Unveiling novel epigenetic regulators of stress resilience and growth in Solanum lycopersicum

Histone deacetylation (HDAC) represents an important process in the transcriptional regulation that underpins plant growth and response to environmental changes. Previously, we have characterized Histone Deacetylase Complex 1 (HDC1) from Arabidopsis thaliana as HDAC ratelimiting factor and a bona-fide member of the HDAC complex which regulates a series of downstream processes in a quantitative manner, including germination, vegetative growth and flowering1,2,3. Recently, we have also demonstrated that HDC1 promotes hypocotyl length in a light-quality manner.  Here, we present the first evidence of HDC1 functional characterization in Solanum lycopersicum. Phenotypical analyses of two independent CRISPR-Cas9 lines show that in tomato HDC1 is required for germination, elongation and growth. Measurements of stomata conductance in adult plants point out that slhdc1 mutants display a lower stomata aperture already in control conditions, suggesting a pre-established stress sensitivity.  RNAseq experiment on four-week-old plants subjected to salt stress reveals a HDC1-mediated reprogramming of gene expression that anticipates plant stress response. Indeed, comparison between mutants and wild type indicates a significant number of Differentially Expressed Genes (DEGs) in both control and stress conditions. Interestingly, under salt, wild type plants show a much higher number of DEGs compared to the slhdc1 lines. Gene ontology analysis suggests a significant enrichment for targets involved in transcriptional regulation, enzymatic activity and hormone process. Overall, our results provide more insights into the deacetylation machinery regulating growth in crops under challenging conditions and it further supports the importance of the link between epigenetic state and transcriptional changes, thereby encouraging the use of HDC1 as active tool to generate novel epi-alleles in plants.