Cereal rust fungi genomics and the pursuit of virulence and avirulence factors

Rust diseases cause significant reductions annually in yield of cereal crops worldwide. Traditional monoculture cropping systems apply significant selection pressure on the pathogen to cause rapid shifts in pathotypes. Plant breeders strive to stay ahead of the evolving pathogens by releasing new crop genotypes with new rust resistance genes or gene combinations. Owing to the limited number of known resistance genes and the lack of molecular understanding of the plant-pathogen interaction, rusts remain challenging organisms to study, both at organismal and molecular levels. This review discusses recent progress by a number of laboratories towards better understanding the molecular component of rust disease resistance.     

Analysis and modelling of effects of leaf rust and Septoria tritici blotch on wheat growth

A model to predict Septoria tritici blotch (STB) and leaf rust effects on wheat growth was constructed and evaluated in two steps. At the leaf scale, Bastiaans' approach that predicts the relative photosynthesis of a wheat leaf infected with a single disease, was extended to the case of two diseases, one biotrophic and one necrotrophic by considering the leaf rust-STB complex. A glasshouse experiment with flag leaves inoculated either singly with one disease or with two diseases combined was performed to check the leaf damage model. No interaction of the two diseases on photosynthesis loss was observed when they occurred simultaneously on the same leaf. In a second step, the single-leaf model was extended to the canopy scale to model the effects of the leaf rust-STB complex on the growth of a wheat crop. The model predicts the effects of disease on the growth of an affected crop relative to the growth of a healthy crop. The canopy model accounted for different contributions to photosynthetic activity of leaf layers, derived from their position in the canopy and their natural leaf senescence. Treatments differing in nitrogen fertilization, microclimatic conditions, and wheat cultivars were implemented in a field experiment to evaluate the model. The model accurately estimated the effect of disease on crop growth for each cultivar, with differences from experimental values lower than 10%, which suggests that this model is well suited to aid an understanding of disease effects on plant growth. A reduction in green leaf area was the main effect of disease in these field experiments and STB accounted for more than 70% of the reduction in plant growth. Simulations suggested that the production of rust spores may result in a loss of biomass from diseased crops and that stem photosynthesis may need to be considered in modelling diseased crop growth.     

Study of rust resistance genes in wheat germplasm with DNA markers

Wheat is a vital dietary component for human health and widely consumed in the world. Wheat rusts are dangerous pathogens and contribute serious threat to its production. In present study, PCR-Based DNA Markers were employed to check the rust resistance genes among 20 wheat genotypes and 22 markers were amplified. NTSYS-pc 2.2 was used to calculate genetic diversity and Nei and Li''s coefficients ranged from 0.55 to 0.95. Cluster analysis was obtained using UPGMA (Unweighted Pair Group Method of Arithmetic Average) algorithm. Maximum no. of genes (23) was amplified from TW-760010 genotype whereas minimum no of genes (14) were amplified from TW-76005 genotype. The data gained from present study open up new ways to produce new varieties by breeding rust resistant germplasm to avoid the economic and food loss and varieties with improved characteristics.     

Characterization of genetic loci conferring adult plant resistance to leaf rust and stripe rust in spring wheat.

Leaf (brown) and stripe (yellow) rusts, caused by Puccinia triticina and Puccinia striiformis, respectively, are fungal diseases of wheat (Triticum aestivum) that cause significant yield losses annually in many wheat-growing regions of the world. The objectives of our study were to characterize genetic loci associated with resistance to leaf and stripe rusts using molecular markers in a population derived from a cross between the rust-susceptible cultivar 'Avocet S' and the resistant cultivar 'Pavon76'. Using bulked segregant analysis and partial linkage mapping with AFLPs, SSRs and RFLPs, we identified 6 independent loci that contributed to slow rusting or adult plant resistance (APR) to the 2 rust diseases. Using marker information available from existing linkage maps, we have identified additional markers associated with resistance to these 2 diseases and established several linkage groups in the 'Avocet S' x 'Pavon76' population. The putative loci identified on chromosomes 1BL, 4BL, and 6AL influenced resistance to both stripe and leaf rust. The loci on chromosomes 3BS and 6BL had significant effects only on stripe rust, whereas another locus, characterized by AFLP markers, had minor effects on leaf rust only. Data derived from Interval mapping indicated that the loci identified explained 53% of the total phenotypic variation (R2) for stripe rust and 57% for leaf rust averaged across 3 sets of field data. A single chromosome recombinant line population segregating for chromosome 1B was used to map Lr46/Yr29 as a single Mendelian locus. Characterization of slow-rusting genes for leaf and stripe rust in improved wheat germplasm would enable wheat breeders to combine these additional loci with known slow-rusting loci to generate wheat cultivars with higher levels of slow-rusting resistance.     

