Integrating genetics and high throughput genomics to identify genes underlying tomato QTL for metabolites that influence fruit quality (TOMQML)
Lead Research Organisation:
Royal Holloway University of London
Department Name: Biological Sciences
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.
People |
ORCID iD |
Paul Fraser (Principal Investigator) | |
Peter Bramley (Co-Investigator) |
Publications
Perez-Fons L
(2014)
A genome-wide metabolomic resource for tomato fruit from Solanum pennellii.
in Scientific reports
Jones MO
(2012)
Characterisation of alleles of tomato light signalling genes generated by TILLING.
in Phytochemistry
Wehrens R
(2014)
Metabolite profiling in LC-DAD using multivariate curve resolution: the alsace package for R
in Metabolomics
Garcia V
(2016)
Rapid identification of causal mutations in tomato EMS populations via mapping-by-sequencing.
in Nature protocols
Fernie AR
(2011)
Recommendations for reporting metabolite data.
in The Plant cell
Mortimer C
(2012)
The identification and rapid extraction of hydrocarbons from Nicotiana glauca: A potential advanced renewable biofuel source
in Phytochemistry Letters
Karlova R
(2011)
Transcriptome and metabolite profiling show that APETALA2a is a major regulator of tomato fruit ripening.
in The Plant cell
Fitzpatrick TB
(2012)
Vitamin deficiencies in humans: can plant science help?
in The Plant cell
Description | This was entered on the previous Jes system. 1. The metabolite screening of sub-ILs (113 Chr2 and 41 Chr3 marker defined QTL-NILs, 10 tagged fruits) have identified and delivered a number of small (25 to 50 cM) regions from exotic tomato species that can be introgressed into tomato backgrounds that confer consumer traits. Thus to the breeder the project has delivered the molecular tools necessary to breed new tomato varieties with improved consumer health traits. Presently these regions are undergoing evaluation in Syngenta's elite germplasm. 2. MS libraries have been extended and spectral information provided to the Golm Metabolome Database (GMD), gmd.mpimp-golm.mpg.de 3. The fruit tissue from all the sub-ILs has been archived as a freeze-dried powder. This provides a valuable resource for other projects, including epigenetic and functional screening. 4. Macros and algorithms have been developed and modified to facilitate the processing of the large datasets generated. This has created a pipeline or workflow to enhance the data processing outputs, especially data derived from direct infusion MS. 5. The datasets created provided a valuable resource for future systems biology projects that could help construct a virtual fruit interface. This resource will soon be available as FruitNet. Fundamental scientific advances have been generated to address (i) the role of metabolite profiling in identifying QTL, (ii) the organization of fruit metabolism, (iii) molecular markers for improved traits and (iv) the processing and management of large datasets. 6. The RNA-Seq has revealed candidates that could act as markers and new regulators for quality traits in tomato fruit ripening. 7. New QTL for tocopherols identified. |
Exploitation Route | Applying for BBSRC grants - unfortunately the innovative system of finance is not compatible with the Syngenta system. |
Sectors | Agriculture, Food and Drink,Chemicals,Education,Environment,Manufacturing, including Industrial Biotechology,Retail |
URL | http://pure.rhul.ac.uk/admin/workspace |
Description | This was entered on the previous Jes system 1. The S.pennellii and S.habrochaites datasets include 2000 molecular features for each IL in the collections. These data has been deposited with SGN (www.solgenomics.net) and can be accessed via Lukas Mueller (Iam87@cornell.edu). 2. In addition it has also been deposited with Phenome-networks (www.phenome-networks.com), contact; Dr Yaniv Semel, Yaniv@phenome-networks.com. 3. The datasets will also been available on the FruitNet website which is being developed at Nottingham. In all cases (1 to 3) interfaces are being developed to enable easy of use and visualization of the data. A disclaimer and MTA have been provided for the use of the data to ensure the correct acknowledgements are used and proof of concept research be carried out. If commercial enterprises wish to use the datasets then an agreement has to be agreed and put in place first, via the research and enterprise offices at RHUL and Nottingham. 4. Chr2 ad 3 metabolite datasets will be subjected to the same procedure. These are close to being deposited once the manuscript is ready for submittion and Syngenta have an opportunity to capture IP. 1. The expertise developed in metabolomics has led to the following collaboration with CIAT and developing crops: Capturing biochemical and genetic diversity in Root, tuber and banana for developing countries, Total £450, 000 (18% overheads) start 01.01.13 to 31.12.16. 2. TomCom: Tomato fruit composition Horticulture Development Council funded, £22,000 01.05.12 to 27.02.13 3. TomNET Link award with Syngenta: The validation, characterisation and translation of outputs derived from network analysis and QTL mapping of tomato fruit quality traits. PI-Dr Fraser, BBSRC-LINK. (total £1.2 million, £600,000 to RHUL), duration: 3 years 01.10.12 to 31.09.15. 4. BBSRC-Syngneta Industrial CASE award: Understanding colour intensity and retention in Capsicum fruit and products as a means of improving product quality. PI-Dr Fraser, BBSRC, BB/10155.90/1. £104,816, duration: 4 years 01.10.11 to 30.09.15. 