The validation, characterisation and translation of outputs derived from network analysis and QTL mapping of tomato fruit quality traits (TomNET)

Tomato (Solanum lycopersicum) is the most important fruit crop in the world by volume consumed, with annual production of 150 million metric tons. Tomatoes are high value products with an annual value in 2009 of around 32 billion US dollars covering both processed and fresh products. They are a major component of healthy diets and provide ready sources of vitamins A, C, E and K, minerals including K and Fe and the lipophilic antioxidant lycopene (the pigment responsible for the characteristic red colour of ripe tomato fruit). There is a wealth of scientific evidence that now exists to corroborate that the consumption of fruits and vegetables is beneficial to human health. These benefits have been attributed to the presence of health promoting phytochemicals or "bioactives" in the food matrix. The challenge, particularly, in Western societies, is to deliver to the consumer better tasting, more nutritious tomatoes and other fruit which have a prolonged shelf-life at a cost affordable to the majority of consumers. The most important quality traits in tomato are colour, texture, flavour and nutritional content. Texture can also impact on taste, the release of nutrients and perhaps most importantly shelf-life. In the UK it is estimated that 40% of the food waste is uneaten fruits and vegetables.
In addition to its economic and societal role, tomato has become a well established scientific model for understanding the development and ripening of fleshy fruit bearing crops, with strong evidence that many of the gene networks controlling ripening have been conserved across different taxa. In fruit crops, the key controller of quality traits is the process of ripening. The aim of TomNET project is to deliver better quality tomato fruit. Our approach will integrate systems analysis and quantitative genetic studies to identify and modulate regulatory genes that allow precise control of fruit development and the ripening process. By harnessing tomato wild-species variation, we can deliver these scientific discoveries into commercial practice in collaboration with Syngenta; our industrial partner in this LINK project.
The project will build on several important resources and findings. Firstly a regulatory network holistically describing the interaction of gene transcripts during fruit development and ripening. Using computational approaches putative regulators of the ripening process have been identified. We have shown that one of these regulators can improve tomato fruit colour. Simultaneously, flavour related compounds responsible for good tasting fruit products are increased. In this project we will use the gene networks to identify additional regulators of ripening that display the potential to alter key fruit quality traits. For the transcriptional activator termed high pigment-4 (HP4), which we have validated as an important modulator of ripening related traits, detail characterisation at multiple levels of regulation will be carried out to ascertain the underlying mechanisms by which the gene product can exert its effects and influence the ripening process. The other key foundation of this project is the identification of genes underlying a complex QTL for texture. Within the target region several interacting components have been identified. In the project the function and interaction between these components will be elucidated by using stable transgenic lines. Combining the enhanced colour and texture traits will also be attempted. Finally natural variation will be exploited to deliver these traits into commercial elite backgrounds thus translating science discovery through to commercial practice.

Building on outputs derived from transcriptional networks constructed for tomato fruit development and ripening and from quantitative genetics studies. We will now validate, characterise and translate the molecular tools identified into commercial backgrounds using the following technical approach.
1. Exploitation of the ripening regulatory network. Following our successful identification of a network derived transcription activator (HP4), involved in fruit pigmentation. Further functional testing of candidate genes regulating ripening and especially colour, texture and flavour will be carried out using Virus Induced Gene Silencing (VIGS) and through the generation of stable transgenic lines.
2. Characterisation of the HP4 transcriptional activator. In order to elucidate the underlying mechanisms associated with the action of HP4 in conferring ripening associated quality traits, we will perform an integrative multi-level approach to characterisation of the phenotype including detailed metabolomics.
3. Testing the involvement of QTL derived candidates in altering fruit texture. Candidate genes underlying texture QTL on tomato chromosomes 2 and 3 will be tested in transgenic plants. Detailed phenotypic assessment including texture, determinations, transcript and metabolite profiling and cell wall analysis will elucidate the biochemical and molecular mechanisms responsible for the enhancement of texture and shelf-life in our target QTL regions.
4. Combining enhanced colour and texture phenotypes. Crosses will be performed to ascertain how mutant alleles and QTLs responsible for colour and texture-based traits will function in combination and if they act in a synergistic manner.
5. Delivery of the traits into commercial practice. Using the unique resources of our industrial partner we will demonstrate the translational potential of candidate genes or QTL regions by marker assisted introgression into the parent of an elite hybrid.

The outputs from the proposal will have significant economic and societal impacts. The economic beneficiaries will include Syngenta, the largest UK affiliated Global Agricultural Biotechnology Business. This multinational company with one of its major International R+D sites at Jealott's Hill near Bracknell and the industrial partner in this LINK application. The Syngenta Vegetable Seeds business is worth several £ bn to the company annually. Tomato is the highest value crop. Syngenta will benefit from the development of new elite tomato lines that add significant value to their seeds portfolio. The IP will be capture through international patent applications. They will also benefit from enhanced knowledge that can be applied to other crops including other Solanaceae such as sweet pepper fruits. There is now compelling evidence that genes regulating ripening are conserved across fleshy fruit species offering opportunities to exploit knowledge from TomNET for crop improvement of other fleshy fruit bearing species. We anticipate that TomNET will have benefits beyond our industrial sponsor. The British Tomato Growers utilize Syngenta lines and improved products normally lead to increased demand from the consumer. The UK fresh market in tomato products, has a retail value in excess of £0.5bn / year at present and the market is expanding. Fresh produce is of course a major line of business for retailers such as Tesco, Sainsbury, Waitrose, which are some of the largest companies in the UK. They will benefit by the added value of improved product quality, nutritional status and shelf-life resulting in higher profits from consumer demand and repeat purchase. The most important benefits should be to consumers in the UK and elsewhere. Benefits to the UK public should include improved products with longer shelf-life. Also better quality foods encourage repeat purchasing and increasing the consumption of fruit and vegetables is a major target for improving diet and towards healthier aging for the population. A secondary economic benefit will be that the UK Government benefits through enhanced tax receipts from the companies and success in the private sector can lead to job creation.
To be competitive and reap the benefits this brings in a global economy, the UK needs a strong R+D base and a skilled workforce. The UK R+D sector will benefit from projects that attract industrial investment. TomNET provides training for PDRAs within the context of the demands of an industrial sponsor. This will enhance skills in the work force and the competitiveness of UK R+D. Syngenta have access to global R+D efforts and are under no obligation to make a UK based investment on criteria other than internationally competitive science coupled with value for money. The pathways for communicating the results to industry and academia are well established and will involve high impact publications and dissemination through scientific and public events such as the International Solanaceae Conference, UK Plant Science Federation events and also the tomato growers annual conference and the Society of Biology. The UK must be involved in internationally competitive projects using state of the art multidisciplinary and integrative biology approaches that take science discovery through to commercial practice.