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New PCR primers applied to characterize distribution of Botrytis cinerea populations in French vineyards

Abstract : The phytopathogenic fungus Botrytis cinerea is a complex of two main genetic groups, Group-I and Group-II, the latter including different TE types distinguished by the presence or absence of two transposable elements (TE), Boty and Flipper. In populations from Bordeaux vineyards (n = 470), the frequency distribution into these genetic subdivisions showed that Group-I isolates were rare (2.3%) whereas, within Group-II, four TE types were identified by dot blot in very different proportions: II-transposa (59.8%), II-boty (21.3 %), II-vacuma (15.5%) and II-flipper (1.1%). To distinguish the TE types by PCR, a first primer pair was designed within the Flipper sequence which yielded a not-expected 2287 bp fragment. The 5' extremity of this fragment was sequenced revealing a potential genomic insertion site of the Flipper element allowing the design of a new overlapping PCR primer. Detection of the Flipper element by two newly developed PCR tests and a published one (F300-F1550) was consistent with dot blot results in Group-I and II-transposa (concordance rates from 94.6% to 100%). However, discrepancies between PCR and dot blot were noticeable especially in II-boty, but also in II-vacuma (concordance rates from 33.3% to 38.0% and from 62% to 81.2%, respectively). On the basis of TE-type identification strengthened by combining different PCR and dot blot results, the spatiotemporal distribution of the Group-II isolates was assessed according to the developmental stage and the host organ of grapevine. In Bordeaux as in Loire valley vineyards, similar distribution patterns were described showing significant differences between the most sampled TE types. The II-transposa isolates predominated on grape berries at the end of the season, whereas the II-vacuma ones were detected mostly at flowering. Lastly, the II-boty isolates were more often detected on grapevine leaves than on flowers or berries.
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https://hal.inrae.fr/hal-02666271
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Submitted on : Sunday, May 31, 2020 - 8:24:24 AM
Last modification on : Tuesday, June 15, 2021 - 2:56:08 PM

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Fabián Martínez, Marie-France Corio-Costet, Caroline Levis, Morvan Coarer, Marc Fermaud. New PCR primers applied to characterize distribution of Botrytis cinerea populations in French vineyards. Vitis, 2008, 47 (4), pp.217-226. ⟨hal-02666271⟩

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