Generation and characterisation of a tomato epigenetic recombinant inbred line (epiRIL) population

Heritable changes in gene expression, which are not due to alterations in the DNA sequence, are termed epigenetic modifications and they play an important role in plant development (Pickaard and Scheid, 2014). These changes include those in DNA methylation, chromatin remodelling and levels of small RNAs. This project focuses on the effects of variations in DNA methylation on the cultivated tomato (Solanum lycopersicum). In Arabidopsis, the effects of DNA methylation on plant development have been investigated using mutants in DNA methyltransferase genes. These mutants have also been used to develop epigenetic recombinant inbred line (epiRIL) populations where the genetic background of individuals in the population is identical, but they show variation in genome wide DNA methylation. The aim of this project was to generate and characterize a novel population of tomato epiRILs and identify the effects of the epigenetic variation on the development of tomato. We have established an epiRIL population in a cherry tomato line (WVA 106) where methyltransferase 1 (MET1) gene has been silenced. F2 seeds were generated by colleagues at INRA, (France). Then the epiRIL population, generations F3-F8, were propagated in Nottingham. The population was screened for altered phenotypes. Morphological changes were observed including twisted and fasciated stems, abnormal leaves, exerted style, twisted stamens and low fruit weight. Targeted analysis of the expression of candidate genes underlying the potential phenotypes focused on genes including FW2.2, SlEZ1 and TM8. RNASeq analysis indicated significant changes in gene expression across the genome of selected epiRILs including altered expression of transposons. Analysis using the enzyme McrBC showed that the level of methylation for target genes was lower in the epiRILs than wild type. Changes in DNA methylation in epiRIL lines was also demonstrated using bisulfite conversion and targeted Sanger sequencing and whole genome bisulfite sequencing. The epiRIL population provides a unique resource for investigating the epigenetic basis of trait variation in tomato which could also be applied in other crop species