Microsatellite Analysis and Urediniospore Dispersal Simulations Support the Movement of Puccinia graminis f. sp. tritici from Southern Africa to Australia

Phylogenetics of the rust fungi (Pucciniales) of South Africa, with notes on their life histories and possible origins

South Africa has an indigenous rust (Pucciniales) funga of approximately 460 species. This funga was sampled with species from as many genera as possible. The nuclear ribosomal large subunit (28S) region was amplified from samples representing 110 indigenous species, as well as the small subunit (18S) region and the cytochrome c oxidase subunit 3 (CO3) in some cases, and these were used in phylogenetic analyses. One new species is described, 12 new combinations made, six names reinstated, and two life history connections made. The life histories of this funga were summarized; it is dominated by species with contracted life histories. The majority of species are autoecious, with a small proportion being heteroecious. Of the autoecious species, many will likely be homothallic with no spermagonia. A shortened life history with homothallism allows for a single basidiospore infection to initiate a local population buildup under the prevailing unpredictable climatic conditions. Suggestions are made as to the possible origin of this funga based on the development of the modern South African flora. It is postulated that the rusts of South Africa are of relatively recent origin, consisting of three groups. Firstly, there is an African tropical element with members of the Mikronegerineae (Hemileia), the Sphaerophragmiaceae (Puccorchidium, Sphaerophragmium), and certain Uredinineae (Stomatisora). Their immediate ancestors likely occurred in the tropical forests of Africa during the Paleogene. Secondly, there is a pantropical element including the Raveneliaceae (e.g., Diorchidium, Maravalia, Ravenelia sensu lato, Uropyxis). This likely diversified during the Neogene, when the mimosoids became the dominant trees of the developing savannas. Thirdly, the Pucciniaceae invaded Africa as this continent pushed northward closing the Tethys Sea. They diversified with the development of the savannas as these become the dominant habitat in most of Africa, and are by far the largest component of the South African rust funga.

Characterization of a partially saturated and glycosylated apocarotenoid from wheat that is depleted upon leaf rust infection

Recent semi-targeted metabolomics studies have highlighted a number of metabolites in wheat that associate with leaf rust resistance genes and/or rust infection. Here, we report the structural characterization of a novel glycosylated and partially saturated apocarotenoid, reminiscent of a reduced form of mycorradicin, (6E,8E,10E)-4,9-dimethyl-12-oxo-12-((3,4,5-trihydroxy-6-(2-hydroxyethoxy)tetrahydro-2H-pyran-2-yl)methoxy)-3-((3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl)oxy)dodeca-6,8,10-trienoic acid, isolated from Triticum aestivum L. (Poaceae) variety 'Thatcher' (Tc) flag leaves. While its accumulation was not associated with any of Lr34, Lr67 or Lr22a resistance genes, infection of Tc with leaf rust was found to deplete it, consistent with the idea of this metabolite being a glycosylated-storage form of an apocarotenoid of possible relevance to plant defense. A comparative analysis of wheat transcriptomic changes shows modulation of terpenoid, carotenoid, UDP-glycosyltransferase and glycosylase -related gene expression profiles, consistent with anticipated biosynthesis and degradation mechanisms. However, details of the exact nature of the relevant pathways remain to be validated in the future. Together these findings highlight another example of the breadth of unique metabolites underlying plant host-fungal pathogen interactions.

Global dispersal and diversity of rust fungi in the context of plant health

Long-distance dispersal of plant pathogens at the continental scale may have strong implications on plant health, in particular when incursions result in spread of disease to new territories where the disease was previously absent or insignificant. These dispersions may be caused by airborne transmission of spores or accidental spread via human travel and trade. Recent surveillance efforts of cereal rust fungi have demonstrated that incursion of new strains with superior fitness into areas where the disease is already established may have similar implications on plant health. Since dispersal events are highly stochastic, irrespective of transmission mechanism, critical mitigation efforts include preparedness by coordinated pathogen surveillance activities, host crop diversification, and breeding for disease resistance with low vulnerability to sudden changes in the pathogen population.

