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Development of a Multiplex-PCR diagnostic tool for the main pathogenic fungi causing cranberry fruit rot

Matteo Conti: Université Laval, département de phytologie

<div><em>Vaccinium macrocarpon</em>, the most cultivated species of cranberry, is known to host a large spectrum of pathogenic fungi, responsible for 25-33% of production losses through fruit rot. Currently, the diagnosis of fungal pathogens is carried out with standard plating and microscopic techniques, requiring both time and excellent mycological knowledge. Therefore, the aim of this study was to develop a Multiplex-PCR diagnostic tool able to analyse and detect rapidly and precisely the most important fungal pathogens of cranberry fruit. For this purpose, the most common barcode DNA regions were screened to identify potentially discriminant specific markers. In order to confirm the interspecific polymorphism, the selected markers were sequenced for all targeted pathogen species and compared with sequences of related species available on usual nucleotide databases. It was possible to design specific primers able to amplify DNA fragments of different length for each pathogen. For practical purposes, the twelve primer pairs were split up in three groups of four primers per PCR-reaction. This allowed a simpler visualisation on the electrophoresis gel. Having established the optimum PCR conditions, the multiplex test was validated with pure fungal specimens of the pathogens and with infected fruits. This diagnostic tool will assist cranberry growers in defining with precision 1) the major fungal pathogens present in their field and 2) the control methods to implement based on this diagnosis.</div>