Other studies have shown that Cercomonas spp. and Bacillus spp. interact, suppressing Fusarium spp. The systematics of protists is in a stage of active development, and molecular methods make it possible to identify new species promising for biocontrol. However, the risks mentioned above must be taken into account (Fujino et al., 2025).

5.5. Compatibility of Biocontrol with Other Protection Methods

Biocontrol is rarely used in isolation. As a rule, it is integrated with other protection methods within an integrated pest management (IPM) system. Hasanuzzaman (2019) emphasizes that IPM is a strategy that combines cultural, mechanical, genetic, and biological methods, considering chemical control as a last resort.

The compatibility of biocontrol with other methods is crucial. For example, some chemical pesticides may be toxic to biocontrol agents. Therefore, when choosing pesticides, their compatibility with beneficial organisms must be taken into account. Hasanuzzaman (2019) notes that the use of selective pesticides that do not kill entomophages makes it possible to integrate chemical and biological control.

Cultural methods can also increase the effectiveness of biocontrol. For example, the use of cover crops, crop rotation, and proper irrigation creates conditions favorable for the survival and activity of antagonists. Haverkort and Anisimov (2007) note that in potato breeding for resistance to diseases and pests, both genetic resources and biocontrol agents are used. For example, cultivars resistant to nematodes reduce the need for chemical nematicides and create conditions for the activity of natural enemies of nematodes.

5.6. Monitoring Effectiveness and Safety

After releasing a biocontrol agent, it is necessary to monitor its effectiveness and safety. This includes assessing the reduction in pest or pathogen numbers, assessing the survival and spread of the agent, and assessing the impact on non-target organisms.

Fujino et al. (2025) emphasize that the interaction between protists and pathogens must be thoroughly studied before they are used as biocontrol agents. This includes specificity tests, assessment of risks of pathogen transfer, and assessment of effects on beneficial microorganisms. Systematics provides tools for such assessment: molecular methods make it possible to identify the agent and the target, while phylogenetic analysis makes it possible to predict potential non-target effects (Fujino et al., 2025).

Hasanuzzaman (2019) notes that monitoring the effectiveness of biocontrol should be part of the overall IPM system. This includes regular field surveys, the use of traps for monitoring pests, and assessment of economic effectiveness. Systematics helps in identifying both pests and biocontrol agents, which is necessary for accurate monitoring.

EPPO (2025) notes that the use of biocontrol agents is regulated by national and international standards. For example, EPPO develops standards for assessing the risks associated with the introduction of biocontrol agents. This includes assessing specificity, assessing potential impact on non-target species, and developing measures to prevent undesirable effects. Systematics is the basis for such assessments, since it makes it possible to identify the agent and assess its phylogenetic relationships with other species (EPPO, 2025).

6.1. Agrocenoses as Part of the Biosphere

Agricultural lands occupy about 40% of the land surface. This is a huge territory that cannot be considered in isolation from natural ecosystems. Agrocenoses are not “empty” spaces filled only with cultivated plants. They are complex ecosystems inhabited by hundreds and thousands of species: soil microorganisms, insects, birds, mammals, and weeds. Many of these species are beneficial or neutral, and some are harmful.

Hasanuzzaman (2019) emphasizes that sustainable agriculture is impossible without taking biodiversity into account. Cultural methods such as cover crops, intercrops, crop rotation, and mulching not only reduce pest and disease numbers but also support beneficial organisms: pollinators, entomophages, and antagonists of pathogens. For example, cover crops increase the numbers of ground beetles and spiders that feed on pests. Intercropping legumes with cereals reduces disease incidence and increases yield (Hasanuzzaman, 2019).

Fujino et al. (2025) add that soil protists are a most important component of biodiversity that directly influences plant health. Predatory protists regulate the numbers of bacteria and fungi, including pathogens, and promote nutrient cycling. Their diversity is an “insurance” for the agrocenosis, since different species perform different functions. The loss of this diversity makes the system less resistant to stresses.

