Publications HAL du labo/EPI 37751;1002097 de la collection INRAE

2023

Theses

titre
Pathogen evolution on partially resistant pepper : impact on their in planta multiplication, their virulence and on host tolerance
auteur
Thibaud Jayet
article
Sciences agricoles. Université d'Avignon, 2023. Français. ⟨NNT : 2023AVIG0613⟩
resume
Breeding resistant cultivars is an efficient way of preventing the development of plant pathogens and of avoiding the use of pesticides. Partial resistance with polygenic determinism imposes a lower selection pressure on pathogen populations than total resistance with monogenic determinism, and is thus considered to have a higher durability potential. Moreover, host tolerance, which reduces the damages due to pathogen infection, is also considered as an efficient and potentially durable way to reduce economic losses. The main objective of this PhD thesis is to highlight factors influencing the pathogen adaptation to plant resistance. First, an analytical review of the literature showed that the statistical interaction between the resistance type (total vs. partial) and the pathogen group is a key factor determining the durability of plant resistance. Secondly, an experimental evolution protocol was carried out to assess the evolutionary potential of Potato virus Y (PVY) and the oomycete Phytophthora capsici on several pepper lines contrasted for alleles at quantitative trait loci (QTLs) controlling the host resistance. Depending on the pepper line, experimentally-evolved PVY populations showed a higher or lower within-plant accumulation and a higher or lower virulence (i.e. intensity of damages induced to their host) compared to the initial strains. Lower host tolerance was associated with all PVY populations that evolved towards a higher virulence. In contrast, a lower host tolerance was associated with a single PVY populations showing significant increase of within-plant accumulation. Increases in viral accumulation within the host were observed specifically on the most resistant pepper line, which also imposed a lower level of genetic drift at the inoculation step on the PVY populations. Mutations which occurred during the experimental evolutions were associated with changes in virulence and viral accumulation, and their role will be further assessed by reverse genetics using a PVY infectious clone. Considering P. capsici, more virulent populations were selected on the pepper line carrying exclusively minor-effect QTLs, while the pepper line carrying a major-effect resistance QTL selected populations with a lower level of adaptation. Point mutations and larger mutational events associated to these changes will also be assessed. Hence, this PhD showed that pathogen adaptation to host resistance is influenced by (i) the statistical interaction between the resistance type and the pathogen group, (ii) the combination of resistance alleles at QTLs carried by the host, and (iii) the level of genetic drift imposed by the host on the pathogen. Experimental evolution is therefore recommended to identify new genetic determinants increasing host durability and to deploy cultivars with the most durable resistance, in order to improve current strategies for deployment of resistant and tolerant cultivars.
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https://theses.hal.science/tel-04265283/file/These_TJayet.pdf BibTex
titre
Adaptation of Aphis gossypii, the melon aphid, to both non-host resistance and resistance conferred by the Vat gene
auteur
Pierre Sadon
article
Sciences agricoles. Université d'Avignon, 2023. Français. ⟨NNT : 2023AVIG0611⟩
resume
Although a relatively small group among insects, aphids are a serious problem in agriculture and plant resistance to these pests remains understudied. In general, aphids must manipulate the plant's defenses to establish a compatible relationship with the vascular system of their host, the phloem, and thus feed sustainably. This strategy of aphids corresponds to the paradigm of plant-pathogen interactions. This paradigm is based on the recognition, by plant receptors encoded by NLR (Nucleotide-binding domain Leucine-rich Repeat containing) type genes, of molecules produced by pathogenic agents (effectors). Aphis gossypii is an extremely polyphagous aphid species with populations structured into host races specialized in different crops, including one specialized in cucurbits. In melon, the NLR Vat gene is unique since it confers both resistance to A. gossypii and to the viruses it transmits. Surprisingly, the study of the diversity of Vat/A. gossypii showed that, in general, the adaptation of aphids to an NLR-type resistance was not explained by a polymorphism in a salivary effector. This point raises the question of a potential diversity of adaptation pathways of A. gossypii to the resistance NLR Vat. In an original way, A. gossypii could exploit the unique architecture of the melon vascular system, partitioned into two phloems with divergent properties to circumvent Vat resistance. First, we sought to determine whether the clones of A. gossypii adapted on cucurbits and those adapted to Vat use the particular phloem of cucurbits as an alternate food source when faced with susceptible or resistant melons. We have shown, through an approach based on the detection of metabolites representative of each of the two phloems of cucurbits, that clones of A. gossypii belonging to the host race specialized in cucurbits exploit the classic phloem when they feed on non-Vat melon and that the circumvention of Vat resistance by certain clones did not imply the use of the particular phloem of cucurbits. Secondly, we tried to identify, in the frame of reference of plant-pathogen interactions, the salivary effector of A. gossypii which interacts directly or indirectly with the melon VAT protein. For this, we performed comparative analyzes of expression data of clones triggering or not triggering Vat resistance in order to identify candidates for the role of effector triggering this resistance. Notably, one candidate stands out but its validation in planta remains to be done. This research work deals with an adaptation pathway not considered in the reference paradigm for plant-pathogen interactions and in particular offers the possibility of studying the Vat phenotype as a key to reading the mechanisms of heritable resistance.
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https://hal.inrae.fr/tel-04066792/file/These_Pierre_SADON.pdf BibTex

2022

Theses

titre
Molecular determinants of resistance to green aphid (Myzus persicae) in peach (Prunus persica) : multi-omic study of responses to infestation
auteur
Pauline Le Boulch
article
Sciences agricoles. Université d'Avignon, 2022. Français. ⟨NNT : 2022AVIG0371⟩
resume
Of the many pests that plants face, aphids are certainly the most damaging to crops due to their rapid multiplication, the direct damage they cause and the plant pathogenic viruses they transmit. The green peach aphid (Myzus persicae, Sulzer) is a generalist pest that attacks a wide range of plants including peach, its primary host, but also numerous secondary hosts from various botanical families including different cultivated species. Previous work has highlighted peach accessions with resistance to M. persicae conferred by the Rm locus that was characterised by an antixenosis phenomenon that rapidly causing the aphids to leave. The objective of our study was to identify, using an integrated transcriptomics and metabolomics approach, the factors involved in the expression of resistance to M. persicae in peach trees in order to obtain a quasi-exhaustive description of the biological functions activated or repressed by the infestation. We compared the responses to infestation of two peach genotypes, GF305 susceptible to M. persicae and Rubira carrying the Rm2 resistance gene, 48 h post-infestation, a period corresponding to the effective establishment of Rm2-induced resistance.Comparative transcriptomic and metabolomic analysis of the two peach varieties revealed a very limited response of GF305 to infestation while profound reconfigurations in Rubira were observed. The transcriptional reconfiguration resulted in a repression of genes involved in growth and development functions and an overexpression of defence genes, indicating a reorientation of cell function towards defence. This observation was confirmed by the significant reduction in metabolic pools of carbon, nitrogen and sulphur and by the accumulation of caffeic acid conjugates with anti-appetent or toxic properties towards aphids. Among the defence genes, the overexpression of PRR and NLR receptors suggested a joint activation of both branches of the plant immune system, PTI and ETI. Furthermore, the enrichment of oxidative stress-related genes, coupled with the activation of H2O2-generating metabolic pathways such as photorespiratory glyoxylate synthesis and P5C/proline futile cycle activation, underlineed the probable involvement of ROS synthesis in Rubira resistance to M. persicae. The appearance of necrotic lesions indicative of a hypersensitive reaction could also be attributed to an oxidative burst in response to infestation. The triggering of an acquired systemic response was also suggested by the activation of salicylic and pipecolic acid metabolism. Finally, as the involvement of pipecolic acid in plant resistance to aphids is poorly documented and in order to determine the role of this compound in peach resistance, the effect of an exogenous supply of pipecolic acid on the escape behaviour of M. persicae and on the development of aphid colonies, as well as on the metabolic profile of the apices was investigated. Although this experiment did not show the capacity of pipecolic acid to induce resistance, it provided new informations concerning the metabolic markers inducible by this molecule. To conclude, this work illustrates the extent and complexity of the expression of resistance to M. persicae conferred by Rm2 and underlines the interest of integrating transcriptomic and metabolomic data for the analysis of the plant/aphid interaction. This functional knowledge will be crucial in order to exploit natural sources of resistance and sustainably control aphid populations.
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https://theses.hal.science/tel-04055663/file/These_PLeBoulch.pdf BibTex

2021

Theses

titre
Contribution of genomic and phenomic selection to genetic improvement programmes for several traits of interest in Apricot (Prunus armeniaca L.)
auteur
Mariem Nsibi
article
Amélioration des plantes. Montpellier SupAgro, 2021. Français. ⟨NNT : 2021NSAM0021⟩
resume
Harnessing technological breakthroughs in data acquisition to genetic improvement of animal and crop species has allowed the advent of novel selection strategies grounded on high-throughput data. The genetic progress issued from unravelling the genetic architecture of agronomically relevant traits resulted in a paradigm shift from extensive characterization of selection candidates to a prediction strategy of their response to environmental variation.Thus, genomic selection (GS) based on the contribution of several tens of thousands of markers covering the entire genome has revolutionized breeding programs. It has overcome the problem of missing heritability encountered in marker-assisted selection (MAS), which relies on minimal fractions of genetic variance accounted for by a few quantitative trait loci (QTL), identified by linkage analysis or genome-wide association studies (GWAS). The constraints of GS, notably linked to the missing heritability unaccounted for by MAS, have recently paved the way for a novel selection strategy denoted as phenomic selection (PS), which is based on infrared spectroscopy and seems to offer a potentially valuable alternative to SG.In this perspective, this PhD project aims at evaluating the potential of the recourse to high throughput data in favor of the genetic improvement of apricot tree, Prunus armeniaca, for which conventional breeding is hindered by various biological limitations and long selection cycles and thus tends to impede the genetic progress. Therefore, the drive behind the use of large-scale data is to hasten the genetic gain per unit time and create genetically superior varieties with improved genetic constitution in order to meet the expectations and needs of apricot sector stakeholders.Within this context, we evaluated the performance of GS and PS models in terms of prediction accuracy for different agronomic traits within a biparental pseudo-testcross population (Goldrich × Moniqui) and a collection of genetic resources encompassing a wide range of diversity.To this end, a cross-validation strategy was performed to predict a panel of traits of agronomic interest such as fruit quality, phenology (flowering and maturity dates) and disease susceptibility. Our findings highlighted the efficiency of GS and PS approaches for several traits with contrasting quantitative genetic architectures. Furthermore, we proposed scenarios for optimizing the prediction accuracy through weighting GS and PS models using the information brought by genetic architecture of these traits. In addition, we assessed a multivariate modelling approach where the emphasis was placed on proxy traits in order to predict costly and difficult-to-measure target traits such as ethylene production. The potential place of both strategies within apricot breeding programs is discussed and their respective contributions to selection decisions is evaluated.
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https://theses.hal.science/tel-04067940/file/21-0021_Nsibi.pdf BibTex
titre
Model reduction, parameter estimation for a population of genotypes and genetic control analysis : Case of the metabolism of sugars in peachDevelop an approach of ideotype design based on a kinetic model of sugar metabolism in peach fruit
auteur
Hussein Kanso
article
Statistiques [math.ST]. Université d'Avignon, 2021. Français. ⟨NNT : 2021AVIG0727⟩
resume
Genotype-phenotype models are seen as future tools for designing new varieties, as they can help to test the performance of genotypes under different climates and cultural practices. However, progress is still needed to include complex genetic control in process-basedmodels and to achieve the integration of information (metabolism, enzyme control, quantitative genetics) from gene to plant. A kinetic model of sugar metabolism was developed by Desnoues et al. (2018) to simulate the concentrations of different sugars during the development of the peach fruit. The objectives of my thesis work are (a) to estimate the inter-genotype variability of themodel parameter values and (b) to study the architecture of genetic control of genotype-dependent parameters. To achieve these objectives, it is necessary to estimate the values of the influential parameters of the model for all 106 genotypes for which few data are available. The number of parameters and the non-linearity of the modelmake the calibration of the model inaccurate (in particular because of the large number of parameters compared to the number of available data and the correlations between the parameters) and costly in terms of calculation time. Therefore, we have developed a reduction strategy for the initial model to reduce the number of parameters and to simplify the model structure while maintaining the network structure and the identity of the variables to facilitate their biological interpretation. The estimation of the 9 parameters of the reduced model obtained was carried out at population scale using a nonlinear mixedmodel(Baey et al. 2018) approach, which makes it possible to simultaneously estimate the values of the parameters of all genotypes. This strategy was compared to more conventional methods which carry out the estimation of the values of the parameters individually, genotype by genotype. We showed that the reliability of the estimates is greatly improved and those correlations between the estimated parameters are reduced. The last step consisted in estimating the links between the genome markers and the genotype-dependent parameters (QTL analyses). We compared the results of a so-called independent analyse (estimation of parameters then detection of the genomic regions involved) with a joint analysis method (Onogi 2020). This PhD work constitutes a crucial step towards the development of a tool that takes into account a complex genetic control of traits to design ideotypes.
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https://theses.hal.science/tel-03281201/file/manuscritFINAL.pdf BibTex

