The past, present and future of breeding rust resistant wheat

Two classes of genes are used for breeding rust resistant wheat. The first class, called R (for resistance) genes, are pathogen race specific in their action, effective at all plant growth stages and probably mostly encode immune receptors of the nucleotide binding leucine rich repeat (NB-LRR) class. The second class is called adult plant resistance genes (APR) because resistance is usually functional only in adult plants, and, in contrast to most R genes, the levels of resistance conferred by single APR genes are only partial and allow considerable disease development. Some but not all APR genes provide resistance to all isolates of a rust pathogen species and a subclass of these provides resistance to several fungal pathogen species. Initial indications are that APR genes encode a more heterogeneous range of proteins than R proteins. Two APR genes, Lr34 and Yr36, have been cloned from wheat and their products are an ABC transporter and a protein kinase, respectively. Lr34 and Sr2 have provided long lasting and widely used (durable) partial resistance and are mainly used in conjunction with other R and APR genes to obtain adequate rust resistance. We caution that some APR genes indeed include race specific, weak R genes which may be of the NB-LRR class. A research priority to better inform rust resistance breeding is to characterize further APR genes in wheat and to understand how they function and how they interact when multiple APR and R genes are stacked in a single genotype by conventional and GM breeding. An important message is do not be complacent about the general durability of all APR genes.

Comparative Analysis Highlights Variable Genome Content of Wheat Rusts and Divergence of the Mating Loci

Three members of the Puccinia genus, Pucciniatriticina (Pt), Pstriiformis f.sp. tritici (Pst), and Pgraminis f.sp. tritici (Pgt), cause the most common and often most significant foliar diseases of wheat. While similar in biology and life cycle, each species is uniquely adapted and specialized. The genomes of Pt and Pst were sequenced and compared to that of Pgt to identify common and distinguishing gene content, to determine gene variation among wheat rust pathogens, other rust fungi, and basidiomycetes, and to identify genes of significance for infection. Pt had the largest genome of the three, estimated at 135 Mb with expansion due to mobile elements and repeats encompassing 50.9% of contig bases; in comparison, repeats occupy 31.5% for Pst and 36.5% for Pgt We find all three genomes are highly heterozygous, with Pst [5.97 single nucleotide polymorphisms (SNPs)/kb] nearly twice the level detected in Pt (2.57 SNPs/kb) and that previously reported for Pgt Of 1358 predicted effectors in Pt, 784 were found expressed across diverse life cycle stages including the sexual stage. Comparison to related fungi highlighted the expansion of gene families involved in transcriptional regulation and nucleotide binding, protein modification, and carbohydrate degradation enzymes. Two allelic homeodomain pairs, HD1 and HD2, were identified in each dikaryotic Puccinia species along with three pheromone receptor (STE3) mating-type genes, two of which are likely representing allelic specificities. The HD proteins were active in a heterologous Ustilago maydis mating assay and host-induced gene silencing (HIGS) of the HD and STE3 alleles reduced wheat host infection.

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.

Ecological genetic interactions between a clonal host plant (Spartina pectinata) and associated rust fungi Puccinia seymouriana and Puccinia sparganioides

The spatial scale of genetic diversity among patches of a host plant could affect the likelihood of pathogen adaptation to the host. If host patches are genetically distinct, pathogen adaptation to local host genotypes may occur. To study this issue, we focused on the ecological and genetic interactions between two rust fungi, Puccinia seymouriana and P. sparganioides, and the clonal prairie grass, Spartina pectinata. In a field transplant experiment, disease levels differed among plants from different patches, suggesting variation in resistance. Over a 4.5-km scale, disease levels were not higher on plants transplanted back into their source patch as opposed to other locations, providing no evidence for local adaptation in the pathogen. However, on the spatial scales examined (ranging from 0.2 km to 120 km), there was no relationship between the physical distance separating host patches and their similarity in isozyme banding patterns, implying that plants from more distant patches are not necessarily more genetically distinct than plants from nearby patches. Plants derived from the most distant location had, on average, the lowest mean number of pustules at the end of the summer, suggesting the need for reciprocal transplant studies to be performed on a larger spatial scale.