Thus, biodiversity conservation in agrocenoses is not only the conservation of rare species but also the maintenance of functional diversity that ensures the productivity and sustainability of agriculture.

6.2. The Role of Systematics in Assessing Diversity

How can biodiversity be assessed? How many species inhabit an agrocenosis? Which of them are rare, which are common, which are invasive? It is impossible to answer these questions without systematics.

Pandey (2021) emphasizes that systematics is the basis for all biology, since organisms cannot be discussed scientifically until a classification is achieved that allows them to be recognized and named. Biodiversity assessment begins with inventory: collecting specimens, identifying them, and describing them. For this, morphological keys, molecular methods (DNA barcoding), reference collections, and databases are used.

Judd et al. (2018) note that a phylogenetic approach to systematics makes it possible not only to list species but also to assess their evolutionary uniqueness. Phylogenetic diversity is a measure that takes into account not only the number of species but also their evolutionary relationships. For example, conserving two closely related species is less valuable from the standpoint of evolutionary history than conserving two species belonging to different major clades. Such an approach makes it possible to set conservation priorities (Judd et al., 2018).

Caliskan et al. (2023) show how systematics is used to assess potato diversity. Section Petota of the genus Solanum includes about 200 species distributed from the southwestern United States to central Argentina. Molecular markers (SSR, SNP) make it possible to assess genetic diversity within and between species, identify duplicates in collections, and identify unique genotypes. Without such assessment, it is impossible to manage gene banks effectively and use resources for breeding (Caliskan et al., 2023).

Biancardi et al. (2012) similarly describe the assessment of Beta maritima diversity. Molecular markers and morphological characters make it possible to identify populations that are sources of valuable genes and to determine priorities for their conservation. For example, populations from the Po Delta in Italy proved to be a source of resistance to Cercospora leaf spot, while populations from Denmark proved to be a source of resistance to rhizomania (Biancardi et al., 2012).

6.3. Indicator Species, Rare and Endangered Species

In biodiversity conservation, indicator species play a special role — species that react sensitively to environmental changes and can serve as a “litmus test” for assessing the state of an ecosystem. For example, many soil invertebrates (springtails, mites, earthworms) are indicators of soil health. Their diversity and abundance reflect the level of organic matter, moisture, pH, and the presence of pollutants.

Systematics is necessary for identifying indicator species. An error in identification can lead to incorrect conclusions about the state of the ecosystem. Molecular methods, such as DNA barcoding, make it possible to identify species quickly and accurately, even if they are represented by fragments or larvae.

Rare and endangered species are a special category. Red books, national and international lists of protected species — all of these are built on systematic data. For example, EPPO (2025) includes in list A2 invasive plants such as Ambrosia artemisiifolia, Heracleum sosnowskyi, and Solidago canadensis. These species cause damage to agriculture and natural ecosystems, and their identification is the first step toward control.

In agrocenoses, rare species may be not only “Red Book” species but also local cultivars, landraces, and wild relatives of cultivated plants. Caliskan et al. (2023) note that local potato landraces in the Andes number more than 3,000 forms, many of which are adapted to specific conditions and possess valuable traits. Their loss means the loss of genetic diversity that may be necessary for future breeding.

6.4. Conservation Strategies

Biodiversity conservation includes two main approaches: in situ and ex situ.

In situ conservation is the conservation of populations in their natural habitat. This method makes it possible to preserve not only genes but also ecological interactions, evolutionary processes, and adaptive potential. Biancardi et al. (2012) emphasize the importance of in situ conservation of Beta maritima, since many populations of this species are threatened with extinction due to habitat destruction. They note that it is necessary to identify not only the species subject to protection but also to determine measures for their in situ and ex situ conservation (Biancardi et al., 2012).

