Waterlogging significantly reduces crop yield and quality, but its molecular effects on cowpea ( Vigna unguiculata (L.) Walp.) across different developmental stages remain poorly understood. Employing RNA-seq, this study investigates the transcriptomic responses of two contrasting cowpea genotypes, UCR369 and Epicselect.4, under control and waterlogging conditions during the vegetative, flowering, and maturity stages. Differential expression analysis revealed stage-specific and genotype-dependent transcriptional responses to waterlogging, with UCR369 demonstrating more dynamic adjustment, particularly at flowering and maturity, highlighting its improved regulatory plasticity under stress. KEGG pathway enrichment analysis showed increases in phenylpropanoid, flavonoid, and isoflavonoid metabolism, starch-sucrose metabolism, and cutin-suberin-wax biosynthesis, which were most prominent in UCR369 during flowering and maturation, indicating a genotype-specific change in metabolic defense and cell-surface/barrier remodeling. Pathview maps also revealed continuous activation of core flavonoid and isoflavonoid steps throughout development stages in both genotypes, implying an antioxidant and membrane-protective program during waterlogging. Transcription factor activity was tracked longitudinally across development stages: MYBs showed larger expression changes at the vegetative stage, bHLHs at flowering and maturation, and ERFs throughout; this matches up with phenylpropanoid, carbon partitioning, and hormone/redox control, along with additional ROS- and hormone-integrating families (WRKY, HD-ZIP, HSF) identified in our TF clustering. WGCNA detected 35 modules across the genes and developmental stages: the greenyellow module was associated with starch and phenolics production and was enriched for plastid/redox hub genes; coral3 monitored sucrose metabolism and contained genes for sugar interconversion and senescence; firebrick3/bisque4 were associated with plastid and pigment functions that matched photosynthetic adjustment; and brown4 was related to membrane stability (MSI). XGBoost machine-learning analysis condensed these transcriptome-scale patterns into a compact collection of predictor genes that recapitulated the KEGG and WGCNA signals and covered major functional axes including cuticle and membrane integrity, plastid and redox homeostasis, ethylene and senescence signaling, and yield determination; this panel consisted of LTP3, NIA2/NR2, CER1/CER22, CASPL1D1, HSP21, ACS6, ICL, SAG12, ATDI21/DI21, ACO1, and two uncharacterized loci, Vigun07g271600 and Vigun08g155100. Together, these findings reveal the architecture of a multilayered regulatory scheme for waterlogging tolerance, as well as suggesting practical gene targets/markers for breeding more resilient cultivars.

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 CO 2 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 CO 2 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 (Ф 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. Rather, UCR 369 rapidly developed adventitious roots (ARs), maintained biomass accumulation, and elongated stems, enabling the genotypeto 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 larger decline in EpicSelect.4. Overall, our findings suggest that rapid AR formation and stem elongation appear to play critical roles in cowpea’s waterlogging tolerance, with the waterlogging-tolerant genotype also maintaining considerable carbon fixation during the reproductive stage.

Waterlogging induces growth and developmental changes in sensitive crops such as cucumber ( Cucumis sativus L.) during early plant development. However, information on the physiological mechanisms underpinning the response of cucumber plants to waterlogging conditions is limited. Here, we investigated the effects of 10-day waterlogging stress on the morphology, photosynthesis, and chlorophyll fluorescence parameters in two cultivars of cucumber seedlings. Waterlogging stress hampered cultivars’ growth, biomass accumulation, and photosynthetic capacity. Both cultivars also developed adventitious roots (ARs) after 10 days of waterlogging (DOW). We observed differential responses in the light- and carbon-dependent reactions of photosynthesis, with an increase in light-dependent reactions. At the same time, carbon assimilation was considerably inhibited by waterlogging. Specifically, the CO 2 assimilation rate ( A) in leaves was significantly reduced and was caused by a corresponding decrease in stomatal conductance (g s). The downregulation of the maximum rate of Rubisco (V cmax) and the maximum rate of photosynthetic electron transport (J max) were non-stomatal limiting factors contributing to A reduction. Exposure of cucumber to 10 DOW affected the PSII photochemistry by downregulating the PSII quantum yield (Φ PSII). The redox state of the primary quinone acceptor in the lake model (1-qL), a measure of the regulatory balance of the light reactions, became more oxidized after 10 DOW, indicating enhanced electron sink capacity despite a reduced A. Overall, the results suggest that waterlogging induces alterations in the photochemical apparatus efficiency of cucumber. Thus, developing cultivars that resist photodamage while maintaining PSII photochemistry is a potential approach for increasing crops’ tolerance to waterlogged environments.