New insights into the fungal diversity of cranberry fruit rot in Québec farms through a large-scale molecular analysis.

Cranberry fruit rot (CFR) pathogens are widely reported in the literature but performing large-scale analysis of their presence inside fruit has always been challenging. In this study, a new molecular diagnostic tool, capable of identifying simultaneously 12 potential fungal species causing CFR, was exploited to better define the impact of CFR across cranberry fields in Quebec. For this purpose, 126 fields and 7,825 fruit were sampled in three cranberry farms distributed throughout the province and subjected to comparative analyses of fungal presence and abundance according to cultural practices, sampling times and cranberry cultivars. All 12 pathogens were detected throughout the study but, as a first major finding, the analyses revealed that four species, Godronia cassandrae, Colletotrichum fructivorum, Allantophomopsis cytisporea, and Coleophoma empetri were consistently predominant regardless of the parameters studied. Conventional productions versus organic ones showed a significant reduction in fungal richness and relative abundance. Interestingly, Monilinia oxycocci was found almost exclusively in organic productions indicating that fungicides had a strong and persistent effect on its population. Surprisingly, there were no significant differences in fungal relative abundance or species richness between fruit sampled at harvest or in storage, suggesting that there may not exist a clear distinction between field and storage rot, as it was previously thought. Comparative analysis of fungal species found on eight different cranberry cultivars indicated that they were all infected by the same fungi, but could not rule out differences in genetic resistance. This large-scale analysis allows us to draw an exhaustive picture of CFR in Quebec and provides new information with respect to its management.