When resistance gene pyramids are not durable-the role of pathogen diversity

A New Threat to Limber Pine (Pinus flexilis) Restoration in Alberta and Beyond: First Documentation of a Cronartium ribicola Race (vcr4) Virulent to Cr4-Controlled Major Gene Resistance

The coevolution of virulence reduces the effectiveness of host resistance to pathogens, posing a direct threat to forest species and their key ecosystem functions. This is a threat to limber pine (Pinus flexilis), an endangered species in Canada due to rapid decline mainly driven by white pine blister rust caused by Cronartium ribicola. We present the first report of a new, virulent race of C. ribicola (designated vcr4) that overcomes limber pine major gene (Cr4) resistance (MGR). Field surveys found that three parental trees (pf-503, pf-508, and pf-2015-0070) were cankered with white pine blister rust in Alberta, but their progenies showed MGR-related phenotypic segregation postinoculation with an avirulent race of C. ribicola (Avcr4). Genotyping of their progenies using Cr4-linked DNA markers and a genome-wide association study provided additional support that these cankered parental trees had Cr4-controlled MGR. To confirm the presence of vcr4, aeciospores were collected from the cankered pf-503 tree to inoculate resistant seedlings that had survived prior inoculation using the Avcr4 race, as well as seedlings of two U.S. seed parents, one previously confirmed with MGR (Cr4) and one without MGR, respectively. All inoculated seedlings showed clear stem symptoms, confirming that the virulent race is vcr4. These results provide insights into the evolution of C. ribicola virulence and reinforce caution on deployment of Cr4-controlled MGR. The information will be useful for designing a breeding program for durable resistance by layering both R genes with quantitative trait loci for resistance to white pine blister rust in North America.

Current status of molecular rice breeding for durable and broad-spectrum resistance to major diseases and insect pests

In the past century, there have been great achievements in identifying resistance (R) genes and quantitative trait loci (QTLs) as well as revealing the corresponding molecular mechanisms for resistance in rice to major diseases and insect pests. The introgression of R genes to develop resistant rice cultivars has become the most effective and eco-friendly method to control pathogens/insects at present. However, little attention has been paid to durable and broad-spectrum resistance, which determines the real applicability of R genes. Here, we summarize all the R genes and QTLs conferring durable and broad-spectrum resistance in rice to fungal blast, bacterial leaf blight (BLB), and the brown planthopper (BPH) in molecular breeding. We discuss the molecular mechanisms and feasible methods of improving durable and broad-spectrum resistance to blast, BLB, and BPH. We will particularly focus on pyramiding multiple R genes or QTLs as the most useful method to improve durability and broaden the disease/insect spectrum in practical breeding regardless of its uncertainty. We believe that this review provides useful information for scientists and breeders in rice breeding for multiple stress resistance in the future.

High-Resolution Disease Phenotyping Reveals Distinct Resistance Mechanisms of Tomato Crop Wild Relatives against Sclerotinia sclerotiorum

Besides the well-understood qualitative disease resistance, plants possess a more complex quantitative form of resistance: quantitative disease resistance (QDR). QDR is commonly defined as a partial but more durable form of resistance and, therefore, might display a valuable target for resistance breeding. The characterization of QDR phenotypes, especially of wild crop relatives, displays a bottleneck in deciphering QDR's genomic and regulatory background. Moreover, the relationship between QDR parameters, such as infection frequency, lag-phase duration, and lesion growth rate, remains elusive. High hurdles for applying modern phenotyping technology, such as the low availability of phenotyping facilities or complex data analysis, further dampen progress in understanding QDR. Here, we applied a low-cost (<1.000 €) phenotyping system to measure lesion growth dynamics of wild tomato species (e.g., Solanum pennellii or Solanum pimpinellifolium). We provide insight into QDR diversity of wild populations and derive specific QDR mechanisms and their cross-talk. We show how temporally continuous observations are required to dissect end-point severity into functional resistance mechanisms. The results of our study show how QDR can be maintained by facilitating different defense mechanisms during host-parasite interaction and that the capacity of the QDR toolbox highly depends on the host's genetic context. We anticipate that the present findings display a valuable resource for more targeted functional characterization of the processes involved in QDR. Moreover, we show how modest phenotyping technology can be leveraged to help answer highly relevant biological questions.

Coming of age for Microbiome gene breeding in plants

The plant microbiota can complement host functioning, leading to improved growth and health under unfavorable conditions. Microbiome engineering could therefore become a transformative technique for crop production. Microbiome genes, abbreviated as M genes, provide valuable targets for shaping plant-associated microbial communities.

Optimizing Clubroot Management and the Role of Canola Cultivar Mixtures

The sustainable cultivation of canola is under threat from clubroot disease (Plasmodiophora brassicae). The pathogen's resting spores can survive in the soil for extended periods, complicating disease management. Therefore, effective clubroot control requires a combination of tactics that provide multiple layers of protection. Management strategies have focused on pathogen avoidance and reducing disease levels in infested fields. The sanitation of machinery and field equipment remains the most effective method for preventing the pathogen's introduction into non-infested fields. For disease reduction, crop rotation, liming, chemical control, and host resistance are commonly employed, with the use of clubroot-resistant cultivars being the most effective to date. However, resistance breakdown has been observed within four years of the introduction of new cultivars, jeopardizing the long-term effectiveness of this approach. A promising yet underexplored strategy is the use of cultivar mixtures. This approach leverages mechanisms such as the dilution effect, the barrier effect, induced resistance, disruptive selection, and the compensatory effect to control the disease. Cultivar mixtures have the potential to reduce the impact of clubroot on canola production while preserving pathogen population structure, thereby minimizing the likelihood of resistance breakdown. Given its potential, further research into cultivar mixtures as a management strategy for clubroot disease is warranted.

Breeding and management of major resistance genes to stem canker/blackleg in Brassica crops

Blackleg (also known as Phoma or stem canker) is a major, worldwide disease of Brassica crop species, notably B. napus (rapeseed, canola), caused by the ascomycete fungus Leptosphaeria maculans. The outbreak and severity of this disease depend on environmental conditions and management practices, as well as a complex interaction between the pathogen and its hosts. Genetic resistance is a major method to control the disease (and the only control method in some parts of the world, such as continental Europe), but efficient use of genetic resistance is faced with many difficulties: (i) the scarcity of germplasm/genetic resources available, (ii) the different history of use of resistance genes in different parts of the world and the different populations of the fungus the resistance genes are exposed to, (iii) the complexity of the interactions between the plant and the pathogen that expand beyond typical gene-for-gene interactions, (iv) the incredible evolutionary potential of the pathogen and the importance of knowing the molecular processes set up by the fungus to "breakdown' resistances, so that we may design high-throughput diagnostic tools for population surveys, and (v) the different strategies and options to build up the best resistances and to manage them so that they are durable. In this paper, we aim to provide a comprehensive overview of these different points, stressing the differences between the different continents and the current prospects to generate new and durable resistances to blackleg disease.