Caliskan et al. (2023) note that in situ conservation of wild potato relatives is especially important, since it allows genetic diversity and the adaptive potential of populations to be preserved. However, this method is vulnerable to natural disasters, anthropogenic impact, and climate change.

Ex situ conservation is the conservation of plant material outside its natural habitat. This is the most widespread method, including the creation of gene banks where seeds, tubers, DNA, and pollen are stored, as well as in vitro collections and cryopreservation. Haverkort and Anisimov (2007) describe the collection of the All-Russian Institute of Plant Genetic Resources (VIR), which contains about 9,000 potato accessions, including 3,000 accessions of wild species. About 300 old cultivars created 60 or more years ago are unique because they are preserved only in the VIR gene bank (Haverkort and Anisimov, 2007).

Caliskan et al. (2023) provide data on the largest potato gene banks: the International Potato Center (CIP) in Peru (4,727 accessions of cultivated potato and 4,052 accessions of wild potato), the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) in Germany (6,200 accessions), the U.S. Potato Gene Bank (5,700 accessions), and the All-Russian Institute of Plant Genetic Resources (VIR) (about 10,000 accessions). In vitro collections play a special role for potato, since it propagates vegetatively and its tubers cannot be stored for long periods. Cryopreservation is the most promising method of long-term storage, making it possible to preserve material at -196 °C indefinitely (Caliskan et al., 2023).

Agroecological schemes are an approach that integrates biodiversity conservation into agricultural practice. Hasanuzzaman (2019) describes the use of cover crops, intercrops, crop rotation, mulching, and biocontrol to support beneficial organisms. For example, cover crops increase the numbers of ground beetles and spiders that feed on pests. Intercropping legumes with cereals reduces disease incidence and increases yield (Hasanuzzaman, 2019). Such schemes not only conserve biodiversity but also increase the resilience of agrocenoses.

Farmer cultivars and landraces are an important reservoir of genetic diversity. Caliskan et al. (2023) note that local potato landraces in the Andes number more than 3,000 forms, many of which are adapted to specific conditions and possess valuable traits. Their conservation is not only the conservation of genes but also the conservation of traditional knowledge and cultural heritage. Biancardi et al. (2012) emphasize that old beet cultivars created 60 or more years ago are unique and preserved only in gene banks. Their loss means the loss of genetic diversity that may be necessary for future breeding.

6.5. Citizen Science and Monitoring

Biodiversity conservation is impossible without monitoring. It is necessary to know which species live where, how their numbers change, and what threats they face. Citizen science is an approach that involves volunteers in collecting biodiversity data. For example, platforms such as iNaturalist, eBird, and PlantNet allow anyone to photograph a plant or animal and receive help in identification. These data are used by scientists to monitor the distribution of species, including invasive and rare ones.

Judd et al. (2018) note that herbaria and other scientific collections are a most important resource for biodiversity monitoring. They contain specimens collected over centuries that make it possible to track changes in the distribution and morphology of species. Digitization of collections and the creation of online databases make these resources accessible to a wide audience.

EPPO (2025) maintains the EPPO Global Database — an online database that contains information on quarantine organisms, their distribution, and methods of detection and identification. The database includes more than 90,000 records on pests and their hosts. It is available to plant quarantine specialists worldwide (EPPO, 2025).

Citizen science and monitoring are not only data collection but also education. Participation in such projects increases people’s awareness of biodiversity and its importance. This is especially important for agronomists, who work daily with living organisms and can make a significant contribution to monitoring.

6.6. Examples: From Beta maritima to Soil Protists

Let us consider several concrete examples to illustrate how systematics works in biodiversity conservation.

Beta maritima. Biancardi et al. (2012) describe that B. maritima is distributed along the coasts of the Mediterranean and North Seas. Many populations of this species are threatened with extinction due to habitat destruction, urbanization, and climate change. However, B. maritima is a valuable source of genes for resistance to Cercospora leaf spot, rhizomania, and nematodes. Conservation of this species is not only biodiversity conservation but also conservation of a resource for future breeding. Biancardi et al. (2012) emphasize the need for both in situ and ex situ conservation of B. maritima, including seed collection, creation of gene banks, and protection of natural populations.

