Genome-Wide Characterization of the INDETERMINATE DOMAIN (IDD) Zinc Finger Gene Family in Solanum lycopersicum and the Functional Analysis of SlIDD15 in Shoot Gravitropism

The plant-specific <i>IDD</i> transcription factors (TFs) are vital for regulating plant growth and developmental processes. However, the characteristics and biological roles of the <i>IDD</i> gene family in tomato (<i>Solanum lycopersicum</i>) are still largely unexplored. In this study, 17 <i>SlIDD</i> genes were identified in the tomato genome and classified into seven subgroups according to the evolutionary relationships of IDD proteins. Analysis of exon-intron structures and conserved motifs reflected the evolutionary conservation of <i>SlIDDs</i> in tomato. Collinearity analysis revealed that segmental duplication promoted the expansion of the <i>SlIDD</i> family. Ka/Ks analysis indicated that <i>SlIDD</i> gene orthologs experienced predominantly purifying selection throughout evolution. The analysis of <i>cis</i>-acting elements revealed that the promoters of <i>SlIDD</i> genes contain numerous elements associated with light, plant hormones, and abiotic stresses. The RNA-seq data and qRT-PCR experimental results showed that the <i>SlIDD</i> genes exhibited tissue-specific expression. Additionally, Group A members from <i>Arabidopsis thaliana</i> and rice are known to play a role in regulating plant shoot gravitropism. QRT-PCR analysis confirmed that the expression level of <i>SlIDD15</i> in Group A was high in the hypocotyls and stems. Subcellular localization demonstrated that the SlIDD15 protein was localized in the nucleus. Surprisingly, the loss-of-function of <i>SlIDD15</i> by CRISPR/Cas9 gene editing technology did not display obvious gravitropic response defects, implying the existence of functional redundant factors within <i>SlIDD15</i>. Taken together, this study offers foundational insights into the tomato <i>IDD</i> gene family and serves as a valuable guide for exploring their molecular mechanisms in greater detail.