18-BTT: Epi-TOM: The development and characterization of an EpiRIL TOMato population
Lead Research Organisation:
Royal Holloway University of London
Department Name: Biological Sciences
Abstract
Tomato (Solanum lycopersicum) is the most important commercial fruit crop in the world with an estimated global net production value well in excess of $50bn [www.fao.org]. On the basis of volume consumed (fresh and processed) tomato products play a crucial role in the human diet, providing essential minerals, vitamins and health promoting bioactive phytochemicals. Presently Marker Assisted Selection (MAS) has been the method of choice to deliver new varieties/hybrids with improved consumer and agronomic traits. MAS is reliant on the exploitation of natural variation. However, it has become apparent that in many crop species including tomato, phenotypic diversity is higher than that expected based on the available genetic variation alone. One explanation for this phenomena is the emerging evidence in plant species that stable inherited epigenetic variation can provide a basis for Darwinian evolution independent of DNA sequence changes.
Using the model plant Arabidopsis, genetically identical recombinant inbred lines harbouring mosaics of methylation (epiRILs) have been created. This has been achieved by crossing two genetically identical lines with the exception that one of the parents is impaired in DNA methyltransferase MET1, a gene required for propagating cytosine methylation during DNA replication. In subsequent generations mosaics of methylation are fixed by self-pollination and single seed descent to F8. a unique epiRIL population in tomato of near homozygous lines with respect to their epigenomes, which will form the foundation of the current project and provide a valuable genetic/chemical community resource. The population consists of 115 lines. To date observable phenotypic differences are evident within the population (e.g. plant height and fruit size) However, the extent of chemical variation linked to consumer and agronomic traits awaits assessment within the remit of the proposed epi-TOM project. The project will deliver important information on the role of epigenetic variation on chemo/phenotypes in a complex genome, which can be exploited for the elucidation of novel quantitative traits with an epigenetic basis (epi-QTL).
Using the model plant Arabidopsis, genetically identical recombinant inbred lines harbouring mosaics of methylation (epiRILs) have been created. This has been achieved by crossing two genetically identical lines with the exception that one of the parents is impaired in DNA methyltransferase MET1, a gene required for propagating cytosine methylation during DNA replication. In subsequent generations mosaics of methylation are fixed by self-pollination and single seed descent to F8. a unique epiRIL population in tomato of near homozygous lines with respect to their epigenomes, which will form the foundation of the current project and provide a valuable genetic/chemical community resource. The population consists of 115 lines. To date observable phenotypic differences are evident within the population (e.g. plant height and fruit size) However, the extent of chemical variation linked to consumer and agronomic traits awaits assessment within the remit of the proposed epi-TOM project. The project will deliver important information on the role of epigenetic variation on chemo/phenotypes in a complex genome, which can be exploited for the elucidation of novel quantitative traits with an epigenetic basis (epi-QTL).
Technical Summary
Tomato is the most important fruit crop in the world and a crop model for plant biology, genomics and fleshy fruit. Fresh and processed tomato products play a crucial role in the human diet, providing essential minerals, vitamins and health promoting phytochemicals. In many crops including tomato, phenotypic diversity is higher than expected based on DNA sequence variation alone. One explanation for this phenomena is emerging evidence that stable inherited epigenetic variation can provide a basis for Darwinian evolution independent of DNA sequence changes. Using the model plant Arabidopsis, genetically identical recombinant inbred lines harbouring mosaics of methylation (epiRILs) were created. This was achieved by crossing two genetically identical lines with the exception that one is impaired in DNA methyltransferase MET1, a gene required for propagating cytosine methylation during DNA replication. In subsequent generations mosaics of methylation are fixed by self-pollination and single seed descent to F8. U The population consists of 115 lines (F8 by autumn 2018). Clear phenotypic differences are evident in the population. The extent of chemical variation for consumer and agronomic traits awaits assessment here. Our goal is to evaluate this population of genetically identical tomato lines with an experimentally induced, mosaic of epigenetic variation (epiRILs) for: (i) their potential to impact agronomic and quality traits, (ii) determine the stability of epigenetic variation under different environmental conditions, and (iii) generate foundational data for further molecular characterization of this population.The extent of chemical variation for consumer and agronomic traits awaits assessment here. Our goal is to evaluate this population of genetically identical tomato lines with an experimentally induced, mosaic of epigenetic variation (epiRILs).
Planned Impact
Global Food Security is and will continue to be a pressing issue. A major component of the solution will be the ability to breed new fit for purpose varieties, delivering higher yields in combination with improved stress tolerance and product quality. This will demand new sources of biological variation accessible within elite backgrounds and suitable for modern intensive but sustainable agriculture. EpiTom will create a new exploitable paradigm in natural variation. The outputs will be important and novel because they address the under explored and poorly understood role of epigenetic variation. This is a new frontier in harnessing natural variation that may help crops withstand abiotic and biotic stress while
delivering high quality nutritious food products. The know-how from this project could be used by breeders to improve performance and quality in tomato and translated to other fruit and vegetable crops. The data will also benefit researchers in universities and industry working on biological variation and the mechanistic basis of plant phenotypes. A revolution in our understanding of molecular mechanisms underlying plant development and the contribution of epigenetics to animal and plant variation is underway and this information will be of general interest.
delivering high quality nutritious food products. The know-how from this project could be used by breeders to improve performance and quality in tomato and translated to other fruit and vegetable crops. The data will also benefit researchers in universities and industry working on biological variation and the mechanistic basis of plant phenotypes. A revolution in our understanding of molecular mechanisms underlying plant development and the contribution of epigenetics to animal and plant variation is underway and this information will be of general interest.
