Antioxidant activation, cell wall reinforcement, and reactive oxygen species regulation promote resistance to waterlogging stress in hot pepper (Capsicum annuum L.)

BACKGROUND: Hot pepper (Capsicum annuum L.) is one of the world’s oldest domesticated crops. It has poor waterlogging tolerance, and flooding frequently results in plant death and yield reduction. Therefore, understanding the molecular mechanisms associated with pepper waterlogging tolerance is essential to grow new varieties with stronger tolerance. RESULTS: In this study, we discovered that after 5 days of flooding, the growth rate of waterlogging-tolerant pepper cultivars did not reduce to a large extent. Physiological data revealed that chlorophyll concentration was not significantly affected by flooding; however, stomatal conductance was altered considerably 0–5 days after flooding, and the net photosynthesis rate changed substantially 5–10 days after flooding. In addition, the root activity of waterlogging-tolerant varieties was substantially higher after flooding for 10 days than that of the control. This implies that the effect of flooding is associated with changes in the root environment, which ultimately affects photosynthesis. We evaluated changes in gene expression levels between two pepper types at the same time point and the same pepper variety at different time points after flooding stress treatment and performed a screening for multiple potential genes. These differentially expressed genes (DEGs) were further analyzed for functional enrichment, and the results revealed that antioxidase genes, cell wall synthesis pathway genes, and calcium ion regulation pathway genes might be associated with waterlogging tolerance. Other genes identified in peppers with waterlogging tolerance included those associated with lignin synthesis regulation, reactive oxygen species (ROS) regulation pathways, and others associated with stress resistance. Considerable changes in the expression levels of these genes were recorded 5 days after waterlogging, which was consistent with a considerable increase in oxidase content that was also noted on the fifth day after flooding. The quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) findings revealed that among the 20 selected DEGs, including genes such as mitogen-activated protein kinase 3 (MPK3) and calcium-binding protein 4 (CML4), approximately 80% of the gene expression patterns were consistent with our RNA-seq dataset. CONCLUSIONS: The findings of this study suggest that ROS modulation, increased antioxidase activity, lignin formation, and the expression of stress resistance genes help peppers with waterlogging tolerance resist flooding stress in the early stages. These findings provide a basis for further investigation of the molecular mechanisms responsible for waterlogging tolerance in pepper and may be a critical reference for the breeding of hot pepper. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-022-03807-2.