Differentiating the effects of origin and frequency in reciprocal transplant experiments used to test negative frequency-dependent selection hypotheses

Reciprocal transplant experiments have been used to estimate the probability that negative frequency-dependent selection by natural enemies has occurred in host populations by determining whether pest populations are less adapted to "foreign" (rare) hosts, which originate from a population with which the pests have not coevolved. However, these experiments usually confound the effects of frequency and origin: the rare genotypes are also genotypes that did not originate at a site. When clonal organisms are used, and the clones occur in more than one population, it is possible to separate the effects of origin and frequency. Here I present the results of an experiment in which Arabis clones of known frequency were reciprocally transplanted among sites. Contrary to expectations, clones at their site of origin had less disease, less herbivory, and higher fitness than foreign clones. However, variation within and among sites in herbivory and infection was large, suggesting that the number of sites and clones needed to thoroughly test the hypothesis of negative frequency-dependent selection in this system is very large: thus, these results are suggestive but not conclusive.

Rust pathogen effectors: perspectives in resistance breeding

Identification and functional characterization of plant pathogen effectors promise to ameliorate future research and develop effective and sustainable strategies for controlling or containing crop diseases. Wheat is the second most important food crop of the world after rice. Rust pathogens, one of the major biotic stresses in wheat production, are capable of threatening the world food security. Understanding the molecular basis of plant-pathogen interactions is essential for devising novel strategies for resistance breeding and disease management. Now, it has been established that effectors, the proteins secreted by pathogens, play a key role in plant-pathogen interactions. Therefore, effector biology has emerged as one of the most important research fields in plant biology. Recent advances in genomics and bioinformatics have allowed identification of a large repertoire of candidate effectors, while the evolving high-throughput tools have continued to assist in their functional characterization. The repertoires of effectors have become an important resource for better understanding of effector biology of pathosystems and resistance breeding of crop plants. In recent years, a significant progress has been made in the field of rust effector biology. This review describes the recent advances in effector biology of obligate fungal pathogens, identification and functional analysis of wheat rust pathogens effectors and the potential applications of effectors in molecular plant biology and rust resistance breeding in wheat.

Brachypodium as an emerging model for cereal-pathogen interactions

BACKGROUND

Cereal diseases cause tens of billions of dollars of losses annually and have devastating humanitarian consequences in the developing world. Increased understanding of the molecular basis of cereal host-pathogen interactions should facilitate development of novel resistance strategies. However, achieving this in most cereals can be challenging due to large and complex genomes, long generation times and large plant size, as well as quarantine and intellectual property issues that may constrain the development and use of community resources. Brachypodium distachyon (brachypodium) with its small, diploid and sequenced genome, short generation time, high transformability and rapidly expanding community resources is emerging as a tractable cereal model.

SCOPE

Recent research reviewed here has demonstrated that brachypodium is either susceptible or partially susceptible to many of the major cereal pathogens. Thus, the study of brachypodium-pathogen interactions appears to hold great potential to improve understanding of cereal disease resistance, and to guide approaches to enhance this resistance. This paper reviews brachypodium experimental pathosystems for the study of fungal, bacterial and viral cereal pathogens; the current status of the use of brachypodium for functional analysis of cereal disease resistance; and comparative genomic approaches undertaken using brachypodium to assist characterization of cereal resistance genes. Additionally, it explores future prospects for brachypodium as a model to study cereal-pathogen interactions.

CONCLUSIONS

The study of brachypodium-pathogen interactions appears to be a productive strategy for understanding mechanisms of disease resistance in cereal species. Knowledge obtained from this model interaction has strong potential to be exploited for crop improvement.

Durable resistance to the wheat rusts: Integrating systems biology and traditional phenotype-based research methods to guide the deployment of resistance genes

Genes which confer partial resistance to the rusts in wheat figure prominently in discussions of potential durable resistance strategies. The positional cloning of the first of these genes, Lr34/Yr18 and Yr36, has revealed different protein structures, suggesting that the category of partial resistance genes, as defined by phenotype, likely groups together suites of functionally heterogenous genes. With the number of mapped partial rust resistance genes increasing rapidly as a result of ongoing advances in marker and sequencing technologies, breeding programs needing to select and prioritize genes for deployment confront a fundamental question: which genes or gene combinations are more likely to provide durable protection against these evolving pathogens? We argue that a refined classification of partial rust resistance genes is required to start answering this question, one based not merely on disease phenotype but also on gene cloning, molecular functional characterization, and interactions with other host and pathogen proteins. Combined with accurate and detailed disease phenotyping and standard genetic studies, an integrated wheat-rust interactome promises to provide the basis for a functional classification of partial resistance genes and thus a conceptual framework for their rational deployment.

