Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

The aim of this review was to survey all fungal pathologists with an association with the journal Molecular Plant Pathology and ask them to nominate which fungal pathogens they would place in a 'Top 10' based on scientific/economic importance. The survey generated 495 votes from the international community, and resulted in the generation of a Top 10 fungal plant pathogen list for Molecular Plant Pathology. The Top 10 list includes, in rank order, (1) Magnaporthe oryzae; (2) Botrytis cinerea; (3) Puccinia spp.; (4) Fusarium graminearum; (5) Fusarium oxysporum; (6) Blumeria graminis; (7) Mycosphaerella graminicola; (8) Colletotrichum spp.; (9) Ustilago maydis; (10) Melampsora lini, with honourable mentions for fungi just missing out on the Top 10, including Phakopsora pachyrhizi and Rhizoctonia solani. This article presents a short resume of each fungus in the Top 10 list and its importance, with the intent of initiating discussion and debate amongst the plant mycology community, as well as laying down a bench-mark. It will be interesting to see in future years how perceptions change and what fungi will comprise any future Top 10.

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The Top 10 fungal pathogens in molecular plant pathology

Root-colonizing non-pathogenic bacteria can increase plant resistance to biotic and abiotic stress factors. Bacterial inoculates have been applied as biofertilizers and can increase the effectiveness of phytoremediation. Inoculating plants with non-pathogenic bacteria can provide 'bioprotection' against biotic stresses, and some root-colonizing bacteria increase tolerance against abiotic stresses such as drought, salinity and metal toxicity. Systematic identification of bacterial strains providing cross-protection against multiple stressors would be highly valuable for agricultural production in changing environmental conditions. For bacterial cross-protection to be an effective tool, a better understanding of the underlying morphological, physiological and molecular mechanisms of bacterially mediated stress tolerance, and the phenomenon of cross-protection is critical. Beneficial bacteria-mediated plant gene expression studies under non-stress conditions or during pathogenic rhizobacteria-plant interactions are plentiful, but only few molecular studies on beneficial interactions under abiotic stress situations have been reported. Thus, here we attempt an overview of current knowledge on physiological impacts and modes of action of bacterial mitigation of abiotic stress symptoms in plants. Where available, molecular data will be provided to support physiological or morphological observations. We indicate further research avenues to enable better use of cross-protection capacities of root-colonizing non-pathogenic bacteria in agricultural production systems affected by a changing climate.

https://www.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-3040.2009.02028.x

Plant-rhizobacteria interactions alleviate abiotic stress conditions.

Global food production must increase by 50% to meet the projected demand of the world’s population by 2050. Meeting this difficult challenge will be made even harder if climate change melts portions of the Himalayan glaciers to affect 25% of world cereal production in Asia by influencing water availability. Pest and disease management has played its role in doubling food production in the last 40 years, but pathogens still claim 10–16% of the global harvest. We consider the effect of climate change on the many complex biological interactions affecting pests and pathogen impacts and how they might be manipulated to mitigate these effects. Integrated solutions and international co-ordination in their implementation are considered essential. Providing a background on key constraints to food security, this overview uses fusarium head blight as a case study to illustrate key influences of climate change on production and quality of wheat, outlines key links between plant diseases, climate change and food security, and highlights key disease management issues to be addressed in improving food security in a changing climate.

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Climate change, plant diseases and food security: an overview

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The Top 10 fungal pathogens in molecular plant pathology: Top 10 fungal pathogens

Strobilurin fungicides or quinone outside inhibitors (QoIs) have been used successfully to control Septoria leaf blotch in the United Kingdom since 1997. However, QoI-resistant isolates of Mycosphaerella graminicola were reported for the first time at Rothamsted during the summer of 2002. Sequence analysis of the cytochrome b gene revealed that all resistant isolates carried a mutation resulting in the replacement of glycine by alanine at codon 143 (G143A). Extensive monitoring using real-time polymerase chain reaction (PCR) testing revealed that fungicide treatments based on QoIs rapidly selected for isolates carrying resistant A143 (R) alleles within field populations. This selection is driven mainly by polycyclic dispersal of abundantly produced asexual conidia over short distances. In order to investigate the role of sexually produced airborne ascospores in the further spread of R alleles, a method integrating spore trapping with real-time PCR assays was developed. This method enabled us to both quantify the number of M. graminicola ascospores in air samples as well as estimate the frequency of R alleles in ascospore populations. As expected, most ascospores were produced at the end of the growing season during senescence of the wheat crop. However, a rapid increase in R-allele frequency, from 35 to 80%, was measured immediately in airborne ascospore populations sampled in a wheat plot after the first QoI application at growth stage 32. After the second QoI application, most R-allele frequencies measured for M. graminicola populations present in leaves and aerosols sampled from the treated plot exceeded 90%. Spatial sampling and testing of M. graminicola flag leaf populations derived from ascospores in the surrounding crop showed that ascospores carrying R alleles can spread readily within the crop at distances of up to 85 m. After harvest, fewer ascospores were detected in air samples and the R-allele frequencies measured were influenced by ascospores originating from nearby wheat fields.

https://apsjournals.apsnet.org/doi/pdf/10.1094/PHYTO-95-0933

Role of Ascospores in Further Spread of QoI-Resistant Cytochrome b Alleles (G143A) in Field Populations of Mycosphaerella graminicola.

