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1.
ABSTRACT Plant pathogen culture collections are essential resources in our fight against plant disease and for connecting discoveries of the present with established knowledge of the past. However, available infrastructure in support of culture collections is in serious need of improvement, and we continually face the risk of losing many of these collections. As novel and reemerging plant pathogens threaten agriculture, their timely identification and monitoring depends on rapid access to cultures representing the known diversity of plant pathogens along with genotypic, phenotypic, and epidemiological data associated with them. Archiving such data in a format that can be easily accessed and searched is essential for rapid assessment of potential risk and can help track the change and movement of pathogens. The underexplored pathogen diversity in nature further underscores the importance of cataloguing pathogen cultures. Realizing the potential of pathogen genomics as a foundation for developing effective disease control also hinges on how effectively we use the sequenced isolate as a reference to understand the genetic and phenotypic diversity within a pathogen species. In this letter, we propose a number of measures for improving pathogen culture collections.  相似文献   

2.
The primary and secondary centres of origin of domesticated plants are often also the places of origin of their pathogens. Therefore, the Near Eastern cradle of agriculture, where crop plants, their wild progenitors, and other con-generic taxa grow sympatrically, may hold some clues on the biology of the pathogens of the respective crops. Unlike the situation in the well-studied Near Eastern cereals and their important diseases, hardly any data are available on basic questions regarding grain legumes. What is the role of genetic diversity at resistance loci of the wild hosts and is it greater compared with the cultigens? Are populations of Ascochyta pathogens infecting wild legumes genetically distinct from populations infecting their domesticated counterparts, and if so, is this differentiation related to differences in host specialization or to adaptation to different ecological conditions? Do isolates originating from wild taxa exhibit a similar level of aggressiveness and have different aggressiveness alleles compared with those originating from domesticated grain legumes? In this review we propose an experimental framework aimed at gaining answers to some of the above questions. The proposed approach includes comparative epidemiology of wild vs. domesticated plant communities, co-evolutionary study of pathogens and their hosts, phenotypic and genetic characterization of fungal isolates from wild and domesticated origins, and genetic analyses of pathogenicity and parasitic fitness among progeny derived from crosses between isolates from wild and domesticated hosts.  相似文献   

3.
The huge amount of genomic data now becoming available offers both opportunities and challenges for epidemiologists. In this “preview” of likely developments as the field of ecological genomics evolves and merges with epidemiology, we discuss how epidemiology can use new information about genetic sequences and gene expression to form predictions about epidemic features and outcomes and for understanding host resistance and pathogen evolution. DNA sequencing is now complete for some hosts and several pathogens. Microarrays make it possible to measure gene expression simultaneously for thousands of genes. These tools will contribute to plant disease epidemiology by providing information about which resistance or pathogenicity genes are present in individuals and populations, what genes other than those directly involved in resistance and virulence are important in epidemics, the role of the phenotypic status of hosts and pathogens, and the role of the status of the environmental metagenome. Conversely, models of group dynamics supplied by population biology and ecology may be used to interpret gene expression within individual organisms and in populations of organisms. Genomic tools have great potential for improving understanding of resistance gene evolution and the durability of resistance. For example, DNA sequence analysis can be used to evaluate whether an arms race model of co-evolution is supported. Finally, new genomic tools will make it possible to consider the landscape ecology of epidemics in terms of host resistance both as determined by genotype and as expressed in host phenotypes in response to the biotic and abiotic environment. Host phenotype mixtures can be modeled and evaluated, with epidemiological predictions based on phenotypic characteristics such as physiological age and status in terms of induced systemic resistance or systemic acquired resistance.  相似文献   

4.
Spinach (Spinacia oleracea) has become an increasingly important vegetable crop in many parts of the world. Significant changes in production practices, particularly in the U.S. and E.U., have occurred in the past 10–15 years as a result of increased product demand. These changes likely increased the incidence and severity of downy mildew, caused by Peronospora farinosa f. sp. spinaciae. Recently, progress has been made to define the genetics of resistance to this pathogen and the closely related white rust pathogen, Albugo occidentalis. In this paper, we outline the genetic and genomic resources currently available for spinach, draw parallels between spinach diseases and more thoroughly characterized pathosystems, and describe efforts currently underway to develop new genetic and genomic tools to better understand downy mildew and white rust of spinach. Presently, many crucial tools and resources required to define the molecular underpinnings of disease are unavailable for either spinach or its pathogens. New resources and information for spinach genomics would provide a jumpstart for ongoing efforts to define (and deploy) genetic resistance against downy mildew and white rust.  相似文献   

