Genome-Wide Identification and Characterization of the C3H Gene Family in Maize (Zea mays L.) and Expression Profiling Under Low-Phosphorus and High-Nitrogen Conditions

CCCH-type zinc finger proteins (C3H transcription factors) play essential roles in plant growth, development, and responses to environmental stresses. Although several maize (Zea mays L.) C3H genes have been reported, a comprehensive genome-wide analysis based on the updated maize reference genome remains lacking. In this study, 64 C3H gene family members were systematically identified from the maize reference genome (Zm-B73-REFERENCE-NAM-5.0) and designated as ZmC3H01 to ZmC3H64 according to their chromosomal locations. Phylogenetic analysis classified the ZmC3H family into four distinct subgroups, exhibiting conserved yet subgroup-specific motif compositions. Synteny analysis revealed that segmental duplication events played an important role in the expansion and evolution of the ZmC3H gene family. Cis-acting regulatory element analysis suggested that ZmC3H genes may participate in multiple stress-responsive and developmental regulatory pathways. Furthermore, transcriptome analysis and quantitative real-time PCR (qRT-PCR) validation identified five candidate ZmC3H genes (ZmC3H33, ZmC3H36, ZmC3H39, ZmC3H52, and ZmC3H57) that exhibited differential expression under low-phosphorus and high-nitrogen conditions in the maize inbred lines 082, Ye107, and B73. These genes were selected based on their differential expression under nutrient stress and their representative distribution across phylogenetic subfamilies, providing preliminary candidates for further functional investigation. Subcellular localization and yeast transcriptional activation assays demonstrated that ZmC3H33, ZmC3H36, and ZmC3H57 are nuclear-localized proteins with transcriptional activation activity. Furthermore, dual-luciferase assays showed that all three proteins activated the maize Phosphate Starvation Response 1 (ZmPHR1) promoter, with ZmC3H57 exhibiting the strongest activation effect, suggesting that these ZmC3H proteins may act as potential upstream regulators of ZmPHR1-mediated low-phosphorus responses. Collectively, these findings provide valuable insights into the evolutionary characteristics and potential biological functions of the maize C3H gene family and identify putative candidate genes for improving phosphorus-use efficiency.