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

Tomato is a paradigm of crop domestication: a widely cultivated and consumed vegetable but with reduced genetic diversity and therefore highly vulnerable to emerging diseases and climate change. Fortunately, tomato is rich in genetic resources and information to overcome those difficulties and a coalition of scientists and breeding experts which have generated a large amount of this information have been organized under an effective management structure and a series of objectives to overcome those threats. HARNESSTOM aims to demonstrate that increasing use of Genetic Resources is key for food safety and security and can lead to innovation and benefit all stakeholders. By capitalizing on the large effort done recently in several EU-funded projects to connect phenotypes/genotypes in a large number of accessions from different germplasm banks and academia, HARNESSTOM will first collect, centralize and normalize this wealth of information in a way that is easily searchable and displayed in a user-friendly manner adapted to different type of users. Second, HARNESSTOM will develop four prebreeding programs addressing the major challenges of the field: 1) introducing resistances against major emerging diseases, 2) improving tomato tolerance to climate change, 3) improving quality 4) increasing resilience in traditional European tomato by participatory breeding. And additional goal is to increase speed and efficiency in prebreeding what is needed to be able to respond to the emerging challenges in a timely and effective manner. Joint leadership of both academia and industry in each of the WP and the participation of two NGOs representing different stakeholders guarantees the results of the project will have an impact in industry innovation and also in the society. An efficient management and outreach and communication platform is also in place to make sure the project runs smoothly and the interests of all stakeholders are protected

Resilience to salinity in tomato Summary Agriculture will have to feed an increasing world population, using a decreasing arable land surface. This is all the more challenging, since the quality of some of our best soils is under threat. Salinity is an increasing problem, in particular in coastal or irrigated areas. Due to climate change, these traditionally fertile areas suffer from increases in soil salinity, reaching concentrations higher than tolerated by current cultivation practices. In the near future these areas will no longer be suitable for cultivating food unless we adopt novel production practices, including the use of novel resilient plant varieties and/or treating plants with natural agents that make them more resilient. For plants to be resilient to abiotic stresses like salinity and drought, the root system is of vital importance. Roots are the primary organs that adapt their architecture and physiology to drought and salt stress. Their performance is key to the ability of the whole plant to recruit nutrients and water. However, we have limited knowledge of how the root functions and this translates into a limited capability to control plant resilience to abiotic stress. In recent years we have started to discover the role and importance of root architecture, stress QTLs and the interaction of plant roots with mycorrhiza. Novel developments in biostimulants show that it is possible to affect root functioning and resilience towards abiotic stress such as high-salinity. However, despite the potential for agriculture, there is very limited knowledge on the mechanisms through which biostimulants act. The goal of ROOT is firstly to provide fundamental knowledge on how to improve the resilience of crop root systems towards salinity stress. We will focus on tomato because it is an important field crop in European areas threatened by salinization, and it has many well-organized resources (well-annotated genome, genetic resources). Key aspects to be addressed by ROOT: Control tomato root architecture by identifying key regulating genes in tomato. Identify QTLs and markers that are predictive for adaptive root architectures and resilience to salt stress in tomato. Understand the mechanism by which biostimulants contribute to tomato resilience under salinity stress conditions, and understand their mode of action. Secondly, ROOT will provide practical knowledge on strategies for reinforcing tomato resilience towards abiotic stress, and go from the lab to the field. ROOT will contribute to developing future cultivation systems for tomato in areas threatened by salinization. The biostimulants that we work with in ROOT will contribute to tomato resilience in the short term, and will create novel opportunities for farmers to operate in areas which are under threat of salinity. The QTLs and markers for root adaptability to salt stress discovered in ROOT will contribute to more resilient tomato varieties in the longer term. We unite the complementary know-how and expertise of European research groups from four different countries to develop strategies for resilient and salt-tolerant root systems in tomato. The industrial partners in ROOT will not only advise the research project from their market-oriented viewpoint, but will also actively participate in work packages, will perform a field experiment, provide their network for stakeholder involvement and will take the lead in the transfer of knowledge into application.

Root-knot and cyst forming nematodes are important pathogens. Nematicides were means in nematode control, but since they threatened environment and human health they were banned (EC directive 2007/619/EC). Natural plant resistance is an available and safe option, but strongly limited by the number of available genotypes and the occurrence of resistance breaking nematode populations. Furthermore, climate change positively regulates the nematode infection capacity inducing more intense infestations and greater risks to European agriculture. Therefore novel strategies must be developed. Molecular mechanisms of plant resistance to pathogens have been extensively studied and are now applied in pest management but knowledge of plant susceptibility and disease development is still limited. It is now well established that pathogens corrupt elementary plant functions and influence defence responses. Identification of plant genes which are essential for pathogens to exploit the host opens a perspective to develop new approaches to plant resistance. Members of this consortium already performed genome-wide expression profiling in Arabidopsis and tomato demonstrating that essential plant functions are manipulated during feeding site development induced by root-knot nematodes (RKN) and beet cyst nematodes (BCN). Morever, functional analysis of differentially expressed genes identify key genes essential for the development of feeding site and RKN or BCN. The NESTOR project will combine the efforts of 5 public research labs and 4 private companies to (i) discover and characterize Arabidopsis genes which are essential for disease susceptibility towards RKN and BCN and (ii) to discover target sequences in crops based on a set of genes for which an important role in feeding cell development has been shown, to generate novel resistance sources in crop plants. Orthologs of Arabidopis genes will be identified in tomato, cucumber, and sugar beet. New alleles will be generated by TILLING or Eco TILLING and tested for enhanced nematode resistance. Those with increased resistance without affecting plant development will be selected as targets. The nematology labs will first define plant susceptibility genes based on microarrays results and Arabidopsis mutant phenotyping. TILLING platforms will identify mutant lines in crops, while private companies will identify orthologues of Arabidopsis susceptibility genes in crop plant candidates and will genotype and phenotype these plants. NESTOR will increase our knowledge on plant-pathogen interactions and will generate resistance towards a large spectrum of nematode species on tomato, cucumber and sugar beet. The expected results of the project will be released to the public domain in the form of as scientific publications. They will have direct implication and application for the production of safer and healthier food by a novel approach replacing banned chemical nematicides.

Melon is an attractive model species that may help to understand the molecular differences between non-climacteric and climacteric fruit ripening because it contains both types of genotypes. This proposal involves the simultaneous use of transcriptome and metabolome analysis in climacteric and non-climacteric melon lines in order to understand the molecular differences between both types of fruit ripening. A search and analysis of melon mutants in key genes in fruit ripening will also be performed. The TILLING and EcoTILLING technologies will enable the identification of mutants that do not have a distinctive visible phenotype. The discovery of such novel variants could directly lead to the creation of new melon hybrid cultivars with commercial interest, a task that will be undertaken by the two private partners that participate in this proposal.