Mathilde Causse

• PhD
• Research Director at French National Institute for Agriculture, Food, and Environment (INRAE)

Background Tomato mating systems were strongly affected by domestication events. Mutations disrupting self-incompatibility paralleled by changes retracting the stigma position (SP) within the staminal cone conferred strict autogamy and self-fertility to the cultivated forms. Although major genes affecting these changes have been identified, SP cont...

The tomato mating system was strongly affected by domestication events. Mutations disrupting self-incompatibility paralleled by changes retracting the stigma position (SP) within the staminal cone conferred strict autogamy and self-fertility to the cultivated forms. Although major genes affecting these changes have been identified, SP control in do...

Soil salinity is a serious concern for tomato culture, affecting both yield and quality parameters. Although some genes involved in tomato salt tolerance have been identified, their genetic diversity has been rarely studied. In the present study, we assessed salt tolerance‐related traits at juvenile and adult stages in a large core collection and i...

Optimising plant nitrogen (N) usage and inhibiting N leaching loss in the soil-crop system is crucial to maintaining crop yield and reducing environmental pollution. This study aimed at identifying quantitative trait loci (QTLs) and differentially expressed genes (DEGs) between two N treatments in order to list candidate genes related to nitrogen-r...

Soil salinity is a serious concern for tomato culture, affecting both yield and quality parameters. Although some genes involved in tomato salt tolerance have been identified, their genetic diversity has been rarely studied. In the present study, we assessed salt tolerance-related traits at juvenile and adult stages in a large core collection and i...

Meeting the challenges of agroecological transition in a context of climate change requires the use of various strategies such as biological regulations, adapted animal and plant genotypes, diversified production systems, and digital technologies. Seeds and plants, through plant breeding, play a crucial role in driving these changes. The emergence...

La domestication des plantes, des animaux et des micro-organismes a permis le développement de l’agriculture, de l’élevage, de la transformation de leurs produits et finalement des civilisations.Les espèces concernées par la domestication, les régions du monde où elle s’est déroulée, les indices permettant d’identifier l’ancêtre sauvage, les propri...

Optimising plant nitrogen (N) usage and inhibiting N leaching loss in the soil-crop system is crucial to maintain crop yield and reduce environmental pollution. This study aimed at identifying quantitative trait loci (QTL) and differential expressed genes (DEGs) between two N treatments in order to list candidate genes related to nitrogen-related c...

The stable production of high vigorous seeds is pivotal to crop yield. Also, a high longevity is essential to avoid progressive loss of seed vigour during storage. Both seed traits are strongly influenced by the environment during seed development. Here, we investigated the impact of heat stress (HS) during fruit ripening on tomato seed lifespan du...

Genome-wide association studies (GWAS) are powerful for identifying genomic regions, or even directly the causal loci, controlling the variation of quantitative traits impacted by multiple loci. First proposed for the discovery of genetic loci controlling human diseases, GWAS rapidly became a method of choice in plant genetic studies, once the numb...

European traditional tomato varieties have been selected by farmers given their consistent performance and adaptation to local growing conditions. Here we developed a multipurpose core collection, comprising 226 accessions representative of the genotypic, phenotypic and geographical diversity present in European traditional tomatoes, to investigate...

Consumers began to complain about the taste of tomato varieties in the late 1990’s. Although tomato taste is influenced by environmental and post-harvest conditions, varieties show a large diversity for fruit quality traits. We herein review our past and present research work intended to improve tomato fruit quality. First, results from sensory ana...

Flavour and nutritional quality are important goals for tomato breeders. This study aimed to shed light upon transgressive behaviors for fruit metabolic content. We studied the metabolic contents of 44 volatile organic compounds (VOCs), 18 polyphenolics, together with transcriptome profiles in a factorial design comprising six parental lines and th...

The Mediterranean basin countries are considered secondary centres of tomato diversification. However, information on phenotypic and allelic variation of local tomato materials is still limited. Here we report on the evaluation of the largest traditional tomato collection, which includes 1499 accessions from Southern Europe. Analyses of 70 traits r...

