Differential expression of stress-responsive microRNAs and their target genes under PEG6000-induced osmotic stress in wild and mutation-bred tomato genotypes

Water deficit, intensified by global warming and climate change, is a major constraint on crop productivity, making it essential to understand and enhance plant adaptation to limited water availability. MicroRNAs (miRNAs), small non-coding RNAs of ~ 20–22 nucleotides, are key post-transcriptional regulators of gene expression and important mediators of plant responses to water-deficit and osmotic stress. Here we compared the expression of drought-associated miRNAs and their validated target genes in two mutation-bred tomato lines (M4.5 and M3.409, developed by gamma-irradiation) and the naturally stress-tolerant wild relative Solanum pennellii. Seedlings were exposed in vitro to 0%, 4% or 6% (w/v) PEG6000 to impose osmotic stress. After 14 days, plantlet height was unaffected by PEG6000 in S. pennellii (0%: 3.85 ± 0.13; 4%: 3.82 ± 0.10; 6%: 4.04 ± 0.07 cm) and M4.5 (0%: 4.44 ± 0.10; 4%: 4.66 ± 0.08; 6%: 4.70 ± 0.18 cm), whereas M3.409 showed a reduction at 6% PEG6000 (0%: 4.04 ± 0.15; 4%: 4.02 ± 0.11; 6%: 3.16 ± 0.10 cm). Using qRT-PCR, we profiled thirteen drought-responsive miRNAs: nine were downregulated (miR1446, miR830, miR479, miR170a, miR170b, miR170c, miR828, miR398 and miR157b) and four were upregulated (miR473, miR2111, miR2118a and miR2118b) under stress. The six analysed target genes displayed the expected inverse expression patterns. Overall, the mutation-bred lines reproduced the miRNA signatures of the wild tolerant genotype, identifying candidate miRNA-target modules that may support the breeding of drought-resilient tomato.