Pathogen Identification and Factors Influencing Infection Frequency and Severity of Fungal Rust in Four Native Grasses in Hulunber Grassland, China

A serious rust infection present in 2014 and 2015 on the dominant grass species (Leymus chinensis) in the Hulunber grassland of Inner Mongolia, China, and also present on three other grass species (Agropyron cristatum [wheat grass], Bromus inermis, and Festuca ovina) was investigated. Field surveys, laboratory determination of morphological characteristics, pathogenicity tests, and molecular identification methods were integrated to identify two rust-causing pathogens on L. chinensis. It was found that Puccinia elymi was the major pathogen of L. chinensis, and also infected A. cristatum and F. ovina. This is the first report of P. elymi on A. cristatum in China. P. striiformis caused stripe rust on L. chinensis and B. inermis. The incidence and severity of rust infection increased through the growing season, presumably from asexual spread by urediniospores, and was higher on grass species phylogenetically more closely related to common crop hosts of the pathogens. High host grass density and presence of a potential alternate host for P. elymi, Thalictrum squarrosum, were two further factors promoting rust incidence. These results provide insight into ecological factors linked to the rust epidemic and provide a theoretical basis for the formulation of control strategies.

Genetic Diversity and Population Structure Reveal Cryptic Genetic Variation and Long Distance Migration of Puccinia graminis f. sp. tritici in the Indian Subcontinent

Stem rust caused by Puccinia graminis f. sp. tritici (Pgt) is a devastating disease of wheat worldwide since time immemorial. Several wheat stem rust outbreaks have been reported worldwide including India. Approximately 7 mha wheat area in central and peninsular India is highly vulnerable to stem rust epidemics. In this study, a repository of 29 single genotype uredospore pathotypes, representing five geographical regions, was characterized by investigating their virulence phenotype and simple sequence repeat (SSR) genotypes using 37 reproducible polymorphic SSR markers, 32 of which had ≥ 0.50 polymorphic information content (PIC) value. Virulence phenotypes were used to evaluate the virulence frequency (VF) and construct a hypothetical evolutionary hierarchy of these pathotypes. We projected seven lineages to explain the evolutionary pattern of the Pgt population. The VF of these pathotypes ranged between 0% and 100%. The virulence-based neighbor-joining (NJ) cluster analysis grouped Pgt pathotypes into five virulence groups. Likewise, five molecular groups were categorized using molecular genotypes. The molecular grouping was supported by principal coordinate analysis (PCoA), which revealed 25% of the cumulative variance contributed by the first two axes. Analysis of molecular variance (AMOVA) revealed 8 and 92% of the variation among and within the populations, respectively. The Mantel test confirmed a positive but weak correlation (R 2 = 0.15) between virulence phenotypes and SSR genotypes. The highest and lowest values of different genetic diversity parameters (Na, Ne, I, He, uHe, and %P) revealed maximum and minimum variability in the Pgt population from Maharashtra and Uttar Pradesh, respectively. The population structure analysis clustered 29 Pgt pathotypes into two subpopulations and an admixture. Our results demonstrated that there was significant genetic diversity among Pgt pathotypes resulting from their long-distance dispersal ability complemented by gene flow. These findings provide insights into the virulence patterns, genetic variations, and possible evolution of Pgt pathotypes, which would support strategic stem rust resistance breeding.

Global Analysis of Hemileia vastatrix Populations Shows Clonal Reproduction for the Coffee Leaf Rust Pathogen Throughout Most of Its Range

Hemileia vastatrix is the most important fungal pathogen of coffee and the causal agent of recurrent disease epidemics that have invaded nearly every coffee growing region in the world. The development of coffee varieties resistant to H. vastatrix requires fundamental understanding of the biology of the fungus. However, the complete life cycle of H. vastatrix remains unknown, and conflicting studies and interpretations exist as to whether the fungus is undergoing sexual reproduction. Here we used population genetics of H. vastatrix to infer the reproductive mode of the fungus across most of its geographic range, including Central Africa, Southeast Asia, the Caribbean, and South and Central America. The population structure of H. vastatrix was determined via eight simple sequence repeat markers developed for this study. The analyses of the standardized index of association, Hardy-Weinberg equilibrium, and clonal richness all strongly support asexual reproduction of H. vastatrix in all sampled areas. Similarly, a minimum spanning network tree reinforces the interpretation of clonal reproduction in the sampled H. vastatrix populations. These findings may have profound implications for resistance breeding and management programs against H. vastatrix.

