Onion (Allium cepa L.) is an economically important vegetable in the United States. Though considered a minor crop in terms of total acreage, onions have high value when compared to other crops and, nationally, their value approaches $800 million. Because harvested onions are routinely stored for long periods, disease can be a major obstacle to the industry. The primary disease reported in stored onions is botrytis neck rot caused by the fungus Botrytis allii (syn. B. aclada). Losses from neck rot can approach 35% of the stored crop. In order to accurately quantify the level of B. allii inoculum in bulbs at harvest to be able to predict potential botrytis neck rot in storage, a quantitative real-time PCR test to quantify levels of B. allii DNA present in onion bulb tissue has been developed. We have employed the TaqMan real time PCR assay and report log-linear (R2= 0.9915) relationship between B. allii DNA concentration and cycle threshold (Ct) value with a detection limit of 5 pico gram/microliter DNA. In addition, a log-linear standard curve plotting mycelial dry weight against Ct value has been developed to allow prediction of mycelial weight in onion tissue at harvest. Currently, the ability of this test to predict botrytis neck rot during storage is being tested.
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