RNA interference-based strategies to control Botrytis cinerea infection in cultivated strawberry

KEY MESSAGE

Gene silencing of BcDCL genes improves gray mold disease control in the cultivated strawberry. Gene silencing technology offers new opportunities to develop new formulations or new pathogen-resistant plants for reducing impacts of agricultural systems. Recent studies offered the proof of concept that the symptoms of gray mold can be reduced by downregulating Dicer-like 1 (DCL1) and 2 (DCL2) genes of Botrytis cinerea. In this study, we demonstrate that both solutions based on dsRNA topical treatment and in planta expression targeting BcDCL1 and BcDCL2 genes can be used to control the strawberry gray mold, the most harmful disease for different fruit crops. 50, 70 and 100 ng μL-1 of naked BcDCL1/2 dsRNA, sprayed on plants of Fragaria x ananassa cultivar Romina in the greenhouse, displayed significant reduction of susceptibility, compared to the negative controls, but to a lesser extent than the chemical fungicide. Three independent lines of Romina cultivar were confirmed for their stable expression of the hairpin gene construct that targets the Bc-DCL1 and 2 sequences (hp-Bc-DCL1/2), and for the production of hp construct-derived siRNAs, by qRT-PCR and Northern blot analyses. In vitro and in vivo detached leaves, and fruits from the hp-Bc-DCL1/2 lines showed significantly enhanced tolerance to this fungal pathogen compared to the control. This decreased susceptibility was correlated to the reduced fungal biomass and the downregulation of the Bc-DCL1 and 2 genes in B. cinerea. These results confirm the potential of both RNAi-based products and plants for protecting the cultivated strawberry from B. cinerea infection, reducing the impact of chemical pesticides on the environment and the health of consumers.

Long-term and rapid evolution in powdery mildew fungi

The powdery mildew fungi (Erysiphaceae) are globally distributed plant pathogens with a range of more than 10,000 plant hosts. In this review, we discuss the long- and short-term evolution of these obligate biotrophic fungi and outline their diversity with respect to morphology, lifestyle, and host range. We highlight their remarkable ability to rapidly overcome plant immunity, evolve fungicide resistance, and broaden their host range, for example, through adaptation and hybridization. Recent advances in genomics and proteomics, particularly in cereal powdery mildews (genus Blumeria), provided first insights into mechanisms of genomic adaptation in these fungi. Transposable elements play key roles in shaping their genomes, where even close relatives exhibit diversified patterns of recent and ongoing transposon activity. These transposons are ubiquitously distributed in the powdery mildew genomes, resulting in a highly adaptive genome architecture lacking obvious regions of conserved gene space. Transposons can also be neofunctionalized to encode novel virulence factors, particularly candidate secreted effector proteins, which may undermine the plant immune system. In cereals like barley and wheat, some of these effectors are recognized by plant immune receptors encoded by resistance genes with numerous allelic variants. These effectors determine incompatibility ("avirulence") and evolve rapidly through sequence diversification and copy number variation. Altogether, powdery mildew fungi possess plastic genomes that enable their fast evolutionary adaptation towards overcoming plant immunity, host barriers, and chemical stress such as fungicides, foreshadowing future outbreaks, host range shifts and expansions as well as potential pandemics by these pathogens.

Determinants of rapid adaptation in species with large variance in offspring production

The speed of population adaptation to changing biotic and abiotic environments is determined by the interaction between genetic drift, positive selection and linkage effects. Many marine species (fish, crustaceans), invertebrates and pathogens of humans and crops, exhibit sweepstakes reproduction characterized by the production of a very large amount of offspring (fecundity phase) from which only a small fraction may survive to the next generation (viability phase). Using stochastic simulations, we investigate whether the occurrence of sweepstakes reproduction affects the efficiency of a positively selected unlinked locus, and thus, the speed of adaptation since fecundity and/or viability have distinguishable consequences on mutation rate, probability and fixation time of advantageous alleles. We observe that the mean number of mutations at the next generation is always the function of the population size, but the variance increases with stronger sweepstakes reproduction when mutations occur in the parents. On the one hand, stronger sweepstakes reproduction magnifies the effect of genetic drift thus increasing the probability of fixation of neutral allele and decreasing that of selected alleles. On the other hand, the time to fixation of advantageous (as well as neutral) alleles is shortened by stronger sweepstakes reproduction. Importantly, fecundity and viability selection exhibit different probabilities and times to fixation of advantageous alleles under intermediate and weak sweepstakes reproduction. Finally, alleles under both strong fecundity and viability selection display a synergistic efficiency of selection. We conclude that measuring and modelling accurately fecundity and/or viability selection are crucial to predict the adaptive potential of species with sweepstakes reproduction.

Pattern recognition receptors as potential therapeutic targets for developing immunological engineered plants

There is an urgent need to combat pathogen infestations in crop plants to ensure food security worldwide. To counter this, plants have developed innate immunity mediated by Pattern Recognition Receptors (PRRs) that recognize pathogen-associated molecular patterns (PAMPs) and damage- associated molecular patterns (DAMPs). PRRs activate Pattern-Triggered Immunity (PTI), a defence mechanism involving intricate cell-surface and intracellular receptors. The diverse ligand-binding ectodomains of PRRs, including leucine-rich repeats (LRRs) and lectin domains, facilitate the recognition of MAMPs and DAMPs. Pathogen resistance is mediated by a variety of PTI responses, including membrane depolarization, ROS production, and the induction of defence genes. An integral part of intracellular immunity is the Nucleotide-binding Oligomerization Domain, Leucine-rich Repeat proteins (NLRs) which recognize and respond to effectors in a potent manner. Enhanced understanding of PRRs, their ligands, and downstream signalling pathways has contributed to the identification of potential targets for genetically modified plants. By transferring PRRs across plant species, it is possible to create broad-spectrum resistance, potentially offering innovative solutions for plant protection and global food security. The purpose of this chapter is to provide an update on PRRs involved in disease resistance, clarify the mechanisms by which PRRs recognize ligands to form active receptor complexes and present various applications of PRRs and PTI in disease resistance management for plants.