Changing the Game: Using Integrative Genomics to Probe Virulence Mechanisms of the Stem Rust Pathogen Puccinia graminis f. sp. tritici

The recent resurgence of wheat stem rust caused by new virulent races of Puccinia graminis f. sp. tritici (Pgt) poses a threat to food security. These concerns have catalyzed an extensive global effort toward controlling this disease. Substantial research and breeding programs target the identification and introduction of new stem rust resistance (Sr) genes in cultivars for genetic protection against the disease. Such resistance genes typically encode immune receptor proteins that recognize specific components of the pathogen, known as avirulence (Avr) proteins. A significant drawback to deploying cultivars with single Sr genes is that they are often overcome by evolution of the pathogen to escape recognition through alterations in Avr genes. Thus, a key element in achieving durable rust control is the deployment of multiple effective Sr genes in combination, either through conventional breeding or transgenic approaches, to minimize the risk of resistance breakdown. In this situation, evolution of pathogen virulence would require changes in multiple Avr genes in order to bypass recognition. However, choosing the optimal Sr gene combinations to deploy is a challenge that requires detailed knowledge of the pathogen Avr genes with which they interact and the virulence phenotypes of Pgt existing in nature. Identifying specific Avr genes from Pgt will provide screening tools to enhance pathogen virulence monitoring, assess heterozygosity and propensity for mutation in pathogen populations, and confirm individual Sr gene functions in crop varieties carrying multiple effective resistance genes. Toward this goal, much progress has been made in assembling a high quality reference genome sequence for Pgt, as well as a Pan-genome encompassing variation between multiple field isolates with diverse virulence spectra. In turn this has allowed prediction of Pgt effector gene candidates based on known features of Avr genes in other plant pathogens, including the related flax rust fungus. Upregulation of gene expression in haustoria and evidence for diversifying selection are two useful parameters to identify candidate Avr genes. Recently, we have also applied machine learning approaches to agnostically predict candidate effectors. Here, we review progress in stem rust pathogenomics and approaches currently underway to identify Avr genes recognized by wheat Sr genes.

A brief overview of the size and composition of the myrtle rust genome and its taxonomic status

Using de novo assembly of 46 million paired end sequence reads of length 250 bp for a myrtle rust isolate, we have estimated its genome size to be between 103 and 145 Mb and the number of proteins as >19,000. Annotation of the contigs found a very large percentage of proteins are associated with molecular functions of DNA binding or binding in biological processes for DNA integration and RNA-dependent DNA replication. A large proportion of these activities are attributed to the transposable elements (TEs). These elements are estimated to comprise 27% of the genome with 22% retrotransposons and 5% DNA transposons. The exon and intron boundaries of 46 genes occurring on contigs >20,000 bp have been determined. The number of introns range from 2 to 20 with a mean of 7. Phylogenetic analyses using partial COXI, 18S rRNA and 28S rRNA genes have placed myrtle rust in the Pucciniaceae lineage on a separate taxonomic branch from the families of Pucciniaceae, Phragmidiaceae, Sphaerophragmiaceae, Phragmidiaceae, Uropyxidaceae, Chaconiaceae and Phakopsoraceae. Further work is thus required to determine the family placement of myrtle rust in the Pucciniaceae of Pucciniales.

A comparative analysis of nonhost resistance across the two Triticeae crop species wheat and barley

BACKGROUND

Nonhost resistance (NHR) protects plants against a vast number of non-adapted pathogens which implicates a potential exploitation as source for novel disease resistance strategies. Aiming at a fundamental understanding of NHR a global analysis of transcriptome reprogramming in the economically important Triticeae cereals wheat and barley, comparing host and nonhost interactions in three major fungal pathosystems responsible for powdery mildew (Blumeria graminis ff. ssp.), cereal blast (Magnaporthe sp.) and leaf rust (Puccinia sp.) diseases, was performed.