5.
ABSTRACT Genetic resistance often fails because a resistance-breaking (RB) pathogen genotype increases in frequency. On the basis of an analysis of cellular plant pathogens, it was recently proposed that the evolutionary potential of a pathogen is a major determinant of the durability of resistance. We test this hypothesis for plant viruses, which differ substantially from cellular pathogens in the nature, size, and expression of their genomes. Our analysis was based on 29 plant virus species that provide a good representation of the genetic and biological diversity of plant viruses. These 29 viruses were involved in 35 pathosystems, and 50 resistance factors deployed against them were analyzed. Resistance was found to be durable more often than not, in contrast with resistance to cellular plant pathogens. In a third of the analyzed pathosystems RB strains have not been reported, and in another third RB strains have been reported but have not become prevalent in the virus population. The evolutionary potential of the viruses in the 35 pathosystems was evaluated with a compound risk index based on three evolutionary factors: the population of the pathogen, the degree of recombination, and the amount of gene and genotype flow. Our analysis indicates that evolutionary potential may be an important determinant of the durability of resistance against plant viruses.  相似文献   

6.
Microarrays offer virtually unlimited diagnostics capability, and have already been developed into diagnostic chips for many different plant pests. The full capacity of such chips, however, has lagged far behind their full potential. The main reason for this is that current chip design relies on a priori genetic information for target organisms and on a consensus on the genetic sequences to be used in particular organism groups. Such information is often unavailable and laborious to obtain. Thus, broad-application diagnostic microarrays have been limited to narrow organism groups focused on Genera of pests/pathogens or those affecting individual host crops, without applicability for simultaneous detection of diverse pests affecting many crops. This paper describes the development of a diagnostic microarray platform that has universal application based on genomic fingerprinting of any organism without a need for a priori sequence information. Taxon-specific hybridization patterns are obtained by unique hybridisation of genomic DNA to 100s–1000s of short random oligonucleotide probes. Taxon identification is then achieved by comparison of hybridisation patterns from an unknown sample against a reference-pattern database. Using bacteria as a model pathogen group, these methods deliver highly reproducible hybridisation patterns with high resolution power and enable discrimination at the species and subspecies level.  相似文献   

7.
Genetic diversity assessment and population structure analysis are essential for characterization of pathogens and their isolates. Markers are essential tools for exploring genetic variation among the isolates. False smut of rice caused by Ustilaginoidea virens, formerly Villosiclava virens, is a major emerging disease of rice in India. A high level of variability is observed at the field level, but no information is available from India on genetic diversity and population structure. This is the first report of genetic diversity and population structure of U. virens from India that included 63 isolates distributed across the vast geographical area of eastern and north-eastern India (18.9 to 26.7°N and 82.6 to 94.2°E). Seventeen RAPDs and 14 SSRs were identified as polymorphic and a total of 140 alleles were detected across the populations. The average number of alleles per locus for each primer was 4.5. All the isolates were grouped into two major clusters, with partial geographical segregation that was supported by principal coordinate analysis. Mantel test suggested genetic distance within the isolates increased with increasing geographical distance. Analysis of molecular variation showed more genetic variation within populations and less among populations. This outcome will help in understanding genetic diversity of U. virens from eastern and north-eastern India and in planning effective management strategies.  相似文献   

8.
Fusarium oxysporum f. sp. lycopersici (FOL) races and F. oxysporum f. sp. radicis lycopersici (FORL), the causal agents of root rot and crown rot diseases, respectively, cause serious economic losses in tomato greenhouses where production is intensive in the West Mediterranean region of Turkey. The isolates were collected from West Mediterranean region of Turkey and were characterized by specific primers based on three races (r1, r2, r3), besides pathogenicity tests in in vivo conditions Additionally, a scheme was developed using newly tested ISSR and SRAP markers to a genotyping database and to determine the possible origin of these pathogens. The present study provided new information on these pathogens based on their races and their dominant existence in this region that has not been reported before. Genetic diversity detected in the same races of the pathogen may be associated with difficulties in controlling the pathogen and a possible resistance formation effort exerted by the pathogen to chemicals used in plant protection in tomato greenhouses. Molecular analyses indicated genetic diversity in pathogen isolates identified as r3, r2 and FORL, which may be associated with abiotic stress to which the pathogens were exposed.  相似文献   

