Puccinia Triticina Research Articles

Characterization of durum wheat resistance against leaf rust under climate change conditions of increasing temperature and [CO2

Durum wheat cultivation in Mediterranean regions is threatened by abiotic factors, mainly related to the effects of climate change, and biotic factors such as the leaf rust disease. This situation requires an in-depth knowledge of how predicted elevated temperatures and [CO2] will affect durum wheat-leaf rust interactions. Therefore, we have characterised the response of one susceptible and two resistant durum wheat accessions against leaf rust under different environments in greenhouse assays, simulating the predicted conditions of elevated temperature and [CO2] in the far future period of 2070–2099 for the wheat growing region of Cordoba, Spain. Interestingly, high temperature alone or in combination with high [CO2] did not alter the external appearance of the rust lesions. However, through macro and microscopic evaluation, we found some host physiological and molecular responses to infection that would quantitatively reduce not only pustule formation and subsequent infection cycles of this pathogen, but also the host photosynthetic area under these predicted weather conditions, mainly expressed in the susceptible accession. Moreover, our results suggest that durum wheat responses to infection are mainly driven by temperature, being considered the most hampering abiotic stress. In contrast, leaf rust infection was greatly reduced when these weather conditions were also conducted during the inoculation process, resembling the effects of possible heat waves not only in disease development, but also in fungal germination and penetration success. Considering this lack of knowledge in plant-pathogen interactions combined with abiotic stresses, the present study is, to the best of our knowledge, the first to include the effects of the expected diurnal variation of maximum temperature and continuous elevated [CO2] in the durum wheat-leaf rust pathosystem.

Comparative transcriptomics of stem rust resistance in wheat NILs mediated by Sr24 rust resistance gene

Stem rust of wheat is a deleterious fungal disease across the globe causing severe yield losses. Although, many stem rust resistance genes (Sr) are being used in wheat breeding programs, new emerging stem rust pathotypes are a challenge to important Sr genes. In recent years, multiple studies on leaf and yellow rust molecular mechanism have been done, however, for stem rust such studies are lacking. Current study investigated stem rust induced response in the susceptible wheat genotype C306 and its Near Isogenic Line (NIL) for Sr24 gene, HW2004, using microarray analysis to understand the transcriptomic differences at different stages of infection. Results showed that HW2004 has higher basal levels of several important genes involved in pathogen detection, defence, and display early activation of multiple defence mechanisms. Further Gene Ontology (GO) and pathway analysis identified important genes responsible for pathogen detection, downstream signalling cascades and transcription factors (TFs) involved in activation and mediation of defence responses. Results suggest that generation of Reactive Oxygen Species (ROS), cytoskeletal rearrangement, activation of multiple hydrolases, and lipid metabolism mediated biosynthesis of certain secondary metabolites are collectively involved in Sr24-mediated defence in HW2004, in response to stem rust infection. Novel and unannotated, but highly responsive genes were also identified, which may also contribute towards resistance phenotype. Furthermore, certain DEGs also mapped close to the Sr24-linked marker on Thinopyrum elongatum translocated fragment on wheat 3E chromosome, which advocate further investigations for better insights of the Sr24-mediated stem rust resistance.

Genetic architecture of adult-plant resistance to stripe rust in bread wheat (Triticum aestivum L.) association panel.