RESULTS

In each pathosystem a significant transcriptome reprogramming by adapted- or non-adapted pathogen isolates was observed, with considerable overlap between Blumeria, Magnaporthe and Puccinia. Small subsets of these general pathogen-regulated genes were identified as differentially regulated between host and corresponding nonhost interactions, indicating a fine-tuning of the general pathogen response during the course of co-evolution. Additionally, the host- or nonhost-related responses were rather specific for each pair of adapted and non-adapted isolates, indicating that the nonhost resistance-related responses were to a great extent pathosystem-specific. This pathosystem-specific reprogramming may reflect different resistance mechanisms operating against non-adapted pathogens with different lifestyles, or equally, different co-option of the hosts by the adapted isolates to create an optimal environment for infection. To compare the transcriptional reprogramming between wheat and barley, putative orthologues were identified. Within the wheat and barley general pathogen-regulated genes, temporal expression profiles of orthologues looked similar, indicating conserved general responses in Triticeae against fungal attack. However, the comparison of orthologues differentially expressed between host and nonhost interactions revealed fewer commonalities between wheat and barley, but rather suggested different host or nonhost responses in the two cereal species.

CONCLUSIONS

Taken together, our results suggest independent co-evolutionary forces acting on host pathosystems mirrored by barley- or wheat-specific nonhost responses. As a result of evolutionary processes, at least for the pathosystems investigated, NHR appears to rely on rather specific plant responses.

Mapping of Novel Leaf Rust and Stem Rust Resistance Genes in the Portuguese Durum Wheat Landrace PI 192051

Leaf rust caused by Puccinia triticina Erikss. (Pt) and stem rust caused by Puccinia graminis f. sp. tritici Erikss. & E. Henn (Pgt) are serious constraints to production of durum wheat (Triticum turgidum L). The objective of this study was to identify leaf rust resistance (Lr) and stem rust resistance (Sr) genes/QTL in Portuguese durum landrace PI 192051. Four Pt-isolates, representing three virulence phenotypes (BBBQJ, BBBSJ & EEEEE) and six Pgt-races TTKSK, JRCQC, TKTTF, QFCFC, TPMKC and TMLKC were used to evaluate 180 recombinant inbred lines (RILs) derived from the cross Rusty (rust susceptible) × PI 192051-1 (rust resistant) at the seedling stage. The RILs were also phenotyped at the adult-plant stage in a stem rust nursery in Ethiopia in 2017. The RILs were genotyped using the Illumina iSelect 9K wheat SNP array. PI 192051-1 carries a previously unidentified major Sr gene designated as QSr.ace-7A on chromosome arm 7AS and Lr gene Lr.ace-4A in the pericentromeric region of chromosome 4A. In addition, three minor Sr QTL QSr.ace-1A, QSr.ace-2B and QSr.ace-4A were mapped in PI 192051-1 on chromosomes 1AL, 2BL, and 4A, respectively Lr.ace-4A could be co-located or tightly linked to QSr.ace-4A. Markers linked to the identified QTL/genes can be used for marker assisted selection. These findings enrich the genetic basis of rust resistance in both durum and common wheat.

Pushing the boundaries of resistance: insights from Brachypodium-rust interactions

The implications of global population growth urge transformation of current food and bioenergy production systems to sustainability. Members of the family Poaceae are of particular importance both in food security and for their applications as biofuel substrates. For centuries, rust fungi have threatened the production of valuable crops such as wheat, barley, oat, and other small grains; similarly, biofuel crops can also be susceptible to these pathogens. Emerging rust pathogenic races with increased virulence and recurrent rust epidemics around the world point out the vulnerability of monocultures. Basic research in plant immunity, especially in model plants, can make contributions to understanding plant resistance mechanisms and improve disease management strategies. The development of the grass Brachypodium distachyon as a genetically tractable model for monocots, especially temperate cereals and grasses, offers the possibility to overcome the experimental challenges presented by the genetic and genomic complexities of economically valuable crop plants. The numerous resources and tools available in Brachypodium have opened new doors to investigate the underlying molecular and genetic bases of plant-microbe interactions in grasses and evidence demonstrating the applicability and advantages of working with B. distachyon is increasing. Importantly, several interactions between B. distachyon and devastating plant pathogens, such rust fungi, have been examined in the context of non-host resistance. Here, we discuss the use of B. distachyon in these various pathosystems. Exploiting B. distachyon to understand the mechanisms underpinning disease resistance to non-adapted rust fungi may provide effective and durable approaches to fend off these pathogens. The close phylogenetic relationship among Brachypodium spp. and grasses with industrial and agronomic value support harnessing this model plant to improve cropping systems and encourage its use in translational research.

