Short waterlogging events differently affect morphology and photosynthesis of two cucumber (Cucumis sativus L.) cultivars

Uncovering waterlogging-responsive genes in cucumber through machine learning and differential gene correlation analysis

As climate change intensifies, the frequency and severity of waterlogging are expected to increase, necessitating a deeper understanding of the cucumber response to this stress. In this study, three public RNA-seq datasets (PRJNA799460, PRJNA844418, and PRJNA678740) comprising 36 samples were analyzed. Various feature selection algorithms including Uncertainty, Relief, SVM (Support Vector Machine), Correlation, and logistic least absolute shrinkage, and selection operator (LASSO) were performed to identify the most significant genes related to the waterlogging stress response. These feature selection techniques, which have different characteristics, were used to reduce the complexity of the data and thereby identify the most significant genes related to the waterlogging stress response. Uncertainty, Relief, SVM, Correlation, and LASSO identified 4, 4, 10, 21, and 13 genes, respectively. Differential gene correlation analysis (DGCA) focusing on the 36 selected genes identified changes in correlation patterns between the selected genes under waterlogged versus control conditions, providing deeper insights into the regulatory networks and interactions among the selected genes. DGCA revealed significant changes in the correlation of 13 genes between control and waterlogging conditions. Finally, we validated 13 genes using the Random Forest (RF) classifier, which achieved 100% accuracy and a 1.0 Area Under the Curve (AUC) score. The SHapley Additive exPlanations (SHAP) values clearly showed the significant impact of LOC101209599, LOC101217277, and LOC101216320 on the model's predictive power. In addition, we employed the Boruta as a wrapper feature selection method to further validate our gene selection strategy. Eight of the 13 genes were common across the four feature weighting algorithms, LASSO, DGCA, and Boruta, underscoring the robustness and reliability of our gene selection strategy. Notably, the genes LOC101209599, LOC101217277, and LOC101216320 were among genes identified by multiple feature selection methods from different categories (filtering, wrapper, and embedded). Pathways associated with these specific genes play a pivotal role in regulating stress tolerance, root development, nutrient absorption, sugar metabolism, gene expression, protein degradation, and calcium signaling. These intricate regulatory mechanisms are crucial for cucumbers to adapt effectively to waterlogging conditions. These findings provide valuable insights for uncovering targets in breeding new cucumber varieties with enhanced stress tolerance.

The role of leaf superoxide dismutase and proline on intra-specific photosynthesis recovery of Schima superba following drought

Understanding the physiological and biochemical responses of tree seedlings under extreme drought stress, along with recovery during rewatering, and potential intra-species differences, will allow us to more accurately predict forest responses under future climate change. Here, we selected seedlings from four provenances (AH (Anhui), JX (Jiangxi), HN (Hunan) and GX (Guangxi)) of Schima superba and carried out a simulated drought-rewatering experiment in a field-based rain-out shelter. Seedlings were progressively dried until they reached 50% and 88% loss of xylem hydraulic conductivity (PLC) (i.e. P50 and P88), respectively, before they were rehydrated and maintained at field capacity for 30 days. Leaf photosynthesis (Asat), water status, activity of superoxide dismutase (SOD), and proline (Pro) concentration were monitored and their associations were determined. Increasing drought significantly reduced Asat, relative water content (RWC) and SOD activity in all provenances, and Pro concentration was increased to improve water retention; all four provenances exhibited similar response patterns, associated with similar leaf ultrastructure at pre-drought. Upon rewatering, physiological and biochemical traits were restored to well-watered control values in P50-stressed seedlings. In P88-stressed seedlings, Pro was restored to control values, while SOD was not fully recovered. The recovery pattern differed partially among provenances. There was a progression of recovery following watering, with RWC firstly recovered, followed by SOD and Pro, and then Asat, but with significant associations among these traits. Collectively, the intra-specific differences of S. superba seedlings in recovery of physiology and biochemistry following rewatering highlight the need to consider variations within a given tree species coping with future more frequent drought stress.

Role of salicylic acid in improving the yield of two mung bean genotypes under waterlogging stress through the modulation of antioxidant defense and osmoprotectant levels

Waterlogging (WL) is a major hindrance to the growth and development of leguminous crops, including mung bean. Here, we explored the effect of salicylic acid (SA) pretreatment on growth and yield output of two elite mung bean genotypes (BU Mung bean-4 and BU Mung bean-6) subjected to WL stress. SA pretreatment significantly improved shoot dry weight, individual leaf area, and photosynthetic pigment contents in both genotypes, while those improvements were higher in BU Mung bean-6 when compared with BU Mung bean-4. We also found that SA pretreatment significantly reduced the reactive oxygen species-induced oxidative burden in both BU Mung bean-6 and BU Mung bean-4 by enhancing peroxidase, glutathione S-transferase, catalase, and ascorbate peroxidase activities, as well as total flavonoid contents. SA pretreatment further improved the accumulation of proline and free amino acids in both genotypes, indicating that SA employed these osmoprotectants to enhance osmotic balance. These results were particularly corroborated with the elevated levels of leaf water status and leaf succulence in BU Mung bean-6. SA-mediated improvement in physiological and biochemical mechanisms led to a greater yield-associated feature in BU Mung bean-6 under WL conditions. Collectively, these findings shed light on the positive roles of SA in alleviating WL stress, contributing to yield improvement in mung bean crop.