A general trait-based modelling framework for revealing patterns of airborne fungal dispersal threats to agriculture and native flora

Fungal plant pathogens are of economic and ecological importance to global agriculture and natural ecosystems. Long-distance atmospheric dispersal of fungal spores (LAD) can pose threats to agricultural and native vegetation lands. An understanding of such patterns of fungal spore dispersal and invasion pathways can provide valuable insights into plant protection. Spore traits affect their dispersal abilities. We propose a general trait-based framework for modelling LAD to reveal dispersal patterns and pathways, and assess subsequent threats of arrival (TOA) quantitatively in the context of biosecurity. To illustrate the framework, we present a study of Australia and its surrounding land masses. The overall dispersal pattern covered almost the entire continent of Australia. Fungal spores in the size class of 10 and 20 µm (aerodynamic diameter) posed the greatest TOA. Our study shows the effects of morphological traits on these potential TOA, and how they varied between source regions, size classes, and seasons. Our framework revealed spore dispersal patterns and pathways. It also facilitates comparisons of spatio-temporal dispersal dynamics among fungal classes, gaining insights into atmospheric long-distance dispersal of fungi as a whole, and provides a basis for assessing fungal pest threats in potential source regions based on easily measured spore characteristics.

Incursions of divergent genotypes, evolution of virulence and host jumps shape a continental clonal population of the stripe rust pathogen Puccinia striiformis

Long-distance migration and host adaptation by transboundary plant pathogens often brings detrimental effects to important agroecosystems. Efficient surveillance as a basis for responding to the dynamics of such pathogens is often hampered by a lack of information on incursion origin, evolutionary pathways and the genetic basis of rapidly evolving virulence across larger timescales. Here, we studied these genetic features by using historical isolates of the obligate biotrophic pathogen Puccinia striiformis f. sp. tritici (Pst), which causes one of the most widespread and devastating diseases, stripe (yellow) rust, of wheat. Through a combination of genotypic, phenotypic and genomic analyses, we assigned eight Pst isolates representing putative exotic Pst incursions into Australia to four previously defined genetic groups, PstS0, PstS1, PstS10 and PstS13. We showed that isolates of an additional incursion of P. striiformis, known locally as P. striiformis f. sp. pseudo-hordei, had a new and unique multilocus SSR genotype (MLG). We provide results of overall genomic variation of representative Pst isolates from each genetic group by comparative genomic analyses. We showed that isolates within the PstS1 and PstS13 genetic groups are most distinct at the whole-genome variant level from isolates belonging to genetic group PstS0, whereas the isolate from the PstS10 genetic group is intermediate. We further explored variable gene content, including putative effectors, representing both shared but also unique genetic changes that have occurred following introduction, some of which may additionally account for local adaptation of these isolates to triticale. Our genotypic and genomic data revealed new genetic insights into the evolution of diverse phenotypes of rust pathogens following incursion into a geographically isolated continental region.

Genomics accelerated isolation of a new stem rust avirulence gene-wheat resistance gene pair

Stem rust caused by the fungus Puccinia graminis f. sp. tritici (Pgt) is a devastating disease of the global staple crop wheat. Although this disease was largely controlled in the latter half of the twentieth century, new virulent strains of Pgt, such as Ug99, have recently evolved^1,2. These strains have caused notable losses worldwide and their continued spread threatens global wheat production. Breeding for disease resistance provides the most cost-effective control of wheat rust diseases³. A number of rust resistance genes have been characterized in wheat and most encode immune receptors of the nucleotide-binding leucine-rich repeat (NLR) class⁴, which recognize pathogen effector proteins known as avirulence (Avr) proteins⁵. However, only two Avr genes have been identified in Pgt so far, AvrSr35 and AvrSr50 (refs. ^6,7), and none in other cereal rusts^8,9. The Sr27 resistance gene was first identified in a wheat line carrying an introgression of the 3R chromosome from Imperial rye¹⁰. Although not deployed widely in wheat, Sr27 is widespread in the artificial crop species Triticosecale (triticale), which is a wheat-rye hybrid and is a host for Pgt^11,12. Sr27 is effective against Ug99 (ref. ¹³) and other recent Pgt strains^14,15. Here, we identify both the Sr27 gene in wheat and the corresponding AvrSr27 gene in Pgt and show that virulence to Sr27 can arise experimentally and in the field through deletion mutations, copy number variation and expression level polymorphisms at the AvrSr27 locus.