Structural insights into impact of Y134F mutation and discovery of novel fungicidal compounds against CYP51 in Puccinia triticina

Sterol 14α-Demethylase Cytochrome P450 (CYP51) protein involved in ergosterol biosynthesis pathways turn out to be a crucial target for the fungicidal compound. However, the recognition mechanism and dynamic behavior of CYP51 in wheat leaf rust pathogen, Puccinia triticina, is still obscure. Previously, a mutation at position 134 (Y134F) was reported in five European isolates of P. triticina, conversely, structural basis of this mutation remains unclear. To address this problem, three-dimensional structure of CYP51 protein from P. triticina was successfully built using homology modeling approach. To assess the protein structure stability, wild and mutant-type CYP51 proteins bound with azole fungicide was subjected to 50 ns molecular dynamics (MD) simulations run. Observably, the comparative protein-ligand interaction analysis and binding free energy results revealed that impact of the mutation on the thermodynamics and conformational stability of the CYP51 protein was negligible. In addition, we carried out structure-based virtual screening and identified potent novel fungicidal compounds from four different databases and libraries. Consequently, through MD simulation and thermodynamic integration, four novel compounds such as CoCoCo54211 (CoCoCo database), ZINC04089470 (ZINC database), Allyl pyrocatechol 3,4 diacetate (Natural compound library), and 9-octadecenoic acid (Traditional Chinese Medicine database) has been predicted as potent fungicidal compound against CYP51 with XPGlide docking score of -11.41, -13.64, -7.40, and -6.55 kcal/mol, respectively. These compounds were found to form hydrogen bonds with heme group of CYP51, subsequently disturbing the stability and survival of fungus and can be used to control leaf rust in wheat.

Inhibition of early development stages of rust fungi by the two fungal metabolites cyclopaldic acid and epi-epoformin

BACKGROUND

Rusts are a noxious group of plant diseases affecting major economically important crops. Crop protection is largely based on chemical control. There is a renewed interest in the discovery of natural products as alternatives to synthetic fungicides for control. In this study we tested two fungal metabolites, namely cyclopaldic acid and epi-epoformin, for their effectiveness in reducing early stages of development of two major rust fungi from the genera Puccinia and Uromyces, P. triticina and U. pisi. Spore germination and appressorium formation were assessed on pretreated detached leaves under controlled conditions. Cyclopaldic acid and epi-epoformin were also tested in infected plants in order to evaluate the level of control achieved by treatments both before and after inoculation.

RESULTS

Cyclopaldic acid and epi-epoformin were strongly effective in inhibiting fungal germination and penetration of both rust species studied. This effect was not dose dependent. These results were further confirmed in planta by spraying the metabolites on plant leaves, which reduced fungal developmental of U. pisi and P. triticina at values comparable with those obtained by application of the fungicide.

CONCLUSION

Our results further demonstrate the potential of fungal metabolites as natural alternatives to synthetic fungicides for the control of crop pathogens of economic importance as rusts. © 2016 Society of Chemical Industry.

