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Plant pathogens present a serious threat to seedling establishment and the potential for plant disease epidemics under greenhouse conditions is great. Hence, pathogen exclusion by detection and elimination of infested seedlots remains a requisite tactic for seedling production and disease management. Unfortunately, the numbers of contaminated seed within a lot may be low and infested seed may be asymptomatic making their detection difficult. To address these issues seed detection assays have been developed, but many of them have shortcomings that reduce their effectiveness. 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 and specificity. Recently, the polymerase chain reaction (PCR) has emerged as a tool for detecting microorganisms in many diverse environments. Thus far, it is clear that DNA-based detection systems exhibit higher levels sensitivity than conventional techniques. Unfortunately, PCR-based seed tests require the extraction of PCR-quality DNA from target organisms 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 seed detection. To overcome these limitations several modified PCR protocols have been developed including selective target colony enrichment followed by PCR (BIO-PCR) and immunomagnetic separation and PCR. These techniques seek to selectively concentrate or increase target organism populations to enhance detection and have been successfully applied for detecting bacteria in seed. Other techniques with great potential for rapid detection of seedborne pathogens include magnetic capture hybridization and PCR, and DNA-chip technology. Ultimately, PCR will be available for the detection of all seedborne pathogens and may supersede conventional detection methods.

Mulch (black plastic, wheat straw, or bare ground) and irrigation (drip or overhead sprinkler) treatments were evaluated for their effect on center rot of onion (Allium cepa L.), caused by the bacterium Pantoea ananatis, over the course of two seasons. Irrigation type had no effect on center rot incidence or severity in either year. In contrast, center rot development was delayed by 7 to 14 days on onions grown in straw mulch or bare ground compared to those in black plastic. Straw mulch resulted in later harvest dates and was associated with reduced levels of center rot. In contrast, black plastic increased disease incidence and hastened the onset of the epidemic. The spatial distribution of disease incidence in both years indicated the presence of a primary disease gradient. At harvest, infected plants were segregated by treatment and by duration of infection [based on disease ratings taken from the time of first symptom expression (beginning at 110 to 120 days after transplanting and then every 5 to 10 days until harvest)]. Early-vs. late-infected plants had no significant effect on yield (bulb weight). However, symptom expression in terms of the number of days after planting was significantly correlated with a disease severity index. Amount of rot in bulbs from plants displaying their first symptoms only 1 to 2 days before harvest (late-season infection) was not significant from rot levels in control bulbs at harvest. However, at 4 weeks after harvest, onions from plants with late-season infections exhibited significantly more rot in storage compared to the control.

A real-time polymerase chain reaction (PCR) assay has been developed for the detection and quantification of Botrytis aclada (Fresenius), a causal agent of neck rot in onion (Allium cepa L.) bulbs. The assay uses TaqMan probe-based chemistry to detect an amplicon from the L45-550 region of B. aclada while using a DNA sequence from the onion serine acetyl transferase gene (SAT1) as a control. The assay detection limits for B. aclada and onion were 10 pg·μL⁻¹ of genomic DNA. The detection limit for lyophilized B. aclada mycelium was 1 μg. The presence of onion tissue in the samples did not affect the performance of the real-time PCR assay. The assay distinguished among different amounts of B. aclada mycelium growing on onion disks that were inoculated with 0, 10², or 10⁴ B. aclada conidia. Visual observations during the incubation period corresponded with changes in real-time PCR results. This assay could be used to determine the amount of B. aclada mycelium in bulbs during growth, harvest, and storage, thus giving researchers an objective and efficient tool by which to quantify the growth rate and virulence of B. aclada strains in vivo.