银叶老鹳草(Geranium sylvaticum)种群中诱导保护抗性和病原菌相互作用的研究（英）

本文通过自然植物种群接种实验,人工接种实验和野外调查研究了（Geranium sylvaticum)对老鹳草单孢锈菌（Uromyces geranii)（长生活史）的抗病性在受柄锈菌（Puccinia)（短生活史）感病前后和受2种柄锈菌（P.leveillei或P.morthieri)感病后有无区别,以及在同一季节里感染同一寄主植物的长生活史单孢锈菌和短生活史柄锈菌间的相互作用,病原菌间的相互作用使寄主植物产生诱导保护抗性。结果表明,P.leveillei可诱导寄主植物产生短时间的保护抗性,而P.morthieri可能诱导寄主植物产生长时期的保护抗性,诱导保护抗性可能是影响自然植物种群中植病式样的重要因素之一。     

Exogenous double-stranded RNA inhibits the infection physiology of rust fungi to reduce symptoms in planta

Rust fungi (Pucciniales) are a diverse group of plant pathogens in natural and agricultural systems. They pose ongoing threats to the diversity of native flora and cause annual crop yield losses. Agricultural rusts are predominantly managed with fungicides and breeding for resistance, but new control strategies are needed on non-agricultural plants and in fragile ecosystems. RNA interference (RNAi) induced by exogenous double-stranded RNA (dsRNA) has promise as a sustainable approach for managing plant-pathogenic fungi, including rust fungi. We investigated the mechanisms and impact of exogenous dsRNA on rust fungi through in vitro and whole-plant assays using two species as models, Austropuccinia psidii (the cause of myrtle rust) and Coleosporium plumeriae (the cause of frangipani rust). In vitro, dsRNA either associates externally or is internalized by urediniospores during the early stages of germination. The impact of dsRNA on rust infection architecture was examined on artificial leaf surfaces. dsRNA targeting predicted essential genes significantly reduced germination and inhibited development of infection structures, namely appressoria and penetration pegs. Exogenous dsRNA sprayed onto 1-year-old trees significantly reduced myrtle rust symptoms. Furthermore, we used comparative genomics to assess the wide-scale amenability of dsRNA to control rust fungi. We sequenced genomes of six species of rust fungi, including three new families (Araucariomyceaceae, Phragmidiaceae, and Skierkaceae) and identified key genes of the RNAi pathway across 15 species in eight families of Pucciniales. Together, these findings indicate that dsRNA targeting essential genes has potential for broad-use management of rust fungi across natural and agricultural systems.     

Quantitative trait loci for slow-rusting resistance in wheat to leaf rust and stripe rust identified with multi-environment analysis

Rust diseases are a major cause of yield loss in wheat worldwide, and are often controlled through the incorporation of resistance genes using conventional phenotypic selection methods. Slow-rusting resistance genes are expressed quantitatively and are typically small in genetic effect thereby requiring multiple genes to provide adequate protection against pathogens. These effects are valuable and are generally considered to confer durable resistance. Therefore an understanding of the chromosomal locations of such genes and their biological effects are important in order to ensure they are suitably deployed in elite germplasm. Attila is an important wheat grown throughout the world and is used as a slow-rusting donor in international spring wheat breeding programs. This study identified chromosomal regions associated with leaf rust and stripe rust resistances in a cross between Attila and a susceptible parent, Avocet-S, evaluated over 3 years in the field. Genotypic variation for both rusts was large and repeatable with line-mean heritabilities of 94% for leaf rust resistance and 87% for stripe rust. Three loci, including Lr46/Yr29 on chromosome 1BL, were shown to provide resistance to leaf rust whereas six loci with small effects conferred stripe rust resistance, with a seventh locus having an effect only by epistasis. Disease scoring over three different years enabled inferences to be made relating to stripe rust pathogen strains that predominated in different years.     