Towards Improved Detection and Identification of Rust Fungal Pathogens in Environmental Samples Using a Metabarcoding Approach

The dispersion of fungal inocula such as the airborne spores of rust fungi (Pucciniales) can be monitored through metabarcoding of the internal transcribed spacer 2 (ITS2) of the rRNA gene in environmental DNAs. This method is largely dependent on a high-quality reference database (refDB) and primers with proper taxonomic coverage and specificity. For this study, a curated ITS2 reference database (named CR-ITS2-refDB) comprising representatives of the major cereal rust fungi and phylogenetically related species was compiled. Interspecific and intraspecific variation analyses suggested that the ITS2 region had reasonable discriminating power for the majority of the Puccinia species or species complexes in the database. In silico evaluation of nine forward and seven reverse ITS2 primers, including three newly designed, revealed marked variation in DNA amplification efficiency for the rusts. We validated the theoretical assessment of rust-enhanced (Rust2inv/ITS4var_H) and universal fungal (ITS9F/ITS4) ITS2 primer pairs by profiling the airborne rust fungal communities from environmental samples via a metabarcoding approach. Species- or subspecies-level identification of the rusts was improved by use of CR-ITS2-refDB and the Automated Oligonucleotide Design Pipeline (AODP), which identified all mutations distinguishing highly conserved DNA markers between close relatives. A generic bioinformatics pipeline was developed, including all steps used in this study from in silico evaluation of primers to accurate identification of short metabarcodes at the level of interest for defining phytopathogens. The results highlight the importance of primer selection, refDBs that are resolved to reflect phylogenetic relationships, and the use of AODP for improving the reliability of metabarcoding in phytopathogen biosurveillance.

Microcyclic rusts of hollyhock ( Alcea rosea )

Rust fungi infecting hollyhock and other plants in Malveae are frequently intercepted at ports of entry to the USA, particularly Puccinia malvacearum and P. heterogenea. These two species can be difficult to distinguish and can be further confused with other, less common species of microcyclic rust fungi infecting hollyhock: P. heterospora, P. lobata, P. platyspora, and P. sherardiana. Molecular phylogenetic analysis revealed that P. malvacearum and P. heterogenea are closely related, along with P. sherardiana and P. platyspora. A key to the six microcyclic Puccinia species infecting hollyhock is presented.

Identification and characterization of simple sequence repeats (SSRs) for population studies of Puccinia novopanici

Switchgrass (Panicum virgatum L.) can be severely affected by rust disease. Recently switchgrass rust caused by P. emaculata (now confirmed to be Puccinia novopanici) has received most of the attention by the research community because this pathogen is responsible for reducing the biomass production and biofuel feedstock quality of switchgrass. Microsatellite markers found in the literature were either not informative (no allele frequency) or showed few polymorphisms in the target populations, therefore additional markers are needed for future studies of the genetic variation and population structure of P. novopanici. This study reports the development and characterization of novel simple sequence repeat (SSR) markers from a Puccinia emaculata s.l. microsatellite-enriched library and expressed sequence tags (ESTs). Microsatellites were evaluated for polymorphisms on P. emaculata s.l. urediniospores collected in Iowa (IA), Mississippi (MS), Oklahoma (OK), South Dakota (SD) and Virginia (VA). Puccinia novopanici single spore whole genome amplifications were used as templates to validate the SSR reactions protocol and to assess a preliminary population genetics statistics of the pathogen. Eighteen microsatellite markers were polymorphic (average PIC=0.72) on individual urediniospores, with an average of 8.3 alleles per locus (range 3 to 17). Of the 49 SSRs loci initially identified in P. emaculata s.l., 18 were transferable to P. striiformis f. sp. tritici, 23 to P. triticina, 20 to P. sorghi and 31 to P. andropogonis. Thus, these markers could be useful for DNA fingerprinting and population structure analysis for population genetics, epidemiology and ecological studies of P. novopanici and potentially other related Puccinia species.

Host-Induced Gene Silencing (HIGS) for Elucidating Puccinia Gene Function in Wheat

Biotrophic fungi (Puccinia spp.) cause devastating diseases of wheat and other cereal species globally. The function of large repertories of genes from Puccinia spp. still needs to be discovered to understand the infection process of these obligate parasites, eventually to protect plants from rust diseases. Functional analysis of targeted genes is challenging due to the inherent difficulties with culturing the fungus and transforming the host. RNA interference (RNAi) is a conserved gene regulation process in eukaryotes and known to be a powerful genetic tool in plant biotechnology. More recently, host-induced gene silencing (HIGS) has been developed to assess pathogen gene function in plants. HIGS is an RNAi-based process where double stranded RNA (dsRNA) homologous to a pathogen gene can be expressed in a plant to induce targeted silencing of the pathogen gene. Here we described a detailed HIGS protocol for functional analysis of rust genes from Puccinia species in cereals. As an example we describe an experiment silencing the tryptophan 2-monooxygenase gene (Pgt-IaaM) from Puccinia graminis f. sp. tritici (Pgt) that is involved in virulence to wheat.

