Pan-Genome-Wide Identification, Evolutionary Analysis, and Stress-Responsive Expression Profiling of the Maize DUF668 Gene Family

Background/Objectives: Plant proteins containing Domain of Unknown Function 668 (DUF668) have been implicated in growth, development, and responses to abiotic stress, but the population-level diversity and potential functions of this family in maize remain poorly understood. We therefore characterized this family across the maize pan-genome and examined its expression under abiotic stress. Methods: DUF668 genes identified in 26 maize genomes were evaluated for presence–absence variation, phylogenetic relationships, structural variation, functional annotation, and predicted functional associations. Public RNA-seq data and qRT-PCR were used to profile B73-resident genes under waterlogging, temperature, osmotic, salinity, and UV-B stresses. Results: We identified 51 nonredundant loci, comprising 8 core, 5 near-core, 9 dispensable, and 29 private loci. Phylogenetic analysis of 69 maize, Arabidopsis, and rice proteins resolved two subfamilies. Most loci showed evidence of purifying selection, whereas ZmDUF668-16 had an elevated Ka/Ks ratio; large insertions or deletions were detected for ZmDUF668-4 and ZmDUF668-15. The 19 B73-resident loci exhibited distinct developmental, temporal, and stress-responsive expression patterns. ZmDUF668-1 was also located within the broad chromosome-2 L-ABA/root-ABA1 interval. Conclusions: The maize DUF668 family exhibits substantial variation at the pan-genomic, evolutionary, and transcriptional levels. These findings provide a basis for prioritizing candidate genes for functional validation in maize development and abiotic stress responses.