Fungi are present in a variety of forms, in almost every habitat, where they are often specific in their occurrence on particular types of host (or substrate) and ecological niche. Fungi may also become partners with higher plants and enter complex biological relationships with the host (Clay and Kover 1996; Thrall and Burdon 1997). The term pathogen is defined as "a parasite able to cause disease in a host or range of hosts" (Kirk et al. 2001), and pathogenic fungi can occur on all plants. In this chapter this definition of plant pathogenic fungi will be limited to those that cause diseases of living plants, and therefore does not include the fungi involved in the spoilage of stored plant materials that are often referred to as causing post harvest "diseases." The plant pathogenic fungi consist of a large group of genera and species from diverse areas of the fungal kingdom. Recent developments in the understanding of the evolution of eukaryotic organisms have meant that a number of important plant pathogenic organisms have been reclassified, and are no longer considered as fungi sensu stricto. These include the economically important genera of Phytophthora, Pythium, and other Oomycetes, that are now placed in the Straminipila (Dick 2001). Plant pathogenic fungi have a significant influence on crop productivity. Devastating fungal diseases such as corn smut, potato blight, and black stem rust of wheat can destroy many economically important crops. This situation becomes more critical when the interaction between pathogen and the host plant involves relatively long periods of intimate interaction without apparent damage to the host, and where the pathogen can persist in asymptomatic hosts for many years (Stanosz et al. 1997). The effects of fungi on living plants vary considerably. At one extreme, damage may be limited to small lesions on leaves or stems [e.g., caused by some Alternaria species, see Ellis (1968)], while at the other extreme the plant may be rapidly killed [e.g., by some Verticillium species, see Pegg (1984)].
Much work has been done to control fungal disease through selection and breeding programs, the genetic modification of both host and pathogen, and the introduction of resistant varieties [see Stukely and Crane (1994)]. The success of these efforts depends largely on the understanding of genetic variability in the fungal population and monitoring this variation in nature. Many aspects of the biology of the fungi have important consequences at the population level. This particularly applies to the mode of reproduction (i.e., the relative contributions of sexual and asexual, outcrossing and selfing mechanisms), and to hyphal anastomosis between genetically different individuals (Brasier 1991; Glass and Kuldau 1992; Milgroom et al. 1996). A further consideration is that some fungi are predominantly haploid in their vegetative phase, some are diploid, and some are dikaryotic. In the case of pathogenic fungi, genetic variability can be introduced through a variety of mechanisms, either during sexual reproduction or independently of it (Kistler and Miao 1992). Such variability is significant as it can influence
*British Antarctic Survey, Cambridge, United Kingdom.
tNational Bureau of Agriculturally Important Microorganisms (NBAIM), New Delhi, India.
the host-pathogen interaction as genetic flexibility allows the fungi to readily adapt to changing environmental conditions, including the introduction of new host genotypes.
Understanding the epidemiology of plant pathogenic fungi depends upon on the ability to unambiguously identify sexually produced individuals and asexually produced clones. Classical identification traits, such as morphological, physiological, and disease characters, lack the required sensitivity and accuracy needed for identifying individuals within a population, and this has prevented detailed population studies for many years. Recent developments in molecular techniques now allow population studies on plant pathogenic fungi, and these can be performed with great sensitivity and accuracy. An almost unlimited number of polymorphic loci can be used to detect individual genotypes for the direct assessment of genetic variation in a given fungal population. Application of molecular markers has also allowed the investigation of evolutionary processes in a large number of agriculturally important fungi (Mitchell and Brasier 1994; Milgroom et al. 1996; Valent and Chumley 1991; Vilgalys and Cubeta 1994), and the number and scope of these studies is rapidly expanding.
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