Publications
Berry H
(2023)
The characterisation of phytoene synthase-1 and 2, and 1-D-deoxy-xylulose 5-phosphate synthase genes from red chilli pepper ( Capsicum annuum )
in The Journal of Horticultural Science and Biotechnology
Berry HM
(2022)
Isolation and characterization of sub-plastidial fractions from carotenoid rich fruits.
in Methods in enzymology
Enfissi E
(2021)
New plant breeding techniques and their regulatory implications: An opportunity to advance metabolomics approaches
in Journal of Plant Physiology
Perez-Fons L
(2022)
Metabolomic approaches for the characterization of carotenoid metabolic engineering in planta.
in Methods in enzymology
Vazquez-Vilar M
(2023)
Dually biofortified cisgenic tomatoes with increased flavonoids and branched-chain amino acids content
in Plant Biotechnology Journal
Description | 1. Within the EpRIL population of tomato lines altered genome methylation has been confirmed. Our preliminary data indicates that metabolite changes have arisen. These appear to be linked to fruit ripening .Presently, the project has another year to completion and only the first crop has been analysed. To date the data acquired and phenotypes although not dramatic look promising. 2. Lines with increased human dietary nutrients have been identified. 3. Potentially the ripening of the lines has been altered, so there is the potential for quicker ripening. 4. Volatile profiles within the population has been altered. 5. Volatile profiles on cold storage have been altered. |
Exploitation Route | The output from this project provides a value resource to the community. It one years time with the finish of the project - data representing potential EpiQTL for fruit quality traits will be availble and exploitable. This information can be used by researchers for fundamnetal advances and industry for application leading to direct commerical practice. Industry partners have been contacted to assess interest and if they wish to exploit the findings. |
Sectors | Agriculture Food and Drink Chemicals Environment Pharmaceuticals and Medical Biotechnology |
Description | 1. The resource provides a means of addressing consumer preferences for fruit and vegetables. 2. New nutrient dense lines have bene indentified. 3. Lower input resources as the fruit ripneing quicker. |
First Year Of Impact | 2021 |
Sector | Agriculture, Food and Drink,Retail |
Impact Types | Societal Economic |
Description | Improving volatile profiles in tomato |
Amount | £120,000 (GBP) |
Organisation | Industry Partners |
Sector | Private |
Country | United States |
Start | 08/2020 |
End | 10/2023 |
Description | nutrient dense fruits |
Amount | £120,000 (GBP) |
Organisation | Industry Partners |
Sector | Private |
Country | United States |
Start | 08/2020 |
End | 10/2023 |
Title | Metabolite database of metabolites in epiRIL population |
Description | Metabolomic database |
Type Of Material | Physiological assessment or outcome measure |
Year Produced | 2022 |
Provided To Others? | No |
Impact | Breeding tool to assess traits of interest |
Title | https://doi.org/10.1111/tpj.14649 |
Description | https://doi.org/10.1111/tpj.14649 |
Type Of Material | Database/Collection of data |
Year Produced | 2020 |
Provided To Others? | Yes |
Impact | https://doi.org/10.1111/tpj.14649 |
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 | Industrial partnership |
Organisation | Burpee Europe Ltd |
Country | United Kingdom |
Sector | Private |
PI Contribution | Analysis of breeding lines |
Collaborator Contribution | construction of breeding lines |
Impact | Not yet |
Start Year | 2020 |
Description | metabolite analysis |
Organisation | Syngenta International AG |
Department | Syngenta Ltd (Bracknell) |
Country | United Kingdom |
Sector | Private |
PI Contribution | Staff time to perform the analysis of volatiles |
Collaborator Contribution | Acess to machine time and germplasm resources |
Impact | The project still has one year to run -so to early |
Start Year | 2019 |
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 open day or visit at my research institution |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Public/other audiences |
Results and Impact | Open days involves presentations to the general public and prospective students - as well as demonstarting the analytical platforms |
Year(s) Of Engagement Activity | 2019 |
Description | College Open Days |
Form Of Engagement Activity | Participation in an open day or visit at my research institution |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Public/other audiences |
Results and Impact | Providd explaination of the project and demnstrated the analytical equipment |
Year(s) Of Engagement Activity | 2019 |
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 | 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 | Plant Cell factories for sustainable production |
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 | Two open days for the general public talks and laboratory tours. |
Year(s) Of Engagement Activity | 2024 |
Description | School Visit Reading |
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 | Ran chromatography practices in schools |
Year(s) Of Engagement Activity | 2023 |
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 | School visit, Bracknell |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Schools |
Results and Impact | 20 pupils talk and debate about Plant biotechnology |
Year(s) Of Engagement Activity | 2023 |
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 | solanaceae conference |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Talk at the solanaceae conference in 2022 |
Year(s) Of Engagement Activity | 2022 |
URL | https://sol2022.web.auth.gr/wp-content/uploads/2022/10/XVII-Solanaceae-Conference-2022-PROGRAM_Oct.-... |