Exploiting experimental and natural epigenetic variation for tomato improvement – epiTOM

Tomato is a major crop cultivated worldwide and a fleshy fruit plant model for biologists. Tomato genome contains large heterochromatic regions densely populated by transposons, which are typically targeted by DNA methylation, an epigenetic modification preventing transposons mobility. DNA methylation is not only a hallmark of heterochromatin involved in genome stability but it can also affect the expression of nearby genes and some heritable epialleles were described in tomato. Moreover, extensive DNA methylation dynamics were observed between tomato organs like fruits, with implications for their development. Understanding how epigenetic variation is generated is thus both of fundamental and agronomical interest.
Here, we propose to build on the complementary expertise of both partners to investigate the extent and molecular pathways underlying tomato epigenetic variation by exploring the methylomes of experimental mutants impaired in DNA methylation homeostasis together with a broad panel of non-domesticated and commercial cultivars. Using a combination of (epi)genomic editing techniques, population epigenomics, quantitative epigenetic and bioinformatic approaches we aim to (i) determine the molecular pathways underlying tomato natural epigenetic variation, (ii) assess the contribution of this variation to crop diversity and (iii) develop new epigenome editing tools to manipulate DNA methylation at loci underlying agronomic traits to modify gene expression without altering their underlying DNA sequences.
EpiTOM will provide key knowledge to harness the potential of epigenetics for crop improvement. Determining the extent of natural epigenetic variation in crops, as well as the molecular mechanisms underlying this variation, will significantly empower our capacity to breed crops. Our findings should shed light on a still unresolved question in the post genomics era, namely that of the contribution of heritable epigenetic changes to plant diversity.