A comprehensive collection of 1254 tomato accessions, corresponding to European traditional and modern varieties, early domesticated varieties, and wild relatives, was analyzed by genotyping by sequencing. A continuous genetic gradient between the traditional and modern varieties was observed. European traditional tomatoes displayed very low geneti...

The French National Research Institute for Agriculture, Food and the Environment (INRAE) conserves and distributes five vegetable collections as seeds: the aubergine* (in this article the word aubergine refers to eggplant), pepper, tomato, melon and lettuce collections, together with their wild or cultivated relatives, are conserved in Avignon, Fra...

Improving fruit quality traits such as metabolic composition remains a challenge for tomato breeders. To better understand the genetic architecture of these traits and decipher the demographic history of the loci controlling tomato quality traits, we applied an innovative approach using multiple haplotype-based analyses, aiming to test the potentia...

Water deficit triggers physiological, biochemical, and molecular changes in leaves that could be important for overall plant adaptive response and it can affect tomato yield and quality. To assess the influence of long-term moderate drought on leaves, four tomato accessions from MAGIC TOM populations were selected on the basis of their differences...

A comprehensive collection of 1,254 tomato accessions corresponding to European heirlooms and landraces, together with modern varieties, early domesticates and wild relatives, were analyzed by genotyping by sequencing. A continuous genetic gradient between the vintage and modern varieties was observed. European vintage tomatoes displayed very low g...

Consumer dissatisfaction with the flavor quality of many modern fresh market tomato varieties has fostered breeders’ interest in sensory quality improvement, and the demand for traditional varieties, which are generally associated with better flavor. To achieve further knowledge on the factors influencing the sensory quality and consumers’ preferen...

Tomato flavour is an important goal for breeders. Volatile organic compounds (VOCs) are major determinants of tomato flavour. Although most tomato varieties for fresh market are F1 hybrids, most studies on the genetic control of flavour-related traits are performed on lines. We quantified 46 VOCs in a panel of 121 small fruited lines and in a test...

Tomato is a widely cultivated crop, which can grow in many environments. However, temperature above 30°C impairs its reproduction, subsequently impacting fruit yield. We assessed the impact of high temperature stress (HS) in two tomato experimental populations, a multi‐parental advanced generation intercross (MAGIC) population and a core‐collection...

Tocochromanols constitute the different forms of vitamin E (VTE), essential for the human diet and display a high membrane protectant activity. By combining interval mapping and genome‐wide association studies (GWAS) we unveiled the genetic determinants of tocochromanol accumulation in tomato fruits. To enhance the nutritional value of this highly...

Water deficit (WD) leads to significant phenotypic changes in crops resulting from complex stress regulation mechanisms involving responses at the physiological, biochemical and molecular levels. Tomato growth and fruit quality have been shown to be significantly affected by WD stress. Understanding the molecular mechanism underlying response to WD...

Deciphering the genetic basis of phenotypic plasticity and genotype x environment interaction (GxE) is of primary importance for plant breeding in the context of global climate change. Tomato is a widely cultivated crop that can grow in different geographical habitats and which evinces a great capacity of expressing phenotypic plasticity. We used a...

Tomato (Solanum lycopersicum L.) is an acknowledged model species for research in genetics and genomics, on fruit development and disease resistance, but it also deserves to be a model species for population genomics studies due to the availability of large genetic and genomic resources. In breeding, tomato breeding and genetic improvement largely...

Tomato is the first vegetable consumed in the world. It is grown in very different conditions and areas, mainly in field for processing tomatoes while fresh-market tomatoes are often produced in greenhouses. Tomato faces many environmental stresses, both biotic and abiotic. Today many new genomic resources are available allowing an acceleration of...

Tomato is the first vegetable consumed in the world. It is grown in very different conditions and areas, mainly in field for processing tomatoes while fresh-market tomatoes are often produced in greenhouses. Tomato faces many environmental stresses, both biotic and abiotic. Today many new genomic resources are available allowing an acceleration of...