2020

Theses

titre
Function of the VPS4 protein in susceptibility and resistance to Watermelon mosaic virus (Potyvirus) in melons
auteur
Aimeric Agaoua
article
Sciences agricoles. Université d'Avignon, 2020. Français. ⟨NNT : 2020AVIG0721⟩
resume
Cucurbitaceae are a family of plants represented by a great diversity of species and cultivated crops all around the world. Within this family and in the genus Cucumis, the melon is particularly susceptible to Potyviruses, against which no allele of the translation initiation factor eIF4e gene has been able to induce a resistance. In cucumber, also a Cucurbitaceae in the genus Cucumis, Amano et al. (2013) identified an allele of the gene encoding for the VPS4 protein, which is involved in the resistance to the Potyvirus Zuchini yellow mosaic virus (ZYMV). In the cell, the VPS4 protein belong to the ESCRT complex (Endosomal sorting complexes required for transport) and is involved in the membrane deformation at the endosome level to create multivesicular bodies (MVBs). The ESCRT complex is highly conserved in all eukaryotic organisms and well described in yeasts and mammals. The use of cell membranes by ssRNA(+) viruses through ESCRT and VPS4 has been widely described for viruses infecting animals, including Human Papillomavirus (HPV) and Human Immunodeficiency (HIV) viruses. In recent years, the major role of vesicular transport in viral infection has also been demonstrated in plants. ssRNA(+) viruses form vesicles and quasi-organelles using cell endomembrane, integrating viral replication complexes (VRCs) and all the elements necessary for the replication of viral RNA and for the translation of viral proteins.This thesis focuses on two aspects: (1) the characterization of alleles of the Vps4 gene involved in melon in a recessive resistance to the Potyvirus Watermelon mosic virus (WMV) (2) and the study of the ESCRT involvement in the formation of viral vesicles in Potyvirus.In the first objective, I demonstrated that a point mutation in the gene encoding the VPS4 protein induces resistance to WMV in the melon accession TGR-1551. For this, I used a virus transformed with the wild type allele of Vps4 to infect the TGR-1551 accession. This allowed us to observe the restoration of the susceptibility in the resistant accession. In addition, all accessions from the natural diversity carrying this allele are also resistant to WMV. These results represent the first characterization of the molecular basis of resistance to WMV in melon. Combined with the results of Amano et al. (2013), this work is part of the identification of a gene for resistance to several Potyviruses.In the second objective, I demonstrated the involvement of ESCRT in the replication of Potyviruses. Using a yeast two-hybrid approach adapted to transmembrane proteins, we showed the interaction of the viral protein 6K2 with the CmVPS28, CmVPS2, CmVPS24 and CmVPS4 melon proteins. In addition, we localized the 6K2 / VPS4 interaction at the viral vesicle level in the plant cell. Since ESCRT has been characterized only at the level of MVBs, the presence of VPS4 at the level of viral vesicles, especially at the level of chloroplasts, implies the hijack of the entire ESCRT mechanism by the virus.Taken together, this work provides a better understanding of the viral vesicle formation mechanism during infection of a plant cell by a Potyvirus. It also offers the opportunity to identify new alleles providing resistance to Potyviruses in order to develop new resistant varieties.
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https://theses.hal.science/tel-03217747/file/These_AimericA.pdf BibTex

2019

Theses

titre
Genetic determinants of tomato response to abiotic stresses
auteur
Isidore Diouf
article
Plant breeding. Montpellier SupAgro, 2019. English. ⟨NNT : 2019NSAM0056⟩
resume
Plants can express different phenotypic responses when exposed to different environmental conditions. This ability, commonly described as phenotypic plasticity, has a very important impact on crop productivity and performance. Understanding the molecular basis of phenotypic plasticity is therefore a crucial issue for plant breeding in the coming years, particularly challenged by climate change predictions. The main objective of this thesis was to assess the impact of tomato (Solanum lycopersicum) response to water deficit, high temperature and salinity stresses at the phenotypic level,and to characterize the genetic architecture of phenotypic plasticity.To this end, a multi-parental (MAGIC) population, derived from the cross of eight parental lines wasevaluated in a multi-environment trial (MET) design including optimal culture conditions with adequate water irrigation and water deficit (WD), salinity stress (SS) and high temperature stress (HT) in France,Israel and Morocco. A total of 12 environments were tested, each environment being regarded as acombination of Treatment x Location x Year. Several phenotypic traits were measured in relation toplant vigor, fruit quality, phenology and yield component traits.Phenotypic analyses revealed significant genotype-environment (GxE) interactions for the majority oftraits assessed. These GxE interaction were subsequently decomposed through various parameters ofphenotypic plasticity by estimating the genotypic sensitivities of MAGIC lines to environmental variations. A linkage mapping analysis was performed using regression and mixed linear models,accounting for the haplotype probabilities of the inheritance of parental alleles, to identify the loci(QTL) involved in the variation of mean and phenotypic plasticity phenotypes. The study highlighted acomplex genetic architecture of phenotypic plasticity in tomato, which is predominantly (66% of QTLsof plasticity) controlled by loci different from those affecting the phenotypic means.We proposed several plasticity candidate genes that require further investigation for functionalvalidation and a clear understanding of their mode of action. In the agronomic context, the results presented in this study open interesting perspectives for the development of tomato varieties adaptedto abiotic stresses by presenting on the one hand, interesting genetic markers for marker-assisted orgenomic selection programs and, on the other hand, interesting genotypes to evaluate in future breeding programs.
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https://hal.inrae.fr/tel-02790135/file/19-0056_Diouf.pdf BibTex
titre
Combining Association and Haplotype Studies Towards the Improvement of Fruit Quality in Tomato
auteur
Jiantao Zhao
article
Agricultural sciences. Université d'Avignon, 2019. English. ⟨NNT : 2019AVIG0712⟩
resume
Consumers have been complaining about tomato flavor for decades. Tomato taste is mainly influenced by sugars, acids and a diverse set of volatiles. Improving tomato flavor remains one of the main challenges for improving tomato sensory quality and consumer acceptability in modern tomato breeding. The main purpose of this thesis was to decipher the genetic and evolutionary control of tomato flavor by using high density SNPs and a diverse set of flavor-related metabolites, including sugars, acids, amino acids and volatiles. In the first part, I performed multiple haplotype-based analyses on a tomato core collection. Several approaches were used and compared to identify the genomic regions under selection. Haplotype and SNP-based Bayesian models identified 108 significant associations for 26 traits. Among these associations, some promising candidate genes were identified. I also compared marker local haplotype sharing (mLHS) with LD in determining the candidate regions. In addition, some general benefits of using haplotypes were also provided as general discussions. In the second part, I pioneered in introducing meta-analysis of genome-wide association studies using three tomato association panels. I demonstrated the efficiency of genotype imputation in increasing the genome-wide SNP coverage. Both fixed-effect and random-effect models (for those SNPs with heterogeneity I2 > 25) of meta-analysis were performed in order to control cross-study heterogeneity. A total of 305 significant loci were identified and 211 of which were new. Among them, 24 loci exhibited cis-eQTLs in a previous transcriptome-wide association study in fruit tissue. Enrichment analysis for all associations showed that up to 10 biological processes were significantly enriched and all of which were closely involved in flavor-related metabolites. A list of promising candidate genes was provided, which could be of great interest for functional validation. I also demonstrated the possibility to significantly increase the content of volatiles that positively contribute to consumer preferences while reducing unpleasant volatiles, by selection of the relevant allele combinations. Taken together, this thesis provides a comprehensive knowledge of the genetic control of tomato flavor, which will promote its improvement.
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https://hal.inrae.fr/tel-02790163/file/JiantaoZhaoThesis.pdf BibTex
titre
Finding loss-of-susceptibility resistance genes toward Tospoviruses in Solanaceae
auteur
Zoé Terret
article
Agricultural sciences. Aix Marseille Université, 2019. English. ⟨NNT : ⟩
resume
The Tomato spotted wilt virus (TSWV) is the second most destructive plant virus, particularly in Solanaceae. Because the resistance genes to TSWV available in tomato (Solanum lycopersicum) and pepper (Capsicum annuum) are overcome by resistance breaking isolates, there is an urgent need to develop new durable genetic resistance. Resistance by loss-of-susceptibility is one of the great opportunities to provide such resistances. The aim of this present work is first to characterize a TSWV isolate and then identify tomato host proteins that interact with the viral proteins, aiming at characterizing new resistances. - Firstly, Tomato spotted wilt virus RNA-dependent RNA polymerase adaptive evolution and most constrained domains was analyzed. The TSWV-LYE51 genome was sequenced. We decided to focus on the RNA-dependent RNA polymerase which is the key protein for cycle life by being responsible for both the transcription and replication of the viral genome. A 3D model of this RdRp protein was built by homology modeling and phylogenetic and selection analyses were used to characterize hot-spot of adaptive mutation as well as the most constrained domains. Those results allow to pinpoint RdRP regions of interest toward which efficient resistances can be targeted. - Based on those data, candidates genes implicated in susceptibility to TSWV were sought after. Viruses have to hijack host cellular protein i.e. named susceptibility factors- in order to accomplish their cycle and infect their host. Those factors can be turned into genetic resistance through their absence or modification. To characterize such susceptibility factors in tomato, yeast-two hybrid screenings were carried out using the identified RdRP constrained domain as a bait. We identify several candidates genes currently being validated. This work, by obtaining new information about TSWV infectious mechanism and its adaptation to plan, may bring new perspectives in order to develop loss-of-susceptibility resistances to TSWV in crops by using natural or induced variability.
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titre
Comparative analyses of the molecular footprint of domestication in three Solanaceae species : eggplant, pepper and tomato
auteur
Stéphanie Arnoux
article
Agricultural sciences. Université d'Avignon, 2019. English. ⟨NNT : 2019AVIG0351⟩
resume
Domestication started thousand years ago when human shifted from hunter-gatherer to agrarian societies. They started selecting wild plants for phenotypes related to consumption andyield. This evolutionary process induced changes in the gene pool of domesticated plants. This thesis focuses on genetic footprints induced by domestication within a trio of Solanaceae species: the eggplant (Solanum melongena), the pepper (Capsicum annuum) and the tomato (S. lycopersicum).Crop plants have been selected for thousand years on phenotypic traits, but the molecularconsequences of such selection remain unknown at the genome-wide scale. The study was performed on a RNAseq data set; using comparative methods between crops and their wild relatives,I studied, at the intra-specific scale, the demographic history, and, both the nucleotide diversity and the gene expression changes due to domestication. Comparing these three independent events ofdomestication, is a great opportunity to decipher the interspecific genetic changes, converging for the three species, during the human selection process.The first chapter is a book chapter about population genomics in model species. It details thestate of art of hundred years of research on tomato as model species (S. lycopersicum). Tomato is amodel species in genetics, as well as in population genomics thanks to the important collection of genomic data that have been accumulating over years. Tomato has the strongest economic importance within the trio of studied species. By highlighting the importance of crop wild relative species for adaptability improvement of modern cultivars, this chapter describes the scientific context of this thesis work.The two next chapters are following these researches and show the importance to both conserve and study the crop wild relative species.In the second chapter, I hypothesize that demographic changes within the three species experience a convergence, despite their independent domestication events. The comparative studyof demographic inferences allows the reconstruction of each domesticated species demographichistory. Theses inferences facilitate the parameter estimations such as the migration rate between crop and wild, the bottleneck strength paired with the human selection and the duration of thedomestication events. This chapter reveals a common bottleneck phenomenon as well as migration rate dependent to the allopatric or sympatric state of the crops with their wild relatives. Knowledge concerning the domestication events dating, for each of the three species, remain poorly studied and this thesis work discloses relative domestication time durations.These new insights bring valuable knowledge to the three species and induce a questioning on thedifferent genome parts that are selected and modified through domestication.The third chapter, test the hypothesis of a convergent evolution of molecular changes,especially transcriptional, induced by domestication and modern breeding. The comparative analysis of crop plants and their wild relatives assesses the convergence of regulation and adaptation mechanisms due to domestication. By testing the correlation between the selection footprints on genes and the gene expression changes in crop compared to their wild relative species, the previous hypothesis was confirmed. This analysis implies that domestication modified gene expression in the three species beyond only nucleotide polymorphisms. The ortholog analysis of our species genes, confirmed that domestication facilitated the fruit development and plant growth but relaxed selective pressure on genes of plant defense and environmental stresses tolerance. Demonstrating demographic changes and molecular footprints of domestication, my PhD thesis highlights several proofs of convergence.
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https://theses.hal.science/tel-02185095/file/pdf2star-1563276098-THESE-SArnoux-Finale.pdf BibTex

