18-BTT: Epi-TOM: The development and characterization of an EpiRIL TOMato population

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).

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).

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.