The regulatory network controlling tomato ripening

Lead Research Organisation: University of Nottingham
Department Name: Sch of Biosciences


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.


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Description Generated time-series gene-expression and metabolite profiling datasets for growing and ripening fruit for wild type and 3 mutant varieties. These data have been used to discover:
(1) novel regulators of developmental transitions and ripening.
(2) the genes responsible for the epigenetic transition that occurs during ripening
Exploitation Route Other factors important for fruit growth and development can now be discovered in the data.
Sectors Agriculture, Food and Drink

Description Patent filed in conjunction with Syngenta
First Year Of Impact 2012
Sector Agriculture, Food and Drink
Impact Types Economic

Description Continuing industrial commitment from Syngenta in the form of a BBSRC LINK grant to Royal Holloway 
Organisation Syngenta International AG
Department Syngenta Seeds
Country Switzerland 
Sector Private 
PI Contribution The validation, characterisation and translation of outputs derived from netword analysis and QTL mapping of tomato fruit quality traits (TomNET) BBSRC BB/J016071/1
Start Year 2012
Description Title: Modulation of Solanaceae fruit ripening. The patent describes an invention rising from systems biological analysis of the fruit ripening process in tomatoes. 
IP Reference WO2012041856 
Protection Patent granted
Year Protection Granted
Licensed No