2018

Theses

titre
Enlargement of ARN viruses resistance spectrum of plants, using the model plant Arabidopsis thaliana
auteur
Anna Bastet
article
Biologie végétale. 2018. Français. ⟨NNT : ⟩
resume
Plants genetic resistances to pathogens is a founding topic in genetics, as well as in crop breeding, in order to limit economical losses caused by diseases. The use of natural resistancesisolated in wild accessions and introgressed into commercial varieties is a common strategy in plant breeding. However, such resistances are not available for all species. The goal of my thesis project was to make up for that lack by identifying and developing new sources of resistance to a major group of plant pathogens, viruses from the Potyvirus family, by two major research axes: - The identification of new plant susceptibility factors to viruses: To realize its viral cycle, viruses hijack several host factors. Those factors can be made into sources of resistance upon being suppressed or modified. I carried out a screening of an Arabidopsis thaliana mutagenized population to search for mutants with decreased viral accumulation, most likely affected in new susceptibility factors. My thesis work allowed to isolate several candidates that remain to be characterized. - New ways of exploiting natural resistances: Point mutations in translation initiation factor eIF4E confer potyvirus resistance in several species, notably in pea. My work aimed at mimicking the genetic variability found in pea to the A.thaliana eIF4E gene to generate resistance. By introducing a synthetic allele carrying the pea resistance mutations into A.thaliana, I made the proof of concept that it was possible to i) transfer resistance to viruses from one species to another, ii) without affecting the eIF4E function in cells, in order to avoid growth or developmental defects and iii) enlarge considerably plant resistance spectrum against viruses. I next showed that this trans-species transfer of resistance signature could be engineered by gene editing technologies paving the way for application to cultivated species.
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titre
Identification and exploitation of Phytophthora capsici effectors to accelerate the development of durable resistance in pepper
auteur
Gaétan Maillot
article
Sciences agricoles. Université d'Avignon, 2018. Français. ⟨NNT : 2018AVIG0350⟩
resume
Plants have developed complex defense mechanisms against pathogens, providing partial to total resistance. Nonetheless, some pathogens effector genes disrupt these mechanisms and help breaking down plant host defenses. Effectors are diverse proteins, with diverse range of evolution constraints. Pathogenomic approaches, such as transcriptomic studies and high-throughput screens of plant resistance factors by effectors, provide information on the effectors molecular functions and their role during the interaction in planta. Quantitative resistances are supposed to be more durable, even though some of them have been overcome by pathogens. This PhD is focused on effectors of Phytophthora capsici deployed during its interaction with pepper (Capsicum annuum) and tomato (Solanum lycopersicum). In Chapter I, I analysed the impact of the plant host genotype on the molecular mechanisms deployed by P. capsici when interacting with pepper, comparing two pathogen’s aggressiveness level and two plant resistance levels. These comparisons revealed differentials expression of genes associated with transport, metabolism and genes encoding pathogenicity effectors. In Chapter II, the avirulence activity of the differentially expressed cytoplasmic effectors was tested. The screening of pepper accessions with in planta transient expression assays revealed a link between expression differences and the ability of the effector to induce the pepper immune responses. Chapter III is focused on analysing effectors polymorphism within 33 isolates P. capsici isolates collected on different hosts and from different geographic regions, using RNA Seq samples at 24 and 72 hours post infection of a susceptible tomato genotype. Effectors showed high levels of diversity, with no correlation between polymorphism and the host on which they were collected. Some expression changes were observed between isolates collected on different hosts or in different geographic regions. Altogether, these results revealed 53 "core" effectors, bringing new insight into P. capsici and pepper/tomato interaction, and providing tools toward durable resistance breeding.
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https://theses.hal.science/tel-02946973/file/these_GaetanMaillot.pdf BibTex

2017

Habilitation à diriger des recherches

titre
Résistance du melon et de la tomate aux hémiptères et aux virus qu’ils transmettent : une analyse du gène au champ
auteur
Nathalie Boissot
article
Zoologie des invertébrés. Université de Montpellier, 2017
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Theses

titre
Adaptation of viral populations to plant resistance and exploitation of plant genetic resources to control this adaptation
auteur
Lucie Tamisier
article
Sciences agricoles. Université d'Avignon, 2017. Français. ⟨NNT : 2017AVIG0696⟩
resume
Plants carrying major resistance genes have been widely used to fight against diseases. However, the pathogensability to overcome the resistance after a few years of usage requires the search for efficient and durable resistances.The objectives of this thesis were (i) to identify plant genomic regions limiting pathogen evolution by inducinggenetic drift effects and (ii) to study the impact of the evolutionary forces imposed by the plant on the pathogenability to adapt to resistance, the goal being to further use these forces to limit pathogen evolution. The pepper(Capsicum annuum) – PVY (Potato virus Y) pathosystem has been mainly used to conduct these researches.Regarding the first objective, quantitative trait loci (QTL) were mapped on a biparental pepper population andthrough genome-wide association on a pepper core-collection. These approaches have allowed the detection ofgenomic regions on chromosomes 6, 7 and 12 controlling viral effective population size during the inoculationstep. Some of these QTLs were common to PVY and CMV (Cucumber mosaic virus) while other were virusspecific.Moreover, the QTL detected on chromosome 6 colocalizes with a previously identified QTL controllingPVY accumulation and interacting with a QTL affecting the breakdown frequency of a major resistance gene.Regarding the second objective, a correlation analysis between the evolutionary forces imposed by the plant andan experimental estimation of the durability of a major resistance gene has been done. Experimental evolution ofPVY populations on plants contrasted for the levels of genetic drift, selection and virus accumulation they imposedhas also been performed. Both studies demonstrated that a plant inducing a strong genetic drift combined to areduction in virus accumulation limits virus evolution and could even lead to the extinction of the virus population.These results open new perspectives to deploy plant genetic factors directly controlling pathogen evolutionarypotential and could help to preserve the durability of major resistance genes.
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https://theses.hal.science/tel-01753184/file/pdf2star-1519813875-Manuscrit-These_Lucie_Tamisier-27-10-2017.pdf BibTex
titre
Genetic and genomic determinants of response to water deficit in tomato (Solanum lycopersicum) and impact on fruit quality
auteur
Elise Albert
article
Agricultural sciences. Université d'Avignon, 2017. English. ⟨NNT : 2017AVIG0688⟩
resume
Water scarcity will constitute a crucial constraint for agricultural productivity in a nearfuture. High throughput approaches in model species have identified hundreds of genespotentially involved in survival under drought conditions, but very few having beneficialeffects on quality and yield in crops plants. Nonetheless, controlled water deficits mayimprove fleshy fruit quality through weaker dilution and/or accumulation of nutritionalcompounds. In this context, the first part of the PhD was aimed at deciphering the geneticdeterminants of the phenotypic response to water deficit in tomato by exploring thegenotype by watering regime (G x W) and QTL by watering regime (QTL x W) interactions intwo populations. The first population consisted in recombinant inbreed lines (RIL) from across between two cultivated accessions and the second was composed of diverse small fruittomato accessions mostly native from South America. Plants were phenotyped for majorplant and fruit quality traits and genotyped for thousands of SNP. Data were analyzed withinthe linkage and association mapping frameworks allowing the identification of QTLs andputative candidate genes for response to water deficit in tomato. The second part of the PhDhad the objective to explore gene regulation in green fruit and leaves of tomato plantsstressed by water deficit. For this purpose, RNA-Seq data were collected on the two parentalgenotypes of the RIL population and their F1 hybrid. Data were analyzed to identifydifferentially expressed genes and allele specific expression (ASE). Then, the expression of200 genes was measured in leaves and fruits of the whole RIL population by high throughputmicrofluidic qPCR. eQTLs and eQTL by watering regime interactions were mapped for thosegenes using linkage mapping. Colocalisations with the phenotypic QTLs were analyzed. Theknowledge produced during this PhD will contribute to a better understanding of the tomatoplant interaction with their environment and provide bases for improvement of fruit qualityunder limited water supply.
Accès au texte intégral et bibtex
https://theses.hal.science/tel-01970364/file/EliseAlbert.pdf BibTex
titre
Genetic and genomic determinants of response to water deficit in tomato (Solanum lycopersicum) and impact on fruit quality
auteur
Elise Albert
article
Biologie végétale. Université d'Avignon et des Pays de Vaucluse, 2017. Français. ⟨NNT : ⟩
resume
Water scarcity will constitute a crucial constraint for agricultural productivity in a near future. High throughput approaches in model species have identified hundreds of genes potentially involved in survival under drought conditions, but very few having beneficial effects on quality and yield in crops plants. Nonetheless, controlled water deficits may improve fleshy fruit quality through weaker dilution and/or accumulation of nutritional compounds. In this context, the first part of the PhD was aimed at deciphering the genetic determinants of the phenotypic response to water deficit in tomato by exploring the genotype by watering regime (G x W) and QTL by watering regime (QTL x W) interactions in two populations. The first population consisted in recombinant inbreed lines (RIL) from a cross between two cultivated accessions and the second was composed of diverse small fruit tomato accessions mostly native from South America. Plants were phenotyped for major plant and fruit quality traits and genotyped for thousands of SNP. Data were analyzed within the linkage and association mapping frameworks allowing the identification of QTLs and putative candidate genes for response to water deficit in tomato. The second part of the PhD had the objective to explore gene regulation in green fruit and leaves of tomato plants stressed by water deficit. For this purpose, RNA-Seq data were collected on the two parental genotypes of the RIL population and their F1 hybrid. Data were analyzed to identify differentially expressed genes and allele specific expression (ASE). Then, the expression of 200 genes was measured in leaves and fruits of the whole RIL population by high throughput microfluidic qPCR. eQTLs and eQTL by watering regime interactions were mapped for those genes using linkage mapping. Colocalisations with the phenotypic QTLs were analyzed. The knowledge produced during this PhD will contribute to a better understanding of the tomato plant interaction with their environment and provide bases for improvement of fruit quality under limited water supply.
Accès au texte intégral et bibtex
https://hal.inrae.fr/tel-02790004/file/EliseAlbert.these_1.pdf BibTex

