Genome-wide identification and expression analysis of the ZIP (ZRT, IRT-like protein) family in Solanum lycopersicum

Abstract Iron (Fe), zinc (Zn), manganese (Mn), and copper (Cu) are essential micronutrients for plant growth and development, but their low bioavailability in soil limits crop growth and yield. The ZIP (ZRT/IRT-like protein) family plays critical roles in the uptake and distribution of these divalent metal ions. Here, we performed a genome-wide identification of the ZIP family in tomato (Solanum lycopersicum) and analyzed their expression profiles under various metal deficiencies. A total of 14 SlZIP genes were identified and classified into three clades based on phylogenetic analysis. Conserved motif and gene structure analyses revealed that SlZIP genes within the same clade share similar exon/intron organization and protein motifs. The 14 SlZIP genes are unevenly distributed across eight chromosomes of tomato, and their promoters contain multiple iron- and copper-deficiency-responsive cis-elements. To further explore the potential functions of these SlZIP genes, we quantified their expression levels in tomato roots under metal-deficient conditions and found that SlIRT1, SlIRT2, and SlZIP4 were significantly induced by Fe deficiency, while SlZIP2 and SlZIP11 were specifically induced by Cu deficiency, and SlZIP13 and SlZIP14 by Mn deficiency. These results provide a comprehensive resource for the tomato ZIP family and lay a foundation for future functional studies of SlZIP genes in metal uptake and transport in tomato.