Stripe rust, caused by Puccinia striiformis f. sp. tritici, is a severe disease in wheat worldwide, including Ethiopia, causing up to 100% wheat yield loss in the worst season. The use of resistant cultivars is considered to be the most effective and durable management technique for controlling the disease. Therefore, the present study targeted the genetic architecture of adult plant resistance to yellow rust in 178 wheat association panels. The panel was phenotyped for yellow rust adult-plant resistance at three locations. Phonological, yield, yield-related, and agro-morphological traits were recorded. The association panel was fingerprinted using the genotyping-by-sequencing (GBS) platform, and a total of 6,788 polymorphic single nucleotide polymorphisms (SNPs) were used for genome-wide association analysis to identify effective yellow rust resistance genes. The marker-trait association analysis was conducted using the Genome Association and Prediction Integrated Tool (GAPIT). The broad-sense heritability for the considered traits ranged from 74.52% to 88.64%, implying the presence of promising yellow rust resistance alleles in the association panel that could be deployed to improve wheat resistance to the disease. The overall linkage disequilibrium (LD) declined within an average physical distance of 31.44 Mbp at r2=0.2. Marker-trait association (MTA) analysis identified 148 loci significantly (p = 0.001) associated with yellow rust adult-plant resistance. Most of the detected resistance quantitative trait loci (QTLs) were located on the same chromosomes as previously reported QTLs for yellow rust resistance and mapped on chromosomes 1A, 1B, 1D, 2A, 2B, 2D, 3A, 3B, 3D, 4A, 4B, 4D, 5A, 5B, 6A, 6B, 7A, and 7D. However, 12 of the discovered MTAs were not previously documented in the wheat literature, suggesting that they could represent novel loci for stripe rust resistance. Zooming into the QTL regions in IWGSC RefSeq Annotation v1 identified crucial disease resistance-associated genes that are key in plants' defense mechanisms against pathogen infections. The detected QTLs will be helpful for marker-assisted breeding of wheat to increase resistance to stripe rust. Generally, the present study identified putative QTLs for field resistance to yellow rust and some important agronomic traits. Most of the discovered QTLs have been reported previously, indicating the potential to improve wheat resistance to yellow rust by deploying the QTLs discovered by marker-assisted selection.

Parental selection proposal strategy for recurrent selection in tropical wheat breeding

AbstractRecurrent selection is an effective breeding method for improving complex traits in wheat (Triticum aestivum L.) breeding. In this study, we propose a genitor selection strategy, employing a multi‐trait selection approach and genetic diversity analysis. To evaluate our proposed method, we conducted a lattice design trial during the winter seasons of 2020 and 2021 in Viçosa, MG, Brazil, comprising 87 lines and 13 commercial cultivars. It assessed various traits such as plant height, days to heading, wheat leaf rust, tan spot of wheat, a hundred grain mass, hectoliter weight, and grain yield, and the best linear unbiased predictor (BLUP) was obtained for each trait via restricted maximum likelihood. Next, a genotypic distance matrix, derived from principal component analysis using the BLUP values, was computed to perform hierarchical clustering via the unweighted pair group method with arithmetic mean. The selection of superior genotypes was made utilizing the multi‐trait genotype‐ideotype distance index, resulting in the identification of eight lines and two commercial cultivars as candidates. Furthermore, the genetic diversity analysis revealed distinct clusters among the selected genotypes. To assess the divergence of the chosen genitors, this study proposes a complementarity matrix using factor analysis. Our results indicate that this selection strategy effectively directed the identification of the best and divergent genitors. The complementarity matrix developed in this paper to evaluate the crossings proposal can also be used to evaluate combinations in any panel selected via a multi‐trait approach and can be easily applied and interpreted by breeders of various programs.

Immunological Evaluation of Winter Triticale Varieties to Pyrenophora tritici-repentis and Puccinia triticina under the Conditions of the South of Russia

Immunological Evaluation of Winter Triticale Varieties to Pyrenophora tritici-repentis and Puccinia triticina under the Conditions of the South of Russia

The Underexplored Mechanisms of Wheat Resistance to Leaf Rust

Wheat leaf rust, caused by the obligate biotrophic fungus Puccinia triticina Eriks. (Pt), is one of the most common wheat foliar diseases that continuously threatens global wheat production. Currently, the approaches used to mitigate pathogen infestation include the application of fungicides and the deployment of resistance genes or cultivars. However, the continuous deployment of selected resistant varieties causes host selection pressures that drive Pt evolution and promote the incessant emergence of new virulent races, resulting in the demise of wheat-resistant cultivars after several years of planting. Intriguingly, diploid wheat accessions were found to confer haustorium formation-based resistance to leaf rust, which involves prehaustorial and posthaustorial resistance mechanisms. The prehaustorial resistance in the interaction between einkorn and wheat leaf rust is not influenced by specific races of the pathogen. The induced defense mechanism, known as systemic acquired resistance, also confers durable resistance against a wide array of pathogens. This review summarizes the host range, pathogenic profile, and evolutionary basis of Pt; the molecular basis underlying wheat–Pt interactions; the cloning and characterization of wheat leaf rust resistance genes; prehaustorial and posthaustorial resistance; systemic acquired resistance; and the role of reactive oxygen species. The interplay between climatic factors, genetic features, planting dates, and disease dynamics in imparting resistance is also discussed.

Chiral analysis and semi-preparative separation of metconazole stereoisomers by supercritical fluid chromatography and cytotoxicity assessment in vitro.

