Diagnosis and Detection of Seed-Borne Fungal Phytopathogens

Food losses due to crop infections caused by different pathogens such as bacteria, viruses and fungi are persistent issues in agriculture for centuries across the globe. The timely detection and appropriate identification of casual agents associated with diseases of crop plants or seeds are considered to be the most important issue in formulating the management strategies. Seed health testing to detect seed-borne pathogens is an important step in the management of crop diseases. Specificity, sensitivity, speed, simplicity, cost-effectiveness and reliability are the main requirements for the selection of seed health test methods. Examples of frequently used seed assays include visual examination, selective media, seedling grow-out and serological assays which, while appropriate for some pathogens, often display inadequate levels of sensitivity, specificity and accuracy. Polymerase chain reaction (PCR) has emerged as a tool for the detection of microorganisms from diverse environments. Thus far, it is clear that nucleic acid-based detection protocols exhibit higher level of sensitivity than conventional methods. Unfortunately, PCR-based seed tests require the extraction of PCR-quality DNA from target pathogens in backgrounds of saprophytic organisms and inhibitory seed-derived compounds. The inability to efficiently extract PCR-quality DNA from seeds has restricted the acceptance and application of PCR for the detection of seed-borne pathogens. To overcome these limitations, several modified PCR protocols have been developed including selective target colony enrichment followed by PCR (Bio-PCR). These techniques seek to selectively concentrate or increase target organism populations to enhance detection and have been successfully applied for detecting fungi in seed. Ultimately, improved protocols based upon PCR, ELISA, etc. will be available for the detection of all seed-borne pathogens and may supersede conventional detection methods. This chapter provides a comprehensive overview of conventional and modern tools used for the early detection and identification of seed-borne fungal pathogens.