SPPADBASE: the first on-line searchable database of PCR primers for phytopathogenic fungi

The fast and unambiguous identification of microbial pathogens affecting plants or plant products is
an essential prerequisite for obtaining high-quality and safe production. Ecologically friendly practice
of the modern agriculture requires the adoption of diagnostic techniques able to detect minimum
inoculum levels of pathogens in soil, seeds, transplants or crops, to limit the raise of epidemics and
to address the adoption of rational and efficient control means. Moreover, there is an increasing
public and official awareness of the potential threat of bio-terrorism directed against food and
agriculture (Monke, 2004). Rapid detection techniques for bioweapon agents are a critical need for
the first-responder community.
Among the nucleic acid-based diagnostic techniques, those involving the Polymerase Chain
Reaction (PCR; Mullis and Faloona, 1987) are the most suited for early detection of phytopathogenic
agents, due to their high sensitivity and the potential for automation. Many sequence source types
could be selected and used as target for specific primer design. These may include, for instance,
Random Amplified Polymorphic DNAs (Williams et al., 1990; Welsh and McClelland, 1990), internal
transcribed spacer (ITS) regions of the ribosomal RNA genes (White et al., 1990) or other specific
gene sequences. Primer sets can be designed to target specificity at the genus, species, or physiological
race level, to distinguish a particular pathogen from closely related organisms.
A common and tedious task for researchers and technicians is to search for and retrieve
bibliographic references of published and validated specific primer sets for a given pathogen querying
the Internet, abstract collections and monthly journals’ tables of contents. Very few examples of
specific primer set collections for phytopathogenic agents have been released: a summary of primers for the diagnostic characterization of phytopathogenic bacteria seems to be the only one printed so far (Louws et al., 1999). Moreover, among 719 molecular biology databases publicly available
recorded by Galperin (2006) or among the 2470 BMC biomedical databases catalog available at
http://databases.biomedcentral.com/, no online repository of primer sets of this kind is accessible. To
overcome this lack of information, we released the first online searchable database of primer sets
useful for the detection and identification of plant pathogenic fungi.