Molecular Tools for Detection of Plant Pathogenic Fungi and Fungicide Resistance

Abstract

Plant pathogenic fungi are the causal agents of the most detrimental diseases in plants, including economically important crops, provoking considerable yield losses worldwide. Fungal pathogens can infect a wide range of plant species or be restricted to one or few host species. Some of them are obligate parasites requiring the presence of the living host to grow and reproduce, but most of them are saprophytic and can survive without the presence of the living plant, in the soil, water or air. Isolates of a fungal species can be differentiated by morphological characteristics, host range (formae speciales), pathogenic aggressiveness (pathotypes or races) or their ability to form stable vegetative heterokaryons by fusion between genetically different strains (belonging to the same vegetative compatibility group, VCG). Detection and accurate identification of plant pathogens is one of the most important strategies for controlling plant diseases to initiate preventive or curative measures. Special interest should be taken in the early detection of pathogens in seeds, mother plants and propagative plant material to avoid the introduction and further spreading of new pathogens in a growing area where it is not present yet. For that reason, the availability of fast, sensitive and accurate methods for detection and identification of fungal pathogens is increasingly necessary to improve disease control decision making. Traditionally, the most prevalent techniques used to identify plant pathogens relied upon culture-based morphological approaches. These methods, however, are often time-consuming, laborious, and require extensive knowledge of classical taxonomy. Other limitations include the difficulty of some species to be cultured in vitro, and the inability to accurately quantify the pathogen (Goud & Termorshuizen, 2003). These limitations have led to the development of molecular approaches with improved accuracy and reliability. A high variety of molecular methods have been used to detect, identify and quantify a long list of plant pathogenic fungi. Molecular methods have also been applied to the study of the genetic variability of pathogen populations, and even for the description of new fungal species. In general, these methods are much faster, more specific, more sensitive, and more accurate, and can be performed and interpreted by personnel with no specialized taxonomical expertise. Additionally, these techniques allow the detection and identification of non-culturable microorganisms, and due to its high degree of specificity, molecular techniques can distinguish closely related organisms at different taxonomic levels. Here, we review the most important tools for molecular detection of plant pathogenic fungi, their applicability, and their implementation in horticultural and agricultural practices. On the other hand, once the pathogenic fungus is already established in a given crop growing area, the use of synthetic fungicides constitutes the main strategy to control plant diseases, since these compounds act quickly and effectively. The disadvantages of continued use of fungicides are their limited spectrum and the emergence of resistant fungal isolates. This fact leads to many yield losses as control systems are not longer effective. The development of resistance to fungicides in fungal pathogens and the growing public concern over the health and environmental hazards associated with the high level of pesticide have resulted in a significant interest in knowing more about fungal resistance. The emergence of more stringent regulations regarding pesticide residues means that one of the main priorities is to ensure food security by reducing the use of fungi toxics. For this reason, it is important to identify and characterize the mechanisms involved in the emergence of strains resistant to fungicides used for control diseases and to know the molecular methods currently available to detect them