Effects of pathogen reproduction system on the evolutionary and epidemiological control provided by deployment strategies for two major resistance genes in agricultural landscapes

Resistant cultivars are of value for protecting crops from disease, but can be rapidly overcome by pathogens. Several strategies have been proposed to delay pathogen adaptation (evolutionary control), while maintaining effective protection (epidemiological control). Resistance genes can be (i) combined in the same cultivar (pyramiding), (ii) deployed in different cultivars sown in the same field (mixtures) or in different fields (mosaics), or (iii) alternated over time (rotations). The outcomes of these strategies have been investigated principally in pathogens displaying pure clonal reproduction, but many pathogens have at least one sexual event in their annual life cycles. Sexual reproduction may promote the emergence of superpathogens adapted to all the resistance genes deployed. Here, we improved the spatially explicit stochastic model landsepi to include pathogen sexual reproduction, and we used the improved model to investigate the effect of sexual reproduction on evolutionary and epidemiological outcomes across deployment strategies for two major resistance genes. Sexual reproduction favours the establishment of a superpathogen when single mutant pathogens are present together at a sufficiently high frequency, as in mosaic and mixture strategies. However, sexual reproduction did not affect the strategy recommendations for a wide range of mutation probabilities, associated fitness costs, and landscape organisations.

Resistant or Susceptible? How Central European Oat (A. sativa L.) Cultivars React to B. graminis f. sp. avenae Infection

In accordance with the postulates of integrated plant protection, the use of cultivars with genetically determined resistance is one of the main strategies for preventing losses caused by fungal pathogens. The development of breeding programs aimed at increasing resistance to pathogens should be preceded by a characterization of the resistance of cultivars grown in a given area. This allows us to determine the number of genes used in breeding and their effectiveness. It also allows us to estimate the pressure that the pathogen may exert on varieties with specific resistance genes. The presented work aimed to determine the level of resistance of oat varieties currently cultivated in Central Europe and the number of effective powdery mildew resistance genes currently used in oat breeding programs. The research showed that out of 46 varieties, only 5 were resistant to powdery mildew. Analysis of the infection profiles allowed us to postulate the presence of the Pm7 gene in four of them. In the Merlin variety from the Czech Republic, it was not possible to determine which of the previously described genes determines resistance to powdery mildew. Due to the observed climate changes and the rapid adaptation of pathogens to new environmental conditions, it is crucial to introduce a wider pool of genes that determine the pathogen resistance of cultivars.

Polymorphism of Avirulence Genes and Adaptation to Brassica Resistance Genes Is Gene-Dependent in the Phytopathogenic Fungus Leptosphaeria maculans

The fungal phytopathogen Leptosphaeria maculans, which causes stem canker (blackleg) of rapeseed (Brassica napus), is mainly controlled worldwide by genetic resistance, which includes major resistance genes (Rlm). This model is one of those for which the highest number of avirulence genes (AvrLm) has been cloned. In many systems, including the L. maculans-B. napus interaction, intense use of resistance genes exerts strong selection pressure on the corresponding avirulent isolates, and the fungi may rapidly escape resistance through various molecular events which modify the avirulence genes. In the literature, the study of polymorphism at avirulence loci is often focused on single genes under selection pressure. In this study, we investigate allelic polymorphism at 11 avirulence loci in a French population of 89 L. maculans isolates collected on a trap cultivar in four geographic locations in the 2017-2018 cropping season. The corresponding Rlm genes have been (i) used for a long time, (ii) recently used, or (iii) unused in agricultural practice. The sequence data generated indicate an extreme diversity of situations. For example, genes submitted to an ancient selection may have either been deleted in populations (AvrLm1) or replaced by a single-nucleotide mutated virulent version (AvrLm2, AvrLm5-9). Genes that have never been under selection may either be nearly invariant (AvrLm6, AvrLm10A, AvrLm10B), exhibit rare deletions (AvrLm11, AvrLm14), or display a high diversity of alleles and isoforms (AvrLmS-Lep2). These data suggest that the evolutionary trajectory of avirulence/virulence alleles is gene-dependent and independent of selection pressure in L. maculans. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

The transcriptional landscape of plant infection by the rice blast fungus Magnaporthe oryzae reveals distinct families of temporally co-regulated and structurally conserved effectors

The rice blast fungus Magnaporthe oryzae causes a devastating disease that threatens global rice (Oryza sativa) production. Despite intense study, the biology of plant tissue invasion during blast disease remains poorly understood. Here we report a high-resolution transcriptional profiling study of the entire plant-associated development of the blast fungus. Our analysis revealed major temporal changes in fungal gene expression during plant infection. Pathogen gene expression could be classified into 10 modules of temporally co-expressed genes, providing evidence for the induction of pronounced shifts in primary and secondary metabolism, cell signaling, and transcriptional regulation. A set of 863 genes encoding secreted proteins are differentially expressed at specific stages of infection, and 546 genes named MEP (Magnaportheeffector protein) genes were predicted to encode effectors. Computational prediction of structurally related MEPs, including the MAX effector family, revealed their temporal co-regulation in the same co-expression modules. We characterized 32 MEP genes and demonstrate that Mep effectors are predominantly targeted to the cytoplasm of rice cells via the biotrophic interfacial complex and use a common unconventional secretory pathway. Taken together, our study reveals major changes in gene expression associated with blast disease and identifies a diverse repertoire of effectors critical for successful infection.

Genetic architecture of rust resistance in a wheat (Triticum turgidum) diversity panel

Introduction

Wheat rust diseases are widespread and affect all wheat growing areas around the globe. Breeding strategies focus on incorporating genetic disease resistance. However, pathogens can quickly evolve and overcome the resistance genes deployed in commercial cultivars, creating a constant need for identifying new sources of resistance.

Methods

We have assembled a diverse tetraploid wheat panel comprised of 447 accessions of three Triticum turgidum subspecies and performed a genome-wide association study (GWAS) for resistance to wheat stem, stripe, and leaf rusts. The panel was genotyped with the 90K Wheat iSelect single nucleotide polymorphism (SNP) array and subsequent filtering resulted in a set of 6,410 non-redundant SNP markers with known physical positions.