Historical Development of the Puccinia triticina Population in South Africa

In contrast to many other countries, the virulence and genetic diversity of the South African Puccinia triticina population before 1980 is unknown, because of the absence of regular and systematic race analysis data and viable rust cultures. Herbarium specimens housed at the National Collection of Fungi, Biosystematics Unit, Plant Health and Protection, Agricultural Research Council, Pretoria, South Africa (SA), provided the opportunity to investigate the genetic development of the population using isolates collected between 1906 and 2010. Five subpopulations that survived between 21 and 82 years in the field were found. While three of these could represent the original races that entered SA during European settlement, two appear to be recent exotic introductions into SA, most probably from other African countries. The demise of the three oldest subpopulations might be from the release of resistant wheat cultivars. The population is clonal, where new virulence develops through single step mutations and selection for virulence. Although a possible case of somatic hybridization was found, sexual reproduction appears to be absent in SA. This study confirmed the importance of annual surveys in SA and its neighboring countries for the timely detection of new virulent races that could threaten wheat production in SA.

Host Adaptation and Virulence in Heteroecious Rust Fungi

Rust fungi (Pucciniales, Basidiomycota) are obligate biotrophic pathogens that cause rust diseases in plants, inflicting severe damage to agricultural crops. Pucciniales possess the most complex life cycles known in fungi. These include an alternation of generations, the development of up to five different sporulating stages, and, for many species, the requirement of infecting two unrelated host plants during different parts of their life cycle, termed heteroecism. These fungi have been extensively studied in the past century through microscopy and inoculation studies, providing precise descriptions of their infection processes, although the molecular mechanisms underlying their unique biology are poorly understood. In this review, we cover recent genomic and life cycle transcriptomic studies in several heteroecious rust species, which provide insights into the genetic tool kits associated with host adaptation and virulence, opening new avenues for unraveling their unique evolution.

Phenotypic and Genotypic Variation of Puccinia helianthi in South Africa

Sunflower (Helianthus annuus L.) is the third largest grain crop by area planted in South Africa (SA). The annual yield is negatively affected by sunflower rust caused by Puccinia helianthi Schw. (Phe). Four Phe races were described in SA in the middle 1990s, but since then, no new race descriptions have been conducted. This has resulted in an information gap on the current Phe population, making it difficult to explain increased disease incidence and loss of resistance in previously resistant hybrids. To address this, 114 Phe field isolates along with 23 historic isolates were phenotyped using the international set of 11 sunflower differentials containing the R₁, R₂/R₁₀, R₃, R_4a, R_4b, R_4c, R_4d, R₅, Pu₆, and R_adv resistance genes. Three new Phe races were identified, bringing the total number of South African races recorded to seven. No avirulence was detected attributable to the R₁ gene, with the R_4d and R_adv genes remaining effective. Four main genetic lineages were detected with no obvious correlation between phenotype and genotype. The detection of three genetic lineages consisting exclusively of field isolates collected post-2006 suggested the possible recent entry of exotic introductions into SA. This, combined with the fact that one lineage consisted exclusively of the most virulent race Phe7721, confirmed a clear shift in the Phe population that could explain the increased virulence and occurrence of the disease in SA.

Accomplishments in wheat rust research in South Africa

Rust diseases, although seasonal, have been severe constraints in wheat production in South Africa for almost 300 years. Rust research gained momentum with the institution of annual surveys in the 1980s, followed by race identification, an understanding of rust epidemiology, and eventually a focused collaboration amongst pathologists, breeders and geneticists. Diversity in South African populations of Puccinia triticina, P. graminis f. sp. tritici and P. striiformis f. sp. tritici has been described and isolates are available to accurately phenotype wheat germplasm and study pathogen populations at national, regional and global levels. Sources of resistance have been, and still are, methodically analysed and molecular marker systems were developed to incorporate, stack and verify complex resistance gene combinations in breeding lines and cultivars. Vigilance, capacity, new technologies, collaboration and sustained funding are critical for maintaining and improving the current research impetus for future management of these important diseases.

