Tackling the re-emergence of wheat stem rust in Western Europe

Saunders, Diane G. O.; Pretorius, Z. A.; Hovmøller, Mogens S.

doi:10.1038/s42003-019-0294-9

Cited by 66 publications

(67 citation statements)

References 13 publications

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“…Population genetic information drives the selection of isolates for activities as diverse as basic mechanistic research and plant germplasm screening for disease resistance. It also helps to pinpoint the origin of pandemic strains and the evolutionary potential of different pathogen populations [7][8][9][10][11][12] . A thorough understanding of the global population structure is essential for any surveillance program that aims at rapidly detecting pathogen incursions into new geographical areas.…”

Section: Introductionmentioning

confidence: 99%

Recently expanded clonal lineages of the rice blast fungus display distinct patterns of presence/absence of effector genes

Latorre

Reyes-Avila

Malmgren

et al. 2020

Preprint

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Background: Understanding the mechanisms and timescales of plant pathogen outbreaks requires a detailed genome-scale analysis of their population history. The fungus Magnaporthe (Syn. Pyricularia ) oryzae -the causal agent of blast disease of cereals-is among the most destructive plant pathogens to world agriculture and a major threat to the production of rice, wheat and other cereals. Although M. oryzae is a multihost pathogen that infects more than 50 species of cereals and grasses, all rice-infecting isolates belong to a single genetically defined lineage. Here, we combined multiple genomics datasets to reconstruct the genetic history of the rice-infecting lineage of M. oryzae based on 131 isolates from 21 countries. Results: The global population of the rice blast fungus consists of a diverse set of individuals and three well-defined genetic groups. Multiple population genetic tests revealed that the rice-infecting lineage of the blast fungus probably originated from a recombining diverse group in South East Asia followed by three independent clonal expansions that took place over the last~200 years. Patterns of allele sharing identified a subpopulation from the recombining diverse group that introgressed with one of the clonal lineages before its global expansion. Remarkably, the four genetic lineages of the rice blast fungus vary in the number and patterns of presence/absence of candidate effector genes. In particular, clonal lineages carry a reduced repertoire of effector genes compared with the diverse group, and specific combinations of effector presence/absence define each of the pandemic clonal lineages. Conclusions: Our analyses reconstruct the genetic history of the rice-infecting lineage of M. oryzae revealing three clonal lineages associated with rice blast pandemics. Each of these lineages displays a specific pattern of presence/absence of effector genes that may have shaped their adaptation to the rice host and their evolutionary history.

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Section: Introductionmentioning

confidence: 99%

Recently expanded clonal lineages of the rice blast fungus display distinct patterns of presence/absence of effector genes

Latorre

Reyes-Avila

Malmgren

et al. 2020

Preprint

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“…Currently, 80% of the world's wheat cultivars are vulnerable to infection (Singh et al, 2008;Lewis et al, 2018) and worldwide yearly grain losses attributed to the disease are estimated at 6.2 million tonnes, equivalent to~1% of the annual wheat yield (valued at USD 1.12 billion; (Beddow et al, 2013). However, this masks crop losses at local or regional levels, which can reach 40% or more (Schumann and Leonard, 2000;Saunders et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

Mutagenesis of Puccinia graminis f. sp. tritici and Selection of Gain-of-Virulence Mutants

et al. 2020

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Wheat stem rust caused by the fungus Puccinia graminis f. sp. tritici (Pgt), is regaining prominence due to the recent emergence of virulent isolates and epidemics in Africa, Europe and Central Asia. The development and deployment of wheat cultivars with multiple stem rust resistance (Sr) genes stacked together will provide durable resistance. However, certain disease resistance genes can suppress each other or fail in particular genetic backgrounds. Therefore, the function of each Sr gene must be confirmed after incorporation into an Sr-gene stack. This is difficult when using pathogen disease assays due to epistasis from recognition of multiple avirulence (Avr) effectors. Heterologous delivery of single Avr effectors can circumvent this limitation, but this strategy is currently limited by the paucity of cloned Pgt Avrs. To accelerate Avr gene cloning, we outline a procedure to develop a mutant population of Pgt spores and select for gain-of-virulence mutants. We used ethyl methanesulphonate (EMS) to mutagenize urediniospores and create a library of > 10,000 independent mutant isolates that were combined into 16 bulks of~658 pustules each. We sequenced random mutants and determined the average mutation density to be 1 single nucleotide variant (SNV) per 258 kb. From this, we calculated that a minimum of three independently derived gain-of-virulence mutants is required to identify a given Avr gene. We inoculated the mutant library onto plants containing Sr43, Sr44, or Sr45 and obtained 9, 4, and 14 mutants with virulence toward Sr43, Sr44, or Sr45, respectively. However, only mutants identified on Sr43 and Sr45 maintained their virulence when reinolculated onto the lines from which they were identified. We further characterized 8 mutants with virulence toward Sr43. These also maintained their virulence profile on the stem rust international differential set containing 20 Sr genes, indicating that they were most likely not accidental contaminants. In conclusion, our method allows selecting for virulent mutants toward targeted resistance (R) genes. The development of a mutant library from as little as 320 mg spores creates a resource that enables screening against several R genes without the need for multiple rounds of spore multiplication and mutagenesis.

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“…In 1998 new races of this pathogen (called Ug99) were detected in Uganda that were virulent against resistance genes present in wheat varieties widely grown in East Africa, leading to local but severe epidemics in the region (Singh et al ., 2015). International efforts to generate and deploy resistant varieties helped to limit impacts from races of these new lineages (Singh et al ., 2015), but the recent detection of stem rust in different parts of Europe is now threatening wheat production in this part of the world (Saunders et al ., 2019). A third and recent example of strain introduction is that of Puccinia striiformis f. sp.…”

Section: Introductionmentioning

confidence: 99%

A polyetic modelling framework for plant disease emergence

et al. 2020

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Plant disease emergences have dramatically increased recently as a result of global changes, especially with respect to trade, host genetic uniformity, and climate change. A better understanding of the conditions and processes determining epidemic outbreaks caused by the emergence of a new pathogen, or pathogen strain, is needed to develop strategies and inform decisions to manage emerging diseases. A polyetic process‐based model is developed to analyse conditions of disease emergence. This model simulates polycyclic epidemics during successive growing seasons, the yield losses they cause, and the pathogen survival between growing seasons. This framework considers one immigrant strain coming in a single event into a system where a resident strain is already established. Outcomes are formulated as probability of emergence, time to emergence, and yield loss, resulting from deterministic and stochastic simulations. An analytical solution to determine a threshold for emergence is also derived. Analyses focus on the effects of two fitness parameters on emergence: the relative rate of reproduction (epidemic speed), and the relative rate of mortality (decay of population between seasons). Analyses revealed that stochasticity is a critical feature of disease emergence. The simulations suggest that: (a) emergence may require a series of independent immigration events before a successful invasion takes place; (b) an explosion in the population size of the new pathogen (or strain) may be preceded by many successive growing seasons of cryptic presence following an immigration event; and (c) survival between growing seasons is as important as reproduction during the growing season in determining disease emergence.

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Tackling the re-emergence of wheat stem rust in Western Europe

Cited by 66 publications

References 13 publications

Recently expanded clonal lineages of the rice blast fungus display distinct patterns of presence/absence of effector genes

Recently expanded clonal lineages of the rice blast fungus display distinct patterns of presence/absence of effector genes

Mutagenesis of Puccinia graminis f. sp. tritici and Selection of Gain-of-Virulence Mutants

A polyetic modelling framework for plant disease emergence

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