Wild potato relatives. Caliskan et al. (2023) note that wild potato relatives are distributed from the southwestern United States to central Argentina. They possess enormous genetic diversity and are a source of resistance to late blight, viruses, nematodes, and insects. However, many populations are threatened by changes in land use and climate change. Conservation of these resources requires both in situ protection of natural habitats and ex situ conservation in gene banks. Caliskan et al. (2023) describe the largest potato gene banks, including CIP, IPK, VIR, and others, which preserve thousands of accessions of wild species. Cryopreservation makes it possible to preserve material indefinitely, which is especially important for vegetatively propagated crops (Caliskan et al., 2023).

Soil protists. Fujino et al. (2025) open a new page in biodiversity conservation. Soil protists are a huge and poorly studied group of organisms that plays a key role in the functioning of soil ecosystems. Predatory protists regulate the numbers of bacteria and fungi, including pathogens, and promote nutrient cycling. Their diversity is an “insurance” for the agrocenosis. However, knowledge about the diversity of protists is still very limited. Fujino et al. (2025) emphasize that further study of protists and their interactions with pathogens is necessary in order to use them for sustainable management of plant pathogens. Conservation of this invisible diversity is conservation of the functional basis of healthy soils (Fujino et al., 2025).

7.1. Systematics as an Integrative Discipline

Systematics is not one of many biological disciplines. It is the discipline that unites them all. Pandey (2021) emphasizes that systematics is the basis for all biology, since organisms cannot be discussed scientifically until a classification is achieved that allows them to be recognized and named. Systematics collects and summarizes everything known about the characteristics of organisms: geographical, morphological, physiological, genetic, ecological, and molecular (Pandey, 2021).

In agronomy this is especially important, since the agronomist works with living organisms from different taxonomic groups. Cultivated plants belong to flowering plants (Angiospermae), but their pathogens may be fungi (Fungi), oomycetes (Oomycota), bacteria (Bacteria), viruses, viroids, and phytoplasmas. Pests are insects (Insecta), mites (Acari), nematodes (Nematoda), rodents (Rodentia), and birds (Aves). Weeds are representatives of dozens of families of flowering plants. Beneficial organisms are entomophages (insects and mites), antagonists (fungi and bacteria), and pollinators (insects, birds, mammals).

Without systematics, the agronomist cannot orient himself in this diversity. He does not know which organisms are beneficial, which are harmful, and which are neutral. He does not know how they interact, how to identify them, or how to manage their populations. Systematics is the “map” that makes it possible to navigate the living world.

Judd et al. (2018) note that systematics occupies a central position in evolutionary biology and plays an increasingly important role in many other disciplines, including ecology, molecular biology, developmental biology, and even anthropology. In agronomy, systematics unites botany, zoology, mycology, microbiology, virology, nematology, entomology, and other disciplines into a unified system of knowledge about the living organisms with which the agronomist works.

7.2. Phylogeny as an Evolutionary Perspective

Phylogeny is the evolutionary history of a group of organisms, which is reconstructed on the basis of the analysis of characters. Judd et al. (2018) emphasize that a phylogenetic approach to systematics makes it possible not only to list species but also to understand their evolutionary relationships. A phylogenetic tree is a diagram reflecting kinship relationships between ancestors and descendants (Judd et al., 2018).

In agronomy, phylogeny has direct practical significance. Biancardi et al. (2012) show how phylogenetic relationships between Beta maritima and cultivated beet made it possible to purposefully transfer genes for resistance to Cercospora leaf spot, rhizomania, and nematodes. Caliskan et al. (2023) describe how the phylogeny of the genus Solanum (section Petota) serves as the basis for searching for sources of resistance to late blight, viruses, nematodes, and insects among wild potato species.

