Comprehensive identification, characterization, and stress response analysis of the ZmSPL gene family in maize (Zea mays L.)

Maize ( Zea mays L.) represents a globally significant food crop. Environmental stresses markedly compromise its agronomic yield and grain quality. The SPL ( SQUAMOSA PROMOTER BINDING PROTEIN – LIKE ) gene family is a plant-specific class of transcription factors that play pivotal roles in the regulation of lateral branching, developmental phase transitions, flowering time, and stress responses. However, comprehensive characterization of the ZmSPLs has yet to be reported. This study conducted a systematic genome-wide identification of the SPL gene family in the latest maize reference genome and analyzed their expression profiles. Based on sequence homology, 36 ZmSPLs were identified in the newly assembled B73 reference genome of maize (RefGen_v5, Zm–B73–REFERENCE–NAM–5.0). They display an uneven distribution pattern across all ten maize chromosomes. Maximum–likelihood phylogenetic analysis classified the 36 ZmSPLs into five distinct clades, with significant variation in sizes across different subgroups. Comparative analysis revealed ZmSPLs belonging to the same subclade shared highly conserved gene structures and protein motif architectures. Collinearity analysis indicated that ZmSPLs have undergone purifying selection during evolution, with segmental duplication serving as the primary driving force for its expansion; Furthermore, ZmSPL genes exhibited conserved genomic correspondence with rice counterparts. The promoter regions of 36 ZmSPLs contained light–responsive, stress–responsive, hormone–responsive, and development–related elements. RNA–seq data combined with RT–qPCR analysis indicated that six ZmSPLs ( ZmSPL3 / 8 / 14 / 18 / 22 / 30 ) highly express in multiple tissues and are significantly induced or reduced in response to salinity and temperature stresses; Suggesting their versatile roles in maize growth, development, and stress response pathways, might be the prime targets for downstream functional investigation. However, the specific biological functions of these genes remain to be experimentally validated. Collectively, our genome-wide characterization of the ZmSPLs offers new perspectives on their evolutionary dynamics and intergenic relationships, thereby providing a foundation for future functional studies.