Integrated miRNA and mRNA Transcriptome Analysis Reveals Eggplant’s (Solanum melongena L.) Responses to Waterlogging Stress

Abstract

Waterlogging stress poses a significant threat to eggplants (Solanum melongena L.), causing root oxygen deficiency and subsequent plant damage. This study aims to explore the morphological changes and chlorophyll and lignin indicators of eggplant seedlings under different time points (0, 3, 6, 12, 24, 48 h) of waterlogging stress. High-throughput sequencing was used to identify differentially expressed miRNAs and mRNAs in response to waterlogging stress in eggplants. The results showed that the content of chlorophyll a significantly decreased during the early stage of waterlogging stress, while the degradation of chlorophyll b intensified with prolonged stress, and carotenoid content remained relatively stable. Additionally, this study investigated changes in root lignin, indicating its role in enhancing cell wall stability and tolerance to cope with hypoxic stress. Using DESeq2, 246 differentially expressed miRNAs were identified, among which significant changes were observed in the miR156, miR166, miR167, and miR399 families. These miRNAs may play a crucial regulatory role in eggplant’s adaptation to the hypoxic environment after waterlogging stress. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that differentially expressed genes were mainly related to cellular physiological processes, metabolic processes, and the biosynthesis of secondary metabolites, influencing the seedlings’ stress resistance under different waterlogging conditions. Furthermore, by constructing a regulatory miRNA–target gene network that pertains to eggplant’s response to waterlogging stress, we have laid the foundation for revealing the molecular mechanisms of eggplant’s response to waterlogging stress.