Ethylene-induced improvement in photosynthetic performance of Zanthoxylum armatum under reoxygenation conditions

In this study, we evaluated the photosynthetic performance of Zanthoxylum armatum seedlings to test the tolerance to reoxygenation after waterlogging. The experiment included a control group without waterlogging (NW) and three reoxygenation groups with reoxygenation after 1day (WR1), 2days (WR2) and 3days (WR3). Seedlings were pretreated with concentrations of 0, 200 and 400μmolL-1 of ethylene. The results showed that reoxygenation after waterlogging for 1-3days decreased photosynthetic pigments content, enzymes activity, stomatal conductance (G s ), net photosynthetic rate (P n ), transpiration rate (T r ) and water-use efficiency (WUE). However, pretreatment with ethylene increased photosynthetic pigments content, enzymes activity and gas exchange parameters under both NW and WR3 treatments. The chlorophyll fluorescence results showed that the maximum quantum yield of PSII (F v /F m ) and actual photochemical efficiency of PSII (Φ PSII ) remained no significant changes under the NW and WR1 treatments, while they were significantly reduced with an increase in waterlogging days followed by reoxygenation under WR2 and WR3 treatments. Exogenous ethylene inhibited F v /F m and the non-photochemical quenching coefficient (NPQ), while enhanced Φ PSII and electron transfer efficiency (ETR) under WR2 treatments. Moreover, the accumulation of exogenous ethylene reduced photosynthetic ability. These findings provide insights into the role of ethylene in enhancing the tolerance of Z. armatum to reoxygenation stress, which could help mitigate the impact of continued climate change.

Waterlogging during the reproductive growth stage causes physiological and biochemical modifications in the leaves of cowpea (Vigna unguiculata L.) genotypes with contrasting tolerance

Waterlogging causes various metabolic, physiological, and morphological changes in crops, resulting in yield loss of most legumes in rainfed and irrigated agriculture. However, research on cowpea genotypes using physiological and biochemical traits as a measure of tolerance to waterlogging stress is limited. We evaluated the impacts of 7 days of waterlogging (DOW) and 7 days of recovery (DOR) on the physiology and biochemistry of two cowpea (Vigna unguiculata (L.) Walp) genotypes (UCR 369 and EpicSelect.4) with contrasting waterlogging tolerance. Cowpea genotypes were grown in a controlled environment until the R2 stage and then subjected to 7 DOW. Later, the waterlogged plants were reoxygenated for an additional 7 DOR. Overall, cowpea genotypes had a contrasting response to waterlogging using different mechanisms. Compared to the control, the photosynthetic parameters of both cowpea genotypes were impaired under 7 DOW and could not recover at 7 DOR, with a larger decline in EpicSelect.4.7 DOW caused significant loss in the chlorophyll and carotenoid content of both genotypes. However, only waterlogged UCR 369 was not photo-inhibited and able to restore the levels of chlorophyll and carotenoids at 7 DOR. In addition, 7 DOW induced intense stress in UCR 369 with increased zeaxanthin, sucrose, and flavonoid content, while these metabolites were decreased in EpicSelect.4. On the other hand, glucose, fructose, and phenolic content were increased in EpicSelect.4 but decreased in UCR 369 at 7 DOR. In summary, compared to EpicSelect.4, UCR 369 restored their photosynthetic pigments and metabolites to the control levels at 7 DOR, indicating a likely tolerance to waterlogging stress.

Growth and Photosynthetic Responses of Cowpea Genotypes under Waterlogging at the Reproductive Stage

Waterlogging is an important environmental stress limiting the productivity of crops worldwide. Cowpea (Vigna unguiculata L.) is particularly sensitive to waterlogging stress during the reproductive stage, with a consequent decline in pod formation and yield. However, little is known about the critical processes underlying cowpea’s responses to waterlogging during the reproductive stage. Thus, we investigated the key parameters influencing carbon fixation, including stomatal conductance (g_s), intercellular CO₂ concentration, chlorophyll content, and chlorophyll fluorescence, of two cowpea genotypes with contrasting waterlogging tolerance. These closely related genotypes have starkly contrasting responses to waterlogging during and after 7 days of waterlogging stress (DOW). In the intolerant genotype (‘EpicSelect.4’), waterlogging resulted in a gradual loss of pigment and decreased photosynthetic capacity as a consequent decline in shoot biomass. On the other hand, the waterlogging-tolerant genotype (‘UCR 369’) maintained CO₂ assimilation rate (A), stomatal conductance (g_s), biomass, and chlorophyll content until 5 DOW. Moreover, there was a highly specific downregulation of the mesophyll conductance (g_m), maximum rate of Rubisco (V_cmax), and photosynthetic electron transport rate (J_max) as non-stomatal limiting factors decreasing A in EpicSelect.4. Exposure of EpicSelect.4 to 2 DOW resulted in the loss of PSII photochemistry by downregulating the PSII quantum yield (F_v/F_m), photochemical efficiency (Φ_PSII), and photochemical quenching (qP). In contrast, we found no substantial change in the photosynthesis and chlorophyll fluorescence of UCR 369 in the first 5 DOW. Instead, UCR 369 maintained biomass accumulation, chlorophyll content, and Rubisco activity, enabling the genotype to maintain nutrient absorption and photosynthesis during the early period of waterlogging. However, compared to the control, both cowpea genotypes could not fully recover their photosynthetic capacity after 7 DOW, with a more significant decline in EpicSelect.4. Overall, our findings suggest that the tolerant UCR 369 genotype maintains higher photosynthesis under waterlogging stress attributable to higher photochemical efficiency, Rubisco activity, and less stomatal restriction. After recovery, the incomplete recovery of A can be attributed to the reduced g_s caused by severe waterlogging damage in both genotypes. Thus, promoting the rapid recovery of stomata from waterlogging stress may be crucial for the complete restoration of carbon fixation in cowpeas during the reproductive stage.