Genome-wide identification and expression analysis of IDD gene family in Gossypium hirsutum L

The INDETERMINATE DOMAIN (IDD) proteins are a plant-specific class of zinc finger transcription factors crucial for development and stress adaptation. In this study, genome-wide identification and expression analysis of IDD gene family was conducted. 66 IDD proteins were identified in Gossypium hirsutum. Protein sequence alignment revealed that the N-terminal regions of GhIDD members were highly conserved, but the C-terminal MSATALLQKAA and TR/LDFLG motifs were missing in some members. Gene duplication analysis showed that whole-genome duplication (WGD) or segmental duplication was the main driving force for IDD gene amplification in cotton. Furthermore, the IDD gene family in cotton is under purifying selection during evolution. Expression analysis showed that GhIDD members were preferentially expressed in stems, leaves and pistils. AtIDD3 has been reported to interact with many GRAS family proteins. Therefore, its cotton homolog, GhIDD38, was selected for further analysis. Subcellular localization analysis confirmed that GhIDD38 is localized in the nucleus, supporting its role as a transcription factor. Gene expression analysis showed that the GhIDD38 gene was expressed at higher levels in leaves than in stems of the glandless stem line T582. The expression patterns of GhIDD38 and GoSPGF under MeJA and GA treatments were similar. Notably, GoSPGF encodes a GRAS protein involved in the glandless stem phenotype. Meanwhile, yeast two-hybrid analysis revealed that GhIDD38 interacts with GoSPGF. Therefore, we speculate that GhIDD38 and GoSPGF form a complex to regulate gland development via hormonal signals. These findings provide a basis for further understanding the biological functions of GhIDD members in cotton.