Evolution of virulence in rust fungi - multiple solutions to one problem

Rust fungi are major pathogens that negatively affect crops and ecosystems. Recent rust disease epidemics driven by the emergence of strains with novel virulence profiles demand a better understanding of the evolutionary mechanisms of these organisms. Here, we review research advances in genome-scale analysis coupled with functional validation of effector candidate genes that have been instrumental to elucidate processes that contribute to changes in virulence phenotypes. We highlight how haplotype-phased genome references have paved the road to link these processes to the reproductive phases of rust fungi and have provided evidence for somatic exchange between strains as an important mechanism for generating diversity in asexual populations. With increasing data availability, we envision the future development of molecular virulence diagnostic tools.

How Target-Sequence Enrichment and Sequencing (TEnSeq) Pipelines Have Catalyzed Resistance Gene Cloning in the Wheat-Rust Pathosystem

The wheat-rust pathosystem has been well-studied among host-pathogen interactions since last century due to its economic importance. Intensified efforts toward cloning of wheat rust resistance genes commenced in the late 1990s with the first successful isolation published in 2003. Currently, a total of 24 genes have been cloned from wheat that provides resistance to stem rust, leaf rust, and stripe rust. Among them, more than half (15) were cloned over the last 4 years. This rapid cloning of resistance genes from wheat can be largely credited to the development of approaches for reducing the genome complexity as 10 out of the 15 genes cloned recently were achieved by approaches that are summarized as TEnSeq (Target-sequence Enrichment and Sequencing) pipelines in this review. The growing repertoire of cloned rust resistance genes provides new tools to support deployment strategies aimed at achieving durable resistance. This will be supported by the identification of genetic variation in corresponding Avr genes from rust pathogens, which has recently begun. Although developed with wheat resistance genes as the primary targets, TEnSeq approaches are also applicable to other classes of genes as well as for other crops with complex genomes.

Breeding Wheat for Durable Leaf Rust Resistance in Southern Africa: Variability, Distribution, Current Control Strategies, Challenges and Future Prospects

Leaf or brown rust of wheat caused by Puccinia triticina (Pt) is one of the most damaging diseases globally. Considerable progress has been made to control leaf rust through crop protection chemicals and host plant resistance breeding in southern Africa. However, frequent changes in the pathogen population still present a major challenge to achieve durable resistance. Disease surveillance and monitoring of the pathogen have revealed the occurrence of similar races across the region, justifying the need for concerted efforts by countries in southern Africa to develop and deploy more efficient and sustainable strategies to manage the disease. Understanding the genetic variability and composition of Pt is a pre-requisite for cultivar release with appropriate resistance gene combinations for sustainable disease management. This review highlights the variability and distribution of the Pt population, and the current control strategies, challenges and future prospects of breeding wheat varieties with durable leaf rust resistance in southern Africa. The importance of regular, collaborative and efficient surveillance of the pathogen and germplasm development across southern Africa is discussed, coupled with the potential of using modern breeding technologies to produce wheat cultivars with durable resistance.

Virulence Dynamics and Breeding for Resistance to Stripe, Stem, and Leaf Rust in Canada Since 2000

Wheat (Triticum spp.) is a major field crop in Canada in terms of acreage, annual production, and export market value. There are nine classes of Canadian wheat based on growth habit (winter or spring), kernel hardness (hard or soft), seed coat color (red or white), and quality factors (grain protein content and gluten strength). Wheat was described by Newman in 1928 as "the economic fairy to the industrial and commercial life of Canada, having built practically the whole economic structure of the Prairie Provinces." Wheat production in Canada is affected by several biotic and abiotic stresses. The major abiotic stresses are frost damage, drought, and heat stress. Among biotic stresses, diseases caused by fungal pathogens are the most important although wheat streak mosaic virus (WSMV) has caused some localized outbreaks in some years. In context of cultivar registration in Canada, there are certain diseases that breeders have to take into account while developing resistant cultivars. The Prairie Recommending Committee for Wheat, Rye, and Triticale (PRCWRT) classify wheat diseases into priority one, priority two, and priority three depending on prevalence and potential damage they can cause. However, priority one diseases are more of a concern and a minimum level of resistance in commercial cultivars is recommended for those.