Green Rust Formation from the Bioreduction of γ –FeOOH (Lepidocrocite): Comparison of Several Shewanella Species

Green rusts are mixed ferrous/ferric hydroxides that typically form under weakly acidic to alkaline conditions in suboxic environments. The recent identification of green rusts as products of the reduction of Fe(III) oxides and oxyhydroxides by Shewanella putrefaciens, a dissimilatory iron-reducing bacterium (DIRB), suggests that green rusts may play a role in the redox cycling of Fe in many aquatic and terrestrial environments. We examined the potential for green rust formation resulting from the bioreduction of lepidocrocite(γ -FeOOH) by a series of Shewanella species (S. alga BrY, S. amazonensis SB2B, S. baltica OS155, S. denitrificans OS217T, S. loihica PV-4, S. oneidensis MR-1, S. putrefaciens ATCC 8071, S. putrefaciens CN32, S. saccharophilia, and Shewanella sp. ANA-3). All Shewanella species, with the exception of S. denitrificans OS217T, were able to couple the oxidation of formate to the reduction of Fe(III) in lepidocrocite; however there were significant differences among species with respect to the rate and extent of Fe(II) production. Despite these differences, green rust was the only Fe(II)-bearing solid phase formed under our experimental conditions, as indicated by X-ray diffraction, Mössbauer spectroscopy, and scanning electron microscopy. The formation of green rust by Shewanella species isolated from a wide range of habitats and possessing varied metabolic capabilities suggests that under favorable conditions biogenic green rusts may be formed by a diverse array of DIRB.     

A model of the effect of fungicides on disease-induced yield loss, for use in wheat disease management decision support systems

A model of the effect of foliar-applied fungicides on disease-induced yield loss is described, parameterised and tested. The effects of fungicides on epidemics of Septoria tritici (leaf blotch), Puccinia striiformis (yellow rust), Blumeria graminis f.sp. tritici (powdery mildew) and Puccinia triticina (brown rust) on winter wheat were simulated using dose–response curve parameters. Where two or more active substances were applied together, their joint action was estimated using an additive dose model where the active substances had the same mode of action or a multiplicative survival model where the modes of action differed. By coupling the model with models of wheat canopy growth and foliar disease published previously, it was possible to estimate disease-induced yield loss for a prescribed fungicide programme. The difference in green canopy area and, hence, interception of photosynthetically active radiation between simulated undiseased and diseased (but treated) crop canopies was used to estimate yield loss. The model was tested against data from field experiments across a range of sites, seasons and wheat cultivars and was shown to predict the observed disease-induced yield loss with sufficient accuracy to support fungicide treatment decisions. A simple method of accounting for uncertainty in the predictions of yield loss is described. Fungicide product, dose and spray timing combinations selected using the coupled models responded appropriately to disease pressure and cultivar disease resistance.     

Role of abiotic factors on the severity of stripe rust of wheat

During last decades, stripe rust has emerged as a major disease of wheat causing considerable yield loss in northern western plain and northern hill zones of India. Considering significant impact of the disease on wheat crop, field experiments were conducted during rabi seasons of 2013 and 2015 to evaluate the effect of different abiotic factors in different varieties (HD 2967, RSP 561, Agra Local and PBW 343) on the progress and spread of the disease as well as development of a predictive model to predict the disease initiation and spread in the field. Statistical analysis of data revealed that existing of low temperature (10–12 °C), high relative humidity (90%) along with intermittent rainfall was found conducive for disease onset. Thermic variables (atmospheric, canopy and soil temperature) along with age of crop in the selected varieties showed significant positive correlation with disease severity. Step-wise regression showed high R² of 0.919, 0.885, 0.967 and 0.956 for the predicative model of stripe rust in RSP 561, HD 2967, Agra Local and PBW 343, respectively.     