2016

Theses

titre
Etude de la variabilité génétique de la sensibilité à la pourriture brune au cours du développement du fruit chez la pêche en lien avec l'évolution des caractéristiques biochimiques du fruit
auteur
Leandro de Oliveira-Lino
article
Sciences du Vivant [q-bio]. Université d'Avignon et des Pays de Vaucluse, 2016. Français. ⟨NNT : ⟩
resume
La pourriture brune des fruits (BR), causée par les champignons du genre Monilinia, est une maladie courante qui peut provoquer jusqu’à 30 à 40% de pertes de récolte chez la pêche. Actuellement, toutes les pêches cultivées sont plus ou moins sensibles à la moniliose. Aucune alternative aux traitements chimiques n’est disponible à ce jour, ce qui rend nécessaire les applications de fongicides jusqu'au stade pré-récolte. Ces applications sont préjudiciables pour l'environnement et peuvent laisser des résidus sur les fruits. Nous avons réalisé une revue de la littérature pour compiler les connaissances disponibles sur le couple pêcher-monilioses. Le but de cette étude est d'étudier les facteurs de résistance du fruit à M. laxa à différents stades de croissance des fruits chez la pêche et de déterminer leur contrôle génétique par l'étude de génotypes contrastés et d’une descendance interspécifique. Nous avons tout d’abord focalisé notre étude sur quelques cultivars pour étudier l'évolution de la sensibilité des fruits à M. laxa au cours de leur développement en relation avec les caractéristiques structurales et biochimiques des fruits, par exemple la conductance cuticulaire du fruit, les micro-fissures de l’épiderme et des composés de surface des fruits. Certains composés ont été détectés pour la première fois chez la pêche. Les résultats ont confirmé que lors de la phase I les fruits immatures sont sensibles à la moniliose. La conductance cuticulaire des fruits était élevée probablement parce que la densité de stomates est forte et la cuticule en formation est mince. En revanche, au stade de durcissement du noyau, les fruits étaient résistants. A ce stade la conductance cuticulaire était faible et les niveaux de composés de surface présentaient un pic de teneurs. A l’approche de la maturité, les fruits sont devenus sensibles de nouveau. Avec le développement rapide du fruit au cours de cette étape, les composés de surface ont été dilués et des micro-fissures sont sans doute apparues entrainant une augmentation de la conductance cuticulaire. Au stade I, nous avons exploré les différentes caractéristiques physiques du fruit immature en relation avec la sensibilité à M. laxa. Une centaine de génotypes d'une descendance interspécifique de pêchers appelée BC2 a été caractérisée par une infection au laboratoire, un suivi de pertes transpiratoires des fruits et une estimation de la densité de stomates (uniquement pour les nectarines). Des symptômes inattendus (une ‘tache claire’ qui ne progresse pas) ont été observés. La conductance cuticulaire était significativement liée à la probabilité d'infection, par contre le nombre de stomates n’a montré aucun effet sur la probabilité d'infection. Des QTL contrôlant la résistance des fruits à la moniliose, à la conductance cuticulaire et au nombre de stomates ont été identifiés et des co-localisations observées. A la maturité, nous avons étudié le contrôle génétique de la résistance à la moniliose conjointement avec des composés biochimiques de l'épiderme des fruits. Pendant trois ans, les fruits de la descendance BC2 ont été infectés avec deux modalités d'infection artificielle avec une suspension de spores de champignon: une pulvérisation au verger pour mesurer la probabilité d'infection et un dépôt d’une goutte dans des conditions contrôlées en laboratoire afin d’estimer le délai d’apparition des symptômes, la progression de la lésion et la vitesse de progression de la lésion. La descendance de BC2 a affiché une forte variabilité de résistance à la moniliose. Malgré une faible stabilité entre les années, des génotypes à haut niveau de résistance ont été identifiés. De plus en 2015, nous avons exploré la variation des composés de l'épiderme des fruits au sein de la descendance de BC2. Les composés phénoliques, les terpènes et dérivés ont été quantifiés par HPLC. La relation entre la résistance à la moniliose et la présence et / ou les niveaux de certains composés de l'épiderme et le contrôle génétique de ces composés ont été étudiés. La moniliose des fruits de pêche est un problème complexe qui est encore loin d'être résolu. Des progrès ont été accomplis dans la connaissance des caractéristiques structurales et biochimiques impliquées dans la résistance et des régions du génome qui pourraient conférer une certaine tolérance à la maladie ont été détectées. Des travaux supplémentaires sont nécessaires pour développer des marqueurs moléculaires pour la sélection assistée par marqueurs. Les résultats obtenus suggèrent que des solutions pour l'avenir résident dans l’association de cultivars tolérants _ moins sensibles aux micro-fissures et à haute teneur en composés épidermiques potentiellement inhibiteurs du développement du champignon _ avec des pratiques culturales réduisant les risques de fissuration des fruits et d'apparition de conditions climatiques favorables à la propagation de la moniliose.
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titre
Study of the genetic variability of peach in susceptibility to brown rot during fruit development in relation with changes in physical and biochemical characteristics of the fruit
auteur
Leandro de Oliveira Lino
article
Agricultural sciences. Université d'Avignon, 2016. English. ⟨NNT : 2016AVIG0677⟩
resume
Brown rot (BR) in peach fruit caused by the fungus Monilinia spp. is a common disease that can provoke as much as 30 to 40% losses of crop. Currently, all cultivated peaches are more or less sensitive to BR. No other alternative than chemical treatment is available, hence fungicide applications are required until pre-harvest. Such applications are damaging the environment and may let residues in fruits. A review of literature was accomplished to compile the knowledge scattered in the literature from many years. The aim of this study is to investigate the factors of resistance of the fruit to M. laxa at different stages of fruit growth and their genetic control by studying contrasted genotypes and an interspecific peach progeny. The first focus was made on few cultivars to study the evolution of sensibility of fruits to M. laxa during their development in relation with structural and biochemical characteristics of the fruit, e.g. cuticular conductance, micro-cracks and fruit surface compounds. Some compounds were detected for the first time on peach fruit. The results confirmed that during the stage I immature fruits are susceptible to BR. Fruit cuticular conductance was high probably due to high density of stomata and thin cuticule in formation. In contrary, at pit hardening stage fruits were resistant, cuticular conductance was low and the levels of surface compounds exhibit a peak. When maturity approaches, fruit become susceptible again. With rapid development of the fruit during this stage, the surface compounds were diluted and micro-cracks often appear which resulted in high cuticular conductance. At stage I we explored the different physical characteristics of the immature fruit in relation with susceptibility to M. laxa. A hundred of individuals of an interspecific peach progeny called BC2 were characterized through laboratory infection, monitoring of fruit transpiratory losses and estimating stomata density (only for nectarines). Unexpected symptoms (not progressing ‘clear spot’) were observed. The cuticular conductance was significantly linked to the likelihood of infection, but the stomata number had no effect on the likelihood of infection. QTL controlling fruit resistance to BR, cuticular conductance and stomata number have been identified and some co-locations observed. At maturity stage we investigated the genetic control of BR resistance together with biochemical compounds of fruit epidermis. For three years, mature fruits from the BC2 progeny were infected with two modalities of infection: spray until runoff in the orchard to measure infection probability and drop in the laboratory conditions in order to observe the characters of beginning, progression and speed of infection. The BC2 progeny displayed high variability for BR resistance. Despite low stability between years, genotypes with high level of resistance were identified. In addition in 2015, we explored the variation in epidermis compounds of fruit within the BC2 progeny. Phenolic compounds, terpenoids and derivatives were quantified by HPLC. The relationship between BR resistance and presence and/or levels of certain epidermis compounds and the genetic control of these compounds were investigated. BR of peach fruit is a complex problem which is still far from resolved. Progress has been made in the knowledge of structural and biochemical characteristics involved in BR resistance and regions of the genome that could confer certain disease tolerance have been detected. Further work is needed to develop molecular markers for marker assisted selection. The results obtained suggest that solutions for the future lie in associations of tolerant cultivars _ less susceptible to micro-cracks and with high content of epidermis compounds potential inhibitor of the fungus development _ with cultural practices reducing both risks of fruit cracking and occurrence of micro-climatic conditions favorable to BR spread and sporulation.
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https://theses.hal.science/tel-01635960/file/pdf2star-1487069659-These_finalenvoyerparmail_Leandro_DE_OLIVEIRA_LINO.pdf BibTex
titre
Study of the molecular basis of recognition of the fungal effector AVR-Pia by the rice immune receptor RGA5
auteur
Diana Vallejo Ortiz
article
Life Sciences [q-bio]. SupAgro, 2016. English. ⟨NNT : ⟩
resume
Plant diseases caused by fungi constitute a worldwide threat to food security and disease resistance (R) genes that allow to breed resistant crops are key elements for efficient disease control. The vast majority of R genes code for NLR multi domain proteins characterized by nucleotide-binding and leucine-rich repeat domains and acting as intracellular immune receptors for pathogen-secreted virulence factors termed effectors. Phytopathogenic fungi possess huge effector repertoires that are dominated by hundreds of sequence-unrelated small secreted proteins. The first question I addressed in my PhD thesis is: how is the tremendous diversity of fungal effectors generated? A structural analysis had identified the family of sequence-unrelated but structurally conserved MAX-effectors (Magnaporthe Avrs and ToxB like) that has expanded specifically in Magnaporthe oryzae the causal agent of rice blast disease. By expression analysis, I confirmed that the majority of M. oryzae MAX-effectors are expressed specifically during early infection suggesting important functions during host colonization. MAX effectors are the first structurally defined family of effectors in fungi and this study gives therefore news clues for the identification of candidate effectors in fungi and constitutes a crucial step towards a better understanding of effector evolution. In fact, the scenario observed for MAX-effectors leads to the hypothesis that the enormous number of sequence-unrelated fungal effectors belong in fact to a restricted set of structurally conserved effector families. The second question I investigated in my PhD thesis is: what are the molecular mechanisms of effector recognition by NLR immune receptors? I addressed this question by studying recognition of the M. oryzae effector AVR-Pia by the rice NLR pair RGA4/RGA5. Previous work has shown that RGA5 acts as a receptor that binds directly to AVR-Pia while RGA4 acts as a constitutively active signaling protein that is, in the absence of pathogen, repressed by RGA5. This functional interaction involves formation of an RGA4/RGA5 receptor complex. By protein-protein interaction studies, I showed that complex formation involves interactions between the RA4 and RGA5 NB-ARC and LRR domains, in addition to previously identified interactions between the coiled-coil domains. AVR-Pia recognition seems not to induce dissociation of the RGA4/RGA5 complex but a ternary RGA4/RGA5/AVR-Pia complex could also not be detected consistently. How effector recognition is translated into receptor complex activation remains therefore to be elucidated in more detail in the future. Previous work has shown that a domain of RGA5 normally not present in NLRs and related to the copper chaperone ATX1 (RATX1 domain) interacts physically with AVR-Pia and may be crucial for effector recognition. The RATX1 domain was hypothesized to mimic the true host targets of AVR-Pia leading to the development of the ‘integrated decoy’ model that states that unconventional domains in NLRs act as decoys in the recognition of effector proteins. By detailed structure-informed analysis of AVR-Pia, I could confirm the pivotal role of the AVR-Pia-RATX1 interaction for effector recognition lending important support to the integrated decoy model. In addition, I could precisely characterize the interaction surface with which AVR-Pia binds to the RGA5 RATX1 domain. Finally, I detected interactions of AVR-Pia with other parts of RGA5, in particular the NB-ARC and the LRR domains. Based on these results, I developed a model that explains how such binding to several independent sites in NLRs leads to high overall affinity and robust effector recognition that is resilient to effector mutations. Taken together, this study provides important novel insight into NLR function and effector recognition and contributes by this to a better understanding of plant immunity which is crucial for generating durable disease resistance in crops.
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https://hal.inrae.fr/tel-03906152/file/Thesis%20Study%20of%20the%20molecular%20basis%20of%20recognition%20of%20the%20fungal%20effector%20AVR-Pia%20by%20the%20rice%20immune%20receptor%20RGA5.pdf BibTex
titre
Analyse de la diversité de processus de développement racinaire chez les Prunus. Aptitude au bouturage et réponses à la contrainte hybride
auteur
Nabil El Debbagh
article
Sciences agricoles. 2016. Français. ⟨NNT : ⟩
resume
ln breeding programs of Prunus rootstocks the aim is to use the existing genetic variability within Prunus species in order to create new rootstock genotypes with excellent agronomie traits, and improved resistance to biotic and abiotic stresses. Exploitation of the genetic variability is based on the evaluation of phenotypic variation among individuals within genetic collections for desirable traits. This make possible to select specifie genotypes to improve a given trait. This study consists of two parts; we explored the genetic diversity within the genus Prunus regarding two important characteristics: rooting ability of hardwood cuttings and responses of some rootstocks to water stress. ln the first part, rooting ability of hardwood cuttings was evaluated among 222 genotypes preserved in genetic collection. The results show considerable variability among the sub genus Amygdalus, Prunophora, and also an interspecific variability within each of them. Rooting ability by hardwood cutting was significantly improved in interspecific hybrids if one parent belongs to P cerasifera species. ln the second part of this study we studied the responses of nine genotypes, commonly used rootstocks, to water stress. We applied three treatments: control, water stress and recovering. Soil moisture was maintained at field capacity through ail stages of the experiment for the control plants. On the contrary we stopped watering during 14 days for the stressed plants, and then we rewatered the recovered plants for 10 days. During this experience, we performed morphological and physiological measurements on the above ground parts of plants and we excavated plants at the end of each phase to observe root system modifications. Aboveground parts of plant responded to water stress by a significant decrease in net photosynthesis, total transpiration, stomatal conductance and leaf expansion. Root system responded to water stress by several modifications: Four genotypes (GF305, Montclar, GF677 and Myrobolan) showed a significant increase in root to shoot ratio under drought conditions. We also detected morphological modifications on the different traits of root architecture in response to water stress. The length of the apical unbranched zone LAUZ and the apical diameter were decreased for ail genotypes, consequently, roots became finer and reduced their rate of elongation. Fine roots enhance the surface of contact between roots and soil which in turn improve the acquisition of water under drought condition. The inter-branch distance also responded, and it tended to decrease under the water stress treatment. The decrease in inter-branch distance can be explained by a production of more lateral roots in deep layers, where water was more available, moreover these new laterals roots were also finer. Qualitatively, a common response to water stress was observed on the different traits of the root system architecture, but we showed a genotypic effect determining the level of the response.
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https://hal.inrae.fr/tel-02796600/file/Nabil%20El%20Debbagh%202016%20Th%C3%A8se_1.pdf BibTex