Metconazole is one of the widely-used chiral triazole fungicides in controlling wheat leaf rust, powdery mildew, Fusarium head blight with high efficacy, and so forth. In the current work, the effects of chiral stationary phases, alcoholic modifiers, and column temperature on the chiral separation of metconazole were discussed in detail. Amylose tris(3,5-dimethylphenylcarbamate)-coated chiral stationary phase exhibited much stronger chiral recognition ability toward metconazole stereoisomers in the CO2 /ethanol mixture as compared to the others. Then, a two-step semi-preparative separation of metconazole was performed through supercritical fluid chromatography and high-performance liquid chromatography, and the enantiomeric excess values of four stereoisomers were achieved over 98%. Moreover, the enantioselective cytotoxicity of cis-metconazole against HepG2 cells has been investigated, and the order of the cell proliferation toxicity against HepG2 cells was (1R, 5S)-metconazole>(1S, 5R)-metconazole>the mixture. Briefly, this study would provide valuable information in the preparative separation of optically pure metconazole products through chromatographic techniques and their environmental risk assessment.

Biotechnological Strategies Adopted for Sugarcane Disease Management in Tucumán, Argentina

Sugarcane diseases can be controlled by an integrated management approach where biotechnological tools can successfully contribute. The Obispo Colombres Agroindustrial Experimental Station (EEAOC) in Tucumán (Argentina’s main sugarcane producer) has successfully implemented multiple strategies that greatly enhance the productivity of sugarcane fields. The local breeding program develops resistant varieties by applying molecular markers to reveal the presence of Bru1 gene for brown rust resistance throughout the EEAOC germplasm collection. In addition, SNP alleles linked to novel sources of resistance were identified following a selective genotyping strategy. Another strategy is the implementation of a seed cane sanitation project using hydrothermal therapy, an in vitro culture technique, molecular diagnosis of diseases, and bionanoparticles. As a result, the incidence of systemic diseases has significantly decreased in the production fields. More recently, the use of biological products has shown to be effective for disease control in EEAOC varieties. In summary, several biotechnological strategies including molecular markers associated with resistant sources, in vitro culture of apical meristems, molecular diagnostic techniques, and the use of bioproducts are being successfully used for the sustainable management of sugarcane diseases in Tucumán, Argentina.

Complete biodegradation of fungicide carboxin and its metabolite aniline by Delftia sp. HFL-1

Fungicide carboxin was commonly used in the form of seed coating for the prevention of smut, wheat rust and cotton damping-off, leading carboxin and its probable carcinogenic metabolite aniline to directly enter the soil with the seeds, causing residual pollution. In this study, a novel carboxin degrading strain, Delftia sp. HFL-1, was isolated. Strain HFL-1 could use carboxin as the carbon source for growth and completely degrade 50 mg/L carboxin and its metabolite aniline within 24 h. The optimal temperatures and pH for carboxin degrading by strain HFL-1 were 30 to 42 °C and 5 to 9, respectively. Furthermore, the complete mineralization pathway of carboxin by strain HFL-1 was revealed by High Resolution Mass Spectrometer (HRMS). Carboxin was firstly hydrolyzed into aniline and further metabolized into catechol through multiple oxidation processes, and finally converted into 4-hydroxy-2-oxopentanoate, a precursor of the tricarboxylic acid cycle. Genome sequencing revealed the corresponding degradation genes and cluster of carboxin. Among them, amidohydrolase and dioxygenase were key enzymes involved in the degradation of carboxin and aniline. The discovery of transposons indicated that the aniline degradation gene cluster in strain HFL-1 was obtained via horizontal transfer. Furthermore, the degradation genes were cloned and overexpressed. The in vitro test showed that the expressed degrading enzyme could efficiently degrade aniline. This study provides an efficient strain resource for the bioremediation of carboxin and aniline in contaminated soil, and further revealing the molecular mechanism of biodegradation of carboxin and aniline.

Occurrence of Tegolophus brunneus and Phyllocoptruta oleivora (Acari: Eriophyidae) on the main citrus belt of Brazil and the differential toxicity of the acaricides to these species.

