Genome-Wide Identification of the IQD Gene Family in Eggplant and Effects of SmIQD9 Overexpression on Tomato Fruit Shape

The IQ67-domain (IQD) gene family is a plant-specific protein family involved in calcium signaling, microtubule dynamics, and organ morphogenesis, with documented roles in fruit shape regulation in several crops. However, little is known about this family in eggplant (Solanum melongena L.), a globally important vegetable with remarkable fruit shape diversity. In this study, we performed a genome-wide identification of the IQD family in eggplant and characterized the function of SmIQD9 in fruit shape regulation. A total of 30 IQD genes were identified in the eggplant genome and designated SmIQD1 to SmIQD30. These genes were unevenly distributed across 10 chromosomes, with segmental duplication serving as the primary driver of family expansion. Phylogenetic analysis classified the IQD proteins from eggplant, Arabidopsis, rice, and tomato into eight groups, revealing both conserved and lineage-specific subgroups. Gene structure and motif analyses showed that SmIQD proteins share the conserved IQ67-domain but exhibit substantial structural diversity, with subfamily-specific motifs suggesting functional specialization. Expression profiling in developing ovaries revealed three distinct expression clades, with Clade C2 members—including SmIQD9—showing a transient peak at 10 or 7 DBA (days before anthesis), coinciding with the critical window for fruit shape determination. Ectopic overexpression of SmIQD9 in tomato resulted in significantly elongated fruits, reduced fruit width, and increased fruit shape index. Histological analysis demonstrated that SmIQD9 promotes fruit elongation primarily by enhancing cell expansion. Collectively, our findings provide a comprehensive genomic framework for the IQD family in eggplant and identify SmIQD9 as one of the positive regulators of fruit elongation, offering a promising candidate for future molecular breeding of eggplant fruit shape.