Results

Population structure and phylogenetic analyses revealed that the diversity panel could be divided into three subpopulations based on phylogenetic/geographic relatedness. Marker-trait associations (MTAs) were detected for two stem rust, two stripe rust and one leaf rust resistance loci. Of them, three MTAs coincide with the known rust resistance genes Sr13, Yr15 and Yr67, while the other two may harbor undescribed resistance genes.

Discussion

The tetraploid wheat diversity panel, developed and characterized herein, captures wide geographic origins, genetic diversity, and evolutionary history since domestication making it a useful community resource for mapping of other agronomically important traits and for conducting evolutionary studies.

Recent developments in plant-downy mildew interactions

Downy mildews are obligate oomycete pathogens that attack a wide range of plants and can cause significant economic impacts on commercial crops and ornamental plants. Traditionally, downy mildew disease control relied on an integrated strategies, that incorporate cultural practices, deployment of resistant cultivars, crop rotation, application of contact and systemic pesticides, and biopesticides. Recent advances in genomics provided data that significantly advanced understanding of downy mildew evolution, taxonomy and classification. In addition, downy mildew genomics also revealed that these obligate oomycetes have reduced numbers of virulence factor genes in comparison to hemibiotrophic and necrotrophic oomycetes. However, downy mildews do deploy significant arrays of virulence proteins, including so-called RXLR proteins that promote virulence or are recognized as avirulence factors. Pathogenomics are being applied to downy mildew population studies to determine the genetic diversity within the downy mildew populations and manage disease by selection of appropriate varieties and management strategies. Genome editing technologies have been used to manipulate host disease susceptibility genes in different plants including grapevine and sweet basil and thereby provide new soucres of resistance genes against downy mildews. Previously, it has proved difficult to transform and manipulate downy mildews because of their obligate lifestyle. However, recent exploitation of RNA interference machinery through Host-Induced Gene Silencing (HIGS) and Spray-Induced Gene Silencing (SIGS) indicate that functional genomics in downy mildews is now possible. Altogether, these breakthrough technologies and attendant fundamental understanding will advance our ability to mitigate downy mildew diseases.

Strong Genetic Differentiation between Generalist Populations of Venturia inaequalis and Populations from Partially Resistant Apple Cultivars Carrying Rvi3 or Rvi5

The ascomycete fungus Venturia inaequalis causes scab disease, a major problem in apple production. The utilization of resistant cultivars is hindered by emerging new pathogen races, which erode their resistance. Increasing our knowledge on the population genetic processes of the fungus can contribute to the development of resistance gene deployment strategies and more durable resistance. We investigated the effect of four scab race indicator cultivars, ‘Gala’ (no R-gene), ‘Golden Delicious’ (Rvi1), ‘Geneva’ (Rvi3, complex), and OR45t132 (Rvi5), on the V. inaequalis population genetic structure and diversity. Sixty-six monosporic fungal isolates from the four cultivars were genotyped with seven simple sequence repeat primers. Furthermore, the partial resistance of the indicators and the pathogenicity profile of the conidia from each host were assessed. The genetic diversity and structure of the investigated V. inaequalis subpopulations correspond to the partial resistance of the original hosts as well as the subpopulations’ pathogenicity profiles. Indicators carrying Rvi3 and Rvi5 had strongly diverged and specialized V. inaequalis populations on them and fewer symptoms on the field. In line with the complete breakdown of the Rvi1 gene, the population from ‘Golden Delicious’ did not segregate from the susceptible ‘Gala’, and virulence towards Rvi1 was present in all subpopulations.

The Characterization of Pathotypes in Grapevine Downy Mildew Provides Insights into the Breakdown of Rpv3, Rpv10, and Rpv12 Factors in Grapevines

We describe a standard method for characterizing the virulence profile of Plasmopara viticola, the causal agent of grapevine downy mildew. We used 33 European strains to inoculate six grapevine varieties carrying the principal factors for resistance to downy mildew (Rpv1, Rpv3.1, Rpv3.2, Rpv5, Rpv6, Rpv10, and Rpv12) and the susceptible Vitis vinifera 'Chardonnay'. For each interaction, we characterized the level of sporulation by image analysis and the intensity of the grapevine hypersensitive response by visual score. We propose a definition for the breakdown of grapevine quantitative resistances combining these two traits. Among the 33 strains analyzed, 28 are virulent on at least one resistance factor. We identified five different pathotypes across the 33 strains analyzed: two pathotypes overcoming a single resistance factor (vir3.1 and vir3.2) and three complex pathotypes overcoming multiple resistance factors (vir3.1,3.2; vir3.2,12; vir3.1,3.2,10). Our findings confirm the widespread occurrence of P. viticola strains overcoming the Rpv3 haplotypes (28 strains). We also detected the first breakdown of resistance to the Rpv10 by a strain from Germany and the breakdown of Rpv12 factors by a strain from Hungary. The pathotyping method proposed here and the associated differential host range lay the groundwork for the early detection of resistance breakdown in grapevines. This approach will also facilitate the monitoring of the evolution of P. viticola populations at large spatial scales. This is an essential step forward to promoting durable management of the resistant grapevine varieties currently available.

Twenty Years of Leptosphaeria maculans Population Survey in France Suggests Pyramiding Rlm3 and Rlm7 in Rapeseed Is a Risky Resistance Management Strategy

Strategies for plant resistance gene deployment aim to preserve their durability to highly adaptable fungal pathogens. While the pyramiding of resistance genes is often proposed as an effective way to increase their durability, molecular mechanisms by which the pathogen can overcome the resistance also are important aspects to take into account. Here, we report a counterexample where pyramiding of two resistance genes of Brassica napus, Rlm3 and Rlm7, matching the Leptosphaeria maculans avirulence genes AvrLm3 and AvrLm4-7, respectively, favored the selection of double-virulent isolates. We previously demonstrated that the presence of a functional AvrLm4-7 gene in an isolate masks the Rlm3-AvrLm3 recognition. Rlm7 was massively deployed in France since 2004. L. maculans populations were surveyed on a large scale (>7,600 isolates) over a period of 20 years, and resistance gene deployment at the regional scale was determined. Mutations in isolates overcoming both resistance genes were analyzed. All data indicated that the simultaneous success of Rlm7, the deployment of varieties pyramiding Rlm3 and Rlm7, along with the decrease in areas cultivated with Rlm3 only, contributed to the success of virulent isolates toward Rlm7, and more recently to both Rlm3 and Rlm7. Experimental field assays proved that resistance gene alternation was a better strategy compared with pyramiding in this context. Our study also illustrated an unusually high sequence diversification of AvrLm3 and AvrLm4-7 under such a selection pressure, and identified a few regions of the AvrLm4-7 protein involved in both its recognition by Rlm7 and in its AvrLm3-Rlm3 masking ability. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

