Know your enemy - Phytophthora

credit: Naomi Williams

A web-based molecular identification tool for the plant pathogenic fungus Phytophthora promises to revolutionize taxonomic identification, making it more objective, accurate and reproducible and thereby aid the control of the diseases caused by this widespread, economically damaging, and yet poorly understood genus. What is unique about the DFID and SERAD-funded identification system, which has been developed by scientists at the Scottish Crop Research Institute (SCRI) and CAB International, is that it links a molecular database to an algorithmic isolate identification search facility. It also provides links to morphological and epidemiological information.

Phytophthora infestans, the causal agent of late blight of potato, gained unequalled notoriety when it devastated crops in many parts of Europe in the 19th century. Although most often associated with the great famine in Ireland, it also caused crop failure, famine and emigration over several years in many other countries. The development of preventive sprays reduced the risk of loss but it remains an abiding threat awaiting the right climatic conditions, and any lapse in prophylactic treatment, to totally destroy potato crops. What plant pathologists recognize (but few others may appreciate) is that the genus includes numerous relatives of P. infestans, some 60 species, most of which can cause a range of diseases in innumerable plants of economic and ecological importance. P. palmivora alone attacks over 80 plant species including cocoa (where it causes blackpod, canker, leaf blight and root rot), coconut, rubber, pepper, pineapple, oilpalm and papaya. Several root rots, including those of avocado and citrus, are caused by Phytopthora spp., as are stem cankers, leaf blights, fruit rots and damping-off in crops ranging from soybean to sisal.

However, despite its worldwide importance there is much to learn about the genus Phytophthora. For example, species identification remains a major difficulty for pathologists, agronomists and plant health regulators. With a shortage of distinct and stable species-specific morphological characters, even specialists can have difficulty in identification beyond the genus level. Many isolates are therefore misidentified or remain as 'unknown Phytophthora sp.'. Such inadequacy may result in a delay in identification of new threats and a failure to rapidly evaluate current problems. Accurate identification is also crucial to plant health legislation and plant quarantine issues.

Appropriate DNA-based molecular methods now offer an objective tool to assist in identification. Work at SCRI has focused on a 900 base pair fragment of rDNA, termed the internal transcribed spacer (ITS) region which, after digestion with a range of restriction enzymes, gives rise to a restriction profile, or genetic 'fingerprint', that can be visualised on agarose gels (see figure). Sophisticated band matching software allows alignment and comparison of digestion profiles of each Phytophthora isolate. Such software is not available in all laboratories so a database comprising species-specific data sets is available through the website. The current database, upon which the new identification tool operates, includes some 450 isolates and represents almost all known taxa. Additional sources of complimentary, electronic information for those attempting to identify Phytopthora spp. include CABI's Crop Protection Compendium and IMI Description Sheets of Fungi and Bacteria.

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