Many mites of the family Eriophyidae are important pests worldwide. In citrus crops, the eriophyid Phyllocoptruta oleivora stands out for the economic losses caused. The pest's injuries cause the darkening of leaves, twigs, and fruits, making them unfit for the fresh fruit market and affecting plant productivity. Another species that causes similar symptoms was described in Brazil recently, the brown citrus rust mite, Tegolophus brunneus. Although studies have not been performed with this species, growers and technicians have attributed the rise in rust damages in Brazil to T. brunneus, affirming that this mite is more aggressive and resistant to acaricides than P. oleivora. In this study, the distribution of T. brunneus in the main Brazilian citrus belt and the differential toxicity of the acaricides sulfur and abamectin were evaluated for both species. Infested fruits were collected from different orchards in many municipalities, covering the main citrus species and cultivars grown, aiming to show the main T. brunneus hosts. It was observed that only plants of Tahiti acid lime (Citrus latifolia) were infested by T. brunneus, whereas P. oleivora infested all citrus cultivars and species evaluated (Citrus spp.). In our study, T. brunneus and P. oleivora were never observed coinfesting the same fruit/leaf or plant. The acute toxicity test of sulfur and abamectin as acaricides showed that T. brunneus has greater tolerance to abamectin than P. oleivora. However, the acute toxicity of sulfur was similar for both species. These results showed T. brunneus specificity to infest Tahiti acid lime, causing important damage to this crop, and suggest that attention should be paid to managing this mite using abamectin.

Phenotypic response of a core collection of Aegilops triuncialis accessions to wheat leaf rust and expression pattern of genes involved in resistance

AbstractLeaf rust caused by Puccinia triticina Eriks. is a serious threat to wheat production worldwide. Exploiting wild relatives can effectively help to improve the genetic resistance of wheat against rust. This study aimed to evaluate the responses of 34 Aegilops triuncialis accessions to seven Pt pathotypes and to analyse expression of genes associated with resistance at the seedling stage. Following multipathotype testing, two accessions with contrasting resistance were analysed at 0, 6, 12 and 24 h post‐inoculation for the expression profile of genes related to PR1, PR2, PR4, PR9, phenylalanine ammonia‐lyase and ATP‐binding cassette transporter. Of the accessions tested, eight showed high infection types of “3” to at least one Pt pathotype, while the remaining accessions had low ITs (“0;=” to “2+”) against all pathotypes. The relative expressions of all candidate genes increased at all‐time points, but the expression level in the incompatible interaction was significantly higher than that of the compatible. The close relationship between PR proteins, PAL, salicylic acid‐ and jasmonic acid‐responsive proteins, as well as the proteins involved in the production of reactive oxygen species and lignin, could point to the specific recognition of the pathogen followed by the timely and intense induction of the expression of PR genes as the main reasons for resistance in incompatible interaction. In conclusion, the present study identified potentially new sources of resistance in this Ae. triuncialis population, which can be exploited in wheat breeding programs.

A landscape-scale field survey demonstrates the role of wheat volunteers as a local and diversified source of leaf rust inoculum

Deploying disease-resistant cultivars is one of the most effective control strategies to manage crop diseases such as wheat leaf rust, caused by Puccinia triticina. After harvest, this biotrophic fungal pathogen can survive on wheat volunteers present at landscape scale and constitute a local source of primary inoculum for the next cropping season. In this study, we characterised the diversity of P. triticina populations surveyed on wheat volunteer seedlings for six consecutive years (2007–2012) at the landscape scale. A total of 642 leaf rust samples classified in 52 virulence profiles (pathotypes) were collected within a fixed 5-km radius. The pathotype composition (identity and abundance) of field-collected populations was analyzed according to the distance between the surveyed wheat plots and to the cultivars of origin of isolates. Our study emphasised the high diversity of P. triticina populations on wheat volunteers at the landscape scale. We observed an impact of cultivar of origin on pathogen population composition. Levels of population diversity differed between cultivars and their deployment in the study area. Our results suggest that wheat volunteers could provide a significant though highly variable contribution to the composition of primary inoculum and subsequent initiation of leaf rust epidemics.

How to Differentiate between Resistant and Susceptible Wheat Cultivars for Leaf Rust Fungi Using Antioxidant Enzymes and Histological and Molecular Studies?