2015

Habilitation à diriger des recherches

titre
Demande pour prétendre au diplôme d'habilitation à diriger des recherches
auteur
Jean-Luc J.-L. Gallois
article
Sciences agricoles. Aix Marseille Université, 2015
Accès au texte intégral et bibtex
https://hal.inrae.fr/tel-02795973/file/Gallois%202015%20R%C3%A9sum%C3%A9%20HDR_1.pdf https://hal.inrae.fr/tel-02795973/file/Gallois%202015%20R%C3%A9sum%C3%A9%20HDR_2.docx BibTex

Theses

titre
Oxidation and degradation of ascorbate in tomato and impact on growth and metabolism
auteur
Vincent Truffault
article
Sciences agricoles. Université d'Avignon et des Pays de Vaucluse, 2015. Français. ⟨NNT : ⟩
resume
Ascorbate metabolism and particularly ascorbate redox status are involved in stress tolerance and growth processes of plant cells. The concentration of ascorbate and its redox status are under control of (i) its biosynthetic pathways, (ii) the ascorbate-glutathione cycle allowing recycling of semi-oxidized and oxidized forms of ascorbate and (iii) its degradation rate. These processes are under environmental control. Transgenic lines modified for the activity of monodehydroascorbate reductase (involved in ascorbate-glutathione cycle) and ascorbate oxidase were generated in cherry and large-fruited genotypes of tomato. Physiological and metabolic modifications related to the modification of these enzyme activities were studied. We observed large phenotypic alterations that affected fruit yield under both stress conditions and normal growth conditions. Links between ascorbate recycling and sugar metabolism, photosynthesis and stomatal conductance were also revealed. An imbalance between the oxidizing and reducing activities of these enzymes is the first step leading to ascorbate degradation. We have shown that the degradation rate was very low under light, whereas under darkness the degradation compounds oxalate, threonate and oxalyl-threonate accumulated in tomato leaves. Also, the degradation rate is correlated with MDHAR activity. These results highlight the crucial role of the redox status of the ascorbate / monodehydroascorbate couple in growth processes and yield stability in tomato, and the impact on ascorbate degradation.
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titre
From gene to phenotype : Genetic control and modeling of sugar metabolism in peach
auteur
Elsa Desnoues
article
Sciences agricoles. Université d'Avignon, 2015. Français. ⟨NNT : 2015AVIG0667⟩
resume
Fruit quality is a multi-criteria character with frequent antagonistic relationships. The perceptionof the fruit quality is highly dependent on the balance between the levels of sugars and acids. Among thethree so-called major sugars in fruit that are sucrose, glucose and fructose, fructose is the sweetest and itsconcentration is the factor that most affects the fruit sweetness. The objective of the present thesis is toanalyze the sugar metabolism in peach fruit from metabolic, enzymatic and genetic aspects and integrateinto a mathematical model all information obtained. This work focuses on the identification of the effect of alow fructose concentration on the whole sugar metabolism and the understanding of the mechanismsresponsible of this phenotype called ‘low-fructose-to-glucose-ratio’. A nearly exhaustive biochemicalcharacterization of sugar metabolism was conducted along peach fruit development. For this, 6 metabolitesand 12 enzyme capacities were assayed in 106 genotypes of a population derived from an interspecific cross.This study revealed a high stability of the enzyme capacities despite large variations of metabolites. Based ondata from 10 genotypes, a kinetic metabolic model that simulates the sugar accumulation in fruit wasdeveloped and validated. This model simulates contrasting phenotypes and helps in understanding theunderlying mechanisms of the ‘low-fructose-to-glucose-ratio’ phenotype. The biochemical characterizationof the population gave the opportunity to perform a QTL research. It highlighted the instability of the effectof certain loci along fruit development and QTL collocations of metabolites, enzyme capacities and candidategenes. It also confirmed the genomic region responsible for the ‘low-fructose-to-glucose-ratio’ phenotypewithin which a functional candidate gene was identified. It is a gene homologous to fructose vacuolartransporter (SWEET17) recently discovered in Arabidopsis. An analysis of this gene was engaged to validateits function and its responsibility in the ‘low-fructose-to-glucose-ratio’ phenotype. In the future, theintegration of the genetic control into the metabolic model will allow simulating virtual genotypes withdifferent combinations of alleles and predict their sugar content. Optimizing allele combinations to increasesugar concentrations in peach fruit will undoubtedly give new breeding opportunities.
Accès au texte intégral et bibtex
https://theses.hal.science/tel-01366023/file/pdf2star-1448626495-THESE-Elsa_Desnoues-def.pdf BibTex
titre
From gene to phenotype : Genetic control and modeling of sugar metabolism in peach
auteur
Elsa Desnoues
article
Sciences agricoles. Université d'Avignon et des Pays de Vaucluse, 2015. Français. ⟨NNT : ⟩
resume
Fruit quality is a multi-criteria character with frequent antagonistic relationships. The perceptionof the fruit quality is highly dependent on the balance between the levels of sugars and acids. Among thethree so-called major sugars in fruit that are sucrose, glucose and fructose, fructose is the sweetest and itsconcentration is the factor that most affects the fruit sweetness. The objective of the present thesis is toanalyze the sugar metabolism in peach fruit from metabolic, enzymatic and genetic aspects and integrateinto a mathematical model all information obtained. This work focuses on the identification of the effect of alow fructose concentration on the whole sugar metabolism and the understanding of the mechanismsresponsible of this phenotype called ‘low-fructose-to-glucose-ratio’. A nearly exhaustive biochemicalcharacterization of sugar metabolism was conducted along peach fruit development. For this, 6 metabolitesand 12 enzyme capacities were assayed in 106 genotypes of a population derived from an interspecific cross.This study revealed a high stability of the enzyme capacities despite large variations of metabolites. Based ondata from 10 genotypes, a kinetic metabolic model that simulates the sugar accumulation in fruit wasdeveloped and validated. This model simulates contrasting phenotypes and helps in understanding theunderlying mechanisms of the ‘low-fructose-to-glucose-ratio’ phenotype. The biochemical characterizationof the population gave the opportunity to perform a QTL research. It highlighted the instability of the effectof certain loci along fruit development and QTL collocations of metabolites, enzyme capacities and candidategenes. It also confirmed the genomic region responsible for the ‘low-fructose-to-glucose-ratio’ phenotypewithin which a functional candidate gene was identified. It is a gene homologous to fructose vacuolartransporter (SWEET17) recently discovered in Arabidopsis. An analysis of this gene was engaged to validateits function and its responsibility in the ‘low-fructose-to-glucose-ratio’ phenotype. In the future, theintegration of the genetic control into the metabolic model will allow simulating virtual genotypes withdifferent combinations of alleles and predict their sugar content. Optimizing allele combinations to increasesugar concentrations in peach fruit will undoubtedly give new breeding opportunities.
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titre
Diversification de cible hôte pour promouvoir la résistance aux Potyvirus et aux Bégomovirus chez la tomate
auteur
Camille Gauffier
article
Sciences agricoles. 2015. Français. ⟨NNT : ⟩
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2014

Theses

titre
Génétique d’association chez la tomate – Une stratégie pour identifier des locus importants pour la qualité du fruit
auteur
Guillaume Bauchet
article
Sciences du Vivant [q-bio]. 2014. Français. ⟨NNT : ⟩
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2013

Habilitation à diriger des recherches

titre
Vers un modèle intégré de conception d’idéotypes de pêchers adaptés à une agriculture durable
auteur
Bénédicte Quilot-Turion
article
Biodiversité et Ecologie. Université d'Avignon et des Pays de Vaucluse, 2013
resume
1. Génétique quantitative de la qualité des fruits et synténie chez les Prunus 1.1 Les bases génétiques des composantes de la qualité dans la population BC2 1.2 Extension au métabolisme secondaire et à d’autres populations de Prunus 1.3 Les déterminants génétiques de la couleur rouge de la chair chez le pêcher 1.4 Analyse basée sur pedigree et génétique d’association 2. Intégration de l’information génétique dans le ‘Fruit Virtuel’ 2.1 Vers une démarche de sélection variétale assistée par des modèles écophysiologiques et génétiques. (Travaux de thèse) 2.2 Adaptation et test du modèle ‘Fruit Virtuel’ intégrant de l’information génétique 3. Contrôle génétique et modélisation de l’accumulation des sucres 3.1 Description du métabolisme des sucres au cours de la croissance des fruits 3.2 Etude du déterminisme du caractère ‘peu de fructose’ 3.3 Etude du déterminisme génétique secondaire du métabolisme des sucres 3.4 Modélisation du métabolisme des sucres 4. Vers la conception d’idéotypes : cas du couple pêcher-monilioses 3.5 Etude expérimentale du couple pêcher-Monilinia 3.6 Modélisation des interactions GxExM pour limiter la contamination en verger 3.7 Ecole-chercheurs ‘Conception d’idéotypes de plantes pour une agriculture durable’
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https://hal.inrae.fr/tel-02810089/file/Quilot%202013%20m%C3%A9moireHDR_1.pdf BibTex

