Investigation of DNA methylation dynamics in pollination-dependent and auxin-induced fruit set in tomato

Fruit formation comprises a series of developmental shifts among which the fruit set process is essential in determining crop yield. We investigated the epigenetic and transcriptomic reprogramming underlying pollination-dependent and auxin-induced flower-to-fruit transitions in the tomato using combined genome-wide transcriptomic profiling, global ChIP-sequencing and whole genomic DNA bisulfite sequencing (WGBS). For the overwhelming majority of genes (80 to 90%), variation in expression was associated with change in histone mark distribution whereas changes in DNA methylation concerned a minor fraction (23 to 28%) of differentially expressed genes. Reprogramming of genes involved in pathways and processes instrumental to fruit set strongly correlated with their H3K9ac or H3K4me3 marking status but not with changes in Cytosine methylation, indicating that histone post translational modifications rather than DNA methylation are associated with the remodeling of the epigenetic landscape underpinning the flower-to-fruit transition. Given the prominent role previously assigned to DNA methylation in reprogramming key genes of the transition to ripening, the outcome of the present study supports the idea that the two main developmental transitions in fleshy fruit and the underlying transcriptomic programming are associated with different modes of epigenetic regulations.