Phylogenetic positions of rust fungi parasitic on ferns: Evidence from 18S rDNA sequence analysis

Molecular phylogenetic analyses of fern rusts were carried out based on 18S rDNA sequences. We sequenced the 18S rDNAs of fern rusts (Hyalopsora polypodii andUredinopsis intermedia) and non-fern rusts (Aecidium epimedii, Coleosporium asterum, Ochropsora kraunhiae, Puccinia suzutake andPhysopella ampelopsidis) and analyzed their phylogenetic relationships with other members of the Urediniomycetes. Our bootstrapped neighbor-joining tree obtained from these analyses showed that rust fungi were apparently monophyletic at high confidence level (100% bootstrap confidence). In this molecular phylogenetic tree, the two fern rusts did not occupy the basal position within the rust fungal lineage and did not form a monophyletic lineage. Two species of the Cronartiaceae (Peridermium harknessii, Cronartium ribicola) and one species of the Coleosporiaceae (Coleosporium asterum) grouped with the fern rusts. Therefore, our results suggested that the two fern rusts were not primitive. On the other hand,Mixia osmundae, which is parasitic on the primitive fernOsmunda, was phylogenetically far from the fern rusts.     

A mutagenesis-derived broad-spectrum disease resistance locus in wheat

Wheat leaf rust, stem rust, stripe rust, and powdery mildew caused by the fungal pathogens Puccinia triticina, P. graminis f. sp. tritici, P. striiformis f. sp. tritici, and Blumeria graminis f. sp. tritici, respectively, are destructive diseases of wheat worldwide. Breeding durable disease resistance cultivars rely largely on continually introgressing new resistance genes, especially the genes with different defense mechanisms, into adapted varieties. Here, we describe a new resistance gene obtained by mutagenesis. The mutant, MNR220 (mutagenesis-derived new resistance), enhances resistance to three rusts and powdery mildew, with the characteristics of delayed disease development at the seedling stage and completed resistance at the adult plant stage. Genetic analysis demonstrated that the resistance in MNR220 is conferred by a single semidominant gene mapped on the short arm of chromosome 2B. Gene expression profiling of several pathogenesis-related genes indicated that MNR220 has an elevated and rapid pathogen-induced response. In addition to its potential use in breeding for resistance to multiple diseases, high-resolution mapping and cloning of the disease resistance locus in MNR220 may lead to a better understanding of the regulation of defense responses in wheat.     

Inheritance and QTL analysis of durable resistance to stripe and leaf rusts in an Australian cultivar, Triticum aestivum 'Cook'.

An F4-derived F6 recombinant inbred line population (n = 148) of a cross between the durable stripe (yellow) rust (caused by Puccinia striiformis) and leaf (brown) rust (caused by Puccinia triticina) resistant cultivar, Triticum aestivum 'Cook', and susceptible genotype Avocet-YrA was phenotyped at several locations in Canada and Mexico under artificial epidemics of leaf or stripe rusts and genotyped using amplified fragment length polymorphism (AFLP) and microsatellite markers. Durable adult plant resistance to stripe and leaf rusts in 'Cook' is inherited quantitatively and was based on the additive interaction of linked and (or) pleiotropic slow-rusting genes Lr34 and Yr18 and the temperature-sensitive stripe rust resistance gene, YrCK, with additional genetic factors. Identified QTLs accounted for 18% to 31% of the phenotypic variation in leaf and stripe rust reactions, respectively. In accordance with the high phenotypic associations between leaf and stripe rust resistance, some of the identified QTLs appeared to be linked and (or) pleiotropic for both rusts across tests. Although a QTL was identified on chromosome 7D with significant effects on both rusts at some testing locations, it was not possible to refine the location of Lr34 or Yr18 because of the scarcity of markers in this region. The temperature-sensitive stripe rust resistance response, conditioned by the YrCK gene, significantly contributed to overall resistance to both rusts, indicating that this gene also had pleiotropic effects.     

Ricerche sperimentali nell' Oltrepò Pavese (Valle Padana) sugli aspetti epidemiologici delle ruggini del frumento