Theses

titre
Analyse fonctionnelle et étude de la régulation de gènes candidats sous-jacents au QTL GpaVspl impliqué dans la résistance au nématode à kyste Globodera pallida chez la pomme de terre
auteur
Patricio Castro Quezada
article
Agricultural sciences. Université d'Avignon et des Pays de Vaucluse; université, 2013. English. ⟨NNT : ⟩
resume
Les nématodes à kystes sont l’un des bioagresseurs causant le plus de dégâts sur les cultures de pommes de terre. La résistance trouvée chez l'accession spl88S.329.18, issue de l'espèce Solanum sparsipilum est caractérisée par un déterminisme oligogénique avec un QTL à effet fort localisé sur le chromosome V (GpaVspl) et un QTL mineur localisé sur le chromosome XI (GpaXIspl). Pour obtenir une résistance de haut niveau, l'effet du QTL GpaVspl, doit être complémenté par celui du QTL à effet faible GpaXIspl. Par génomique comparative, le locus GpaV a été localisé dans un intervalle compris entre 16 et 60 kb sur les génomes de la tomate et des espèces apparentées à la pomme de terre, Solanum demissum et Solanum phureja. Deux gènes ont été annotés dans cet intervalle sur les génomes de la tomate et de S. demissum: le premier appartient à la famille des TIR-NBS-LRR (TNL), famille de gènes de résistance classiques, et le second appartient à la famille des « mitochondrial, transcription termination factor » (mTERF), dont l’implication dans des mécanismes de résistance n’a jamais été démontrée. Les objectifs de ma thèse étaient d'identifier le(s) gène(s) responsable(s) de la résistance à G. pallida, conférée par le locus GpaVspl, et d'étudier sa régulation. Suite à la publication de la séquence du génome de S. phureja, en 2011, nous avons mis en évidence que le locus GpaV était dupliqué chez S. phureja et que cette duplication était également présente chez S. sparsipilum. Les quatre gènes annotés au locus GpaVspl ont été nommés Spl_mTERF18430, Spl_TNL18429, Spl_mTERF18453 et Spl_TNL18428. L'effet des deux gènes Spl_mTERF18430 et Spl_TNL18428 sur la résistance à G. pallida a été analysé via des expériences de transformation génétique suivies par des tests de résistance sur les plantes transformées. Un effet partiel du gène Spl_TNL18428 sur la résistance à G. pallida a été mis en évidence par complémentation de plantes sensibles. Aucun effet significatif n'a été détecté pour le gène Spl_mTERF18430. Des expériences d'extinction génique suggèrent que le deuxième gène TIR-NBS-LRR, Spl_TNL18429, qui est également exprimé dans les racines et qui présente un fort pourcentage d'identité de séquence avec le gène Spl_TNL18428, pourrait également être impliqué dans la résistance à G. pallida. L'expression du gène rapporteur GFP, placé sous le contrôle du promoteur du gène Spl_TNL18428, est fortement induite dans les cellules situées autour du syncytium. Ceci renforce l'hypothèse d'une implication du gène Spl_TNL18428 dans la résistance à G. pallida, car la localisation de l'expression de la GFP est similaire à celle de la nécrose, qui est caractéristique de la réaction développée par les plantes résistantes autour du syncytium induit par les nématodes. En tenant compte des données bibliographiques récentes, montrant que plusieurs gènes NBS-LRR peuvent être indispensables à l'expression d'une résistance, nos résultats suggèrent que les deux gènes Spl_TNL18428 et Spl_TNL18429 sont nécessaires à l'expression de la résistance à G. pallida.
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https://hal.inrae.fr/tel-02810876/file/Castro%20Quezada%20th%C3%A8se%20page%20de%20garde%20et%20r%C3%A9sum%C3%A9_1 BibTex
titre
Functional analysis and regulation of candidate genes underlying the QTL GpaVspl involved in resistance to cyst nematode in potatoes
auteur
Patricio Salvador Castro Quezada
article
Sciences agricoles. Université d'Avignon, 2013. Français. ⟨NNT : 2013AVIG0653⟩
resume
Cyst nematodes are one of the pests that cause the most damage to potato cultures. Resistance found in the accession spl88S.329.18 in Solanum sparsipilum is characterized by oligogenic determinism with a strong effect QTL on chromosome V (GpaVspl) and a minor effect QTL on chromosome XI (GpaXIspl). To obtain a high level of resistance, the effect of QTL GpaVspl must be complemented by the low effect QTL GpaXIspl. By comparative genomics, the GpaV locus was located in a range between 16 and 60 kb in genomes of tomato and potato related species: Solanum demissum and Solanum phureja. Two genes were annotated: the first belonging to the TIR -NBS -LRR gene family (TNL) and the second one belonging to the “mitochondrial transcription termination factor” family (mTERF). The effect of both genes -Spl_TNL18428 and Spl_mTERF18430- on resistance to G. pallida were analyzed via genetic transformation experiments followed by resistance tests on transformed plants. A partial effect of Spl_TNL18428 on resistance to G. pallida was identified by complementation of susceptible plants. Gene silencing experiments suggested that Spl_TNL18429, which occurs in roots and presents a high percentage of sequence identity with the gene Spl_TNL18428, is also involved in resistance to G. pallida. The expression of the GFP reporter gene, under the control of the Spl_TNL18428 gene promoter, is strongly induced in cells located around the syncytium. This strengthens the hypothesis of an involvement of Spl_TNL18428 gene in resistance to G. pallida, because the location of GFP expression is similar to necrosis, which is characteristic of resistant plants. Taking into account that recent data showing that several NBS-LRR genes may be essential for the expression of resistance, our results suggest that both Spl_TNL18428 and Spl_TNL18429 genes are necessary for the expression of resistance to G. pallida
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https://theses.hal.science/tel-00991628/file/pdf2star-1399992907-Version-pour-mise-en-ligne_Castro_FAC_1.pdf BibTex
titre
Genetic and functional bases of the durability of polygenic resistance to Potato virus Y (PVY) in pepper (Capsicum annuum)
auteur
Julie Quenouille Épouse Lederer Quenouille-Lederer
article
Sciences agricoles. Université d'Avignon, 2013. Français. ⟨NNT : 2013AVIG0650⟩
resume
Genetic resistances provide an efficient control of crop diseases but are limited by pathogen adaptation.In pepper, the durability of the pvr23 allele, conferring resistance to Potato virus Y (PVY), was demonstrated todepend on the plant genetic background. The aim of my PhD thesis was to characterize the host genetic factorsaffecting the durability of the major resistance gene pvr23 and to answer to the following question s: (i) What istheir action on the evolution of the viral population? (ii) Is there identity between the QTLs (quantitative traitloci) controlling the partial resistance and the QTLs affecting the durability of pvr23? (iii) Are these genetic factorswidespread among the genetic resources of pepper? Various experiments including resistance testing,experimental evolution and competition between various PVY variants, enabled to show that the genetic factorsaffecting the durability of pvr23 acted in: (i) decreasing the viral accumulation, (ii) decreasing the probability ofacquisition of resistance breaking (RB) mutations by PVY and (iii) slowing down the selection of RB variants. QTLdetection and mapping of genetic factors affecting the frequency of pvr23 RB showed that four loci actingadditively and in epistatic interactions explained together 70% of the variance of pvr23 breakdown frequency.Comparative mapping between these QTLs and QTLs affecting partial resistance showed that three of the fourQTLs controlling the frequency of pvr23 RB are also involved in quantitative resistance, suggesting that QTLs forquantitative resistance have a pleiotropic effect on the durability of the major resistance gene. Analysis of acollection of 20 pepper accessions, carrying pvr23 or pvr24 (allele closely related to pvr23) in various geneticbackgrounds, showed that genetic backgrounds favorable to the durability of the pvr2-mediated resistance arewidespread in the genetic resources of pepper. These results highlight that the durability of a major resistancegene can be strongly increased when associated with genetic factors decreasing the pathogen multiplication.Moreover, the frequency of a major gene RB is a highly heritable trait and QTLs detection for this trait isachievable. The direct selection for such QTLs opens new prospects to preserve the durability of major resistancegenes used by breeders.
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https://theses.hal.science/tel-00982624/file/pdf2star-1398165405-These_Julie_Quenouille_Lederer_Vf_lecteurs.pdf BibTex
titre
Variation phénotypique de la résistance quantitative à Phytophthora capsici dans la diversité naturelle du piment, et diversité moléculaire et profil d'évolution du QTL majeur Pc5.1
auteur
Melissa Cantet
article
Sciences agricoles. Institut National d'Etudes Supérieures Agronomiques de Montpellier, 2013. Français. ⟨NNT : ⟩
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titre
Héredité de la résistance à des virus transmis par Bemisia chez le melon
auteur
Hanan Ibn Oaf
article
Sciences agricoles. University of Gezira, 2013. Français. ⟨NNT : ⟩
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2012

