Understanding mechanisms governing plant adaptation to the environment is a crucial challenge in the light of current issues concerning climate change. The diversity present in natural populations and genetic resources is a vital source of traits and alleles for crops, many of which may have been inadvertently lost during selection. The accumulation of knowledge on genes or traits, which enable the plant to adapt to a changing environment, is necessary for future plant breeding programs. The rise of functional genomic strategies combined with systems biology approaches are a powerful way of linking whole plant physiology, stress adaptation and crop breeding to information on gene transcription and regulation, metabolite variation and networks of interactions. In parallel, functional analysis of candidate genes and key regulators give complementary and precise information on specific pathways and responses. The objective of the project is the identification of useful alleles, genes, QTLs and phenotypes that will enable a plant to maintain yield under conditions of limited water. This trait is defined as water productivity: we therefore do not aim to study drought stress per se as a phenotype but instead something closer to the conditions plants may really have to withstand in the field in a changing environment. We aim to, in a model and economically important crop, tomato: 1. Identify QTLs involved in water productivity and tomato accessions or mutants adapted to water stress useful for breeding purposes. The QTL regions will be dissected in regard to the genome sequence of the parental lines. The segregating population will be analysed in heat and salt stress conditions in order to identify common and specific QTLs 2. Identify regulatory genes (encoding transcription factors or production of signalling molecules) that are candidates for the improvement of yield in cultivated tomato and alleles that can be used directly to improve water productivity. 3. Screen for mutants tolerant to water stress and identify the corresponding genes through DNAseq mapping 4. Continue the characterisation of previously identified candidate genes involved in cellular protection against water limitation by using transgenic tomato plants. 5. Carry out a precise physiological analysis of the response to water limitation and the role of physical barriers to water loss such as the cuticle. 6. Introduce into an ecophysiological model the impact of water stress in interaction with genotypes in order to define ideotypes and test virtual scenarios of plant adaptation. 7. Integrate and manage all the data produced into a common database The project relies on the complementary expertises (genetics, ecophysiology, genomics and physiology) of three laboratories and two breeding companies. It will benefit form a range of resources and preliminary data, such as several populations (accessions, segregating populations and EMS induced mutants) and the availability of the tomato genome sequence as well as the genome sequences of 8 divergent lines used as parents of a MAGIC population

Considering the forecasted world demographic growth and the global changes in climate, it is becoming a major challenge for human society to provide sufficient amounts of high nutritional and sensory quality food. The TomEpiSet project aims to uncover new means and strategies to overcome poor fruit setting and the resulting low yield under elevated temperature using tomato as reference species. Screen tomato germoplasm and available auxin related and epigenetic mutants to select lines that successfully initiate fruit setting without need for pollination, normal or high yield with maintenance of fruit quality under heat stress conditions. The main novelty of the project is to unravel of the epigenetic components of the fruit set process and parthenocarpy in relation to auxin signaling. Genome-wide transcriptomic profiling combined to chromatin immuno-precipitation and DNA methylation studies will generate extensive multidimensional expression maps of epigenetic marks and auxin signaling factors allowing uncovering new components of the fruit set process. These new candidate genes will be analyzed with reverse genetics approaches using transgenic lines mis-expressing these genes to generate loss-of-function mutants by CRISPR/cas9 - RNAi approaches or overexpression plants. Then, the mutant plants will be analyzed at the physiological level for their capacity to produce normal or higher fruit yields in conditions of elevated ambient temperatures. An attempt to setup a new approach for breading using epigenetic information will be developed in the frame of the project. Programmable epigenetic marks based on the CRISPR/Cas9 gene regulation system, consisting of the nuclease-null dCas9 protein fused to the catalytic core histone or DNA modifiers will be in generated to guide for specific epigenetic modifications to candidate genes identified by an integrated approach combining RNA-Seq, ChIP-Seq and BS-Seq approaches. Validated epi-mutants will be phenotyped regarding their ability to display normal or higher fruit yield under elevated temperatures without loss of fruit quality. A major goal of our project will be the integration of all data sets coming from different high throughput approaches. TomEpiSet will take advantage of the tomato transcriptomic platform called TomExpress (http://gbf.toulouse.inra.fr/tomexpress) which has been developed by P1, allows processing and analyzing the data in standardized and unified ways for the whole project. Elucidating the mechanisms underpinning fruit set by integrating epigenetic mechanisms and auxin signaling will represent a major breakthrough in our understanding of reproductive biology and will open the way to the design of new strategies towards improving crop yield, particularly in adverse environmental condition leading to poor flower fertilization. TomEpiSet will highly contribute to enrich the content of high education courses at the national and international level through an Erasmus+ Capacity Building in the Field of Higher Education ‘MABIOVA’ (creation of a Master degree in plant Biotechnology field) project coordinated by P1 and through different partners of the project regarding their involvement in teaching activities at the high education level. The use of our data for tomato breeding will be in the scope of the valorization procedures and we shall use the Partners’ national and international network of contacts, for such perspectives.