MicroRNAs and DNA Damage Response: Modulating stress response during germination in cereals

The ability of plants to endure environmental challenges during germination is important for guaranteeing optimal crop establishment and productivity. Germination is a developmental stage that is especially vulnerable to stress, resulting in DNA damage and diminished seedling vigour. Plants depend on the DNA damage response (DDR), a system of sensors, transducers, and repair effectors, to preserve genomic integrity. However, the post-transcriptional regulation of DDR is not fully comprehended in cereals, despite their importance for global food security. Understanding the role of microRNAs (miRNAs) in modulating DDR during germination may yield novel insights into stress tolerance mechanisms and guide approaches for crop enhancement. This PhD thesis examined the role of miRNAs in modulating DDR during germination in wheat and rice cereals. Two experimental systems were utilised: (1) wheat seeds exposed to gamma (γ)-radiation, and (2) rice seeds subjected to salinity stress. In both cases, in silico predictions were integrated with expression profiling of potential miRNAs and target DDR genes, together with a phenotypic evaluation of germination behaviour under stress. In wheat (Triticum aestivum), the findings indicated that DDR-related genes, encompassing sensors (MRE11, NBS1, RAD50), a transducer (ATM), and repair proteins (BRCA1, TDP1, OGG1), along with their putative miRNAs (miR164, miR5086, miR112), were differentially regulated in a time- and genotype-dependent fashion post-irradiation. A significant negative correlation identified for the tae-miR5086–RAD50 pair offers an indirect evidence for miRNA-gene interaction. The function of RAD50, a dual-purpose element of the MRN complex engaged, in detecting and repairing double-strand breaks highlights the significance of miRNA-mediated modulation on DDR, In rice (Oryza sativa), a bioinformatic selection identified ten DDR genes (MRE11, SOG1, RAD50, NBS1, ATM, ATR, RPA, RBR, RFC, WEE1-like) as potential targets of eight miRNAs (osa-miR414, osa-miR5519, osa-miR818a, osa-miR2879, osa-miR395t, osa-miR2102, osa-miR415, osa-miR2925). Salinity stress was demonstrated to influence rice germination in a dose-dependent way, revealing distinctions between tolerant (IR64, Apollo, Carnaroli, Lomello, Unico, Inpari) and susceptible (Cerere, Rc460) cultivars. Variety-dependent expression patterns of DDR genes and respective miRNAs have been observed, with the osa-miR818a–NBS1 exhibiting a significant negative correlation. Collectively, these data indicate that miRNAs could act as regulators of DDR during germination under stress in cereals. The identified correlations between miRNAs and DDR genes offer an indirect confirmation of this regulatory function while emphasising the potential use of miRNA–gene pairs as indicators of stress tolerance. The possibility to modify miRNA expression presents options for regulating DDR and improving stress resilience. This understanding may influence crop improvement strategies, such as the generation of tolerant cultivars, promoting future sustainable agriculture.