Integrative Transcriptomic and Metabolomic Analyses Reveal Molecular Processes Associated with Differential Embryo Dehydration in Maize

Background/Objectives: Kernel dehydration is an important agronomic trait influencing mechanical harvesting efficiency, post-harvest drying costs, and grain storage quality in maize (Zea mays L.). Although the genetic and molecular basis of whole-kernel dehydration has been increasingly investigated, tissue-specific physiological and molecular patterns, particularly those associated with the embryo, remain insufficiently characterized. In this study, four maize inbred lines with contrasting dehydration capacities were selected to characterize tissue-specific dehydration dynamics and associated molecular patterns. Methods: Moisture content and dehydration rates of kernels, endosperms, and embryos were monitored from 10 to 55 days after pollination (DAP), followed by correlation analyses with kernel- and ear-related agronomic traits. Transcriptome sequencing, weighted gene co-expression network analysis (WGCNA), and untargeted metabolomics were integrated to characterize molecular processes associated with contrasting embryo dehydration phenotypes. Results: Embryo dehydration closely paralleled whole-kernel dehydration, and embryo dehydration rate was strongly associated with kernel dehydration rate. Transcriptomic and WGCNA analyses revealed developmental- and genotype-dependent expression changes, particularly during late maturation, and identified dehydration-associated modules enriched in lipid metabolism, glycolysis, hormone signaling, and stress-responsive processes, including fatty acid metabolism, ABA- and ethylene-related signaling, and MAPK-related genes. FDR-controlled metabolomics further revealed genotype- and developmental-stage-dependent metabolite differences associated with organic acid metabolism, amino acid metabolism, transport-associated processes, and secondary metabolism. Pathway-level integration highlighted ABA- and ethylene-associated candidate processes associated with variation in embryo dehydration. Conclusions: Collectively, these findings provide an embryo-focused characterization of physiological and multi-omics variation associated with maize kernel dehydration and identify candidate molecular processes for further functional investigation. Further validation across broader germplasm panels, environmental conditions, and experimental systems will be required to determine the causal roles and potential breeding relevance of these candidate processes.