Ecological Genomics and Epidemiology (original) (raw)
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Evolutionary Applications, 2015
The management of genes conferring resistance to plant-pathogens should make it possible to control epidemics (epidemiological perspective) and preserve resistance durability (evolutionary perspective). Resistant and susceptible cultivars must be strategically associated according to the principles of cultivar mixture (within a season) and rotation (between seasons). We explored these questions by modeling the evolutionary and epidemiological processes shaping the dynamics of a pathogen population in a landscape composed of a seasonal cultivated compartment and a reservoir compartment hosting pathogen year-round. Optimal deployment strategies depended mostly on the molecular basis of plantpathogen interactions and on the agro-ecological context before resistance deployment, particularly epidemic intensity and landscape connectivity. Mixtures were much more efficient in landscapes in which between-field infections and infections originating from the reservoir were more prevalent than within-field infections. Resistance genes requiring two mutations of the pathogen avirulence gene to be broken down, rather than one, were particularly useful when infections from the reservoir predominated. Combining mixture and rotation principles were better than the use of the same mixture each season as (i) they controlled epidemics more effectively in situations in which within-field infections or infections from the reservoir were frequent and (ii) they fulfilled the epidemiological and evolutionary perspectives.
Evolutionary genomics has recently entered a new era in the study of host-pathogen interactions. A variety of novel genomic techniques has transformed to the identification, detection and classification of both hosts and pathogens, allowing a greater resolution that helps decipher their underlying dynamics and provides novel insights into their environmental context. Nevertheless, many challenges to a general understanding of host-pathogen interactions remain, in particular in the synthesis and integration of concepts and findings across a variety of systems and different spatiotemporal and ecological scales. In this perspective we aim to highlight some of the commonalities and complexities across diverse studies of host-pathogen interactions, with a focus on ecological, spatiotemporal variation, and the choice of genomic methods used. We performed a quantitative review of recent literature to investigate links, patterns and potential tradeoffs between the complexity of genomic, eco...
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Networks are sets of nodes connected by links in various ways (Box 1). Although the properties of random networks have already been systematically investigated in the 1960s, a growing body of literature is now using networks in a range of ecological applications, including the study and management of human, animal, and plant diseases . Given the generality and flexibility of the approach, network representations can be used at a variety of levels in plant pathology, from gene expression during host-pathogen interactions, to the development of plant epidemics among fields, farms, and landscapes and to trade movement of plants infected by pathogens or infested by insects among regions and countries.
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Climate change across the globe has an impact on the occurrence, prevalence, and severity of plant diseases. About 30% of yield losses in major crops are due to plant diseases; emerging diseases are likely to worsen the sustainable production in the coming years. Plant diseases have led to increased hunger and mass migration of human populations in the past, thus a serious threat to global food security. Equipping the modern varieties/hybrids with enhanced genetic resistance is the most economic, sustainable and environmentally friendly solution. Plant geneticists have done tremendous work in identifying stable resistance in primary genepools and many times other than primary genepools to breed resistant varieties in different major crops. Over the last two decades, the availability of crop and pathogen genomes due to advances in next generation sequencing technologies improved our understanding of trait genetics using different approaches. Genome-wide association studies have been ...
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SummaryAssessment of pathogen diversity in agricultural fields is essential for informing management decisions and the development of resistant plant varieties. However, many population genomic studies have relied on culture‐based approaches that do not provide quantitative assessment of pathogen populations at the field‐level or the associated host microbiome. Here, we applied whole‐genome shotgun sequencing of microbial DNA extracted directly from the washings of pooled leaf samples, collected from individual tomato and pepper fields in Alabama that displayed the classical symptoms of bacterial spot disease caused by Xanthomonas spp. Our results revealed that while the occurrence of both X. perforans and X. euvesicatoria within fields was limited, evidence of co‐occurrence of up to three distinct X. perforans genotypes was obtained in 7 of 10 tomato fields sampled. These population dynamics were accompanied by the corresponding type 3 secreted effector repertoires associated with ...
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Plant pathologists have seen many boom-and-bust cycles following the deployment of resistant varieties. These cycles result when pathogen populations adapt to the presence of a major resistance gene by evolving a new population that can overcome this resistance gene. The breakdown of genetic resistance is due to the evolution of the local pathogen population because of selection for mutants, recombinants, or immigrants that are better adapted to the resistant cultivar. To understand the process that leads to breakdown of a resistance gene, we need to understand the processes that govern pathogen evolution. Population geneticists have identified five evolutionary forces that interact to affect the evolution of organisms. We ranked these risks and developed a quantitative framework to predict the risk that a pathogen will evolve to overcome major resistance genes. Our hypothesis is that much of the durability of resistance genes is due to the nature of the pathogen population rather t...
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New Phytologist, 2007
Climate change will affect plant pathosystems at a variety of levels of integration (from genes to populations and from ecosystems to distributional ranges) and in most aspects of epidemic development (from environmental conditions to host vigour and susceptibility, and from pathogen virulence to infection rates). Climate change is likely to have a profound impact on plant–pathogen interactions, and will thus represent a world-wide interdisciplinary challenge not only for the long-term sustainability of crop production but also for the understanding of biodiversity dynamics in a changing world and for the success of conservation biology activities.
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Pathogens are often the main selective agents acting in plant communities, thereby influencing the distribution of polymorphism at loci affecting resistance within and among natural plant populations. In addition, the outcome of plant-pathogen interactions can be drastically affected by abiotic and biotic factors at different spatial and temporal grains. The characterization of the adaptive genetic architecture of disease resistance in native heterogeneous environments is however still missing. In this study, we conducted an in situ Genome-Wide Association study in the spatially heterogeneous native habitat of a highly genetically polymorphic local mapping population of Arabidopsis thaliana, to unravel the adaptive genetic architecture of quantitative disease resistance. Disease resistance largely differed among three native soils and was affected by the presence of the grass Poa annua. The observation of strong crossing reactions norms among the 195 A. thaliana genotypes for diseas...