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Caractérisation des agents phytopathogènes responsables des pertes de la filière ail : mise au point d'une méthode de détection

Abstract : Since the early 2000s and despite a high level of sanitary requirements, the French garlic sector has suffered increasingly significant losses linked to the emergence of a fungal disease causing rotting of the bulbs during storage. The losses endured by some producers can reach 90%. In 2016, a collaboration was established between INRAE and the French garlic industry in order to clarify the etiology of this disease and to develop diagnostic methods in view of the long terms goal of developing effective and sustainable methods of control. The specific objectives of this collaboration were to 1) establish the causes of the disease, 2) characterize the causative agents, 3) elucidate the process of clove penetration and 4) develop a method for detecting the pathogen(s) involved.The first step was to build a collection of strains from a sample of 5,493 cloves from 354 heads collected over 3 seasons, in the two main production basins and on as many varieties of garlic as possible leading to a collection of> 1000 fungal strains. Through molecular identification, two fungal species associated with symptoms were identified: F. proliferatum, the dominant pathogen, and F. oxysporum. Based on the DNA sequences of the so-called housekeeping gene (translation elongation factor 1 alpha) a predominant haplotype within the strains of F. proliferatum was described in addition to twenty other minor haplotypes among the two identified species.A test of aggressiveness on garlic was developed to validate Koch's postulates and to characterize the pathogenicity of strains of F. proliferatum and F. oxysporum. A representative panel of strains was chosen. All of the selected strains recreated garlic symptoms with varying levels of disease intensity. The variability of the aggressiveness of the strains was compared with the genetic diversity observed previously: some haplotypes showed statistically superior aggressiveness than others.In order to understand when and how F. proliferatum penetrates into cloves, histological observations of the root plateau (root growth zone) were carried out in partnership with Avignon University and the 3A microscopy platform. The results showed that, when the fungus is inoculated at the base of the clove, it can penetrate at the level of natural wounds (at the exit point of roots, for example). The root plate can constitute an environment favorable to fungal development and degradation of the tissue by the mycelium happens at a distance from the mycelial front and in all directions.Finally, based on DNA sequences obtained during molecular identification, LAMP primers were designed and tested in vitro as the first step in the method for detecting F. proliferatum. These primers showed specificity to F. proliferatum. The in vivo tests in progress will delimit the final form of the detection method. This method will be passed on to stakeholders in the French garlic sector and will make it possible to elucidate the biological cycle of F. proliferatum on garlic and, in the future, to limit the occurrence of this disease.
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https://tel.archives-ouvertes.fr/tel-03211009
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Submitted on : Wednesday, April 28, 2021 - 12:55:08 PM
Last modification on : Thursday, July 8, 2021 - 9:06:55 AM
Long-term archiving on: : Thursday, July 29, 2021 - 6:40:05 PM

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  • HAL Id : tel-03211009, version 1

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Paul L. Chretien. Caractérisation des agents phytopathogènes responsables des pertes de la filière ail : mise au point d'une méthode de détection. Sciences agricoles. Université d'Avignon, 2021. Français. ⟨NNT : 2021AVIG0363⟩. ⟨tel-03211009⟩

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