Phylogeny also makes it possible to predict the properties of organisms. If two species are close relatives, they probably possess similar biochemical and ecological characteristics. Judd et al. (2018) give the example of the search for medicinal compounds in plants: having discovered cortisone precursors in some species of the genus Dioscorea, researchers began to search for them in closely related species and found higher concentrations. The same principle works in agronomy: knowing phylogeny, one can predict where to look for donors of economically valuable traits.

Finally, phylogeny provides an evolutionary perspective. It makes it possible to understand how certain traits arose, how they evolved, and how they may change in the future. For example, understanding the evolution of resistance to fungicides makes it possible to predict the emergence of resistant strains and develop resistance management strategies (Agrios, 2005).

7.3. Nomenclature as the Basis of Stable Communication

Nomenclature is the formal naming of taxa in accordance with established rules. Pandey (2021) emphasizes that nomenclature is not simply the assigning of names, but a strict system of rules that guarantees that each name is tied to a certain taxon and cannot be used arbitrarily. For plants, algae, and fungi, the International Code of Nomenclature for algae, fungi, and plants (ICNafp) applies. For bacteria — the International Code of Nomenclature of Prokaryotes. For viruses — the International Committee on Taxonomy of Viruses (ICTV).

In agronomy, nomenclature ensures universal communication. Blancard (2012) describes how scientific names of pathogens allow specialists from different countries to understand each other. Alternaria tomatophila is the same name in Russia, Spain, China, and the United States. Without nomenclature, we would speak different languages, and international cooperation in plant protection would be impossible.

Nomenclature also ensures the continuity of knowledge. If a taxonomic revision has split one species into several, the old names are preserved as synonyms so that information in older publications can still be found. This is especially important in agronomy, where data on pathogens and pests accumulate over decades. Blancard (2012) gives the example of Fusarium oxysporum f. sp. lycopersici, which exists as three races, and knowledge of nomenclature makes it possible to interpret data on cultivar resistance correctly.

Nomenclature is constantly developing. EPPO (2025) notes that when the preferred name of a pest changes after its addition to lists A1 and A2, it is updated at the next revision of the lists. If a taxonomic revision leads to the splitting of a species into several or its merging with others, the categorization of all affected species is reviewed by the Panel on Phytosanitary Measures and the Working Group on Phytosanitary Regulations (EPPO, 2025). This means that the agronomist must follow taxonomic changes and use current names.

7.4. Identification as a Practical Skill

Identification is the process of establishing that an unknown specimen belongs to a known taxon. Pandey (2021) emphasizes that identification is the primary function in taxonomy, and, applying nomenclature, it performs an essential role as a means of communication. For identifying plants, taxonomic keys are used, which are usually dichotomous, that is, consist of a series of two contrasting statements (Pandey, 2021).

In agronomy, identification is a practical skill that is used daily. Agrios (2005) emphasizes that most serious diseases of agricultural crops appear on a few plants, spread rapidly, and are difficult to treat after development has begun. Therefore, accurate identification of the pathogen or pest is the first and mandatory step toward successful protection (Agrios, 2005).

Blancard (2012) describes that many symptoms caused by different pathogens can be very similar. For example, spots caused by Alternaria tomatophila, Stemphylium spp., and some bacteria may look almost identical to an inexperienced eye. However, accurate diagnosis requires not only visual inspection but also an understanding of the biology of the causal agent, its taxonomic affiliation, and its life cycle. Only on this basis can the correct protection strategy be chosen (Blancard, 2012).

Identification is also important for plant quarantine. EPPO (2025) publishes lists A1 and A2 of quarantine pests, and for quarantine service inspectors it is critically important to be able to identify these objects and distinguish them from closely related but non-quarantine species. Systematics provides tools for such identification: morphological keys, molecular tests, and reference collections (EPPO, 2025).

