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We review waterlogging and submergence tolerances of forage (pasture) legumes. Growth reductions from waterlogging in perennial species ranged from >50% for Medicago sativa and Trifolium pratense to <25% for Lotus corniculatus, L. tenuis, and T. fragiferum. For annual species, waterlogging reduced Medicago truncatula by ~50%, whereas Melilotus siculus and T. michelianum were not reduced. Tolerant species have higher root porosity (gas-filled volume in tissues) owing to aerenchyma formation. Plant dry mass (waterlogged relative to control) had a positive (hyperbolic) relationship to root porosity across eight species. Metabolism in hypoxic roots was influenced by internal aeration. Sugars accumulate in M. sativa due to growth inhibition from limited respiration and low energy in roots of low porosity (i.e. 4.5%). In contrast, L. corniculatus, with higher root porosity (i.e. 17.2%) and O₂ supply allowing respiration, maintained growth better and sugars did not accumulate. Tolerant legumes form nodules, and internal O₂ diffusion along roots can sustain metabolism, including N₂ fixation, in submerged nodules. Shoot physiology depends on species tolerance. In M. sativa, photosynthesis soon declines and in the longer term (>10 d) leaves suffer chlorophyll degradation, damage, and N, P, and K deficiencies. In tolerant L. corniculatus and L. tenuis, photosynthesis is maintained longer, shoot N is less affected, and shoot P can even increase during waterlogging. Species also differ in tolerance of partial and complete shoot submergence. Gaps in knowledge include anoxia tolerance of roots, N₂ fixation during field waterlogging, and identification of traits conferring the ability to recover after water subsides.

Understanding the mechanisms underlying plant stress tolerance is crucial for improving plant resilience, particularly under challenging environmental conditions. This study investigates the role of long-chain acyl-CoA synthetases in Salix matsudana (SmLACSs), focusing on their evolutionary relationships, functional characterization, and response to environmental stresses. Through a comprehensive analysis, 25 SmLACSs were identified, classified into seven distinct clades, with Clade VII representing a newly discovered subfamily in willow. Evolutionary analysis revealed that segmental duplication and whole-genome duplication were key mechanisms for the expansion of SmLACSs . Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis further indicated that SmLACSs play a role in lipid metabolism, cuticle formation, and stress response pathways. Using RNA-seq and qRT-PCR, differential expression patterns of SmLACSs under salt or submergence stress were observed, highlighting their contribution to stress tolerance, particularly in maintaining cell membrane integrity and lipid homeostasis. These findings provide valuable insights into the roles of SmLACSs in willow’s resilience, and offer potential targets for improving stress tolerance in plants.

Plants have developed elaborate mechanisms for perceiving extracellular stimuli and subsequently activating defense reactions through a multifaceted interaction of signaling cascades. Calcium ion (Ca²⁺), an essential and ubiquitous intracellular second messenger molecules, whose concentration ([Ca 2+ ]cyt) has been observed to rise in response to numerous environmental stresses. The calcium/calmodulin (Ca²⁺/CaM) complex triggers apposite cellular responses through modifying the activities of a varied array of CaM-binding proteins (CBPs). Among CBPs , the CBP60 gene family has been identified as key regulators of stress responses in several crop species. Recently, we have demonstrated the expanded and diversified role of OsCBP60 in rice against devastating pathogens. Here, we analyzed the diversified roles of OsCBP60s in two major abiotic stresses, namely reproductive drought and submergence stress. OsCBP60bcd -2 and OsCBP60g-1/OsSARD1 were consistently upregulated during reproductive drought stress in rice. However, OsCBP60g-5 and OsCBP60g-6 were steadily up-regulated under submergence stress in rice. Interestingly, OsCBP60g-4 was consistently upregulated in both abiotic stresses, except on the third day of reproductive drought. The differential expression of OsCBP60s under water stress highlights the importance of further studying these genes as potential targets for enhancing stress resilience in rice.

