Integrating genetics and high throughput genomics to identify genes underlying tomato QTL for metabolites that influence fruit quality. (TOMQML)

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

Abstract

Fruits are an immensely important part of the human diet. Low fruit and vegetable intake is recognised as a major factor for increased risk of heart disease and certain cancers. Encouraging people to consume more fruit in their diet is not necessarily straight forward and depends on factors including cost and product quality. Some of the most important changes in fruit quality related to ripening involve the accumulation of primary metabolites such as sugars and acids which influence taste. Also alterations in the levels of secondary metabolites such as carotenoids and phenylpropanoids can have a significant impact on nutritional quality. The challenge is to understand how these individual ripening changes are controlled /modulated and develop commercially viable strategies for breeding novel and better fruit products. This project focuses on tomato as it is the most widely consumed fleshy fruit in the human diet, with a global value in excess of $10 bn. It has become the model for studying the development and ripening of fleshy fruits and a wealth of genetic and genomic resources are available. We will use a range of well characterised publicly available tomato lines and novel tomato genetic resources combined with a range of genetic and molecular approaches to identify the genes controlling tomato taste and the accumulation of health enhancing phytochemicals. In concert with these approaches, we will identify the links between major regulators of ripening and their associated metabolite changes. The project will make an important contribution to fundamental knowledge about the molecular basis of fruit ripening. The consortium consists of internationally recognized groups from universities and research institutes in Europe and the USA as well as a global supplier of vegetable seeds, collectively ensuring a framework for innovative excellence.

Technical Summary

Fruits are an immensely important part of the human diet. Low fruit and vegetable intake is recognised as a major factor for increased risk of heart disease and certain cancers. This project focuses on identifying genes in tomato that are involved in the accumulation of primary metabolites such as sugars and acids which influence taste and alterations in the levels of secondary metabolites such as carotenoids and phenylpropanoids that can have a significant impact on nutritional quality. We will combine state of the art high throughput genomics technologies with quantitative genetic approaches for rapid identification of genes underlying tomato metabolite QTL. In concert with these approaches, we will identify the links between major regulators of ripening, e.g. RIN, CNR and their associated metabolite changes. We will achieve our objectives by using the 76 S. pennellii ILs, around 500 publicly available sub-ILs and new fixed recombinant lines (QTL-NILs) from these ILs. Additional populations will be used to capture allelic diversity. QTL for around 20 key primary and secondary metabolites already identified on the 76 S. pennellii ILs will be resolved to specific sub-lines or QTL-NILs. A new screen for ILs bearing QTL that can influence the retention of metabolites after harvest will also be undertaken. Candidate genes will then be nominated based on metabolomics and expression information from the ILs and sub-ILs. This process will be aided by the development of co-expression networks. Concurrently, we will proceed with positional cloning of 8 preselected QTL using a high-throughput marker platform. The project will make an important contribution to fundamental knowledge about the molecular basis of fruit ripening. The consortium consists of 7 internationally recognized groups from universities and research institutes in Europe and the USA as well as a global supplier of vegetable seeds, collectively ensuring a framework for innovative excellence.
 
Description Main objective was to identify candidate genes under a range of metabolite QTL. This has been achieved. Several candidate genes were identified and have subsequently been validated in transgenic plants as part of the BBSRC TomNET project. Some of these are being taken forward by Syngenta as part of their tomato breeding programme. These have included those linked to fruit texture and shelf life on chromosome 2 and 3. Work on colour development and taste-related genes has been published and papers are linked to this award.
Exploitation Route Findings are being taken forward by an industrial partner within their tomato breeding programme
Sectors Agriculture, Food and Drink

 
Description The outputs will influence breeding programmes for fruit and vegetables. Regions of the tomato genome were identified that had a strong effect on enhancing the health promoting compounds and colour of tomato. This information is being used in industrial partners breeding programme for tomato and pepper
First Year Of Impact 2012
Sector Agriculture, Food and Drink
Impact Types Societal,Economic

 
Description SFS-7a-2014: Traditional resources for agricultural diversity and the food chain H20:20
Amount € 295,000 (EUR)
Organisation European Commission 
Department Horizon 2020
Sector Public
Country European Union (EU)
Start 09/2015 
End 03/2018
 
Title Germplasm resources for tomato genetics and crop improvement 
Description Germplasm resources in the form of 20 new S. pennellii marker defined Micro-introgression lines spanning specific regions on tomato chromosome 2 have been supplied to Professor Dani Zamir at the Hebrew University of Jerusalem for distribution to the international community. 
Type Of Material Biological samples 
Year Produced 2011 
Provided To Others? Yes  
Impact The seeds will be distributed to researchers and will facilitate map-based cloning of genes underlying important QTL 
 
Description Interaction on map-based cloning of ripening genes and the mechanistic basis of fruit ripening 
Organisation Cornell University
Country United States 
Sector Academic/University 
PI Contribution Sharing of data and ideas relating to the mechanisms controlling fruit ripening
Collaborator Contribution Provision of ideas and resources including access to data. This has resulted in a number of important papers and the collaboration has helped to formulate the now accepted model for the biological basis of fruit ripening
Impact The Tomato Genome Consortium (including Seymour GB) (2012).The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485:635-641 Seymour GB, Ryder CD, Cevik V, Hammond JP, Popovich A, King GJ, Vrebalov J, Giovannoni JJ and Manning K (2011). A SEPALLATA gene is involved in the development and ripening of strawberry (Fragaria × ananassa Duch.) fruit, a non-climacteric tissue. J. Exp. Bot: 62, 1179-1188. Vrebalov, J., Pan, I.L., Matas Arroyo., A.J., McQuinn, R., Chung, M-Y., Poole, M., Rose, J., Seymour, G., Grandillo, S., Giovannoni, J., Irish, V.F. (2009) Freshy fruit expansion and ripening are regulated by the tomato SHATTERPROOF gene TAGL1. Plant Cell 21 3041-3062. Manning K., Tor, M., Poole M., Hong, Y.,Thompson, A.J., King G., Giovannoni, J. and Seymour, G.B. (2006). A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening. Nature Genetics, 38: 948-952.
 