In biocontrol, identification is also crucial. Fujino et al. (2025) emphasize that accurate identification of the biocontrol agent is critically important, since different species may have different specificity. For example, Colpoda sp. is capable of directly feeding on Ralstonia solanacearum, reducing tomato disease incidence. However, other protist species may not be effective against this pathogen or, conversely, may attack beneficial bacteria. Without systematic knowledge, it is impossible to predict which species will be effective and safe (Fujino et al., 2025).

7.5. Collections and Databases as Infrastructure

Collections and databases are the infrastructure of systematics and agronomy. Without reference specimens, it is impossible to identify a pathogen accurately. Without databases, it is impossible to quickly obtain information on the distribution, biology, and control methods of a quarantine object.

Haverkort and Anisimov (2007) describe the collection of the All-Russian Institute of Plant Genetic Resources (VIR), which is one of the largest in the world. It contains about 9,000 potato accessions, including 3,000 accessions of wild species, 3,500 accessions of cultivated species, 2,100 cultivars, and 400 interspecific hybrids and dihaploids. About 300 old cultivars created 60 or more years ago are unique because they are preserved only in the VIR gene bank (Haverkort and Anisimov, 2007).

Caliskan et al. (2023) provide data on the largest potato gene banks: the International Potato Center (CIP) in Peru, the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) in Germany, the U.S. Potato Gene Bank, the All-Russian Institute of Plant Genetic Resources (VIR), and others. In vitro collections play a special role for potato, since it propagates vegetatively and its tubers cannot be stored for long periods. Cryopreservation is the most promising method of long-term storage, making it possible to preserve material at -196 °C indefinitely (Caliskan et al., 2023).

Databases are also a most important resource. EPPO (2025) maintains the EPPO Global Database — an online database that contains information on quarantine organisms, their distribution, and methods of detection and identification. The database includes more than 90,000 records on pests and their hosts. It is available to plant quarantine specialists worldwide (EPPO, 2025).

Herbaria and other scientific collections are a most important resource for biodiversity monitoring. Judd et al. (2018) note that herbaria contain specimens collected over centuries that make it possible to track changes in the distribution and morphology of species. Digitization of collections and the creation of online databases make these resources accessible to a wide audience (Judd et al., 2018).

7.6. Molecular Methods as a Modern Tool

Molecular methods have revolutionized systematics and diagnostics. Agrios (2005) points out that polymerase chain reaction (PCR) and DNA sequencing make it possible to detect a pathogen in plant tissues at early stages of infection, when its presence is minimal. This is especially important for quarantine objects and for seed material (Agrios, 2005).

Blancard (2012) describes the use of molecular methods for detecting Clavibacter michiganensis subsp. michiganensis (the causal agent of bacterial canker of tomato) in seeds. For this, DNA primers specific to the internal transcribed spacers of ribosomal DNA are used. This makes it possible to identify infected seeds before sowing and prevent the spread of the disease (Blancard, 2012).

Caliskan et al. (2023) describe various types of markers used to characterize potato germplasm: RAPD, AFLP, SSR, ISSR, IRAP, and SNP. SSR (microsatellites) possess high polymorphism, codominance, and reproducibility. SNP (single nucleotide polymorphisms) are the most common type of genetic variation, and the SolCAP Infinium platform allows high-throughput genotyping (Caliskan et al., 2023).

QTL mapping makes it possible to identify loci controlling quantitative traits, such as disease resistance, yield, and tuber quality. Caliskan et al. (2023) describe the mapping of QTL for resistance to late blight, potato virus Y (PVY), nematodes, and other pathogens. GWAS (genome-wide association study) uses historical recombinations in existing natural populations to identify genes associated with phenotypic traits (Caliskan et al., 2023).