Experimental researches in Oltrepò Pavese (Padana Valley), on wheat rust epidemiological aspects related to the climatic conditions Our experimental researches began in 1976 in Oltrepò Pavese, one of the most important seedwheat growing environment in the Padana Valley. Wheat rust epidemiology, on the cv San Pastore, was studied in relation to the following climatic conditions: temperature and rain. Therefore, after having illustrated the modalities of observation and survey of the three rusts, we studied the infection behaviour on plants in field and hence the infection behaviour on the single leaves. In the end, knowing, by statistical analysis, the relations between infections and climatic parameters, it was possible to define as follows. By comparing the three rusts infections in our environment, we noted that San Pastore wheat has been more affected by Puccinia striiformis West. with maximum infection points of 26,4 % on the leaves. We noted the greater development of this infection from the fourth to the sixth observation, in correspondence with average values of T° max rising from 23,7° to 26,4°C; in the same period, precipitations varied with a daily average from 3,0 to 1,7 mm. Both P. striiformis and P. recondita Rob. ex Desm. appeared when the average of the T° max was 20,6°C, and in lack of rain. P. recondita had a development rising from the fourth to the sixth observation showing, with regard to P. striiformis, lower demands of humidity and relatively greater demands of temperature; in fact, it reached a maximum point of infection of 26,4 % on the leaves, assuming a more gradual development than P. striiformis. P. graminis Pers. appeared much later, as it needs higher T° max, followed by rains. Indeed, it appeared with average T° max of 23, 8 °C and with average daily rains of 0,4 mm, rising above all at the sixth observation with 26,4° C and 1,7 mm, respectively. So, we can affirm that the actual experimental investigations point out and confirm what has been already met by other Authors, that is: a) among the three rusts considered, P. striiformis and P. recondita show to begin their development at the same time, in climatic conditions characterized by T° max relatively mild and high environmental humidity; b) P. striiformis shows, afterwards, the highest infections percentages; c) P. graminis appeared much later reaching modest infection percentages.     

Comparison of the Wheat Brown and Yellow Rusts for Monocyclic Sporulation and Infection Processes, and their Polycyclic Consequences

Sporulation capacity and infection efficiency of wheat brown and yellow rusts were measured daily in favourable controlled conditions. Monocyclic sporulation capacity for a single lesion of yellow rust was 9 times greater than for an isolated lesion of brown rust, and 40 times greater than for a lesion of brown rust at medium infection density. Infection efficiency fluctuated and reached about 40 % for brown rust but remained under 5% for yellow rust. For both fungi, sporulation capacity and infection efficiency compensated for each other, but their product, the daily multiplication factor, was greater for yellow rust than for brown rust. Progeny/parent ratio was 3 times greater for yellow rust. Effect of daily multiplication factor variations on epidemic progress was simulated using a simple matrix model. Increase in number of lesions was faster in brown rust than in yellow rust because of a latent period shorter by 2 days. Semi-systemic growth of yellow rust fungus reduced, however, the difference between both fungi when sporulating surface was calculated.     

Dr. Heinz rogoll‐70 Jahre

The wheat crop remains vulnerable to all three rust diseases (leaf rust, stem rust and yellow rust) caused by Puccinia spp. according to the prevalence of the pathogen in different wheat-growing areas worldwide. Stripe rust or yellow rust caused by Puccinia striiformis f. sp. tritici is the most significant rust pathogen which prefers cool, moist areas and highlands. The pathogen is recognised as responsible for huge production losses in wheat. Genetic variation in pathogen makes its control difficult. Therefore, resistance against all the races of the pathogen known as durable or race-non-specific resistance is preferred. The present study was carried out to identify durable resistance against stripe rust in selected wheat cultivars from Pakistan through seedling testing, field evaluation at adult stage, morphological marker studies and marker-assisted selection. Results revealed that 4% of the cultivars were resistant at the seedling stage while the rest were susceptible or intermediate. To confirm their field resistance, the same cultivars were evaluated under field conditions at Cereal Crops Research Institute Pirsabak (located in Khyber Pakhtunkhwa, KP) a hot spot of stripe rust in Pakistan. Observations exhibited that at the adult stage 4% of the cultivars were resistant, 70% intermediate or moderately resistant while the others were highly susceptible. Leaf tip necrosis was observed in 30% of the cultivars. Wheat cultivars showing susceptibility at the seedling stage were highly to moderately resistant at adult stage showing durable resistance. For further validation, morphological markers were also observed in cultivars indicating the presence of Yr18/Lr34 gene. Eleven cultivars (C-518, Mexipak, Kohinoor-83, Faisalabad-83, Zardana-93, Shahkar-95, Moomal-2002, Wattan-94, Pasban-90, Kiran-95, and Haider-2000) were identified, having durable or race non-specific resistance against stripe rust. These cultivars can further be utilised in wheat breeding programmes for deploying durable resistance to attain long lasting control against stripe rust.     