Carotenoid biosynthesis and the evolution of carotenogenesis genes in rust fungi

Diseases caused by rust fungi pose a significant threat to global plant production. Although carotenoid pigments are produced in spores of nearly all rust species, the corresponding biosynthesis pathway(s) have not been investigated. Here, candidate genes for carotenoid biosynthesis in Puccinia graminis f. sp. tritici (Pgt) were identified, cloned and functionally complemented using specifically engineered strains of Escherichia coli. A part of the carotenoid biosynthesis pathway in rust fungi was elucidated, with only two genes, CrtYB and CrtI, catalysing the reactions from geranyl-geranyl diphosphate (GGPP) to γ-carotene. The CrtYB gene encodes a bi-functional lycopene cyclase/phytoene synthase, which catalyses the condensation of two GGPP into phytoene, as well as the cyclisation of the ψ-end of lycopene to form γ-carotene. The CrtI gene encodes a phytoene desaturase that carries out four successive desaturations of phytoene, through the intermediates phytofluene and neurosporene to lycopene. The evolution of carotenoid pigmentation in rust fungi, including Pgt, P. graminis avenae, P. graminis secalis (Pgs), P. graminis lolli, P. striiformis f. sp. tritici, P. striiformis f. sp. pseudohordei, P. striiformis f. sp. hordei, the "scabrum" rust (putative hybrids between Pgt and Pgs), P. triticina, and P. hordei, was investigated by phylogenetic analysis. Both CrtYB and CrtI were found to be closely related among rust fungi, other pathogenic fungi, and some aphids. Our results provide a springboard to increase the understanding of the physiological role(s) of carotenoid pigments in rust fungi, to better understand evolution within the Pucciniales, and to develop robust molecular diagnostics for rust fungi.

High-resolution mapping of genes involved in plant stage-specific partial resistance of barley to leaf rust

Partial resistance quantitative trait loci (QTLs) Rphq11 and rphq16 against Puccinia hordei isolate 1.2.1 were previously mapped in seedlings of the mapping populations Steptoe/Morex and Oregon Wolfe Barleys, respectively. In this study, QTL mapping was performed at adult plant stage for the two mapping populations challenged with the same rust isolate. The results suggest that Rphq11 and rphq16 are effective only at seedling stage, and not at adult plant stage. The cloning of several genes responsible for partial resistance of barley to P. hordei will allow elucidation of the molecular basis of this type of plant defence. A map-based cloning approach requires to fine-map the QTL in a narrow genetic window. In this study, Rphq11 and rphq16 were fine-mapped using an approach aiming at speeding up the development of plant material and simplifying its evaluation. The plant materials for fine-mapping were identified from early plant materials developed to produce QTL-NILs. The material was first selected to carry the targeted QTL in heterozygous condition and susceptibility alleles at other resistance QTLs in homozygous condition. This strategy took four to five generations to obtain fixed QTL recombinants (i.e., homozygous resistant at the Rphq11 or rphq16 QTL alleles, homozygous susceptible at the non-targeted QTL alleles). In less than 2 years, Rphq11 was fine-mapped into a 0.2-cM genetic interval and a 1.4-cM genetic interval for rphq16. The strongest candidate gene for Rphq11 is a phospholipid hydroperoxide glutathione peroxidase. Thus far, no candidate gene was identified for rphq16.

Durable resistance to the wheat rusts: Integrating systems biology and traditional phenotype-based research methods to guide the deployment of resistance genes

Genes which confer partial resistance to the rusts in wheat figure prominently in discussions of potential durable resistance strategies. The positional cloning of the first of these genes, Lr34/Yr18 and Yr36, has revealed different protein structures, suggesting that the category of partial resistance genes, as defined by phenotype, likely groups together suites of functionally heterogenous genes. With the number of mapped partial rust resistance genes increasing rapidly as a result of ongoing advances in marker and sequencing technologies, breeding programs needing to select and prioritize genes for deployment confront a fundamental question: which genes or gene combinations are more likely to provide durable protection against these evolving pathogens? We argue that a refined classification of partial rust resistance genes is required to start answering this question, one based not merely on disease phenotype but also on gene cloning, molecular functional characterization, and interactions with other host and pathogen proteins. Combined with accurate and detailed disease phenotyping and standard genetic studies, an integrated wheat-rust interactome promises to provide the basis for a functional classification of partial resistance genes and thus a conceptual framework for their rational deployment.