Deciphering the genetic basis of phenotypic plasticity and genotype x environment interaction (GxE) is of primary importance for plant breeding in the context of global climate change. Tomato is a widely cultivated crop that can grow in different geographical habitats and which evinces a great capacity of expressing phenotypic plasticity. We used a...

This is the presentation for the SOL2019

Tomato flavor has changed over the course of long-term domestication and intensive breeding. To understand the genetic control of flavor, we report the meta-analysis of genome-wide association studies (GWAS) using 775 tomato accessions and 2,316,117 SNPs from three GWAS panels. We discover 305 significant associations for the contents of sugars, ac...

Tomato (Lycopersicum esculentum), which is used for both processing and fresh markets, is a major crop species that is ranked the first vegetable produced over the world. Tomato is also a model species for research in genetics, fruit development and disease resistances. Genetic resources available in public repositories comprise the 12 wild related...

RNAseq Plant domestication led to considerable phenotypic modifications of floral traits in the transition from wild species to modern varieties. A change in style position with respect to stamens represents one of these adaptations, leading from allogamy of ancestor species (style exserted), to the autogamy of modern counterparts (style inserted)....

Characterizing the natural diversity of gene expression across environments is an important step in understanding how genotype by environment interactions shape phenotypes. Here, we analyzed the impact of water deficit onto gene expression levels in tomato at the genome‐wide scale. We sequenced the transcriptome of growing leaves and fruit pericarp...

Quality is a key trait in plant breeding, especially for fruit and vegetables. Quality involves several polygenic components, often influenced by environmental conditions with variable levels of genotype × environment interaction that must be considered in breeding strategies aiming to improve quality. In order to assess the impact of water deficit...

Haplotype prediction. Each of the 12 tomato chromosomes is represented with the percentage of allelic contribution of every parental line. NA represented all positions on the chromosomes where the parental allelic origin could not be assigned.

Functional annotation of CG retained after the filtering procedure according to allelic parental effect. Only QTL that presented <40 CG were screened. For each QTL, the chromosome and localization (position in pb) were precised. The type of polymorphisms, depending if it is a single nucleotide polymorphism (snp) or insertion deletion (indel) were i...

Distribution of mean values across MAGIC lines for each trait in Exp.1 (A) and Exp.2 (B); For each trait, minimum (dotted lines) and maximum (solid lines) parental values are plotted for control (green) and stress (red) treatment.

Mapchart representation of detected QTL on the genetic map for all chromosomes where a QTL was identified. The dashes on the chromosomes barchart represent the centimorgan distances between markers along the chromosomes. Each trait has a color code representation.

QTL detected in the different conditions. For each trait, all the QTL found are identified by a specific name (QTL name column), the treatment where the QTL was found (Treatment), the chromosome (Chr) and the position (Pos) in cM. The peak region encompassing any QTL is defined by a pair of marker (LeftMrk and RightMrk), corresponding to the lower...

Average variation caused by water deficit (WD), salinity (SS) and control in Exp.2 (Ctrl2) relative to control in Exp.1. The effect of each treatment was measured in percentage of increase or decrease against control in Exp.1.

Allelic effect of parental lines for QTL that were mapped in a confidence interval smaller than 2Mb.

Changing the balance between ascorbate, monodehydroascorbate, and dehydroascorbate in plant cells by manipulating the activity of enzymes involved in ascorbate synthesis or recycling of oxidized and reduced forms leads to multiple phenotypes. A systems biology approach including network analysis of the transcriptome, proteome and metabolites of RNA...

Heatmap showing protein levels in pericarp of fruit 20 days after anthesis (3 pools of 30 fruits) of the transgenic lines and wild-type. All proteins were separated by two-dimensional gel electrophoresis and identified by mass spectrometry. The log2 of the protein ratio with the wild-type for each transgenic line is presented. The scale goes from g...

Gene expression profiles for AO, Solyc04g054690; GLD, Solyc10g079470 and MDHAR, Solyc09g009390 as obtained from the TomExpress tool (http://tomexpress.toulouse.inra.fr).

