Grapes, an important and widespread fruit crop providing multiple products, face increasing flooding risks due to intense and frequent extreme rainfall. It is thus imperative to fully understand the flood-tolerance mechanisms of grapevines. Here, RNA-seq and LC-MS/MS technologies were used to analyze the transcriptome and metabolome changes in the roots of SO4 (tolerant to flooding) and Kyoho (sensitive to flooding) grapes under flooding and post-flooding conditions. The results showed that the abundance of many metabolites in the phenylpropanoids and polyketides, organic acids and their derivatives, and organic oxygen compounds superclasses changed in different patterns between the Kyoho and SO4 grapes under flooding and post-flooding conditions. Jasmonic acid and the ascorbic acid–glutathione cycle played a pivotal role in coping with both hypoxia stress and reoxygenation stress incurred during flooding and post-flooding treatments in the SO4 cultivar. Under flooding stress, the regulatory mechanistic shift from aerobic respiration to anaerobic fermentation under hypoxia is partly missing in the Kyoho cultivar. In the post-flooding stage, many genes related to ethylene, gibberellins, cytokinins, and brassinosteroids biosynthesis and brassinosteroids-responsive genes were significantly downregulated in the Kyoho cultivar, adversely affecting growth recovery; however, their expression was not reduced in the SO4 cultivar. These findings enhance our understanding of the flooding-tolerance mechanisms in grapes.

Drought is one of the most serious abiotic stresses in citrus plantations. It is thus imperative to fully understand the drought-resistant mechanisms in these plants. Here, RNA-seq was used to analyze the transcriptomic changes in the roots of Poncirus trifoliata, a widely used rootstock in citrus plantations, under a 72-day soil drought and a 7-day recovery stage. Our results showed that the genes upregulated under drought were only enriched in the galactose metabolism and protein processing in endoplasmic reticulum pathways. In the galactose metabolism pathway, four genes related to the synthesis of raffinose family oligosaccharides, which act as osmoprotectants and ROS scavengers, were significantly upregulated under long-term drought. Several heat-shock protein (HSP) family genes were significantly upregulated under drought, leading to increased levels of HSPs to alleviate the endoplasmic reticulum-associated degradation of misfolded proteins induced by drought stress. Some other upregulated genes under drought, like late embryogenesis-abundant family genes and lipid transfer protein family genes, might also be crucial to the drought resistance of P. trifoliata roots. MSYJ196370 (heat-shock factor family gene) was the top hub gene in the protein–protein interaction analysis of upregulated genes under drought. These findings supplement the transcriptomic response of P. trifoliata root under long-term drought stress.