Role of the tomato MARS1/ROUGH gene encoding a LYSINE‐SPECIFIC HISTONE DEMETHYLASE 1 in adventitious root and fruit skin formation

In contrast to animals, plants possess a remarkable regenerative capacity and are capable of forming new organs or even entire organisms from a limited number of cells present in adult tissues, in response to injury or environmental changes. In this study, we describe the isolation and characterization of the more adventitious roots1-1 (mars1-1) mutant, which exhibits enhanced regenerative potential upon wounding in tomato hypocotyl explants. Additionally, the mars1-1 fruits exhibited a rough surface because of ectopic subepidermal cell proliferation, resulting in the formation of callus-like structures on their cuticle. The MARS1/ROUGH gene encodes a conserved lysine-specific histone demethylase, SlLDL1, which regulates processes such as cell proliferation, stem cell pluripotency, and embryogenesis in metazoans. Two CRISPR/Cas9 null alleles, mars1-2 and mars1-3, were generated, and their pleiotropic phenotypes were characterized. ChIP-seq analysis revealed elevated levels of methylated lysine 4 in histone 3 within specific regions of the mars1/rough genome. To determine the impact of altered epigenetic marks on gene expression regulation in mars1/rough mutants, we analyzed the transcriptome of tomato hypocotyls during adventitious root formation. Using specific bioinformatic workflows and the resolution of the directional RNA-seq data, we identified several dozen distinct genomic regions with de novo expression in the mars1/rough mutants. One such region includes a novel B-type cyclin gene that is upregulated in mars1/rough mutants and may account for adventitious root and fruit skin phenotypes. Our findings indicate that SlLDL1 plays a role in maintaining silencing in specific genomic regions that are essential for tissue-specific reprogramming.