14 ERA-CAPS Regulating Tomato quality through Expression (RegulaTomE)

The twin objectives of RegulaTomE are to determine the importance of transcriptional regulation of the metabolic pathways defining quality traits in tomato and to identify such transcriptional regulators at the molecular level. The selected quality traits include those determining antioxidant capacity which impacts shelf life and nutritional value as well as those determining fruit flavor and over-ripening which influence organoleptic properties and shelf-life. Loci contributing to abiotic stress tolerance will also be identified toward the combined goals of more nutritious, stable and sustainable crops. RegulaTomE will use the natural variation available in introgression lines (ILs) resulting from wild species crosses to tomato to assess the importance of transcriptional regulation, identify additional regulatory genes and assess underlying genetic and epigenetic variation. RegulaTomE will additionally assess the potential for direct or indirect use of natural variation from a largely untapped wild species resource for crop improvement. To identify genes regulating metabolic pathways using the Solanum lycopersicoides ILs, and to capture as much genetic and epigenetic variation as possible for application to gene discovery and tomato improvement, resources need to be developed, including a genome reference sequence for S. lycopersicoides and metabolite, DNA methylation and transcriptome profiles of IL fruit. Resulting data will be made available without restriction via existing public databases, providing invaluable resources for the community to exploit further the untapped natural variation in S.lycopersicoides. RegulaTomE will lead to regulatory gene identification (an important advance in terms of fundamental understanding), and provide new tools for metabolic engineering of fruit quality. More immediately, the natural variation in fruit quality revealed by the S.lycopersicoides ILs could be applied to tomato improvement either directly through introgression into cultivated varieties or indirectly through the identification of target loci and corresponding allelic variation making positive contributions to quality traits within S. lycopersicum breeding germplasm and in other close relatives of tomato. The cooperation of scientists from five major European organisations and two US Universities producing world-leading research on fleshy fruit and agricultural/horticultural innovation will allow the development of tools and resources on a scale unavailable at a national level. The outputs of RegulaTomE will provide a framework of understanding as well as tools, in the form of genes, target loci and molecular markers, to support development of longer shelf-life, more nutritious and more flavorsome fleshy fruits in other horticultural crops. The effectiveness of these resources and the significance of the knowledge acquired on RegulaTomE will ensure that the project contributes directly to food security and sustainable fruit cultivation.

The twin objectives of RegulaTomE are to determine the importance of transcriptional regulation of the metabolic pathways defining quality traits in tomato and to identify such transcriptional regulators at the molecular level. The selected quality traits include those determining antioxidant capacity which impacts shelf life and nutritional value as well as those determining fruit flavour and over-ripening which influence organoleptic properties and shelf-life. Loci contributing to abiotic stress tolerance will also be identified toward the combined goals of more nutritious, stable and sustainable crops. We will use the natural variation available in introgression lines (ILs) resulting from wild species crosses to tomato to assess the importance of transcriptional regulation, identify additional regulatory genes and assess underlying genetic and epigenetic variation. We will additionally assess the potential for direct or indirect use of natural variation from a largely untapped wild species resource for crop improvement. To identify genes regulating metabolic pathways using the Solanum lycopersicoides ILs, and to capture as much genetic and epigenetic variation as possible for application to gene discovery and tomato improvement, resources need to be developed, including a genome reference sequence for S. lycopersicoides and metabolite, DNA methylation and transcriptome profiles of IL fruit. Resulting data will be made available via existing public databases, providing invaluable resources for the community to exploit further the untapped natural variation in S.lycopersicoides. We will identify regulatory genes, and provide new tools for metabolic engineering of fruit quality. More immediately, the natural variation in fruit quality revealed by the S.lycopersicoides ILs could be applied to tomato improvement either directly through introgression into cultivated varieties or indirectly through the identification of target loci and corresponding allelic variation.

Most efforts in tomato breeding have been to increase yield at the expense of consumer traits, particularly flavour. In RegulaTomE we are focussing on identifying quality traits and the genes that underpin these traits, which are of primary significance to consumers. We are using methods where the variation identified can be applied rapidly to the tomato crop, so that consumers can experience the benefits of longer shelf-life, improved nutritional status and improved flavour relatively quickly.

Useful variation identified in the IL populations that extends the shelf life of tomatoes will also reduce post-harvest spoilage significantly, so reducing waste and improving the sustainability of tomato cultivation. All the antioxidants that RegulaTomE will focus upon are also of nutritional significance (vitamins A, B, C, E and polyphenols). Enhancing the nutritional value of tomato will be very beneficial to consumers, world-wide, to prevent the increasing incidence of diet-related chronic diseases. Tomatoes with enhanced antioxidant capacities could be classified as functional foods, should trials prove their efficacy. Functional food is defined as food that is taken as part of the usual diet and has beneficial effects that go beyond nutritional effects. Functional food is gaining increasing market shares and a recent lower-bound estimate indicated a size of EUR 6.4 billion for the EU market. If it is possible to identify genes regulating the production of these antioxidants, it should also be possible to identify equivalent genes in other fruit crops and enhance antioxidant levels in them, either by breeding, or by genetic engineering. Traits identified will also affect nutritional quality and flavour, which can be introduced relatively rapidly into commercial varieties, to meet consumer demands.

RegulaTomE is unique in its objectives of developing the S.lycopersicoides ILs for capturing currently unused variation. Many other projects in Europe and the US are using ILs from different wild relatives of tomato (for example S.habrochaites, S. pimpinellifolium, S.peruvianum, S.chilense). These are major tools being used by Dani Zamir on his ERC award to improve yield in this crop and RegulaTomE will work very closely with him to develop further the S.lycopersicoides ILs. Some other populations, developed by private companies, are extremely difficult to access by the research community. RegulaTomE has chosen the S.lycopersicoides ILs to develop because they are the result of the widest cross to tomato and should therefore reveal more variation than other populations, and they have been used in only a limited capacity, so far. It is the intention of the Consortium that all the data from RegulaTomE should be publically available at the earliest point possible, so ensuring that the data will benefit the community as well as those involved in the project.

Few groups have linked antioxidant capacity to shelf-life of fruit, although there are many research projects, world-wide, investigating post-harvest physiology of fruit. The efforts invested in RegulaTomE may well underpin new strategies to breed for extended shelf-life in other fruit. The major antioxidants of tomato fruit are all nutritionally beneficial compounds, so the RegulaTomE activities will serve to identify means of enhancing the nutritional value of the fruit as well. Again, there are European groups in Italy (INEA), France (INRA Avignon) and Spain (University of Malaga) and internationally (Plant & Food Research New Zealand) with programs to enhance vitamin content of tomato, but none are undertaking attempts to identify regulators of these pathways. RegulaTomE will attract researchers to use its new tools and resources to identify novel variation or new regulators of metabolism or fruit development, for greater fundamental understanding and further improvement of quality traits in tomato.