Theses

titre
Analysis of molecular and proteomic polymorphism of tomato and identification of QTLs for fruit quality traits in tomato
auteur
Jiaxin Xu
article
Sciences agricoles. Université d'Avignon, 2012. Français. ⟨NNT : 2012AVIG0644⟩
resume
Fruit quality in tomato is highly dependent on genetic variation. Following domestication and modernbreeding, molecular diversity of tomato has been strongly reduced, limiting the possibility to improvetraits of interest. New molecular markers such as single nucleotide polymorphisms (SNP) constituteprecious tools to saturate tomato genetic maps and identify quantitative trait loci (QTL) andassociations in a poorly polymorphic species like tomato. The objectives of this study were tocharacterize tomato genetic diversity at the molecular levels and to try to identify QTLs, genes andproteins responsible for fruit quality traits in tomato. For this purpose, three independent studies wereconducted leading to the discovery of new SNP markers, their use for association study and finally theanalysis of proteome diversity in relation to physiological phenotypes. We first used two nextgenrationsequencing platforms (GA2 Illumina and 454 Roche) to re-sequence targeted sequencescovering about 0.2% of the tomato genome from two contrasted accessions. More than 3000 SNPswere identified between the two accessions. We then validated 64 SNPs by developing CAPS markers.We thus showed the value of NGS for the discovery of SNPs in tomato and we produced low costCAPS markers which could be used to characterize other tomato collections. A SNPlexTM arraycarrying 192 SNPs was then developed and used to genotype a broad collection of 188 accessionsincluding cultivated, cherry type and wild tomato species and to associate these polymorphisms to tenfruit quality traits using association mapping approach. A total of 40 associations were detected andco-localized with previously mapped QTLs. Some other associations were identified in new regions.We showed the potential of using association genetics in tomato. Finally, a new analytical approachcombining proteome, metabolome and phenotypic profiling were applied to study natural geneticvariation of fruit quality traits in eight diverse accessions and their four corresponding F1s at cellexpansion and orange-red stages. We identified 424 variable spots by combining 2-DE and nano LCMS/MS and built the first comprehensive proteome reference map of the tomato fruit pericarp at twodevelopmental stages from the 12 genotypes. In parallel, we measured the variation of 34 metabolites,26 enzyme activities and five phenotypic traits. A large range of variability and several inheritancemodes were described in the four groups of traits. Data integration was achieved through sPLS andcorrelation networks. Many significant associations were detected within level and between levels ofexpression. This systems biology approach provides better understanding of networks of elements(proteins, enzymes, metabolites and phenotypic traits) in tomato fruits
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https://theses.hal.science/tel-00927514/file/pdf2star-1381138291-Thesis_jiaxin_-XU.pdf BibTex
titre
Evolutionary potential and adaptation of lettuce downy mildew populations, Bremia lactucae, face selection pressure of host plant, Lactuca sativa
auteur
Romain Valade
article
Sciences agricoles. Université Paris Sud - Paris XI, 2012. Français. ⟨NNT : 2012PA112088⟩
resume
Resistance genes introgressed into cultivated plants are frequently overcame by pathogens, causing outbreaks and economic losses. Therefore, understanding the evolutionary strategies involved in the adaptation of pathogen populations is needed to improve the sustainable management of resistance. Bremia lactucae, the lettuce downy mildew, is under strong selection pressure exerted by host resistance genes. Under this selection pressure, B. lactucae populations showed a rapid adaptation to host resistance. The study of pathogen genetic structure may help to understand the evolutionary mechanisms involved in the overcoming of resistant genes. Study of the genetic structure (neutral and potentially selected markers) of B. lactucae populations in France was conducted in order to identify the evolutionary forces involved in the adaptation of the plant pathogen and to determine the influence of selective pressure of host resistance genes on the population structure. We developed 12 microsatellites markers, to study genetic structure of B. lactucae populations in France. Over 800 isolates were collected from the most important production areas of the host plant, Lactuca sativa. These isolates were taken from different cultivars grouped according to their resistance gene combinations. Moreover, a prospection in the wild compartment allowed sampling isolates of B. lactucae on the wild host L. serriola. The polymorphism of several RxLR candidate effectors was studied in several Bremia populations. Our results showed clonality in Bremia populations but rare events of sexual reproduction are also suggested. Weak genetic differentiation between populations suggested important gene flow between populations at French regional scale. Gene flow was also found between the wild and the crop pathosystems indicating a possible role of wild host plants as genetic reservoir. Moreover, analyzing the population genetic structure suggests the presence of different clonal lineages, resulting probably from selection pressure of resistance genes. Characterizing the population structure of B. lactucae allowed to highlight the strong evolutionary potential (significant gene flow, mixed mating system, selection by resistance genes) of B. lactucae explaining its rapid adaptation to host resistance. Thus, we can suggest some management strategies of resistance genes as promoting the use of quantitative resistance and use of crop association to improve the durability of resistance.
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https://theses.hal.science/tel-00769939/file/VA2_VALADE_ROMAIN_11062012.pdf BibTex
titre
MDHAR3 : an enzyme at the interface of antioxidant defense, carbon metabolism and fruit quality in tomatoes
auteur
Noé Gest
article
Sciences agricoles. Université d'Avignon, 2012. Français. ⟨NNT : 2012AVIG0328⟩
resume
non identifiée
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https://theses.hal.science/tel-04288793/file/Thesis_ngest.pdf BibTex
titre
MDHAR3 : une enzyme à l'interface de la défense antioxydante, du métabolisme carboné et de la qualité du fruit chez la tomate
auteur
Noé Gest
article
Sciences agricoles. Université d'Avignon et des Pays de Vaucluse, 2012. Français. ⟨NNT : ⟩
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titre
Analyse de la structure génétique de l’abricotier au niveau du bassin Méditerranéen: Histoire et diffusion de l'espèce
auteur
Hedia Bourguiba
article
Sciences agricoles. Université de Tunis, 2012. Français. ⟨NNT : ⟩
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2011

Habilitation à diriger des recherches

titre
Redox, environnement et quelques aspects du développement des plantes. Habilitation à diriger des recherches
auteur
Rebecca Stevens
article
Sciences du Vivant [q-bio]. Université d'Avignon et des Pays de Vaucluse, 2011
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Theses

titre
Selection pressures exerted by the genetic resistances of melon on Aphis gossypii populations
auteur
Sophie Thomas
article
Sciences du Vivant [q-bio]. Université d'Avignon et des Pays de Vaucluse, 2011. Français. ⟨NNT : ⟩
resume
The adaptive response of pest populations to selection pressures exerted by agricultural activities determines the sustainability of control methods. In melon, the Vat gene that confers resistance to Aphis gossypii has been deployed for over 10 years, so there are fears it will be overcome. The challenge is to provide strategic elements to plant breeders, concerning the risk of development of virulent aphids, in order to develop new varieties with durable resistances. In the context of this PhD, we have: i) Estimated the available genetic diversity in populations of A. gossypii from different melon growing areas. The diversity is structured geographically. The great diversity observed in France would have its origine in part from the events of sexual reproduction, suggesting a high evolutionary potential of A. gossypii. ii) Estimated the selection pressure exerted by different resistance combinations (Vat gene and QTLs) on these populations. Population densities are lower on VatR plants than VatS plants and population genetic structure is altered in certain growing areas when the VatR gene is present. The clones multiplying on VatR plants have good fitness and the risk of their spreading is great. No effect of QTLs has been identified in the field. iii) Characterized the clones overcoming the VatR gene. Our results suggest that the adaptation of clones made either by alteration of the avirulence gene of aphids or by adaptation of aphids to resistance effectors. New strategies for Vat resistance management are proposed.
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https://hal.inrae.fr/tel-02811117/file/45159_20111117100128625_1.pdf BibTex
titre
Etude de l'intérêt de l'hermaphrodisme chez le melon.
auteur
Mutasim Elsalir Abdelmohsin
article
Sciences agricoles. 2011. Français. ⟨NNT : ⟩
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2010

Theses

titre
Diversité de Ralstonia solanacearum au Cameroun et bases génétiques de la résistance chez le piment (Capsicum annuum) et les solanacées
auteur
Gabriel Mahbou Somo Toukam
article
Sciences du Vivant [q-bio]. AgroParisTech, 2010. Français. ⟨NNT : ⟩
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https://hal.inrae.fr/tel-02824238/file/49672_20120210022805675_1.pdf BibTex
titre
Analyse du polymorphisme moléculaire de gènes de composantes de la qualité des fruits dans les ressources génétiques sauvages et cultivées de tomate ; recherche d’associations gènes/QTL
auteur
Nicolas N. Ranc
article
Sciences du Vivant [q-bio]. Ecole Nationale Supérieure Agronomique de Montpellier, 2010. Français. ⟨NNT : ⟩
resume
In Tomato (Solanum lycopersicum), breeding for fruit quality is difficult due to the multiplicity and complexity of the traits. QTL mapping has allowed the genetic characterization of these traits. One of the challenges is now to identify the genes underlying these QTLs. Following this aim, we used linkage-disequilibrium (LD) mapping. To avoid hazardous associations between traits and polymorphisms, the genetic structure has to be taken into account for LD mapping. Cultivated tomato showed low genetic diversity reducing mapping resolution. Cherry type tomato (S. lycopersicum var. cerasiforme) genome is described to be admixture between cultivated tomato and its wild ancestor. Such admixture may increase resolution of association mapping. We used a core collection focused on cherry type accessions to validate a candidate gene for a fruit locule-number QTL. We found that two single nucleotide polymorphisms (SNP) were highly associated with the trait. These two SNP evolved differently from the rest of the chromosome 2. They underwent a balanced selection which testifies a selection for fruit morphology diversity by human. Association mapping, focused on whole chromosome 2, allowed us to assess the extent of linkage disequilibrium over genetic and physical distances. Associations of polymorphisms with phenotypes were detected with structured association methods. We thus showed efficiency of genome admixture to overcome the low-resolution limitation of association mapping for an inbred crop. We validated previously identified QTLs and found associations with new QTLs and new candidate genes. An evolutionary model including bottleneck and gene flow between wild and domesticated forms of tomato is also presented.
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https://hal.inrae.fr/tel-02824399/file/36854_20100805104226325_1.pdf BibTex

2009

Theses

titre
Analysis of tomato fruit weight and sugar content via an integrative approach combining ecophysiological, genetic and molecular studies
auteur
Marion Prudent
article
Biologie végétale. Université d'Avignon, 2009. Français. ⟨NNT : ⟩
resume
Fruit weight and sugar content are two complex traits largely involved in tomato quality. The aim of this study is to dissect these two traits via a multidisciplinary approach combining ecophysiology, genetics and genomics. A population of 20 introgression lines of Solanum chmielewskii in the genetic background of S. lycopersicum were grown in 2006 and 2007 under two fruit load conditions in order to modulate carbon availability to fruit. Under high load conditions, trusses were not pruned while under low load conditions, trusses were pruned to one fruit. Indicators of ecophysiological processes involved in tomato fruit weight and sugar content were measured or estimated and allowed the characterization of main processes underlying QTL for quality traits such as cell division and expansion, fruit transpiration or allocation of carbon for the synthesis of structural compounds. A high effect of fruit load was emphasized on QTL expressions, indicating the occurrence of genotype x fruit load interactions. The combined use of an ecophysiological model predicting the final fruit sugar content and QTL detection allowed the identification of co-localizations between QTL for quality traits and QTL for variables involved in fruit functioning such as the assimilate supply to the fruit, the metabolic transformation of sugars into other compounds, or the dilution by water uptake. Finally, an introgression line harbouring QTL for fresh weight and sugar content with opposite allele effects, and the line conferring the genetic background were studied at the transcriptome level during the cell expansion phase. Candidate genes whose expression levels could be associated to the variation of weight and sugar content led by a fruit load change were identified. The kinetic analysis of expressions from a set of candidate genes allowed establishing links between ecophysiological and molecular variables.
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https://theses.hal.science/tel-00600410/file/TheseMPrudent2009.pdf BibTex
titre
Structural diversity of resistance loci to Phytophthora infestans in potato and synteny within Solanaceae
auteur
Sarah Danan
article
Sciences du Vivant [q-bio]. Institut National d'Etudes Supérieures Agronomiques de Montpellier, 2009. Français. ⟨NNT : ⟩
resume
Polygenic resistances to plant pathogens, controlled by QTLs (Quantitative Trait Loci), appear as a durable alternative to monogenic resistances, which are often quickly overcome by new virulences. To facilitate the use of polygenic resistances in plant breeding and in an attempt to better understand their potential durability, the exploration of the host diversity is necessary to inventory the resistance sources and describe the involved loci in the most comprehensive way, according to their genomic distribution and their allelic variability. The aim of this work was to clarify the structural organization of resistance loci to Phytophthora infestans on the potato genome and to make more precise their syntenic relationships with the QTLs of two other Solanaceae. Phytophthora are oomycetes responsible for late blight, and provoke tremendous damages in Solanaceae crops. Many loci of quantitative and qualitative resistances have been described, mostly in potato, but also in tomato and pepper. Three kinds of QTL analyses were used. The analyses in bi-parental independent populations and in connected multi-populations using a factorial mating design allowed the identification of new resistance QTLs in three potato-related wild species, S. sparsipilum, S. spegazzinii and S. berthaultii, with quantitative tests on stems and foliage. A meta-analysis of all available QTL mapping data coming from the present work and from literature highlighted QTL congruency between the different studies, and made colocations clearer between QTLs and major genes of resistance, and with maturity QTLs. Candidate genes of the obtained meta-QTLs have been proposed. From a more prospective point of view, in order to make the syntenic relationships between the three Solanaceae more precise in a region of QTL colinearity, an inter-specific meta-analysis was achieved. Hypotheses were proposed about the molecular nature of the genes underlying the QTLs of the different species, their possible origins and evolution during speciation.
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https://hal.inrae.fr/tel-02823681/file/28041_20091201093933701_1.pdf BibTex
titre
Analyse des variations de poids et de teneurs en sucres du fruit de tomate par une approche intégrative combinant des études écophysiologique, génétique et moléculaire
auteur
Marion Prudent
article
Sciences du Vivant [q-bio]. Université d'Avignon et des Pays de Vaucluse, 2009. Français. ⟨NNT : ⟩
resume
Fruit weight and sugar content are two complex traits largely involved in tomato quality. The aim of this study is to dissect these two traits via a multidisciplinary approach combining ecophysiology, genetics and genomics. A population of 20 introgression lines of Solanum chmielewskii in the genetic background of S. lycopersicum were grown in 2006 and 2007 under two fruit load conditions in order to modulate carbon availability to fruit. Under high load conditions, trusses were not pruned while under low load conditions, trusses were pruned to one fruit. Indicators of ecophysiological processes involved in tomato fruit weight and sugar content were measured or estimated and allowed the characterization of main processes underlying QTL for quality traits such as cell division and expansion, fruit transpiration or allocation of carbon for the synthesis of structural compounds. A high effect of fruit load was emphasized on QTL expressions, indicating the occurrence of genotype x fruit load interactions. The combined use of an ecophysiological model predicting the final fruit sugar content and QTL detection allowed the identification of co-localizations between QTL for quality traits and QTL for variables involved in fruit functioning such as the assimilate supply to the fruit, the metabolic transformation of sugars into other compounds, or the dilution by water uptake. Finally, an introgression line harbouring QTL for fresh weight and sugar content with opposite allele effects, and the line conferring the genetic background were studied at the transcriptome level during the cell expansion phase. Candidate genes whose expression levels could be associated to the variation of weight and sugar content led by a fruit load change were identified. The kinetic analysis of expressions from a set of candidate genes allowed establishing links between ecophysiological and molecular variables.
Accès au texte intégral et bibtex
https://hal.inrae.fr/tel-02819431/file/38940_20100128111652656_1.pdf BibTex

