Abstract
Fungi comprise nearly 70 % of the non-native pathogens introduced into Great Britain over the last 40 years and pose serious plant health risks. The Plant Health Directive requires controls to prevent the introduction and spread of such pathogens and the EC regulated Alternaria diseases of pome fruits is an important case in point. Other Alternaria pathogens have also been intercepted on plant material in the UK recently (e.g. A. panax on Fatsia sp. and Alternaria sp. on Impatiens; CSL-PRA Notes, C. Sansford). Alternaria species are distributed worldwide and are important plant and human pathogens. They cause extensive pre- and post- harvest losses of agricultural produce and are one of the most common allergens. Alternaria species infect a wide range of plants ranking 10th in terms of total number of hosts and encompass a great deal of morphological, physiological and ecological diversity. Several Alternaria taxa form closely related clusters of pathogens and saprobes with poor species definitions. Traditional taxonomy users define species largely by host interactions, but in many cases a continuum of genotypic and phenotypic divergences is witnessed, which makes species definition and diagnosis difficult (Akimitsu et al., 2003; Thomma, 2003). Recent studies have led to clear division of the ‘porri’ and ‘alternata’ species-groups characterised by large and small spores, respectively. Within the species-groups, however, population-species boundaries are blurred and there is considerable controversy among the small-spored taxa related to ‘alternata’. Alternaria blotches of apple and pear are serious diseases and are economically important as they reduce fruit yield and affect fruit quality. The classification of these EC listed non-European species of Alternaria pathogenic to apple, pear and quince remains unresolved. Some researchers describe the apple pathogen as A. mali and the Asian pear pathogen as A. gaisen/A. kikuchiana, whilst others refer to these pathogens as different forms/pathotypes of A. alternata linked to the production of toxins associated with pathogenicity. On a number of other plant hosts such as strawberry, tomato, citrus, kiwifruit, walnut, rosemary and lavender, morphologically similar toxin producing Alternaria pathogens have emerged (the latter two are PHSI interceptions; PH0171, CSL). The relatedness of these to the listed pathogens and the plant health risk posed by them need to be evaluated. Development of rapid and robust diagnostic methodologies is essential due to increased trade and the ineffectiveness of current assays. One of the major problems in addressing these issues has been the poor resolution of the molecular markers commonly used in fungal systematics (e.g. ITS, mtSSU, tubulin, TEF ) and emerging research suggests the potential of genes such as endo-polygalacturonase (Peever et al., 2004; Andrew et al., 2009). The overall aim of the current project is to develop DNA-based methodologies to characterise EC-listed Alternaria pathogens to establish phylogenetically well resolved taxa. And use this as a platform to develop robust diagnostics that meet users’ needs, in the context of disease control, trade and risk analysis as well as to widen links with fungal barcoding initiatives. To achieve this, loci of phylogenetic value in Alternaria species will be identified through comparative analysis of fungal genome sequences. Alternaria pathogens are known to produce host-specific and non-specific toxins. Some progress has been made in identifying the genes responsible for the biosynthesis of host-specific toxins such as AK-toxin produced by the Japanese pear pathogenic isolates/pathotypes of Alternaria (Tsuge, 2003; Strange and Scott, 2005). These toxin genes as well as other pathogenicity-related genes such as those involved in plant cell wall degradation and melanin biosynthesis have the potential to serve as useful markers to identify Alternaria pathotypes and differentiate the pathogenic strains from non-pathogens. The presence and expression of these groups of genes will be analysed in relation to host range and specificity to identify potential functional gene markers. These molecular analyses along with phenotypic assays such as pathogenicity tests will be used to characterise EC-listed Alternaria pathogens originating from pome fruits and related pathogens from important crops and to differentiate pathogenic and non-pathogenic forms. The genotype-phenotype data will be integrated to define population-species boundaries, improve systematics and develop diagnostic methodologies. Warwick HRI have considerable experience in phylogenetics and genomics of diverse fungal systems (Sreenivasaprasad and Talhinhas, 2005; Muthumeenakshi et al., 2007) and Fera staff who will co-supervise the PhD programme have experience in Alternaria pathogens (PH0171). Warwick HRI and Fera collaboration provides complementary expertise and unique resources such as a large collection of relevant Alternaria isolates, differential host varieties and excellent links with international fungal biology research community. Close interaction with and benefit to the Alternaria community will be ensured through various dissemination activities. Warwick HRI and Fera are also part of a newly established UK research group to co-ordinate the development of fungal DNA barcoding technologies, and the proposed project will provide opportunities for wider collaborative links with these approaches. Overall this work relates to Defra’s policy objectives in sustainable farming and food and the UK government initiative to develop capability in modern taxonomic approaches underpinning biodiversity conservation, and food security.
United Kingdom