HD-ZIP proteins (homeodomain–leucine zipper proteins) are a large family of plant-specific transcription factors that play crucial roles in regulating various physiological and developmental processes, including growth, differentiation, response to environmental stress, and reproductive development. Seed size is the main limiting factor affecting the yield of maize (Zea mays). However, the genome-wide identification and characterization of this family in maize and its biological functions in seed size have not been reported. Here, 61 ZmHD-ZIP genes were identified in the genome. Phylogenetic analysis of these ZmHD-ZIP genes revealed that they are clustered into four subfamilies: HD-ZIP I, HD-ZIP II, HD-ZIP III, and HD-ZIP IV. Domain analysis revealed that the distribution of these domains aligns perfectly with the subfamily classification criteria, with members of the same subfamily sharing similar domains. Cis-acting element analysis showed that the ZmHD-ZIP family genes are involved in the regulation of plant reproductive development. In addition, ZmHD-ZIP23-overexpressing Arabidopsis and maize had larger seed with increased grain length and heavier grain weight owing to bigger embryo and endosperm area. These findings could serve as a basis for future studies on the roles of ZmHD-ZIP genes in improving maize yield.

The nuclear factor Y (NF-Y) transcription factor family plays crucial roles in plant growth, development, and stress responses. However, studies on the NF-Y family in maize remain relatively limited. In this study, we identified 53 NF-Ys in the maize genome, which were classified into ZmNF-YA, ZmNF-YB, and ZmNF-YC subfamilies. These genes exhibited diverse physicochemical properties and were unevenly distributed across the 10 chromosomes. Synteny analysis revealed 48 collinear gene pairs between maize and rice, indicating close evolutionary relationships. Gene structure and conserved motif analyses showed both conservation and divergence within the family. Promoter analysis identified abundant cis-acting elements related to hormone response, abiotic stress, light response, and growth regulation. Expression profiling under drought stress revealed that ZmNF-Ys respond differentially, with some showing strong induction. Functional characterization demonstrated that ZmNF-YA7 positively regulates drought tolerance in maize. Overexpression of ZmNF-YA7 enhanced drought tolerance through multiple mechanisms: reducing oxidative damage by increasing antioxidant enzyme activities, accumulating osmoprotectants, and modulating xylem vessel anatomy (larger diameter and lower density under drought). These findings provide comprehensive insights into the ZmNF-Y gene family and highlight ZmNF-YA7 as a promising candidate for improving drought tolerance in maize breeding programs.