Soutenance de thèse - Rahim HASSANALY GOULAMHOUSSEN

devant le jury composé de :

Président/te du jury :

• Cécile SABOURAULT, Professeure, ECOSEAS, Université Côte d'Azur, France

Rapporteurs/trices :

• Nadia PONTS, Chargée de Recherche, MycSA, INRAE Bordeaux, France
• Marc-Henri LEBRUN, Directeur de Recherche, INRAE Grignon, France

Examinateurs/trices :

• Rita REBOLLO, Chargée de Recherche, INSA Lyon, France
• Eric GRENIER, Chargé de Recherche, IGEPP Le Rheu, France
• Eric ROTTINGER, Directeur de Recherche, IRCAN, Université Côte d'Azur, France

Directeur/trice de Thèse :

• Laetitia ZURLETTO, Maîtresse de Conférences Universitaire, ISA , Université Côte d'Azur, France
• Pierre ABAD, Directeur de Recherche, ISA, Université Côte d'Azur, France

Abstract :

Plant parasitic nematodes of the genus Meloidogyne are crop pests of global importance. As such, M. incognita is the emblematic species as it is present all over the world with a wide spectrum of host plants. Currently, the use of resistant plants is the most effective way to control this nematode. However, the emergence of virulent lines able to bypass the plant resistance requires a better understanding of the biology of this species. M. incognita reproduces asexually by obligate mitotic parthenogenesis. Asexual reproduction is often considered as an evolutionary dead end because in this case, individuals adapt poorly to changing environments, due to the absence of meiosis. Despite this apparent lack of genetic plasticity, this species shows an amazing ability to adapt to adverse environments. An example of this is the bypassing of resistance in response to selection pressure exerted by the tomato Mi-1 resistance gene, with the appearance of virulent phenotypic variants in the progeny. The characteristics of the transmission of this trait over generations suggest a non-Mendelian heritability, thus involving an epigenetic component.

In this thesis, the impact of histone post-translational modifications (HPTMs) in the biology of M. incognita was studied. First, the method of chromatin immunoprecipitation in fixed condition was developed and optimized for M. incognita. This optimization, performed for the first time in a parasitic nematode, allowed to show the involvement of five HPTMs in the regulation of genome expression. The conservation of the function of H3K9me3, through its association with transposable elements and low-expressed genes, and of H3K4me3 enriched at the promoter level of highly expressed genes, leads to the hypothesis of the existence of a "histone code" in this species.

The dynamics of the chromatin landscape was studied during the development of this nematode, through the analysis of the regulation of the five HPTMs. These dynamics are marked by the expression of specific genes in association with the activating HPTM H3K4me3, during the transition from the egg stage to the L2 juvenile larval stage. At the egg stage, the predicted functions of the genes regulated by this mark concern cell cycle regulation and embryo development, while at the L2 juvenile larval stage, mainly genes involved in stimulus response were identified.

The importance of HPTMs in the acquisition of virulence of this nematode was also initiated. The identification of differential enrichment profiles between avirulent and virulent lines of M. incognita showed a virulence polymorphism related to the regulation by HPTMs. At the origin of this polymorphism are a class of genes coding for SKP1 proteins, involved in protein degradation pathways. These candidate genes show overexpression in association with H3K4me3 in avirulent lines and decreased expression associated with loss of this HPTM in virulent lines. The precise role of SKP1 proteins in the acquisition of virulence in M. incognita remains to be determined.

All these works contribute to evaluate the importance of epigenetic mechanisms in the adaptation of parthenogenetic organisms to changing environments and to define new control methods against crop pests.

Keywords :

epigenetics, HPTM, root-knot nematode, Meloidogyne incognita, development, virulence