Pan-Genomic Characterization of the Nudix Hydrolase Gene Family and Its Response to Different Pathogen Strains in Maize (Zea mays)

Background: Nudix hydrolases (NHs), characterized by the conserved Nudix motif (GX5EX7REUXEEXGU), hydrolyze nucleoside diphosphate derivatives and play vital roles in plant stress responses and cellular homeostasis. However, the NH gene family has not been systematically characterized in maize (Zea mays L.). Methods: We performed a genome-wide analysis of ZmNH (Nudix hydrolase) genes using a maize pan-genome encompassing 26 high-quality genomes. Results: A total of 73 ZmNH members were identified, comprising 22 core genes (present in all 26 lines), 28 dispensable genes (present in 2–25 lines), and 23 private genes (present in only one line). Phylogenetic analysis clustered them into three subgroups (Type-I, -II, and -III), with Type-III being the largest (28 members). Gene structure and motif analyses revealed conserved exon–intron architectures and 10 conserved motifs. Nonsynonymous/synonymous substitution ratio (Ka/Ks) calculations across the 26 inbred lines indicated that most ZmNH genes were under purifying selection (Ka/Ks < 1), whereas ZmNH2 and ZmNH12 showed evidence of positive selection in some lines. Expression profiling under four stress conditions—Fusarium graminearum, Cercospora zeina, Exserohilum turcicum, and Ostrinia furnacalis—identified 20 differentially expressed ZmNH genes. Notably, ZmNH9 was consistently responsive across multiple pathogen treatments, suggesting a potential role in broad-spectrum disease resistance. Conclusions: These findings provide a foundation for future functional studies of the maize NH gene family.