How large and diverse are field populations of fungal plant pathogens? The case of Zymoseptoria tritici

Pathogen populations differ in the amount of genetic diversity they contain. Populations carrying higher genetic diversity are thought to have a greater evolutionary potential than populations carrying less diversity. We used published studies to estimate the range of values associated with two critical components of genetic diversity, the number of unique pathogen genotypes and the number of spores produced during an epidemic, for the septoria tritici blotch pathogen Zymoseptoria tritici. We found that wheat fields experiencing typical levels of infection are likely to carry between 3.1 and 14.0 million pathogen genotypes per hectare and produce at least 2.1-9.9 trillion pycnidiospores per hectare. Given the experimentally derived mutation rate of 3 × 10-10 substitutions per site per cell division, we estimate that between 27 and 126 million pathogen spores carrying adaptive mutations to counteract fungicides and resistant cultivars will be produced per hectare during a growing season. This suggests that most of the adaptive mutations that have been observed in Z. tritici populations can emerge through local selection from standing genetic variation that already exists within each field. The consequences of these findings for disease management strategies are discussed.

Characterization of the Level and Type of Resistance of Potato Varieties to Late Blight (Phytophthora infestans)

Understanding the level and type of resistance in potato varieties is relevant for integrating varietal resistance into the management of potato late blight. Accordingly, 54 potato varieties were tested for their level and type of resistance to late blight in 2019 and 2020 in Denmark. Spreader rows were artificially inoculated to ensure an even inoculum distribution in the trial. Disease severity was assessed once or twice per week. Cluster analysis (CA) was done based on the weighted mean absolute rate (WMAR), the relative area under the disease progress curve, the onset of disease (Xo), the severity of disease in the middle of the season, the time to reach 1% disease severity, the time to reach final disease severity, and the maximum disease severity. The resistance types were determined by comparing the tested varieties to Bintje (susceptible reference) for Xo and WMAR. The CA ranked the varieties as susceptible, moderately resistant, resistant, and very resistant based on their level of resistance. Except for a few varieties, the expressed resistance levels varied between the years. Several varieties that were susceptible in 2019 were moderately resistant in 2020. Also, the types of resistance that the varieties exhibited varied from year to year. In 2020, most varieties exhibited race-specific resistance, while in 2019 they mostly showed susceptible characteristics. The variation between years for the level and types of resistance of the varieties highlights the importance of regularly monitoring varietal resistance across time and space.

Steroidal Saponins─New Sources to Develop Potato (Solanum tuberosum L.) Genotypes Resistant against Certain Phytophthora infestans Strains

Plant pathogens such as Phytophthora infestans that caused the Irish Potato Famine continue to threaten local and global food security. Genetic and chemical plant protection measures are often overcome by adaptation of pathogen population structures. Therefore, there is a constant demand for new, consumer- and environment-friendly plant protection strategies. Metabolic alterations induced by P. infestans in the foliage and tubers of six different potato cultivars were investigated. Using a combination of untargeted metabolomics, isolation techniques, and structure elucidation by MS and 1D/2D-NMR experiments, five steroidal glycoalkaloids, five oxylipins, and four steroidal saponins were identified. As the steroidal saponins showed antioomycete but no hemolytic activity, they may thus be considered as probably safe target substances for enrichment in breeding programs for disease resistance and as chemical lead structures for the production of nature-derived synthetic antioomycetes.

Genetic diversity and disease: The past, present, and future of an old idea

Why do infectious diseases erupt in some host populations and not others? This question has spawned independent fields of research in evolution, ecology, public health, agriculture, and conservation. In the search for environmental and genetic factors that predict variation in parasitism, one hypothesis stands out for its generality and longevity: genetically homogeneous host populations are more likely to experience severe parasitism than genetically diverse populations. In this perspective piece, I draw on overlapping ideas from evolutionary biology, agriculture, and conservation to capture the far-reaching implications of the link between genetic diversity and disease. I first summarize the development of this hypothesis and the results of experimental tests. Given the convincing support for the protective effect of genetic diversity, I then address the following questions: (1) Where has this idea been put to use, in a basic and applied sense, and how can we better use genetic diversity to limit disease spread? (2) What new hypotheses does the established disease-diversity relationship compel us to test? I conclude that monitoring, preserving, and augmenting genetic diversity is one of our most promising evolutionarily informed strategies for buffering wild, domesticated, and human populations against future outbreaks.

A new avirulence gene of Leptosphaeria maculans, AvrLm14, identifies a resistance source in American broccoli (Brassica oleracea) genotypes

In many cultivated crops, sources of resistance to diseases are sparse and rely on introgression from wild relatives. Agricultural crops often are allopolyploids resulting from interspecific crosses between related species, which are sources of diversity for resistance genes. This is the case for Brassica napus (oilseed rape, canola), an interspecific hybrid between Brassica rapa (turnip) and Brassica oleracea (cabbage). B. napus has a narrow genetic basis and few effective resistance genes against stem canker (blackleg) disease, caused by the fungus Leptosphaeria maculans, are currently available. B. rapa diversity has proven to be a valuable source of resistance (Rlm, LepR) genes, while B. oleracea genotypes were mostly considered susceptible. Here we identified a new resistance source in B. oleracea genotypes from America, potentially effective against French L. maculans isolates under both controlled and field conditions. Genetic analysis of fungal avirulence and subsequent cloning and validation identified a new avirulence gene termed AvrLm14 and suggested a typical gene-for-gene interaction between AvrLm14 and the postulated Rlm14 gene. AvrLm14 shares all the usual characteristics of L. maculans avirulence genes: it is hosted in a genomic region enriched in transposable elements and heterochromatin marks H3K9me3, its expression is repressed during vegetative growth but shows a strong overexpression 5-9 days following cotyledon infection, and it encodes a small secreted protein enriched in cysteine residues with few matches in databases. Similar to the previously cloned AvrLm10-A, AvrLm14 contributes to reduce lesion size on susceptible cotyledons, pointing to a complex interplay between effectors promoting or reducing lesion development.