Description TomQML ERAPG grant BB/G02491X 
Organisation Max Planck Society
Department Max Planck Institute Golm
Country Germany 
Sector Public 
PI Contribution UNOTT provided tomato genetic material for the project
Collaborator Contribution MP colleagues were collaborators on this ERANET grant and provided a wild tomato species genome sequence that has helped identify genes under important QTL
Impact Joint publications
Start Year 2009
 
Description TomQML and TomNet grants 
Organisation University of Wageningen
Country Netherlands 
Sector Academic/University 
PI Contribution We have provided critical information to allow joint discoveries pertaining to the molecular mechanisms controlling fruit ripening
Collaborator Contribution Colleagues at Wageningen have been partners on TomQML and involved in TomNet
Impact One paper already published on the Transcriptional Control of Fruit Ripening and a further publication to come in 2016.
Start Year 2009
 
Title MODULATION OF SOLANACEAE FRUIT RIPENING 
Description The present invention relates to a transcription factor gene that plays a key role in Solanaceae fruit ripening. Plants overexpressing the gene have fruits with deeper pigmentation and ripen more rapidly than controls. The invention also relates to transgenic plants comprising said gene, and methods of making said plants. 
IP Reference WO2012041856 
Protection Patent application published
Year Protection Granted 2012
Licensed Yes
Impact Enhancing colour and health promoting phytochemicals in fruit crops. The application will directly impact tomato and pepper breeding
 
Title TOMATO FRUIT HAVING INCREASED FIRMNESS 
Description Identification of genes underlying tomato firmness and shelf life 
IP Reference WO2011051120 
Protection Patent application published
Year Protection Granted 2011
Licensed Yes
Impact Information is being used to breed better tomato fruit with increased shelf life, but good flavour
 
Description Interview for BBC Farming Today 26th July am 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Interview on Radio 4 Farming today programme related to my discovery of the gene controlling tomato fruit softening and how it will help breed tomato fruits with long shelf life while maintaining excellent taste
Year(s) Of Engagement Activity 2016
 
Description Interview with journalist from the Daily Mail in the UK 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Interview so I could provide information on discovery of gene controlling tomato shelf life and its potential for creating more nutritious tomato products
Year(s) Of Engagement Activity 2016
URL http://www.dailymail.co.uk/sciencetech/article-3707182/Salad-days-Tomato-never-goes-soft-stay-freshe...
 
Description Presentation to the British Tomato Growers about latest developments in tomato research including genome sequence 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Discussion of latest development on tomato genome sequencing project and UK contribution

Tomato Growers showed increased interest and understanding about molecular breeding approaches
Year(s) Of Engagement Activity 2011
 
Description Publicity for the Tomato Genome Project and publication of the project outcomes in Nature 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Media outputs relating to the Genome Sequence and Role of Nottingham University. These included BBSRC and Nottingham University websites for end May and June 2012, BBC website from May 30, 2012.
Example URLs are:
http://www.nature.com/news/tomato-genome-sequence-bears-fruit-1.10751
http://www.bbsrc.ac.uk/news/food-security/2012/120531-pr-international-consortium-sequences-tomato-genome.aspx
http://www.bbc.co.uk/news/science-environment-18253577,
http://www.cbc.ca/news/technology/story/2012/06/01/sci-tomato-genome.html
http://www.eurobiotechnews.eu/news/news/2012-02/tomato-genome-decoded.html
http://news.yahoo.com/tomato-genome-project-bears-fruit-170214265.html
http://www.nytimes.com/2012/05/31/science/the-tomato-ripe-juicy-and-bursting-with-genes.html
http://www.eurobiotechnews.eu/news/news/2012-02/tomato-genome-decoded.html
http://www.thegrocer.co.uk/fmcg/fresh/fruit-and-veg/tomato-genome-set-to-boost-taste-and-health/229610.article


Worldwide publicity about new tomato genome sequence and how it will make a step change in breeding improved varieties. Also how tomato is a model for other Solanceous crops, e.g.potato, pepper, eggplant.
Year(s) Of Engagement Activity 2012
URL http://www.bbc.co.uk/news/science-environment-18253577
 
Description Tomato Growers Conference, Coventry, UK 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Presentation on the Tomato Genome Project to the British Tomato Growers Conference to demonstrate prospects for crop improvement using genomics information

Demonstrated to growers value of rational approaches to breeding that will allow a step change in crop improvement. Also developed contacts that have been useful to extend industry interactions including funding for a recent TSB project on enhancing tomato shelf life.
Year(s) Of Engagement Activity 2011
 
Description public lecture sponsored to the Society of Biology, East Midlands Branch 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Seymour presented a public lecture sponsored to the Society of Biology, East Midlands Branch entitled 'The Tomato
Genome Project' on 17th November 2011 at University of Nottingham.


Discussion around use of molecular breeding
Year(s) Of Engagement Activity 2011
 
Description report in the daily mirror on my work relating to tomato fruit shelf life 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Article in Daily Mirror based on University of Nottingham press release about my discovery of gene controlling tomato fruit softening
Year(s) Of Engagement Activity 2016
URL http://www.mirror.co.uk/science/scientists-create-mutant-tomatoes-could-8496942