Fruit metabolite data (orange fruit pericarp). Quantitative data for the following metabolites: galactose, mannose, glutamate, glutamine, alanine, aspartate, tyrosine, fructose, glucose, sucrose, ascorbate, dehydroascorbate, GABA, citramalate, citrate, malate, chlorogenic acid, caffeic acid glucoside, cis-chlorogenic acid, quercetin derivative, and...

WGCNA module identification. A graphical representation of the data from Supplementary Table S4: module eigengenes are labeled by color and the module membership scale from red (high adjacency, positive correlation) to green (low adjacency, negative correlation) shown for each metabolite and protein. The 7633 genes were used to generate the topolog...

Proteins. Raw data for quantifiable proteins (see Materials and methods) from orange pericarp with spot identifier code for each of the three pools for the wild type, AO, GLD, and MDHAR RNAi lines.

Gene expression profiles for AO, Solyc04g054690; GLD, Solyc10g079470 and MDHAR, Solyc09g009390 as obtained from the Solgenomics expression atlas tool (http://tea.solgenomics.net).

Ascorbate and dehydroascorbate levels in pericarp fruit 20 days after anthesis of transgenic lines and WT. Ascorbate and dehydroascorbate were assayed in the pericarp tissue (3 biological replicates of 30 fruits per pool) of the lines by a spectrophotometric method. Measurements show means with standard error (SE). A comparison of means was carried...

WGCNA. Solyc identifier, gene function, GO terms, module color, module membership (MM or eigengene-based connectivity) and associated p-value for the 38 modules and 7633 genes as generated by the WGCNA R package.

Transcriptome raw data. For each of the 7633 genes mean expression (normalized) in each of the three transgenic lines and wild type with standard error (SE). F values, p-values, false discovery rate corrected p-values and fold change (FC) are also given for each comparison as follows: 1: AO vs. WT, 2: GLD vs. WT, 3: MDHAR vs. WT, 4: AO vs. MDHAR, 5...

•Plant metabolites are important to world food security due to their roles in crop yield and nutritional quality. •Here we report the metabolic profile of 300 tomato accessions (Solanum lycopersicum and related wild species) by quantifying 60 primary and secondary metabolites, including volatile organic compounds, over a period of 2 yr. Metabolite...

Plant domestication has led to considerable phenotypic modifications from wild species to modern varieties. However, although changes in key traits have been well documented, less is known about the underlying molecular mechanisms, such as the reduction of molecular diversity or global gene co-expression patterns. In this study, we used a combinati...

Key message: A panel of 300 tomato accessions including breeding materials was built and characterized with >11,000 SNP. A population structure in six subgroups was identified. Strong heterogeneity in linkage disequilibrium and recombination landscape among groups and chromosomes was shown. GWAS identified several associations for fruit weight, ea...

Tomato fruit quality is a complex trait involving a number of components, including appearance, flavour, aroma and texture. There is a large range of genetic diversity in tomato for fruit quality components. Although a few major mutations may have a huge effect on fruit quality (notably the rin mutation), most of the components have a quantitative...

This book describes the strategy used for sequencing, assembling and annotating the tomato genome and presents the main characteristics of this sequence with a special focus on repeated sequences and the ancestral polyploidy events. It also includes the chloroplast and mitochondrial genomes. Tomato (Solanum lycopersicum) is a major crop plant as we...

Drought stress is a major abiotic stress threatening plant and crop productivity. In case of fleshy fruits, understanding mechanisms governing water and carbon accumulations and identifying genes, QTLs and phenotypes, that will enable trade-offs between fruit growth and quality under Water Deficit (WD) condition is a crucial challenge for breeders...

Water scarcity constitutes a crucial constraint for agriculture productivity. High-throughput approaches in model plant species identified hundreds of genes potentially involved in survival under drought, but few having beneficial effects on quality and yield. Nonetheless, controlled water deficit may improve fruit quality through higher concentrat...

Tomato is a model species for genetic analyses since a long time. Many mutations controlled by a single gene were discovered and the underlying genes were mapped first on the tomato genetic map. Most of these genes are involved in fruit colour and shape, in plant growth and architecture and in disease resistances. With the construction of high-dens...