Resistance in Maize (Zea mays) to Isolates of Puccinia sorghi from Eastern Australia

The causal agent of maize common rust (CR), Puccinia sorghi, has increased in incidence and severity in Australia in recent years, prompting the assessment of sources of resistance and a preliminary survey of the diversity of P. sorghi populations. The maize commercial hybrids tested carried no resistance to 14 isolates of P. sorghi and had infection types comparable with that of a susceptible check. The resistance gene Rp1_D that remained effective in the United States for 35 years was ineffective against 7 of the 14 isolates. Maize lines carrying known "resistance to Puccinia" (Rp) genes were inoculated with the five isolates considered most diverse based on year of collection (2018 or 2019), location (Queensland or Victoria), and host from which they were isolated (maize or sweet corn). Lines carrying the resistance genes RpG, Rp5, Rp1_E, Rp1_I, Rp1_L, RpGDJ, RpGJF, and Rp5GCJ were resistant to all five isolates and to isolates collected in many agroecological regions. These lines were recommended as donors of effective resistance for maize breeding programs in Australia. Lines carrying no known resistance or resistance genes Rp8_A, Rp8_B, Rp1_J, Rp1_M, Rp7, and Rpp9 (conferring resistance to P. polysora) were susceptible to all five isolates. Differential lines carrying resistance genes Rp1_B, Rp1_C, Rp1_D, Rp1_F, Rp1_K, Rp3_D, or Rp4_A were either resistant or susceptible depending upon the isolate used, showing that the isolates varied in virulence for these genes. Urediniospore production was reduced on adult compared with juvenile plants, presumably due to changes in plant physiology associated with age or the presence of adult plant resistance.

Creation and judicious application of a wheat resistance gene atlas

Disease-resistance (R) gene cloning in wheat (Triticum aestivum) has been accelerated by the recent surge of genomic resources, facilitated by advances in sequencing technologies and bioinformatics. However, with the challenges of population growth and climate change, it is vital not only to clone and functionally characterize a few handfuls of R genes, but also to do so at a scale that would facilitate the breeding and deployment of crops that can recognize the wide range of pathogen effectors that threaten agroecosystems. Pathogen populations are continually changing, and breeders must have tools and resources available to rapidly respond to those changes if we are to safeguard our daily bread. To meet this challenge, we propose the creation of a wheat R-gene atlas by an international community of researchers and breeders. The atlas would consist of an online directory from which sources of resistance could be identified and deployed to achieve more durable resistance to the major wheat pathogens, such as wheat rusts, blotch diseases, powdery mildew, and wheat blast. We present a costed proposal detailing how the interacting molecular components governing disease resistance could be captured from both the host and the pathogen through biparental mapping, mutational genomics, and whole-genome association genetics. We explore options for the configuration and genotyping of diversity panels of hexaploid and tetraploid wheat, as well as their wild relatives and major pathogens, and discuss how the atlas could inform a dynamic, durable approach to R-gene deployment. Set against the current magnitude of wheat yield losses worldwide, recently estimated at 21%, this endeavor presents one route for bringing R genes from the lab to the field at a considerable speed and quantity.

Mono-Locus and Pyramided Resistant Grapevine Cultivars Reveal Early Putative Biomarkers Upon Artificial Inoculation With Plasmopara viticola

One of the most economically important grapevine diseases is Downy mildew (DM) caused by the oomycete Plasmopara viticola. A strategy to reduce the use of fungicides to compensate for the high susceptibility of V. vinifera is the selection of grapevine varieties showing pathogen-specific resistance. We applied a metabolomics approach to evaluate the metabolic modulation in mono-locus resistant genotypes carrying one locus associated with P. viticola resistance (Rpv) (BC4- Rpv1, Bianca- Rpv3-1, F12P160- Rpv12, Solaris- Rpv10), as well as in pyramided resistant genotypes carrying more than one Rpv (F12P60- Rpv3-1; Rpv12 and F12P127- Rpv3-1, Rpv3-3; Rpv10) taking as a reference the susceptible genotype Pinot Noir. In order to understand if different sources of resistance are associated with different degrees of resistance and, implicitly, with different responses to the pathogen, we considered the most important classes of plant metabolite primary compounds, lipids, phenols and volatile organic compounds at 0, 12, 48, and 96 h post-artificial inoculation (hpi). We identified 264 modulated compounds; among these, 22 metabolites were found accumulated in significant quantities in the resistant cultivars compared to Pinot Noir. In mono-locus genotypes, the highest modulation of the metabolites was noticed at 48 and 96 hpi, except for Solaris, that showed a behavior similar to the pyramided genotypes in which the changes started to occur as early as 12 hpi. Bianca, Solaris and F12P60 showed the highest number of interesting compounds accumulated after the artificial infection and with a putative effect against the pathogen. In contrast, Pinot Noir showed a less effective defense response in containing DM growth.

A Conserved Oomycete CRN Effector Targets Tomato TCP14-2 to Enhance Virulence

Phytophthora spp. secrete vast arrays of effector molecules during infection to aid in host colonization. The crinkling and necrosis (CRN) protein family forms an extensive repertoire of candidate effectors that accumulate in the host nucleus to perturb processes required for immunity. Here, we show that CRN12_997 from Phytophthora capsici binds a TCP transcription factor, SlTCP14-2, to inhibit its immunity-associated activity against Phytophthora spp. Coimmunoprecipitation and bimolecular fluorescence complementation studies confirm a specific CRN12_997-SlTCP14-2 interaction in vivo. Coexpression of CRN12_997 specifically counteracts the TCP14-enhanced immunity phenotype, suggesting that CRN mediated perturbation of SlTCP14-2 function. We show that SlTCP14-2 associates with nuclear chromatin and that CRN12_997 diminishes SlTCP14-2 DNA binding. Collectively, our data support a model in which SlTCP14-2 associates with chromatin to enhance immunity. The interaction between CRN12_997 and SlTCP14-2 reduces DNA binding of the immune regulator. We propose that the modulation of SlTCP14-2 chromatin affinity, caused by CRN12-997, enhances susceptibility to P. capsici.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

When Does Spatial Diversification Usefully Maximize the Durability of Crop Disease Resistance?