9.
The spot blotch disease of wheat is caused by Bipolaris sorokiniana, which is an anamorph (teleomorph Cochliobolus sativus). The disease mainly occurs in warm, humid wheat‐growing regions, and the Eastern Gangetic Plains (EGP) of South Asia is a hotspot. Significant progress has been made in recent years in characterizing the host–pathogen interaction. The study of the pathogen's life cycle and diversity have been an active area of research. A number of resistance sources have also been identified, characterized and used for breeding. Although immunity has not been observed in any genotype, cultivars displaying a relatively high level of resistance have been developed and made available to farmers. Further progress will require regular use of marker‐assisted breeding, genomic selection, gene editing and transgenic interventions. This review summarizes the current state of knowledge about genetic and breeding efforts on the wheat–B. sorokiniana pathosystem and discusses ways in which emerging tools can be used for future research to understand the mechanism involved in infection and for developing cultivars exhibiting a high level of resistance.  相似文献   

10.
Cucurbit powdery mildew (CPM) is caused most frequently by well-differentiated obligate erysiphaceous ectoparasites Golovinomyces orontii and Podosphaera xanthii, which vary in their ecology and virulence. All economically important cucurbit crops host both of these CPM species. Breeding of cucurbits for CPM resistance is highly important worldwide, but adequate knowledge of CPM species determination, as well as virulence structure, population dynamics, and spatiotemporal variation of these pathogens, has not yet been achieved. New tools have been developed to enhance research on CPM virulence variation for more efficient breeding and seed and crop production. A set of differential genotypes of Cucumis melo, with high differentiation capacity, may contribute substantially to understanding of variation in CPM virulence at both individual and population levels. Long-term observations (2001–2012) of CPM pathogens in the Czech Republic were used to analyse virulence variation within and among annual CPM populations and demonstrate the utility of recently developed tools for studying species variability and virulence variation of CPM pathogens worldwide. Detailed analyses of diversity and spatiotemporal fluctuations in the composition of CPM populations provide crucial information for shaping breeding programmes and predicting the most effective sources of race-specific resistance. The primary aim of this work was to create a uniform framework for determination of CPM species structure and diversity, virulence phenotypes, virulence and phenotype frequencies, phenotype complexity, dynamics, and variation within and among CPM populations. In addition, practical advice is presented on how to select the most relevant data and interpret them for use in cucurbit resistance breeding.  相似文献   

11.
Existing theory suggests that increasing the diversity of resistance and virulence types in host–pathogen interactions will result in qualitative shifts in spatial and temporal dynamics, and greater among-population asynchrony in disease dynamics and prevalence. Here, data are presented from a biologically realistic metapopulation model of gene-for-gene interactions that indicate that population level variation in resistance diversity will be negatively associated with disease prevalence (fraction of individuals infected). The model also predicts that disease incidence (presence/absence) will be positively related to total resistance diversity across the metapopulation, because high resistance diversity also selects for more virulent pathogens. These results are then contrasted with empirical data from a natural host–pathogen system. While the argument that high resistance diversity should generally lead to lower disease levels has been applied extensively in agricultural situations, the connection between genetic diversity, resistance and disease dynamics has never been demonstrated in natural systems. Here, through analysis of multiyear data on disease prevalence in the context of knowledge of resistance variation among host populations in a natural plant host–pathogen metapopulation, the first evidence is provided that observed levels of asynchrony in disease dynamics may indeed be related to resistance structure.  相似文献   

12.
Twelve species of fungi have been found growing on barley leaves in Icelandic fields. The study presented here on the population structure of two of these species, the pathogens Rhynchosporium commune and Pyrenophora teres f. teres, reveals high levels of genetic diversity, low levels of migration, and a significant differentiation from other European populations, despite the short history of continuous barley cultivation in Iceland. The gene diversity for R. commune in Iceland was 0.55 compared to a range of 0.43?C0.73 for six European populations. The gene diversity for P. teres was higher in Iceland than in populations from Russia and Finland. The two mating types were found to overlap in distribution for both fungi making sexual reproduction a possibility, supported by the few clones and the gametic equilibrium within the Icelandic populations. When the high levels of diversity, low levels of migration, and the genetic differentiation observed between Icelandic and Scandinavian populations are put into context with the short history of barley cultivation in Iceland, it raises questions regarding the origin of the Icelandic fungal populations. It also underlines the importance of proper analysis of pathogens prior to starting resistance breeding projects. The findings are an addition to the ongoing analysis of the global diversity of barley fungal pathogens in general and an important input into future barley breeding projects in Iceland in particular.  相似文献   