Interspecies gene transfer provides soybean resistance to a fungal pathogen

Fungal pathogens pose a major challenge to global crop production. Crop varieties that resist disease present the best defence and offer an alternative to chemical fungicides. Exploiting durable nonhost resistance (NHR) for crop protection often requires identification and transfer of NHR‐linked genes to the target crop. Here, we identify genes associated with NHR of Arabidopsis thaliana to Phakopsora pachyrhizi, the causative agent of the devastating fungal disease called Asian soybean rust. We transfer selected Arabidopsis NHR‐linked genes to the soybean host and discover enhanced resistance to rust disease in some transgenic soybean lines in the greenhouse. Interspecies NHR gene transfer thus presents a promising strategy for genetically engineered control of crop diseases.     

Tracking wheat rust on a continental scale

The rusts of wheat are important fungal plant pathogens that can be disseminated thousands of kilometers across continents and oceans by wind. Rusts are obligate parasites that interact with resistance genes in wheat in a gene-for-gene manner. New races of rust develop by mutation and selection for virulence against rust resistance genes in wheat. In recent years, new races of wheat leaf rust, wheat stripe rust, and wheat stem rust have been introduced into wheat production areas in different continents. These introductions have complicated efforts to develop wheat cultivars with durable rust resistance and have reduced the number of effective rust-resistance genes that are available for use. The migration patterns of wheat rusts are characterized by identifying their virulence against important rust resistance genes in wheat and by the use of molecular markers.     

Modelling wheat growth and yield losses from late epidemics of foliar diseases using loss of green leaf area per layer and pre-anthesis reserves

BACKGROUND AND AIMS: Crop protection strategies, based on preventing quantitative crop losses rather than pest outbreaks, are being developed as a promising way to reduce fungicide use. The Bastiaans' model was applied to winter wheat crops (Triticum aestivum) affected by leaf rust (Puccinia triticina) and Septoria tritici blotch (STB; Mycosphaerella graminicola) under a range of crop management conditions. This study examined (a) whether green leaf area per layer accurately accounts for growth loss; and (b) whether from growth loss it is possible to derive yield loss accurately and simply. Methods Over 5 years of field experiments, numerous green leaf area dynamics were analysed during the post-anthesis period on wheat crops using natural aerial epidemics of leaf rust and STB. Key Results When radiation use efficiency (RUE) was derived from bulk green leaf area index (GLAI), RUE(bulk) was hardly accurate and exhibited large variations among diseased wheat crops, thus extending outside the biological range. In contrast, when RUE was derived from GLAI loss per layer, RUE(layer) was a more accurate calculation and fell within the biological range. In one situation out of 13, no significant shift in the RUE(layer) of diseased crops vs. healthy crops was observed. A single linear relationship linked yield to post-anthesis accumulated growth for all treatments. Its slope, not different from 1, suggests that the allocation of post-anthesis photosynthates to grains was not affected by the late occurring diseases under study. The mobilization of pre-anthesis reserves completely accounted for the intercept value. Conclusions The results strongly suggest that a simple model based on green leaf area per layer and pre-anthesis reserves can predict both growth and yield of wheat suffering from late epidemics of foliar diseases over a range of crop practices. It could help in better understanding how crop structure and reserve management contribute to tolerance of wheat genotypes to leaf diseases.     

Global risk levels for corn rusts (Puccinia sorghi and Puccinia polysora) under climate change projections

Common rust (Puccinia sorghi) and southern rust (Puccinia polysora) are two of the most important foliar corn diseases worldwide. These fungi have caused severe economic loss to corn yields worldwide. The current and future potential distribution of these diseases was modelled with CLIMEX using the known current geographic locations of the rusts, growth and stress indices. The models were run under the A2 scenario using CSIRO‐Mk3·0 and MIROC‐H for 2050 and 2100. The current projection shows areas with marginal to optimal suitability in all the continents. The models for future projections display a general reduction in the Southern hemisphere and increase in the Northern hemisphere, especially for the southern rust. The overlay of the General Circulation Models produce an estimation of the common areas under risk for future climate conditions for the simultaneous occurrence for both corn rusts, with a reduction of the medium‐ and high‐risk categories by 2100. This study highlights the possible effects of climate change at a global level for common and southern rust, as well as the risk of occurrence of both diseases in common areas for future climate that could be particularly harmful for crops.