Fruit quality is polygenic, each with variable heritability and difficult to assess. Genomic selection, which allows the prediction of phenotypes based on the whole genome genotype, could strongly help its improvement. The goal of this study is to evaluate the accuracy of genomic selection for several metabolomic and quality traits by cross-validat...

Key message: In tomato, genotype by watering interaction resulted from genotype re-ranking more than scale changes. Interactive QTLs according to watering regime were detected. Differentially expressed genes were identified in some intervals. As a result of climate change, drought will increasingly limit crop production in the future. Studying gen...

Tomato is a model species for genetic analyses since a long time. Many mutations controlled by a single gene were discovered and the underlying genes were mapped first on the tomato genetic map. Most of these genes are involved in fruit colour and shape, in plant growth and architecture and in disease resistances. With the construction of high-dens...

Le bon goût est à la mode dans le potager. Les consommateurs sont de plus en plus exigeants sur la qualité gustative des légumes ou des fruits. Les sélectionneurs en tiennent compte. Voici quatre exemples avec la fraise, la framboise, la tomate et le melon.

Improvement of fruit quality traits is a major goal for tomato breeding. Deciphering the genetic diversity and inheritance of fruit quality components is thus necessary. For this purpose, we carried out a large multi-level omic experiment. Eight contrasted lines and 4 of their F1 hybrids were phenotyped for fruit development traits. Fruit pericarp...

Quantitative trait loci (QTL) have been identified using traditional linkage mapping and positional cloning identified several QTL. However linkage mapping is limited to the analysis of traits differing between two lines and the impact of the genetic background on QTL effect has been underlined. Genome-wide association studies (GWAs) were proposed...

A l’échelle du globe, le réchauffement climatique est aujourd’hui sans équivoque. En particulier, l’eau va devenir un des principaux facteurs limitant pour les productions agricoles dans le bassin méditerranéen. Afin de s’adapter aux contraintes environnementales au court de leur cycle de développement, les plantes ont la capacité de moduler leur p...

In the next decade water will be increasingly limiting crop production, in particular in Mediterranean region. Improving plant water use efficiency by studying genotype x water regime (G x WR) interactions is of main interest to improve plant adaptation to low water availability. At different degrees, plants can change their phenotypes (molecular,...

Background: Domestication modifies the genomic variation of species. Quantifying this variation provides insights into the domestication process, facilitates the management of resources used by breeders and germplasm centers, and enables the design of experiments to associate traits with genes. We described and analyzed the genetic diversity of 1,...

Tomato, grown in drought areas, requires a large amount of water for its production. A slight limitation of water input can have a positive impact on tomato fruit quality by increasing the concentration in taste and nutritional compounds. But the right balance must be found to limit yield loss. Only a small part of the genomic regions involved in t...

Background and Aims In flowering plants, fertilization relies on the delivery of the sperm cells carried by the pollen tube to the ovule. During the tip growth of the pollen tube, proper assembly of the cell wall polymers is required to maintain the mechanical properties of the cell wall. Xyloglucan (XyG) is a cell wall polymer known for maintainin...

Background and Aims In flowering plants, fertilization relies on the delivery of the sperm cells carried by the pollen tube to the ovule. During the tip growth of the pollen tube, proper assembly of the cell wall polymers is required to maintain the mechanical properties of the cell wall. Xyloglucan (XyG) is a cell wall polymer known for maintainin...

Identification of the polymorphisms controlling quantitative traits remains a challenge for plant geneticists. Multiparent advanced generation intercross (MAGIC) populations offer an alternative to traditional linkage or association mapping populations by increasing the precision of quantitative trait loci (QTL) mapping. Here, we present the first...

Background Domestication and selection of crops have notably reshaped fruit morphology. With its large phenotypic diversity, tomato (Solanum lycopersicum) illustrates this evolutive trend. Genes involved in flower meristem development are known to regulate also fruit morphology. To decipher the genetic variation underlying tomato fruit morphology,...