13.
Seed potato degeneration, the reduction in yield or quality caused by an accumulation of pathogens and pests in planting material due to successive cycles of vegetative propagation, has been a long‐standing production challenge for potato growers around the world. In developed countries this problem has been overcome by general access to and frequent use of seed, produced by specialized growers, that has been certified to have pathogen and pest incidence below established thresholds, often referred to as certified seed. The success of certified seed in developed countries has concentrated the research and development agenda on the establishment of similar systems in developing countries. Despite these efforts, certified seed has had little penetration into the informal seed systems currently in place in most developing countries. Small‐scale farmers in these countries continue to plant seed tubers acquired through the informal seed system, i.e. produced on‐farm or acquired from neighbours or local markets. Informal seed tubers frequently have poor health status, leading to significant reductions in yield and/or market value. This review emphasizes the need to refocus management efforts in developing countries on improving the health status of seed tubers in the informal system by integrating disease resistance and on‐farm management tools with strategic seed replacement. This ‘integrated seed health strategy’ can also prolong the good health status of plants derived from certified seed, which would otherwise be diminished due to potential rapid infection from neighbouring fields. Knowledge gaps, development challenges and impacts of this integrated seed health strategy are discussed.  相似文献   

14.
The heterothallic ascomycete Fusarium fujikuroi (teleomorph: Gibberella fujikuroi) is the causal agent of bakanae of rice, a disease of increasing economic importance in the major rice‐producing areas in the world and a serious threat for Italian rice cultivation. A few studies have characterized F. fujikuroi isolates in America and the Philippines but no data are available on the genetic structure of Italian pathogen populations. Microsatellite SSRs are useful tools to study the intraspecific diversity at population level. In this study, 19 polymorphic SSRs have been identified and applied to characterize the genetic variation of 334 isolates of F. fujikuroi coming from eight Italian rice‐growing areas. A high degree of diversity at haplotype level has emerged: in the eight populations, 107 unique haplotypes were scored. Analysis of molecular variance (amova ) showed that 98% of genetic variability occurred within F. fujikuroi Italian populations, as confirmed by the allelic Shannon index ranging from 0.56 to 1.06. The presence of a 1:1 ratio of mating type alleles in six out of eight of the Italian fungal populations suggests a potential for sexual reproduction in the field. However, the high fraction of clonality (43%), confirmed by neighbour‐joining clustering analysis, and the high level of linkage disequilibrium observed, indicates that reproduction of F. fujikuroi is mostly clonal in Italy. All data suggest that the observed genetic variability was probably mediated by human activity and transmission by rice seeds.  相似文献   

15.
The barley powdery mildew pathogen, Blumeria graminis f. sp. hordei (Bgh), exists in numerous haplotypes and displays significant differences in fungicide sensitivity. It causes considerable yield losses throughout the world. Microsatellite SSRs are useful tools to study the population level and biogeographic aspects of intraspecific diversity, but so far none have been defined for Bgh. Here, eight polymorphic microsatellite loci were identified and characterized. Primer pairs amplifying the loci were then applied to 111 isolates of Bgh from Australia. The number of alleles per locus ranged from 4 to 13, and Nei's genetic diversity ranged from 0·25 to 0·76. The microsatellite primers detected several clones among the isolates and defined 97 unique haplotypes. There was little evidence for regional genotypic subdivision, suggesting that gene flow may not be restricted among geographic regions. All data was consistent with high levels of genetic diversity, potentially resulting from random mating and spread within each region.  相似文献   

16.
 采用RAPD技术对分离自河南省各地的43株小麦黑胚病优势病原菌(Alternaria spp.)菌株进行了遗传多样性分析。17个随机引物共扩增出151条清晰的DNA条带,所扩增出的DNA条带均为多态带,说明河南省小麦黑胚病菌存在着丰富的遗传多样性。利用NTSYS软件进行了病原菌的聚类分析,结果表明,河南省小麦黑胚病菌主要有2个种,即Alternaria alternata和A. tenuissima,种间的遗传相似系数的变化幅度为0.62~0.92。来自同一个地区的小麦黑胚病菌菌株基本上聚在了一起,表现出很近的亲缘关系,来自不同地区之间的菌株也可以交叉聚类。病原菌遗传多样性分析进一步验证了形态学的鉴定结果。  相似文献   