Plants resist pathogen attack through a combination of constitutive and inducible defences Different types of induced resistance have been defined based on differences in signalling pathways and spectra of effectiveness Systemic acquired resistance (SAR) occurs in distal plant parts following localized infection by a necrotizing pathogen It is controlled by a signalling pathway that depends upon the accumulation of salicylic acid (SA) and the regulatory protein NPR1 In contrast, induced systemic resistance (ISR) is promoted by selected strains of non-pathogenic plant growth-promoting rhizobacteria (PGPR) ISR functions independently of SA, but requires NPR1 and is regulated by jasmonic acid (JA) and ethylene (ET)Resistance can be induced by treatment with a variety of biotic and abiotic inducers The resistance induced is broad spectrum and can be long-lasting, but is rarely complete, with most inducing agents providing between 0·20 and 0·85 disease control In the field, expression of induced resistance is likely to be influenced by the environment, genotype, crop nutrition and the extent to which plants are already induced Unfortunately, understanding of the impact of these influences on the expression of induced resistance is rudimentary So too is understanding of how best to use induced resistance in practical crop protection This situation will need to change if induced resistance is to fulfil its potential in crop protection

Practical application of induced resistance to plant diseases: an appraisal of effectiveness under field conditions

The phyllosphere is a rich and varied microbial community comprising organisms with diverse functional types. Its composition is strongly influenced by both genotypic and environmental factors, many of which can be manipulated by breeding, agronomy and crop protection strategies in an agricultural context. These factors also affect the complex interactions between the microbes, which in turn affect their interaction with their host plant. Whether or not an organism becomes pathogenic and the subsequent expression of disease are also influenced by all these factors. Understanding the population dynamic balance between the organisms of the phyllosphere as an ecological system should lead to new approaches in agronomy, crop protection and breeding that enhance sustainability, where the previously presumed requirement to eliminate putative pathogens is replaced by management that favours dominance of beneficial organisms and contains putative pathogens in asymptomatic or stable states.

Managing the ecology of foliar pathogens: ecological tolerance in crops

BACKGROUND: In 2004, field isolates of Botrytis cinerea Pers. ex Fr., resistant to strobilurin fungicides (QoIs), were first found in commercial citrus orchards in Wakayama Prefecture, Japan. Subsequently, QoI-resistant isolates of this fungus were also detected in plastic strawberry greenhouses in Saga, Ibaraki and Chiba prefectures, Japan. Biological and molecular characterisation of resistant isolates was conducted in this study.

RESULTS: QoI-resistant isolates of B. cinerea grew well on PDA plates containing kresoxim-methyl or azoxystrobin at 1 mg L−1, supplemented with 1 mM of n-propyl gallate, an inhibitor of alternative oxidase, whereas the growth of sensitive isolates was strongly suppressed. Results from this in vitro test were in good agreement with those of fungus inoculation tests in vivo. In resistant isolates, the mutation at amino acid position 143 of the cytochrome b gene, known to be the cause of high QoI resistance in various fungal pathogens, was found, but only occasionally. The heteroplasmy of cytochrome b gene was confirmed, and the wild-type sequence often present in the majority of resistant isolates, indicating that the proportion of mutated cytochrome b gene was very low.

CONCLUSION: The conventional RFLP and sequence analyses of PCR-amplified cytochrome b gene are insufficient for molecular identification of QoI resistance in B. cinerea. Copyright © 2009 Society of Chemical Industry

Characterisation of QoI‐resistant field isolates of Botrytis cinerea from citrus and strawberry

Barley is one of the world’s most important crops providing food and related products for millions of people. Diseases continue to pose a serious threat to barley production, despite the use of fungicides and resistant varieties, highlighting the impact of fungicide resistance and the breakdown of host plant resistance on the efficacy of control measures. This paper reviews progress towards an integrated approach for disease management in barley in which new methods may be combined with existing measures to improve the efficacy of control in the long-term. Advances have been made in genetic mapping of resistance (R) genes and in identifying novel sources of genes in wild barley populations and land races. Marker assisted selection techniques are being used to pyramid R genes to increase the durability of resistance. Elicitors to induce host resistance used in combination with fungicides can provide effective disease control in the field and could delay the evolution of fungicide insensitivity. Traits that may contribute to disease tolerance and escape have been identified and the extent of genetic variation within barley germplasm is being determined. Tools are being developed to integrate the above methods via an assessment of the risk of economic injury occurring from disease to guide decisions on the requirement for fungicide treatment. Barriers exist to the adoption of integrated management approaches from growers and end-users further down the supply chain (e.g. acceptance of variety mixtures) and policy incentives from government may be required for it to be taken up in practice.

J. M. Fountaine

Papers

Role of Ascospores in Further Spread of QoI-Resistant Cytochrome b Alleles (G143A) in Field Populations of Mycosphaerella graminicola.

Practical application of induced resistance to plant diseases: an appraisal of effectiveness under field conditions

Managing the ecology of foliar pathogens: ecological tolerance in crops

Characterisation of QoI‐resistant field isolates of Botrytis cinerea from citrus and strawberry

Control of foliar diseases in barley: towards an integrated approach