5. BBSRC-Syngenta Industrial Case award:The molecular and biochemical characterisation of a Capsicum derived phytoene synthase-1 underlying an important fruit colour QTL. BB/K01210X/1: £104,816, duration: 4 years 01.10.13 to 30.09.17. 1. The PI organised a pan-European metabolite training school for early stage researchers. There were 140 applicants for 14 places. The 14 participants chosen were from 14 different countries. One day in the four day course was spent at Syngenta. An ideal example of what could be performed in a BBSRC skills school. The PI gave two days of talks and the researcher employed a lecture and practical demonstration. 2. Four training visits in metabolite profiling were provided by the PIs laboratory, two to ESR and two to researchers from developing countries. 3. The researcher employed on the project provided a lecture and training session for School pupils as part of a taster day for schools. 4. Participation in SET days (science open days), including poster presentations and practical demonstrations by the co-PI and researcher. 5. Two placements for school pupils. 6. Two Science talks at local schools. 7. Co-PI provided a general scientific talk to the local community. 8. Small movie describing the scientific approaches used in the project as part of the departments' promotional video. 9. PI presentation to the tomato growers association. 10. PI presentation on modern approaches to tomato breeding to Flavour fresh (vegetable producers) at Preston site. 11. PI presentation on modern approaches to tomato breeding to Wight salads (vegetable producers) at Isle Wight site. 12. PhD outputs have showed new gene functions related to improved ripening. 13. Further transcription factors identified. |
First Year Of Impact | 2016 |
Sector | Agriculture, Food and Drink,Chemicals,Education,Manufacturing, including Industrial Biotechology,Retail |
Impact Types | 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 |
Description | POC award NIBB high value chemicals from plants |
Amount | £50,000 (GBP) |
Funding ID | POCPROVITA |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 07/2017 |
End | 06/2018 |
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 | Industrial collaboration |
Organisation | Syngenta International AG |
Department | Syngenta Ltd (Bracknell) |
Country | United Kingdom |
Sector | Private |
PI Contribution | Analysis of volatiles present in the EpiRil population |
Collaborator Contribution | Funding |
Impact | outputs not ready yet |
Start Year | 2020 |
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 |
Title | Carotenoid standards |
Description | Carotenoid reference standards |
Type Of Technology | New Material/Compound |
Year Produced | 2022 |
Impact | RHUL are selling the carotenoid reference standards. |
Title | MS Libraries for GC/MS |
Description | The customised MS searchable libraries used for the metabolite profiling of metabolites have been updated with new enteries fromthis projects outputs to date. |
Type Of Technology | New/Improved Technique/Technology |
Year Produced | 2019 |
Impact | Improved MS searable libraries for GC/MS |
Description | College open days |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Public/other audiences |
Results and Impact | College open days talks on the projects and discussion groups. |
Year(s) Of Engagement Activity | 2022 |
Description | College public Open days |
Form Of Engagement Activity | Participation in an open day or visit at my research institution |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Public/other audiences |
Results and Impact | Routine 50 school pupils or general public are shown theresearch facilities and ongoing projects are described. A Q and A session is included. |
Year(s) Of Engagement Activity | 2009,2010,2011,2012,2013,2014,2015,2016 |
URL | https://www.royalholloway.ac.uk/science/sciencefestival/home.aspx |
Description | General public |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | Communication forum on New plant breeding techniques "People Jury" virtual |
Year(s) Of Engagement Activity | 2021 |
Description | Industry Wight salads |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Industry/Business |
Results and Impact | Presentation to tomato grower Wight Salads |
Year(s) Of Engagement Activity | 2012 |
Description | Industry visit Flavour fresh preston |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Industry/Business |
Results and Impact | Talk to tomato industry Flavour fresh |
Year(s) Of Engagement Activity | 2011,2012 |
Description | School visit |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Schools |
Results and Impact | Talk and forum by Dr Enfissi on healthy diets and plant based foods |
Year(s) Of Engagement Activity | 2021 |
Description | School visit |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Schools |
Results and Impact | Dr Enfissi provide talks and practical classes (separation of colours by chromatography) to school children. |
Year(s) Of Engagement Activity | 2019 |
Description | Schools taster day |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Schools |
Results and Impact | School science taster day |
Year(s) Of Engagement Activity | 2020 |
Description | Talk to Tomato growers association |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Industry/Business |
Results and Impact | Talk on project to the tomato growers association |
Year(s) Of Engagement Activity | 2013 |
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 |