Eight wheat cultivars, Sakha-94, Giza-171, Sids-1, Sids-12, Sids-13, Shandweel-1, Misr-1, and Misr-2, were evaluated for leaf rust at the seedling and adult stages in the 2021 and 2022 seasons. Biochemical, histological, and genetic analyses were performed to determine the link between cultivars that were either sensitive or resistant to the disease. Misr-2 and Giza-171 cultivars had the highest levels of resistance to leaf rust races in 2021 (LTCGT, STSJT, and TTTST) and 2022 (MBGJT, TTTKS, and TTTTT) at the seedling stage. However, at the adult stage, Sakha-94, Giza-171, Misr-1, and Misr-2 cultivars had the highest levels of resistance; consequently, they had the lowest final disease severity and the lowest values of AUDPC. The correlation between the seedling reaction and adult reaction was non-significant, with values of 0.4401 and 0.4793 in the 2021 and 2022 seasons, respectively. Throughout the biochemical, histological, and genetic analyses, it was observed that catalase, peroxidase, and polyphenol oxidase activities significantly increased in the resistant cultivars. The discoloration of superoxide (O2-) and hydrogen peroxide (H2O2) significantly decreased in resistant and moderately resistant wheat cultivars (Sakha-94, Giza-171, Misr-1, and Misr-2); higher hydrogen peroxide (H2O2) and superoxide (O2-) levels were recorded for the susceptible cultivars compared to the resistant cultivars. Molecular markers proved that the Lr50 gene was detected in the resistant cultivars. Puccinia triticina infections negatively affected most histological characteristics of flag leaves, especially in susceptible cultivars. The thickness of the blade (µ), the thickness of the upper and lower epidermis (UE and LE), the thickness of mesophyll tissue (MT), and bundle length and width in the midrib were decreased in susceptible cultivars such as Sids-1, Sids-13, and Shandwel-1 compared with resistant cultivars.

Use of effective sources of winter wheat resistance in breeding for immunity

Winter wheat is one of the most important crops in Ukraine, and modern varieties have the potential to produce high yields under favourable conditions. The realisation of the genetic yield potential of a variety is the result of a complex interaction of genotype and environmental variables. In order to find effective sources of resistance, a collection of winter wheat accessions of different ecological and geographical origin was studied. The research was conducted in 2017-2019 in the Right-Bank Forest-Steppe, and the analysis of plant resistance of the winter wheat collection of the National Centre of Plant Genetic Resources of Ukraine was tested against a synthetic infectious background of septoria, brown rust and smut as opposed to the natural background of powdery mildew, leaf yellowing (pyrenophorosis) and other root rot. The collection of 32 varieties was represented by 9 countries, most of them of Ukrainian origin. In the field, on artificial and natural infectious backgrounds, we identified varieties characterised by group resistance to pathogens of major diseases. The studies of adult plant resistance under conditions of infectious natural background and the use of the method of artificial complex infectious background have established that it is possible to investigate and identify sources of resistance to both individual pathogens and a complex of pathogens. As a result, no accessions were found to possess group resistance against the six pathogens presented. The selected varieties, Zdoba Kyivska, Vykhovanka Odeska and Feonia, can be used as sources of group resistance, which allows for excellent breeding efforts leading to the development of resistant wheat varieties. The selected sources are suitable for inclusion in breeding programmes as starting material for the development of modern high-yielding winter durum wheat varieties resistant to diseases and other environmental factors

Influence of biotic and abiotic factors on the virulence of Puccinia triticina population in southern Russia

AbstractWheat leaf rust, caused by Puccinia triticina, is reported annually in southern Russia, the main wheat production region in Russia. The effect of biotic (types of cultivar resistance) and abiotic (northern, central and southern agro‐ecological zones) factors on virulence variability of the pathogen was analysed with 43 Lr differentials. Virulence frequencies to Lr genes 1, 2c, 3, 3bg, 11, 14a, 14b, 16, 17, 18, 23, 25, 26, 33, 34, 40 and Kanr exceeded 50% in all populations. A total of 81 virulence phenotypes (based on the standard set of 20 differentials) were identified among 108 isolates. The most common phenotypes were PHSTQ, THTTR, PHTTR and TKTTR. The minimum genetic distance (the highest similarity) was established between the P. triticina populations from susceptible cv. Krasnodarskaya 99 and cv. Brigada with race‐specific resistance. P. triticina populations from the susceptible cultivar in the three agro‐ecological zones were less variable and more similar than the cultivar‐specific and natural pathogen populations. Resistance types of host cultivars seem to have a greater effect on the pathogen population than abiotic factors. Nevertheless, abiotic factors need to be considered when making decisions about deployment of wheat varieties. Our results support the paradigm of a shift in the population of an obligate parasite towards increased virulence in response to the selection pressure of cultivars with race‐specific resistance.

