Loss of Aucsia2 remodels root architecture and enhances salt stress resilience in tomato

Aucsia (Auxin cum silencing action) genes are widespread throughout the green plant lineage and encode miniproteins of 40–60 amino acids characterized by a conserved 16–amino acid motif. In tomato, the Aucsia gene family comprises two members, Aucsia1 and Aucsia2, whose simultaneous silencing has previously revealed a role in auxin biology. Here, we demonstrate that the knockout of Aucsia2, the most highly expressed family member, had a positive effect on fruit set and modified root system architecture. Specifically, Aucsia2 CRISPR-Cas9 mutants (cr-Aucsia2) displayed fewer lateral roots than WT, resulting in a more parsimonious root system that did not compromise shoot growth or overall yield. Under salt stress, cr-Aucsia2 mutants suffered less damage to root and shoot growth and exhibited reduced halotropic response relative to WT plants. Comparative transcriptomic analysis of roots revealed that, under salt stress, WT plants mounted marked transcriptional reprogramming involving genes associated with oxidative stress, cell wall growth and remodeling, and hormone metabolism and signaling, whereas these responses were substantially attenuated in cr-Aucsia2 mutants. Notably, the mutants showed constitutive alterations in ethylene-responsive genes, auxin homeostasis control and distribution, and lower levels of abscisic acid and salicylic acid compared with WT. These features may be advantageous in limiting root damage caused by high accumulation of ethylene and ABA, which is commonly observed under saline stress. Overall, our data suggest that the reduced salt sensitivity of cr-Aucsia2 mutants is likely associated to constitutive metabolic and hormonal changes that confer a pre-adapted state to stress conditions.