Haverkort and Anisimov (2007) note that in recent years molecular genetic methods, including PCR analysis, have been used in potato breeding for genotyping cultivars, studying the variability of meristem lines, identifying mutations, detecting viruses and viroids, and also for studying breeding material using DNA markers of resistance genes to various pathogens (Haverkort and Anisimov, 2007).

Fujino et al. (2025) open new horizons by showing that molecular methods make it possible to study even such poorly studied groups as soil protists. DNA sequencing and metabarcoding make it possible to identify new protist species and assess their role in suppressing pathogens (Fujino et al., 2025).

7.7. Critical Thinking as the Basis of Professionalism

Systematics is not a dogma but a developing field of knowledge. Taxonomic revisions occur constantly: species are renamed, genera are reorganized, phylogenetic trees are refined. A modern agronomist must be prepared for the fact that the names he learned at university may change. But this is not a reason to ignore systematics — on the contrary, it is a reason to follow updates and use modern tools.

Pandey (2021) emphasizes that systematics is the basis for all biology, since organisms cannot be discussed scientifically until a classification is achieved that allows them to be recognized and named. In agronomy this is especially important, because errors in identification can lead to significant economic losses and ecological consequences (Pandey, 2021).

Agrios (2005) notes that most control methods are aimed at protecting plants from disease rather than treating them. Therefore, diagnosis at early stages is the key to success. And systematics is the tool that makes such diagnosis possible (Agrios, 2005).

Hasanuzzaman (2019) emphasizes that integrated plant protection (IPM) is a strategy that combines cultural, mechanical, genetic, and biological methods, considering chemical control as a last resort. Systematics lies at the basis of IPM, since it makes it possible to identify pests and pathogens, understand their biology and ecology, and choose the most effective and safe control methods (Hasanuzzaman, 2019).

Judd et al. (2018) note that our knowledge of plant systematics is growing rapidly. New phylogenetic hypotheses appear at high speed, and significant changes can be expected even in the coming years. Under these conditions, it is impossible for a textbook to remain current, and undoubtedly it will be necessary to supplement the material with additional information, possibly obtained through computer databases (Judd et al., 2018).

Critical thinking is the basis of professionalism. The agronomist must be able to assess the reliability of sources, verify identification, take context into account, and make decisions based on evidence. Systematics provides tools for such thinking, but the final decision remains with the specialist.

7.8. Connection of All Course Modules

Our course consisted of several modules: fundamental concepts of systematics, nomenclature, identification methods, phylogenetic analysis, genetic resources, quarantine, biocontrol, and biodiversity conservation. Each of these modules is a separate tool. But only together do they form a coherent picture.

• Fundamental concepts (taxon, clade, phylogeny) provide the theoretical basis.
• Nomenclature ensures stability and universality of communication.
• Identification is a practical skill that allows one to “recognize” objects in the field.
• Phylogeny provides an evolutionary perspective and predictive power.
• Genetic resources (CWR, gene pools) are the material basis for breeding.
• Quarantine is a regulatory function based on systematic data.
• Biological control is the application of systematic knowledge to manage agrocenoses.
• Biodiversity conservation is an ethical and ecological task that also relies on systematics.

All these modules are interconnected. For example, to choose a biological control agent, one needs to know its phylogenetic relationships with other species (to avoid non-target effects), its nomenclature (to identify it correctly), and its ecological preferences (to create conditions for survival). To include a quarantine object in a list, one needs to know its taxonomy, distribution, and harmfulness. To find a source of resistance, one needs to know the phylogeny of the cultivated species and its wild relatives.

Systematics is not the sum of separate disciplines but their integration. It is the “map” by which the agronomist navigates the living world. It is the “language” in which he communicates with colleagues around the world. It is the “tool” that makes it possible to make well-founded decisions.

8.1. Systematics Is Not a Dogma but a Developing Field of Knowledge

One of the key ideas that I would like to leave with you after this course is that systematics is not a frozen dogma but a dynamically developing field of knowledge. Taxonomic revisions occur constantly: species are renamed, genera are reorganized, phylogenetic trees are refined. What only yesterday seemed an immutable truth may today be revised on the basis of new molecular data.

