Developing a novel platform to determine the epidermal layer transcriptome in plants based on RNA-seq allele-specific expression

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Who will benefit? Those who will benefit from this research are academics working on processes occurring in the epidermis, especially those researching tomato. Bioinformaticians will benefit from our methodology to analyze and visualise RNA-seq data. Through novel discoveries made in our platform industrial contacts will benefit through licensing patents and developing new processes and tomato varieties. Ultimately, as tomato is a key crop that is central to human nutrition and the global diet, this research will benefit the public at large. How will they benefit? Although our research is fundamental it will have many avenues of impact especially as it is designed to be a platform for further experimentation and exploitation. Key to this is the use of tomato that is a model system for fleshy fruit production and also an important crop in its own right. In 2008 tomato production was ~130 million tonnes that had a value of ~$50 billion USD, (FAOSTAT). It is also nutritionally very important providing key sources of anti-oxidants such as lycopene, flavanols and vitamin C. The PI is always keen to maximise the impact of his research and has continued working on tomato because its importance as a food crop. In order to maximise the impact of the research we will place all data in the public domain in a timely manner. We will follow the exemplary lead of our project in sequencing the tomato genome, whereby all sequence data has been placed in the public domain for all to use, almost as soon as it has come off the sequencing machines. We will continue to work on this principle in order to ensure the highest impact of our research. Such communication to the research community is essential and Dr Bishop has been instrumental in setting up the annual UK-SOL meetings (http://www.uk-sol.org/index.htm) in which progress of the tomato genome sequencing programme has been reported along with talks on recent research from leaders in UK and worldwide labs. Representatives from UK industry have also given talks and/or participated in these meetings. He was also one of the leading researchers organising the annual international SOL meeting of ~280 participants. We have requested funds to go to the 2012 SOL meeting and will provide a workshop demonstrating the web-based resources that we have generated. This will ensure rapid dissemination and exploitation of our data. To ensure rapid use of our novel data we have already discussed the underlying idea in confidence with Imperial Innovations, the College's technology transfer company, and also with Syngenta. Initiating such avenues of intellectual property transfer at the early stages of research will enable efficient and timely exploitation of the research outputs when required. It is also evident that although our research is fundamental it will have many potential avenues for benefiting the tomato and related crops. Groups likely to benefit include plant breeders, plant biotechnology companies, agrochemical companies and bioenergy industries. Communicating our project to the public is also critically important to us and we have been involved in generating press releases for the initial phase of the sequencing project that have been used by the national press (The Guardian) the Grower and BBSRC Business. The PI has been trained by the BBSRC in effective communication with the press and will be willing to highlight the key impacts that this research will have especially in the areas that plant breeding companies are striving to improve. This includes the development of stress-tolerant and pathogen/insect-resistant varieties of horticultural crops that will be vital in providing an expanding population with fresh produce but using less input. Also our insights into the genes that encode the fruit epidermal layer will provide important leads to make tomatoes tastier. Similarly all research is communicated to the academic research community via research articles in peer-reviewed journals.