Modeling the Impact of Proportion, Sowing Date, and Architectural Traits of a Companion Crop on Foliar Fungal Pathogens of Wheat in Crop Mixtures.

Diversification of cropping systems is a lever for the management of epidemics. However, most research to date has focused on cultivar mixtures, especially for cereals, even though crop mixtures can also improve disease management. To investigate the benefits of crop mixtures, we studied the effect of different crop mixture characteristics (i.e., companion proportion, sowing date, and traits) on the protective effect of the mixture. We developed a SEIR (Susceptible, Exposed, Infectious, Removed) model of two damaging wheat diseases (Zymoseptoria tritici and Puccinia triticina), which were applied to different canopy components, ascribable to wheat and a theoretical companion crop. We used the model to study the sensitivity of disease intensity to the following parameters: wheat-versus-companion proportion, companion sowing date and growth, and architectural traits. For both pathogens, the companion proportion had the strongest effect, with 25% of companion reducing disease severity by 50%. However, changing companion growth and architectural traits also significantly improved the protective effect. The effect of companion characteristics was consistent across different weather conditions. After decomposing the dilution and barrier effects, the model suggested that the barrier effect is maximized for an intermediate proportion of companion crop. Our study thus supports crop mixtures as a promising strategy to improve disease management. Future studies should identify real species and determine the combination of host and companion traits to maximize the protective effect of the mixture. [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.

Classification of yellow rust of wheat from Sentinel-2 satellite imagery using deep learning artificial neural network

Classification of yellow rust of wheat from Sentinel-2 satellite imagery using deep learning artificial neural network

The analysis of Puccinia triticina field populations in Canada between 2018 and 2020 using restriction site‐associated DNA genotyping‐by‐sequencing

AbstractPuccinia triticina, the causal agent of wheat leaf rust, is a dynamic pathogen causing significant yield losses worldwide. In this study, we analysed the virulence and genetic structure of 98 P. triticina isolates collected in Canada between 2018 and 2020. Isolates from Manitoba and Saskatchewan were found to be highly related for virulence, as were isolates from Quebec and Ontario. Isolates from Alberta had a virulence profile more similar to those from Manitoba and Saskatchewan than to Ontario and Quebec. To study the genetic structure of P. triticina populations, we used the restriction site‐associated DNA (RAD) genotyping‐by‐sequencing method to identify single‐nucleotide polymorphisms (SNPs). The Puccinia DNA sequences were aligned against the reference genome of P. triticina race BBBD and 1898 SNPs were identified. The phylogenetic analysis using SNP markers grouped these P. triticina into three genetic clades. The separation of P. triticina into three genetic clades was also supported by principal component analysis. Isolates from Clade 1 and Clade 2 were found throughout Canada, whereas Clade 3 isolates were only found in Ontario and Quebec. There were differences in virulence profiles among P. triticina isolates from the three genetic clades and a general correlation between virulence phenotypes and SNP genotypes was observed. These results indicate that the SNPs derived from RAD genotyping‐by‐sequencing could be useful in tracking the genetic and virulence dynamics of this pathogen in Canadian wheat.

Development of a Model for Detection and Grading of Stem Rust in Wheat Using Deep Learning

Development of a Model for Detection and Grading of Stem Rust in Wheat Using Deep Learning

Nuclear exchange generates population diversity in the wheat leaf rust pathogen Puccinia triticina

In clonally reproducing dikaryotic rust fungi, non-sexual processes such as somatic nuclear exchange are postulated to play a role in diversity but have been difficult to detect due to the lack of genome resolution between the two haploid nuclei. We examined three nuclear-phased genome assemblies of Puccinia triticina, which causes wheat leaf rust disease. We found that the most recently emerged Australian lineage was derived by nuclear exchange between two pre-existing lineages, which originated in Europe and North America. Haplotype-specific phylogenetic analysis reveals that repeated somatic exchange events have shuffled haploid nuclei between long-term clonal lineages, leading to a global P. triticina population representing different combinations of a limited number of haploid genomes. Thus, nuclear exchange seems to be the predominant mechanism generating diversity and the emergence of new strains in this otherwise clonal pathogen. Such genomics-accelerated surveillance of pathogen evolution paves the way for more accurate global disease monitoring.