Judd et al. (2018) emphasize that our knowledge of plant systematics is growing rapidly. New phylogenetic hypotheses appear at high speed, and significant changes can be expected even in the coming years. Under these conditions, it is impossible for a textbook to remain current, and undoubtedly it will be necessary to supplement the material with additional information, possibly obtained through computer databases (Judd et al., 2018).

This means that a modern agronomist must be prepared for the fact that the names he learned at university may change. For example, in 2025, Tomato brown rugose fruit virus (ToBRFV) was added to EPPO list A2 — a new virus that no one had heard of ten years earlier (EPPO, 2025). Or another example: the genus Clavibacter was reorganized, and some species previously considered subspecies received the status of independent species (Blancard, 2012). An agronomist who does not follow taxonomic updates risks using outdated names and, as a consequence, making incorrect decisions.

8.2. An Agronomist Who Has Mastered Systematics Makes More Precise and Well-Founded Decisions

The second key idea is that systematics is not simply a set of names but a tool for decision-making. Agrios (2005) emphasizes that most control methods are aimed at protecting plants from disease rather than treating them. Therefore, diagnosis at early stages is the key to success. And systematics is the tool that makes such diagnosis possible.

We have seen in concrete examples how systematics helps:

• choose the correct fungicide by distinguishing fungi and oomycetes (Agrios, 2005);
• select a resistant cultivar by knowing the race of the pathogen (Blancard, 2012);
• identify a quarantine object and prevent its introduction (EPPO, 2025);
• choose an effective and safe biocontrol agent (Fujino et al., 2025; Hasanuzzaman, 2019);
• find a source of resistance among wild relatives of cultivated plants (Biancardi et al., 2012; Caliskan et al., 2023).

An agronomist who has mastered systematics makes more precise and well-founded decisions. He knows which pathogen is in front of him, how to control it, where to look for resistant cultivars, which quarantine measures to apply, and which biological agents to use. He understands that an agrocenosis is part of the biosphere, and that managing it requires a systems approach.

Pandey (2021) emphasizes that systematics is the basis for all biology, since organisms cannot be discussed scientifically until a classification is achieved that allows them to be recognized and named. In agronomy this is especially important, because errors in identification can lead to significant economic losses and ecological consequences (Pandey, 2021).

8.3. The Future of Sustainable Agriculture Is Impossible Without the Integration of Systematic Knowledge

The third key idea is that sustainable agriculture is impossible without the integration of systematic knowledge. We live in an era of global challenges: climate change, population growth, reduction of arable land, and biodiversity loss. Agriculture must adapt to these challenges, becoming more sustainable, productive, and environmentally safe.

Hasanuzzaman (2019) emphasizes that integrated plant protection (IPM) is a strategy that combines cultural, mechanical, genetic, and biological methods, considering chemical control as a last resort. Systematics lies at the basis of IPM, since it makes it possible to identify pests and pathogens, understand their biology and ecology, and choose the most effective and safe control methods (Hasanuzzaman, 2019).

Fujino et al. (2025) open new horizons by showing that even such poorly studied groups as soil protists may be the key to sustainable management of agrocenoses. Predatory protists regulate the numbers of bacteria and fungi, including pathogens, and promote nutrient cycling. Their diversity is an “insurance” for the agrocenosis. However, to use this potential, further systematic research is necessary (Fujino et al., 2025).

Caliskan et al. (2023) and Biancardi et al. (2012) show that the genetic resources of wild relatives of cultivated plants are an inexhaustible source of resistance to diseases, pests, and abiotic stresses. But to use these resources effectively, knowledge of systematics, phylogeny, and genetics is necessary. Without this knowledge, we will not be able to find the needed genes and transfer them into cultivated cultivars.