17.
Diagnostic services in developing countries are severely limited by the availability of funding and trained personnel. While common fungal pathogens can be identified with minimal equipment and media, the conventional methods for identification of bacterial pathogens are time-consuming and require a wide range of costly media and reagents. In addition, excessive time and resources are often devoted to the identification of contaminating saprophytic bacteria. The Biolog system for identifying bacteria by metabolic profiles has been evaluated and adapted for use in routine diagnosis in small plant pathology laboratories overseas. Although Biolog is costly, it can be combined with a system for the preliminary identification and elimination of non-pathogens using a limited number of conventional tests. The database of Gram-negative profiles supplied by Biolog needs to be supplemented by user-defined database(s). Bacterial Identifier software (Blackwell Scientific Publications) is advocated as a cost-effective alternative.  相似文献   

18.
The leaf spot form of the barley disease net blotch, caused by the fungus Pyrenophora teres f. maculata (PTM), is an increasingly important foliar disease of barley. Studies of population genetic structure and reproductive mode are necessary to make predictions of the evolutionary potential of the pathogen. Sources of resistance to PTM have been found in Iranian landraces, which may have the potential to improve plant breeding efforts. However, little is known about the population genetic structure of this fungus in Iran. In this study, we analysed the frequency of the mating type genes to assess the potential for sexual mating of PTM collected from four provinces—Khuzestan, Hamadan, Golestan, and East Azerbaijan—and we investigated the population genetic structure using seven simple sequence repeat markers. High genotype diversity, linkage equilibrium, and equal ratios of mating types frequencies in the PTM populations at Khuzestan and Hamadan support the occurrence of sexual reproduction in these populations, while in Golestan and East Azerbaijan populations, significant gametic disequilibrium and relatively low genotype diversity suggest a higher incidence of clonality or different demographic histories. Unequal mating type frequencies in Golestan confirm a predominance of asexual reproduction. Finally, we found significant evidence for strong population structure with most of the genetic variation represented within regional populations (89%). Overall, our study provides evidence for high genetic variation in Iranian PTM populations, which may be the basis for rapid adaptive evolution in this pathosystem. This highlights the need for integrated efforts to control the disease.  相似文献   

19.
Wheat production is threatened by a constantly changing population of pathogen species and races. Given the rapid ability of many pathogens to overcome genetic resistance, the identification and practical implementation of new sources of resistance is essential. Landraces and wild relatives of wheat have played an important role as genetic resources for the improvement of disease resistance. The use of molecular approaches, particularly molecular markers, has allowed better characterization of the genetic diversity in wheat germplasm. In addition, the molecular cloning of major resistance (R) genes has recently been achieved in the large, polyploid wheat genome. For the first time this allows the study and analysis of the genetic variability of wheat R loci at the molecular level and therefore, to screen for allelic variation at such loci in the gene pool. Thus, strategies such as allele mining and ecotilling are now possible for characterization of wheat disease resistance. Here, we discuss the approaches, resources and potential tools to characterize and utilize the naturally occurring resistance diversity in wheat. We also report a first step in allele mining, where we characterize the occurrence of known resistance alleles at the wheat Pm3 powdery mildew resistance locus in a set of 1,320 landraces assembled on the basis of eco-geographical criteria. From known Pm3 R alleles, only Pm3b was frequently identified (3% of the tested accessions). In the same set of landraces, we found a high frequency of a Pm3 haplotype carrying a susceptible allele of Pm3. This analysis allowed the identification of a set of resistant lines where new potentially functional alleles would be present. Newly identified resistance alleles will enrich the genetic basis of resistance in breeding programmes and contribute to wheat improvement.  相似文献   

20.
Ralstonia solanacearum is the causal organism of bacterial wilt of more than 200 species representing 50 families of plants in tropical, subtropical, and warm temperate regions in the world. Traditionally classified into five races based on differences in host range, R. solanacearum has also been grouped into six biovars on the basis of biochemical properties. With recent developments in molecular biology, various DNA-based analyses have been introduced and used to confirm that this binary system does not completely represent the diversity within R. solanacearum strains. Therefore, a new hierarchical classification scheme has been suggested, which defines R. solanacearum as a species complex and reorganized the concept of the species as a monophyletic cluster according to a phylogenetic analysis based on genomic sequence data. Here we discuss the current bacterial wilt situation and genetic relationships based on the recent classification system of Japanese R. solanacearum strains as well as worldwide strains. We also review the genetic, biochemical, and pathological characteristics of R. solanacearum strains, in particular, those affecting potato and Zingiberaceae plants as distinctly important pathogens in relation to continuously problematic and recent emergent diseases in Japan.  相似文献   

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