Maximizing the durability of crop disease resistance genes in the face of pathogen evolution is a major challenge in modern agricultural epidemiology. Spatial diversification in the deployment of resistance genes, where susceptible and resistant fields are more closely intermixed, is predicted to drive lower epidemic intensities over evolutionary timescales. This is due to an increase in the strength of dilution effects, caused by pathogen inoculum challenging host tissue to which it is not well-specialized. The factors that interact with and determine the magnitude of this spatial suppressive effect are not currently well understood, however, leading to uncertainty over the pathosystems where such a strategy is most likely to be cost-effective. We model the effect on landscape scale disease dynamics of spatial heterogeneity in the arrangement of fields planted with either susceptible or resistant cultivars, and the way in which this effect depends on the parameters governing the pathosystem of interest. Our multiseason semidiscrete epidemiological model tracks spatial spread of wild-type and resistance-breaking pathogen strains, and incorporates a localized reservoir of inoculum, as well as the effects of within and between field transmission. The pathogen dispersal characteristics, any fitness cost(s) of the resistance-breaking trait, the efficacy of host resistance, and the length of the timeframe of interest all influence the strength of the spatial diversification effect. A key result is that spatial diversification has the strongest beneficial effect at intermediate fitness costs of the resistance-breaking trait, an effect driven by a complex set of nonlinear interactions. On the other hand, however, if the resistance-breaking strain is not fit enough to invade the landscape, then a partially effective resistance gene can result in spatial diversification actually worsening the epidemic. These results allow us to make general predictions of the types of system for which spatial diversification is most likely to be cost-effective, paving the way for potential economic modeling and pathosystem specific evaluation. These results highlight the importance of studying the effect of genetics on landscape scale spatial dynamics within host-pathogen disease systems.[Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Functional analysis of RXLR effectors from the New Zealand kauri dieback pathogen Phytophthora agathidicida

New Zealand kauri is an ancient, iconic, gymnosperm tree species that is under threat from a lethal dieback disease caused by the oomycete Phytophthora agathidicida. To gain insight into this pathogen, we determined whether proteinaceous effectors of P. agathidicida interact with the immune system of a model angiosperm, Nicotiana, as previously shown for Phytophthora pathogens of angiosperms. From the P. agathidicida genome, we defined and analysed a set of RXLR effectors, a class of proteins that typically have important roles in suppressing or activating the plant immune system. RXLRs were screened for their ability to activate or suppress the Nicotiana plant immune system using Agrobacterium tumefaciens transient transformation assays. Nine P. agathidicida RXLRs triggered cell death or suppressed plant immunity in Nicotiana, of which three were expressed in kauri. For the most highly expressed, P. agathidicida (Pa) RXLR24, candidate cognate immune receptors associated with cell death were identified in Nicotiana benthamiana using RNA silencing-based approaches. Our results show that RXLRs of a pathogen of gymnosperms can interact with the immune system of an angiosperm species. This study provides an important foundation for studying the molecular basis of plant-pathogen interactions in gymnosperm forest trees, including kauri.

What natural variation can teach us about resistance durability

Breeding a crop variety to be resistant to a pathogen usually takes years. This is problematic because pathogens, with short generation times and fluid genomes, adapt quickly to overcome resistance. The triumph of the pathogen is not inevitable, however, as there are numerous examples of durable resistance, particularly in wild plants. Which factors then contribute to such resistance stability over millennia? We review current knowledge of wild and agricultural pathosystems, detailing the importance of genetic, species and spatial heterogeneity in the prevention of pathogen outbreaks. We also highlight challenges associated with increasing resistance diversity in crops, both in light of pathogen (co-)evolution and breeding practices. Historically it has been difficult to incorporate heterogeneity into agriculture due to reduced efficiency in harvesting. Recent advances implementing computer vision and automation in agricultural production may improve our ability to harvest mixed genotype and mixed species plantings, thereby increasing resistance durability.

Genetic modification to improve disease resistance in crops

Plant pathogens are a significant challenge in agriculture despite our best efforts to combat them. One of the most effective and sustainable ways to manage plant pathogens is to use genetic modification (GM) and genome editing, expanding the breeder's toolkit. For use in the field, these solutions must be efficacious, with no negative effect on plant agronomy, and deployed thoughtfully. They must also not introduce a potential allergen or toxin. Expensive regulation of biotech crops is prohibitive for local solutions. With 11-30% average global yield losses and greater local impacts, tackling plant pathogens is an ethical imperative. We need to increase world food production by at least 60% using the same amount of land, by 2050. The time to act is now and we cannot afford to ignore the new solutions that GM provides to manage plant pathogens.

The Current Epidemic of the Barley Pathogen Ramularia collo-cygni Derives from a Population Expansion and Shows Global Admixture

Ramularia leaf spot is becoming an ever-increasing problem in main barley-growing regions since the 1980s, causing up to 70% yield loss in extreme cases. Yet, the causal agent Ramularia collo-cygni remains poorly studied. The diversity of the pathogen in the field thus far remains unknown. Furthermore, it is unknown to what extent the pathogen has a sexual reproductive cycle. The teleomorph of R. collo-cygni has not been observed. To study the genetic diversity of R. collo-cygni and get more insights in its biology, we sequenced the genomes of 19 R. collo-cygni isolates from multiple geographic locations and diverse hosts. Nucleotide polymorphism analyses of all isolates shows that R. collo-cygni is genetically diverse worldwide, with little geographic or host specific differentiation. Next, we used two different methods to detect signals of recombination in our sample set. Both methods find putative recombination events, which indicate that sexual reproduction happens or has happened in the global R. collo-cygni population. Lastly, we used these data on recombination to perform historic population size analyses. These suggest that the effective population size of R. collo-cygni decreased during the domestication of barley and subsequently grew with the rise of agriculture. Our findings deepen our understanding of R. collo-cygni biology and can help us to understand the current epidemic. We discuss how our findings support possible global spread through seed transfer, and we highlight how recombination, clonal spreading, and lack of host specificity could amplify global epidemics of this increasingly important disease and suggest specific approaches to combat the pathogen.

Plant cell surface immune receptor complex signaling

Plant plasma membrane pattern recognition receptors are key to microbe sensing and activation of immunity to microbial invasion. Plants employ several types of such receptors that differ mainly in the structure of their ectodomains and the presence or absence of a cytoplasmic protein kinase domain. Plant immune receptors do not function as single entities, but form larger complexes which undergo compositional changes in a ligand-dependent manner. Here, we highlight current knowledge of molecular mechanisms underlying receptor complex dynamics and regulation, and cover early signaling networks implicated in the activation of generic plant immune responses. We further discuss how an increasingly comprehensive set of immune receptors may be employed to engineer crop plants with enhanced, durable resistance to microbial infection.

