Multi-Omics Analysis Reveals Differential Molecular Responses of RNA Polymerase Common Subunit ZmRPABC5b for Seedling Development in Maize

The normal development of maize (<i>Zea mays</i>) seedling is a prerequisite for achieving high crop yields. Although numerous molecular pathways regulate seedling development, the role of RNA polymerases (RNAPs) in this process remains largely unclear, and the function of common RNAP subunits in plants are not well understood. Here, we characterized the loss-of-function mutant of common subunit ZmRPABC5b, <i>defective kernel 701</i> (<i>dek701</i>), which displays delayed seedling development. To elucidate the role of ZmRPABC5b in maize seedling growth, we conducted transcriptomic and metabolomic analyses. This study found that the loss of <i>ZmRPABC5b</i> function severely impaired early seedling growth, leading to significant reductions in stem length, root length, as well as fresh and dry weight. Transcriptome analysis identified 3780 upregulated and 4385 downregulated differentially expressed genes (DEGs) in <i>dek701</i> seedlings compared to wild type. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of DEGs revealed that significant enrichment in pathways related to RNA biosynthesis, carbohydrate metabolic, hormone stimulus, cellular transporter and ribosome activity. Metabolome analysis identified 501 differentially expressed metabolites (DEMs) in <i>dek701</i> seedlings, which were significantly enriched in the amino acid metabolism, secondary metabolites, carbohydrate metabolism, lipid metabolism, transport and translation. These findings provide substantial insight into the <i>ZmRPABC5b</i> regulatory network, positioning it as a central hub for regulating seedling development in maize.