Emergence of the Ug99 lineage of the wheat stem rust pathogen through somatic hybridisation

Parasexuality contributes to diversity and adaptive evolution of haploid (monokaryotic) fungi. However, non-sexual genetic exchange mechanisms are not defined in dikaryotic fungi (containing two distinct haploid nuclei). Newly emerged strains of the wheat stem rust pathogen, Puccinia graminis f. sp. tritici (Pgt), such as Ug99, are a major threat to global food security. Here, we provide genomics-based evidence supporting that Ug99 arose by somatic hybridisation and nuclear exchange between dikaryons. Fully haplotype-resolved genome assembly and DNA proximity analysis reveal that Ug99 shares one haploid nucleus genotype with a much older African lineage of Pgt, with no recombination or chromosome reassortment. These findings indicate that nuclear exchange between dikaryotes can generate genetic diversity and facilitate the emergence of new lineages in asexual fungal populations.

An early warning system to predict and mitigate wheat rust diseases in Ethiopia

Wheat rust diseases pose one of the greatest threats to global food security, including subsistence farmers in Ethiopia. The fungal spores transmitting wheat rust are dispersed by wind and can remain infectious after dispersal over long distances. The emergence of new strains of wheat rust has exacerbated the risks of severe crop loss. We describe the construction and deployment of a near realtime early warning system (EWS) for two major wind-dispersed diseases of wheat crops in Ethiopia that combines existing environmental research infrastructures, newly developed tools and scientific expertise across multiple organisations in Ethiopia and the UK. The EWS encompasses a sophisticated framework that integrates field and mobile phone surveillance data, spore dispersal and disease environmental suitability forecasting, as well as communication to policy-makers, advisors and smallholder farmers. The system involves daily automated data flow between two continents during the wheat season in Ethiopia. The framework utilises expertise and environmental research infrastructures from within the cross-disciplinary spectrum of biology, agronomy, meteorology, computer science and telecommunications. The EWS successfully provided timely information to assist policy makers formulate decisions about allocation of limited stock of fungicide during the 2017 and 2018 wheat seasons. Wheat rust alerts and advisories were sent by short message service and reports to 10 000 development agents and approximately 275 000 smallholder farmers in Ethiopia who rely on wheat for subsistence and livelihood security. The framework represents one of the first advanced crop disease EWSs implemented in a developing country. It provides policy-makers, extension agents and farmers with timely, actionable information on priority diseases affecting a staple food crop. The framework together with the underpinning technologies are transferable to forecast wheat rusts in other regions and can be readily adapted for other wind-dispersed pests and disease of major agricultural crops.

Multilocus Genotypes of the Wheat Leaf Rust Fungus Puccinia triticina in Worldwide Regions Indicate Past and Current Long-Distance Migration

Many plant pathogenic fungi have a global distribution across diverse ecological zones and agricultural production systems. Puccinia triticina, the wheat leaf rust fungus, is a major pathogen in many wheat production areas of the world. The objective of this research was to determine the genetic relatedness of P. triticina in different worldwide regions. A total of 831 single-uredinial isolates collected from 11 regions were characterized for multilocus genotype at 23 simple sequence repeat loci and for virulence to 20 lines of wheat with single genes for leaf rust resistance. A total of 424 multilocus genotypes and 497 virulence phenotypes were found. All populations had high heterozygosity and significant correlation between virulence and molecular variation, which indicated clonal reproduction. The populations from North America and South America, Central Asia and Russia, and the Middle East and Europe were closely related for multilocus genotypes and many individual isolates from other continental regions were closely related. Twenty-seven multilocus genotypes were found in more than one continental region, and 13 of these had isolates with identical virulence phenotypes. The wide geographic distribution of identical and highly related multilocus genotypes of P. triticina indicated past and more recent migration events facilitated by the spread of clonally produced urediniospores.