Tolerance and overcompensation to infection by Phytophthora infestans in the wild perennial climber Solanum dulcamara

Studies of infection by Phytophthora infestans-the causal agent of potato late blight-in wild species can provide novel insights into plant defense responses, and indicate how wild plants might be influenced by recurrent epidemics in agricultural fields. In the present study, our aim was to investigate if different clones of Solanum dulcamara (a relative of potato) collected in the wild differ in resistance and tolerance to infection by a common European isolate of P. infestans. We performed infection experiments with six S. dulcamara genotypes (clones) both in the laboratory and in the field and measured the degree of infection and plant performance traits. In the laboratory, the six evaluated genotypes varied from resistant to susceptible, as measured by degree of infection 20 days post infection. Two of the four genotypes susceptible to infection showed a quadratic (concave downward) relationship between the degree of infection and shoot length, with maximum shoot length at intermediate values of infection. This result suggests overcompensation, that is, an increase in growth in infected individuals. The number of leaves decreased with increasing degree of infection, but at different rates in the four susceptible genotypes, indicating genetic variation for tolerance. In the field, the inoculated genotypes did not show any disease symptoms, but plant biomass at the end of the growing season was higher for inoculated plants than for controls, in-line with the overcompensation detected in the laboratory. We conclude that in S. dulcamara there are indications of genetic variation for both resistance and tolerance to P. infestans infection. Moreover, some genotypes displayed overcompensation. Learning about plant tolerance and overcompensation to infection by pathogens can help broaden our understanding of plant defense in natural populations and help develop more sustainable plant protection strategies for economically important crop diseases.

Tomato Yellow Leaf Curl Sardinia Virus, a Begomovirus Species Evolving by Mutation and Recombination: A Challenge for Virus Control

The tomato leaf curl disease (TYLCD) is associated with infections of several species of begomoviruses (genus Begomovirus, family Geminiviridae) and causes severe damage to tomatoes throughout tropical and sub-tropical regions of the world. Among others, the Tomato yellow leaf curl Sardinia virus (TYLCSV) species causes damage in the Mediterranean Basin since early outbreaks occurred. Nevertheless, scarce information is available about the diversity of TYLCSV. Here, we study this aspect based on the sequence information accessible in databases. Isolates of two taxonomically differentiated TYLCSV strains can be found in natural epidemics. Their evolution is mostly associated with mutation combined with selection and random genetic drift and also with inter-species recombination which is frequent in begomoviruses. Moreover, a novel putative inter-strain recombinant is reported. Although no significantly new biological behaviour was observed for this latter recombinant, its occurrence supports that as shown for other related begomoviruses, recombination continues to play a central role in the evolution of TYLCD-associated viruses and the dynamism of their populations. The confrontation of resistant tomatoes with isolates of different TYLCD-associated viruses including the novel recombinant demonstrates the existence of a variable virus x plant genotype interaction. This has already been observed for other TYLCD-associated viruses and is a challenge for the control of their impact on tomato production.

Discovering new alleles for yellow spot resistance in the Vavilov wheat collection

GWAS detected 11 yellow spot resistance QTL in the Vavilov wheat collection. Promising adult-plant resistance loci could provide a sustainable genetic solution to yellow spot in modern wheat varieties. Yellow spot, caused by the fungal pathogen Pyrenophora tritici-repentis (Ptr), is the most economically damaging foliar disease of wheat in Australia. Genetic resistance is considered to be the most sustainable means for disease management, yet the genomic regions underpinning resistance to Ptr, particularly adult-plant resistance (APR), remain vastly unknown. In this study, we report results of a genome-wide association study using 295 accessions from the Vavilov wheat collection which were extensively tested for response to Ptr infections in glasshouse and field trials at both seedling an adult growth stages. Combining phenotypic datasets from multiple experiments in Australia and Russia with 25,286 genome-wide, high-quality DArTseq markers, we detected a total of 11 QTL, of which 5 were associated with seedling resistance, 3 with all-stage resistance, and 3 with APR. Interestingly, the novel APR QTL were effective even in the presence of host sensitivity gene Tsn1. These genomic regions could offer broad-spectrum yellow spot protection, not just to ToxA but also other pathogenicity or virulence factors. Vavilov wheat accessions carrying APR QTL combinations displayed enhanced levels of resistance highlighting the potential for QTL stacking through breeding. We propose that the APR genetic factors discovered in our study could be used to improve resistance levels in modern wheat varieties and contribute to the sustainable control of yellow spot.

Mosaics, mixtures, rotations or pyramiding: What is the optimal strategy to deploy major gene resistance?

Once deployed uniformly in the field, genetically controlled plant resistance is often quickly overcome by pathogens, resulting in dramatic losses. Several strategies have been proposed to constrain the evolutionary potential of pathogens and thus increase resistance durability. These strategies can be classified into four categories, depending on whether resistance sources are varied across time (rotations) or combined in space in the same cultivar (pyramiding), in different cultivars within a field (cultivar mixtures) or among fields (mosaics). Despite their potential to differentially affect both pathogen epidemiology and evolution, to date the four categories of deployment strategies have never been directly compared together within a single theoretical or experimental framework, with regard to efficiency (ability to reduce disease impact) and durability (ability to limit pathogen evolution and delay resistance breakdown). Here, we used a spatially explicit stochastic demogenetic model, implemented in the R package landsepi, to assess the epidemiological and evolutionary outcomes of these deployment strategies when two major resistance genes are present. We varied parameters related to pathogen evolutionary potential (mutation probability and associated fitness costs) and landscape organization (mostly the relative proportion of each cultivar in the landscape and levels of spatial or temporal aggregation). Our results, broadly focused on qualitative resistance to rust fungi of cereal crops, show that evolutionary and epidemiological control are not necessarily correlated and that no deployment strategy is universally optimal. Pyramiding two major genes offered the highest durability, but at high mutation probabilities, mosaics, mixtures and rotations can perform better in delaying the establishment of a universally infective superpathogen. All strategies offered the same short-term epidemiological control, whereas rotations provided the best long-term option, after all sources of resistance had broken down. This study also highlights the significant impact of landscape organization and pathogen evolutionary ability in considering the optimal design of a deployment strategy.