Genome-Wide Analysis and Functional Correlation of Tomato JAZ Genes Under Tuta absoluta Infestation and Nanoparticle-Induced Defense

Tomato (<i>Solanum lycopersicum</i>) production is increasingly threatened by <i>Tuta absoluta</i>, a destructive pest that compromises yield and quality. To explore sustainable alternatives to conventional insecticides, we investigated the jasmonate-mediated defense pathway by performing a genome-wide characterization of the JAZ gene family in <i>S. lycopersicum</i>. A total of 39 <i>SlJAZ</i> genes were identified and mapped to 12 chromosomes. Detailed analysis revealed conserved motifs, diverse exon-intron structures, four major phylogenetic groups, and the presence of multiple MeJA- and stress-responsive cis-elements. Synteny analysis indicated gene duplication events and evolutionary conservation with Arabidopsis and potato. Small RNA predictions suggested that 33 <i>SlJAZ</i> genes are targeted by 69 microRNAs, implying multilayered regulation. Transcriptome analysis under four treatment conditions-mesoporous silica nanoparticles (MSNs) ± pest infestation-revealed 21 differentially expressed SlJAZ genes. <i>SlJAZ1</i>, <i>SlJAZ19</i>, <i>SlJAZ20</i>, and <i>SlJAZ22</i> were notably upregulated under the combined MSN and pest treatment, with expression patterns validated by qRT-PCR (R² = 0.92). Phenotypic assessment of leaf damage index, larval survival rate, and number of leaf mines showed reduced pest activity in MSN-treated plants. Regression analysis demonstrated significant negative correlations between expression levels of <i>SlJAZ20</i>, <i>SlJAZ26</i>, and <i>SlJAZ29</i> and pest-related damage traits. These findings indicate that MSNs function as effective elicitors of JA-responsive defense in tomato and modulate the expression of specific JAZ genes linked to enhanced resistance. The study provides a valuable foundation for integrating nanotechnology with molecular defense strategies to promote sustainable pest management.