2007

Theses

titre
Development of a high resolution intra-specific map of pepper (Capsicum annuum L.) and QTL analysis for horticultural traits
auteur
Lorenzo Barchi
article
Life Sciences [q-bio]. Università di Torino; Université Montpellier 2 (Sciences et Techniques), 2007. English. ⟨NNT : ⟩
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https://hal.inrae.fr/tel-02821811/file/45908_20110411112433093_1.pdf BibTex
titre
Caractérisation des déterminants génétiques et moléculaires de composantes de la texture du fruit de tomate
auteur
Jamila Chaïb
article
Sciences du Vivant [q-bio]. Ecole Nationale Supérieure Agronomique de Montpellier, 2007. Français. ⟨NNT : ⟩
resume
La texture est un critère essentiel dans la perception de la qualité organoleptique du fruit de tomate. Cependant, il s’agit d’un caractère complexe dont les différentes composantes (fermeté, farinosité, jutosité) sont essentiellement évaluées par analyses sensorielles. L’objectif de la thèse est d’identifier des mécanismes contrôlant les variations de texture du fruit de tomate, tant au niveau génétique que moléculaire, afin de fournir, à long terme, des outils intéressants pour assister la sélection de ces caractères dans le cadre de l’innovation variétale. Au niveau génétique, la caractérisation des QTL de texture est abordée en cherchant à savoir comment les régions porteuses de QTL interagissent entre elles et comment le fonds génétique peut influencer l’expression de ces QTL. A l’exception de la fermeté, les effets des QTL de qualité ont été retrouvés au niveau des lignées quasi-isogéniques correspondantes dans le fonds génétique utilisé à l’origine pour la détection de QTL. Néanmoins, de fortes interactions entre QTL et fonds génétiques ont été mises en évidence ainsi qu’un effet fort de l’environnement sur l’expression de ces QTL. Parallèlement, la cartographie fine de deux régions où sont localisés des QTL associés à la texture, a été initiée. Les effets des QTL contrôlant la fermeté du fruit ont été détectés au niveau de certaines familles de recombinants et la localisation de ces QTL a été précisée. Au niveau moléculaire, la recherche de gènes candidats dont la fonction et/ou le niveau d’expression sont associés aux variations de texture a été réalisée par des analyses du protéome et du transcriptome. Plusieurs gènes candidats ont été identifiés et la cartographie de certains d’entre eux a révélé une co-localisation avec les QTL cibles.
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https://hal.inrae.fr/tel-02824941/file/19215_20070830060110106_1.pdf BibTex
titre
Caractérisation moléculaire et fonctionnelle de le résistance aux Phytophthora chez les Solanacées
auteur
Julien Bonnet
article
Sciences agricoles. 2007. Français. ⟨NNT : ⟩
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titre
Caractérisation fonctionnelle et évolution moléculaire des gènes codant pour les facteurs d'initiation de la traduction eIF4E : des facteurs clés dans la résistance des plantes aux Potyvirus
auteur
Carine Charron
article
Sciences du Vivant [q-bio]. Université de la Méditerranée (Aix Marseille 2), 2007. Français. ⟨NNT : ⟩
resume
L'objectif de cette étude est de décrire puis analyser et comparer le polymorphisme de séquence des gènes eIF4E (eukaryotic Initiation Factor 4E) de résistance aux potyvirus, afin de mettre en relation ce polymorphisme avec la double fonction des protéines eIF4E dans les processus cellulaires de l'hôte et dans l'interaction avec les potyvirus. La stratégie repose sur l'association d'analyses fonctionnelles et d'études d'évolution moléculaire des gènes eIF4E chez deux Solanacées (piment et tomate) et chez l'espèce modèle Arabidopsis thaliana. En ce qui concerne le rôle de eIF4E dans les processus cellulaires, la pression de sélection purificatrice forte identifiée pour l'ensemble des gènes eIF4E argumente en faveur de l'acquisition d'une spécialisation fonctionnelle, et ce bien que toutes les protéines eIF4E apparaissent capables de complémenter une levure délétée de son gène eIF4E. En ce qui concerne le rôle de eIF4E dans les interactions plantes-potyvirus, une importante diversité de variants alléliques a été identifiée au locus eIF4E1-pvr2 du piment, diversité caractérisée par des substitutions nucléotidiques exclusivement non-synonymes. La plupart de ces substitutions, impliquées dans la résistance aux PVY (Potato virus Y) et TEV (Tobacco etch virus) via une modification de l'interaction avec la protéine virale VPg (Viral Protein genomelinked), sont sous pression de sélection positive. Ces résultats couplés à ceux montrant que des mutations dans la VPg permettent aux potyvirus de s'adapter aux protéines eIF4E1 de résistance, mettent en évidence l'existence d'une coévolution entre eIF4E1 et VPg. Cette coévolution n'est cependant pas retrouvée chez la tomate et A. thaliana, indiquant que leurs caractéristiques biologiques d'interaction avec les potyvirus "in natura" conduisent à des profils différents d'évolution des gènes eIF4E. Plus globalement, ces résultats associés à ceux montrant la conservation de la position des substitutions en acides aminés dans les protéines eIF4E de résistance d'espèces très éloignées suggèrent l'existence d'une évolution convergente
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2005

Theses

titre
Mécanismes de contournement des résistances et évaluation a priori de leur durabilité dans l'interaction piment (Capsicum annuum L.) - virus Y de la pomme de terre (PVY)
auteur
Valérie Ayme
article
Sciences du Vivant [q-bio]. Université Montpellier 2 (Sciences et Techniques), 2005. Français. ⟨NNT : ⟩
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2004

Theses

titre
No English title available
auteur
Amandine Carmeille
article
Biologie végétale. Université de la Réunion, 2004. Français. ⟨NNT : 2004LARE0026⟩
resume
A deep knowledge of the genetic basis of tomato resistance against R.solanacearum is required to control efficiently bacterial wilt disease. The aim of this study is to identify a resistance source against a race 3, phylotype II (r3pII) strain, to characterise the genetic basis of this resistance for comparison with resistance to race 1 strains. The best best source of partial resistance to a Reunion Island r3pII strain was identifid in L.esculentum var. cerasiforme Hawaii 7996 among 82 Lycopersicon sp. accessions. QTL mapping for resistance was performed in a F3 population derived from Hawaii 7996 x L. pimpinellifolium WVa 700 (susceptible) during two seasons and using different resistance criteria (symptoms and bacterial colonisation). A generalist QTL with major effect and several QTLs criterion or season-specific were detected. QTL mapping experiments performed on the F8 population using r1pI and r3pII strains from Reunion Island and comparison with previous studies reveals a phylotype-specificity of some QTLs.
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titre
Cartographie génétique des résistances partielles du melon à la fusariose race 1.2 et au mildiou
auteur
Laure Perchepied
article
Sciences du Vivant [q-bio]. Institut National Agronomique Paris Grignon, 2004. Français. ⟨NNT : ⟩
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titre
Résistances récessives aux potyvirus chez les solanacées et facteurs du complexe d'initiation de la traduction
auteur
Sandrine Ruffel
article
Sciences du Vivant [q-bio]. Université de la Méditerranée (Aix Marseille 2), 2004. Français. ⟨NNT : ⟩
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titre
Cartographie génétique et étude de QTL conférant la résistance au nématode à kyste Globodera pallida (Stone) chez la pomme de terre (Solanum tuberosum ssp. tuberosum L.)
auteur
Bernard Caromel
article
Sciences du Vivant [q-bio]. Université Paris Sud - Paris 11, 2004. Français. ⟨NNT : ⟩
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https://hal.inrae.fr/tel-02831072/file/76502_20120402032951493_1.pdf BibTex

2003

Habilitation à diriger des recherches

titre
Habilitation à diriger des recherches (HDR)
auteur
Carole Caranta
article
Sciences du Vivant [q-bio]. Université de la Méditerranée (Aix Marseille 2), 2003
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Theses

titre
Efficacité de la sélection assistée par marqueurs pour l'amélioration de la qualité organoleptique de la tomate
auteur
L. Lecomte
article
Sciences du Vivant [q-bio]. Université de la Méditerranée (Aix Marseille 2), 2003. Français. ⟨NNT : ⟩
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2002

Theses

titre
Introgression d'une résistance polygénique à l'oïdium chez le pêcher Prunus persica à partir d'une espèce sauvage Prunus davidiana
auteur
Marie Foulongne
article
Sciences du Vivant [q-bio]. Université de la Méditerranée (Aix Marseille 2), 2002. Français. ⟨NNT : ⟩
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titre
Expression de l'ADNc NIA2, codant pour une nitrate réductase de tabac, chez la laitue
auteur
V. Dubois
article
Sciences du Vivant [q-bio]. Université Paris Sud - Paris 11, 2002. Français. ⟨NNT : ⟩
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titre
Identification and inheritance of resistance to watermelon chlorotic stunt virus (WmCSV) in melon (Cucumis melo L.) using molecular and biological techniques
auteur
- Mohamed Taha Yousif Elamin
article
Life Sciences [q-bio]. University of Gezira, 2002. English. ⟨NNT : ⟩
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titre
Construction de résistance polygénique assistée par marqueurs: application à la résistance quantitative du piment (Capsicum annuum L.) à Phytophthora capsici
auteur
A. Thabuis
article
Sciences du Vivant [q-bio]. Institut National Agronomique Paris Grignon, 2002. Français. ⟨NNT : ⟩
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2000

Theses

titre
Construction d'une carte génétique de référence du melon (Cucumis melo L.) et étude du contrôle génétique du développement et de la maturation du fruit
auteur
Christophe Périn
article
Sciences du Vivant [q-bio]. Université Paul Cézanne (Aix Marseille 3), 2000. Français. ⟨NNT : ⟩
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titre
Qualité organoleptique de la tomate : cartographie de QTL des composantes physiques, chimiques et sensorielles
auteur
V. Saliba-Colombani
article
Sciences du Vivant [q-bio]. Université Pierre et Marie Curie - Paris 6, 2000. Français. ⟨NNT : ⟩
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1998

Theses

titre
Caractérisation fonctionnelle de locus impliqués dans les résistances aux maladies chez le piment (Capsicum annuum L.) à l'aide d'une approche gène candidat
auteur
Stéphanie Pflieger
article
Sciences du Vivant [q-bio]. Université Paris Sud - Paris 11, 1998. Français. ⟨NNT : ⟩
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1995

Theses

titre
Cartographie génétique du melon (Cucumis melo L.) et recherche de QTL de la résistance au virus de la mosaïque du concombre et de quelques caractères morphologiques
auteur
S. Baudracco-Arnas
article
Sciences du Vivant [q-bio]. Université Paris Sud - Paris 11, 1995. Français. ⟨NNT : ⟩
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