Dispersal Kernels may be Scalable: Implications from a Plant Pathogen

AIM

Understanding how spatial scale of study affects observed dispersal patterns can provide insights into spatiotemporal population dynamics, particularly in systems with significant long-distance dispersal (LDD). We aimed to investigate the dispersal gradients of two rusts of wheat with spores of similar size, mass, and shape, over multiple spatial scales. We hypothesized that a single dispersal kernel could fit the dispersal from all spatial scales well, and that it would be possible to obtain similar results in spatiotemporal increase of disease when modeling based on differing scales.

LOCATION

Central Oregon and St. Croix Island.

TAXA

Puccinia striiformis f. sp. tritici, Puccinia graminis f. sp. tritici, Triticum aestivum.

METHODS

We compared empirically-derived primary disease gradients of cereal rust across three spatial scales: local (inoculum source and sampling unit = 0.0254 m, spatial extent = 1.52m) field-wide (inoculum source = 1.52 m, sampling unit = 0.305 m, and spatial extent = 91.44 m), and regional (inoculum source and sampling unit = 152 m, spatial extent = 10.7 km). We then examined whether disease spread in spatially explicit simulations depended upon the scale at which data were collected by constructing a compartmental time-step model.

RESULTS

The three data sets could be fit well by a single inverse-power law dispersal kernel. Simulating epidemic spread at different spatial resolutions resulted in similar patterns of spatiotemporal spread. Dispersal kernel data obtained at one spatial scale can be used to represent spatiotemporal disease spread at a larger spatial scale.

MAIN CONCLUSIONS

Organisms spread by aerially dispersed small propagules that exhibit LDD may follow similar dispersal patterns over a several hundred- or thousand-fold expanse of spatial scale. Given that the primary mechanisms driving aerial dispersal remain constant, it may be possible to extrapolate across scales when empirical data are unavailable at a scale of interest.

Assessment of Aggressiveness of Puccinia striiformis on Wheat

A simple point-inoculation method using Novec™ 7100, a volatile engineered fluid, is presented for the assessment of aggressiveness of Puccinia striiformis isolates on seedlings of wheat. The method allows for quantification of the applied inoculum with a minimal risk of cross-contamination of rust from leaves grown side by side. The method is also applicable for the assessment of qualitative differences inferred by compatible and incompatible host-pathogen interactions, and it can be adjusted to other cereal rust and powdery mildew fungi on other host species, and other plant growth stages as appropriate.

Taxonomy and Phylogeny of Rust Fungi on Hamamelidaceae

Hamamelidaceae is composed of woody plant taxa of important economic value; however, reports on diseases affecting these plants are rare. Three kinds of rusts were studied, of which the first one is characterized by catenulate spores in peridiate columnar sori on Sycopsis sinensis, the second one produces two-celled pedicellate teliospores in pulvinate sori on S. sinensis and Corylopsis spp., and the last one produces aeciospores in cup-shaped aecia on Hamamelis spp. Phylogenetic analyses indicated that the three species belong to the same genus in Pucciniaceae. The first fungus is distinct in teliospore morphology, producing one-celled catenulate spores in peridiate columnar sori and molecular phylogeny from species of other genera. Thus, it is described herein as a new genus and species Novopuccinia sycopsis-sinensis in Pucciniaceae. The latter two species were reported as Puccinia corylopsidis and Aecidium hamamelidis, respectively. However, phylogenetic analysis using ITS and 28S genes has revealed that these are closely related to the new genus and species. By combining host, distribution, and evolutionary hypothesis of rust fungi with endocyclic life cycle, these are reclassified as N. corylopsidis and N. hamamelidis. Taxonomic descriptions, illustrations, and a key to rust fungal species occurring in Hamamelidaceae in Asia are provided.