The global tomato industry is worth in excess of $10 billion. More than 100 million metric tonnes of tomatoes are produced each year, and in the United States and Western Europe it is the most important fruit in the human diet in terms of quantity consumed. A diet rich in fruits and vegetables is known to be essential for human health providing protection from heart disease, stroke, high blood pressure and certain cancers. This project focuses on understanding the molecular basis of fruit quality attributes in partnership with Syngenta, a company with a world wide tomato business. The strategy will be to compare the molecular events occurring in the fruits of wild type and naturally occurring non-ripening mutants of tomato. The regulatory genes underlying these mutations have recently been identified. The challenge is to connect the emerging network of regulatory factors with their down-stream effectors and thereby identify control points for the various ripening pathways, for example, colour development and fruit softening. We will achieve this aim by profiling the gene expression and metabolite pools of wild type and mutant tomato fruit at a wide range of stages of fruit development. Mathematical modelling techniques will then be used to associate regulators with down-stream effects and metabolites, to produce an initial regulatory framework. These models can then be tested experimentally by silencing selected transcription factors in transgenic plants and determining how this affects the patterns of gene expression, metabolite pools and ripening. This will allow us to build dynamic models to describe this important developmental process. Our industrial partner will use the information to breed improved tomato varieties.

One of the biggest challenges of our time is to feed the growing global population. World arable land is practically at its maximum capacity, and will decrease in coming years due to climate change and urban development. Therefore, the productivity of our food system must be increased to tackle world hunger and increase food security. One exceptional strategy to achieve this goal is to reduce losses by pests. Barley (Hordeum vulgare) is the fourth most important crop worldwide and second in the UK. Diseases, including those caused by the brown rust Puccinia hordei and Ramulaira collo-cygni, represent the largest threat to barley, causing yield losses of up to 40%. Based on their lifestyle and interaction with the host, pathogenic fungi can be classified as either biotrophic or necrotrophic. The key difference between biotrophic and necrotrophic fungi is that biotrophic fungi derive nutrients from living plant cells, maintaining them alive, while necrotrophic fungi kill the plant tissues and then obtain nutrients from them. However, many pathogenic fungi use sequential biotrophic and necrotrophic infection phases. During the biotrophic phase they invade and extensively colonise the plant with minimum damage, before switching to the often fatalnecrotrophic phase. Importantly, fungicides are most effective at reducing disease when applied during the early biotrophic stages of infection, but since this phase cannot be visually identified, they are often applied too late when the pathogen is already well established. In response to pathogen attack, plants initiate immune responses that are sufficient to fend off most pathogens. However, adapted pathogens secret effector proteins that are capable of suppressing the host immune response and promote successful infection, causing severe crop damage. These effectors are constantly evolving, thereby avoiding existing host resistance or current plant protection strategies. Consequently, alternative methods to enhance crop resistance are required. The use of immune elicitors or protective biostimulants is a highly promising sustainable method for inducing long-lasting disease resistance, but the modes of action and plant cell targets of these chemicals remain unknown. Plants use the conserved protein ubiquitin to regulate immune responses. Ubiquitination is a fast and reversible protein modification that regulates the amplitude and intensity of the immune response. Using a proteomic pipeline developed in our laboratories, we discovered that protein ubiquitination is a far better biomarker for early biotrophic pathogen infection than currently available genomic and transcriptomic markers. Our results in barley cultivars on a field trial with P. hordei showed a general ubiquitin-mediated immune activation of all infected barley cultivars, implying that ubiquitin regulation of the immune system is a conserved mechanism across cultivars. Therefore, in this project we will investigate the ubiquitin-dependent response of barley to elicitors/biostimulants and economically relevant pathogens with changing lifestyles. These will be compared to the ubiquitin proteomes of plant immune hormones responsive to biotrophic and necrotrophic stages, revealing the modes of action of elicitors/biostimulants and precisely identifying when pathogens change their lifestyle, identifying new biomarkers for early detection of the 'invisible' biotrophic disease phase. In summary, this project will address a crucial gap in knowledge and uncover new fundamental insights into the activation and modulation of plant immunity during biotrophic and necrotophic fungal infections, and real the mode of action of elicitors and biostimulants, which will be used to enhance crop resistance. These novel, sustainable approaches will have a significant impact on global food security and drive innovation in the agrifood sector.

Doctoral Training Partnerships: a range of postgraduate training is funded by the Research Councils. For information on current funding routes, see the common terminology at https://www.ukri.org/apply-for-funding/how-we-fund-studentships/. Training grants may be to one organisation or to a consortia of research organisations. This portal will show the lead organisation only.

Doctoral Training Partnerships: a range of postgraduate training is funded by the Research Councils. For information on current funding routes, see the common terminology at https://www.ukri.org/apply-for-funding/how-we-fund-studentships/. Training grants may be to one organisation or to a consortia of research organisations. This portal will show the lead organisation only.

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.