Maize is a valuable raw material for feed and food production. Healthy seed germination is important for improving the yield and quality of maize. However, the molecular mechanisms that regulate maize seed germination remain unclear. In this study, multi-omics was used to reveal the molecular mechanism of seed germination induced by gibberellin (GA) in maize. The results indicated that 25,603 genes were differentially expressed (DEGs) and annotated in the GO database, of which 2515 genes were annotated in the KEGG database. In addition, 791 mature miRNAs with different expression levels were identified, of which 437 were known in the miRbase database and 354 were novel miRNAs. Integrative analysis of DEGs and miRNAs suggested that carbohydrate, lipid, amino acid, and energy metabolisms are the primary metabolic pathways in maize seed germination. Interestingly, a lipid metabolism-related gene named ZmSLP was found to negatively regulate maize germination. We transformed this gene into Arabidopsis thaliana to verify its function. The results showed that the germination rate of transgenic Arabidopsis seeds was obviously decreased, and the growth of seedlings was weaker and slower than that of WT plants, suggesting that this gene plays an important role in promoting seed germination. These findings provide a valuable reference for further research on the mechanisms of maize seed germination.

High seed vigor is crucial for agricultural production owing to its potential in high quality and yield of crops and a better understanding of the molecular mechanism associated with maize seed vigor is highly necessary. To better understand the involvement and regulatory mechanism of miRNAs correlated with maize seed vigor, small RNAs and degradome sequencing of two inbred lines Yu537A and Yu82 were performed. A total of 791 mature miRNAs were obtained with different expressions, among of which 505 miRNAs were newly identified and the rest miRNAs have been reported before by comparing the miRNAs with the sequences in miRbase database. Analysis of miRNA families showed maize seeds contain fewer miRNA families and larger miRNA families compared with animals, indicating that functions of miRNAs in maize seeds were more synergistic than animals. Degradome sequencing was used to identify the targets of miRNAs and the results showed a total of 6,196 targets were obtained. Function analysis of differentially expressed miRNAs and targets showed Glycan degradation and galactose metabolism were closely correlated with improved maize seed vigor. These findings provide valuable information to understand the involvement of miRNAs with maize seed vigor and these putative genes will be valuable resources for improving the seed vigor in future maize breeding.

Maize is an important food and feed crop. Under limited arable land area, the cultivation of high-density-tolerance crops is a key factor in promoting yield improvement. Leaf width and stalk strength are important influences on density tolerance in maize. However, no comprehensive transcriptomic analysis has focused on maize’s leaf width and stalk strength formation mechanisms. In this study, comparative transcriptomic analyses demonstrated that significant transcriptome changes occurred regarding leaf width and stalk strength of narrow-leaved and wide-leaved maize inbred lines, with a total of 5001 differentially expressed genes (DEGs) identified. Enrichment analysis showed that phenylpropanoid biosynthesis, starch and sucrose metabolism, phytohormone signaling, amino acid metabolism, and brassinosteroid biosynthesis were significantly correlated with the formation of maize leaf shape and stalk strength and that the genes in these pathways were primarily involved in cell wall formation. Weighted gene co-expression network analysis identified 2 modules significantly correlated with leaf width and stalk strength, from which 11 hub genes were further identified. The 11 leaf and stem development genes in different pathways were validated using qRT-PCR. These findings can provide a theoretical basis for the mechanism of narrow-leaf and high-strength stalk formation in high-density-tolerance maize and contribute to the proposal of a breeding strategy for yield improvement.