The regulatory network controlling tomato ripening
Lead Research Organisation:
Royal Holloway University of London
Department Name: Biological Sciences
Abstract
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.
Technical Summary
Tomato is probably the most important fruit in the western diet and is also a model for understanding the development and ripening of fleshy fruits. In partnership with Syngenta, we want to understand the molecular basis of fruit ripening and use this information to breed improve tomato varieties. In tomato, there are a small number of distinct single gene mutants where ripening is almost completely abolished. The genes underlying these mutations have been cloned by us and others. In this application we will analyse the transcriptome and metabolome of wild type and non-mutant tomato fruit at 8 stages of fruit development and ripening, and use the information to build dynamic models that describe the ripening process. To achieve this aim we will draw on a range of unique and public genomics resources. The transcriptomics data will be obtained using the Syngenta GeneChip array containing sequences that represent 22000 genes. Syngenta will undertake the metabolomics assays and will capture information on at least 60 compounds in an untargeted screen, as well as targeted quantitative analysis for carotenoids, polyphenols and flavonoids. The data analysis will then be undertaken within the Centre for Plant Integrative Biology (CPIB), but with additional inputs from Syngenta using their proprietary tomato-specific metabolic-network. Time-Series Network Identification and Bayesian Network Reconstruction will be used to build initial network models connecting transcription factors to down-stream genes and metabolites. These and subsequent dynamic models will provide hypotheses for testing in tomato using virus induced gene silencing (VIGS). The models will then be refined from the array and metabolite profiles of the fruit where transcription factor expression has been modulated. A final refined model will be used to select targets for the development of novel varieties.
People |
ORCID iD |
Paul Fraser (Principal Investigator) |
Publications
Fernie AR
(2011)
Recommendations for reporting metabolite data.
in The Plant cell
Jones MO
(2012)
Characterisation of alleles of tomato light signalling genes generated by TILLING.
in Phytochemistry
Pan Y
(2013)
Network inference analysis identifies an APRR2-like gene linked to pigment accumulation in tomato and pepper fruits.
in Plant physiology
Description | RHUL only had a small contribution in this project but from the networks and metabolite data related to fuit ripening that can be exploited to identify metabolite changes. |
Exploitation Route | Candidate genes related fruit ripening can be identiifed and their function characterised in further funding. |
Sectors | Agriculture, Food and Drink,Chemicals,Environment,Manufacturing, including Industrial Biotechology,Retail |
Description | Understanding of cnsumer preference fro fruit quality traits. |
First Year Of Impact | 2015 |
Sector | Agriculture, Food and Drink,Chemicals,Manufacturing, including Industrial Biotechology,Retail |
Impact Types | Societal,Economic |
Description | EU FP7 |
Amount | € 677,000 (EUR) |
Funding ID | DISCO |
Organisation | European Commission |
Sector | Public |
Country | European Union (EU) |
Start | 11/2013 |
End | 10/2017 |
Title | Solanaceae Genome Network |
Description | Inputed large sacle datasets |
Type Of Material | Database/Collection of data |
Year Produced | 2013 |
Provided To Others? | Yes |
Impact | The data has been utilised by other scientists and industry |
URL | https://solgenomics.net/ |
Description | Nottingham University |
Organisation | University of Nottingham |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | The analysis of metabolites and proteins |
Collaborator Contribution | The analysis of metabolites and proteins |
Impact | 1. Two patents 2. Three papers |
Start Year | 2010 |
Description | Syngenta Ltd |
Organisation | Syngenta International AG |
Department | Syngenta Ltd (Bracknell) |
Country | United Kingdom |
Sector | Private |
PI Contribution | Identification of QTL |
Collaborator Contribution | RNA-Seq, elite lines, chemical analysis |
Impact | One patent and one publication |
Title | Modulation of tomato fruit ripening |
Description | Academia and industry partnership |
IP Reference | EPA10183748.2 |
Protection | Patent granted |
Year Protection Granted | 2015 |
Licensed | Yes |
Impact | Syngenta applied the technology into elite backgrounds |
Description | College open days to the public |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Public/other audiences |
Results and Impact | Talks, lab tours and leaflets to 50 members of the general public to explain the research activities. |
Year(s) Of Engagement Activity | 2018 |
Description | Waitrose retailer |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Industry/Business |
Results and Impact | Discussion on collaboration and funding |
Year(s) Of Engagement Activity | 2012,2015 |
Description | traing schools for ESRs |
Form Of Engagement Activity | Participation in an open day or visit at my research institution |
Part Of Official Scheme? | Yes |
Geographic Reach | International |
Primary Audience | Participants in your research and patient groups |
Results and Impact | The scheme was adopted by many COST actions The people attending the course were able to publish in higher impact journals |
Year(s) Of Engagement Activity | 2012 |