Background Submergence stress is a prevalent abiotic stress affecting plant growth and development and can restrict plant cultivation in areas prone to flooding. Research on plant submergence stress tolerance has been essential in managing plant production under excessive rainfall. Red clover ( Trifolium pratense L.), a high-quality legume forage, exhibits low tolerance to submergence, and long-term submergence can lead to root rot and death. Results This study assessed the microstructure, physiological indicators, and the key genes and metabolic pathways under submergence stress in the root system of red clover HL(Hong Long) and ZY(Zi You) varieties under submergence stress at 0 h, 8 h, 24 h, 3 d, and 5 d. Based on 7740 transcripts identified in the leaves at 0 h, 8 h, and 24 h submergence stress, Weighted Gene Co-expression Network Analysis (WGCNA) was performed on the differentially expressed genes (DEGs) at 8 h and 24 h. Functional annotation of the DEGs in the four key modules was obtained. Based on the results, the red clover root system exhibited epidermal cell rupture, enlargement and rupture of cortical thin-walled cells, thickening of the mid-column, and a significant increase in the number of air cavities and air cavity area of aeration tissue with the prolongation of submergence stress. The malondialdehyde content, relative conductivity, peroxidase, and superoxide dismutase initially increased and decreased as submergence stress duration increased. Four specific modules (cyan, purple, light cyan, and ivory) closely correlated with each stress were identified by WGCNA. The 14 obtained Hub genes were functionally annotated, among which six genes, including gene51878, gene11315, and gene11848, were involved in glyoxylate and dicarboxylic acid metabolism, carbon fixation in photosynthetic organisms, carbon metabolism, biosynthesis of pantothenic acid and CoA, flavonoid biosynthesis. Conclusion In this study, using WGCNA, the molecular response mechanisms of red clover to submergence stress was proposed, and the core genes and metabolic pathways in response to submergence stress were obtained, providing a valuable data resource at the physiological and molecular levels for subsequent studies of submergence stress tolerance in plants.

Submergence stress is a limiting factor for direct-seeded rice systems in rainfed lowlands and flood-prone areas of South and Southeast Asia. The present study demonstrated that submergence stress severely hampered the germination and seedling growth of rice, however, seed priming alleviated the detrimental effects of submergence stress. To elucidate the molecular basis of seed priming-induced submergence tolerance, transcriptome analyses were performed using 4-day-old primed (selenium-Se and salicylic acid-SA priming) and non-primed rice seedlings under submergence stress. Genomewide transcriptomic profiling identified 2371 and 2405 transcripts with Se- and SA-priming, respectively, that were differentially expressed in rice compared with non-priming treatment under submergence. Pathway and gene ontology term enrichment analyses revealed that genes involved in regulation of secondary metabolism, development, cell, transport, protein, and metal handling were over-represented after Se- or SA-priming. These coordinated factors might have enhanced the submergence tolerance and maintained the better germination and vigorous seedling growth of primed rice seedlings. It was also found that many genes involved in cellular and metabolic processes such as carbohydrate metabolism, cellular, and metabolic biosynthesis, nitrogen compound metabolic process, transcription, and response to oxidative stress were induced and overlapped in seed priming treatments, a finding which reveals the common mechanism of seed priming-induced submergence tolerance. Taken together, these results may provide new avenues for understanding and advancing priming-induced responses to submergence tolerance in crop plants.

During the energy crisis associated with submergence stress, plants restrict mRNA translation and rapidly accumulate stress granules that act as storage hubs for arrested mRNA complexes. One of the proteins associated with hypoxia-induced stress granules in Arabidopsis thaliana is the calcium-sensor protein CALMODULIN-LIKE 38 (CML38). Here, we show that SUPPRESSOR OF GENE SILENCING 3 (SGS3) is a CML38-binding protein, and that SGS3 and CML38 co-localize within hypoxia-induced RNA stress granule-like structures. Hypoxia-induced SGS3 granules are subject to turnover by autophagy, and this requires both CML38 as well as the AAA + -ATPase CELL DIVISION CYCLE 48A (CDC48A). CML38 also interacts directly with CDC48A, and CML38 recruits CDC48A to CML38 granules in planta. Together, this work demonstrates that SGS3 associates with stress granule-like structures during hypoxia stress that are subject to degradation by CML38 and CDC48-dependent autophagy. Further, the work identifies direct regulatory targets for the hypoxia calcium-sensor CML38, and suggest that CML38 association with stress granules and associated regulation of autophagy may be part of the RNA regulatory program during hypoxia stress.

Leaf senescence is an irreversible growth process that determines plant productivity and survival, especially under environmental stress. Among water stresses, drought and submergence significantly influence senescence pathways through distinct molecular mechanisms. Drought stress accelerates leaf senescence by impairing photosynthesis, reducing leaf expansion, and disrupting water balance, with transcription factors such as NAC, WRKY, and AP2/ERF playing critical roles in its regulation. In particular, the NAC transcription factor family modulates key senescence-associated genes, while WRKY and AP2/ERF members coordinate stress responses through ABA-dependent and independent pathways. Submergence, on the other hand, induces ethylene-mediated senescence, primarily through hypoxia-induced metabolic shifts and light deprivation. ERF transcription factors, particularly ERFVII, regulate hypoxia-responsive genes, whereas bHLH and WRKY transcription factors contribute to ethylene-induced senescence. Furthermore, NAC family regulators, along with EIN3, modulate dark-induced senescence under submergence, revealing mechanistic overlap with natural senescence processes. Recent advances further reveal that epi-genetic modifications dynamically alter chromatin accessibility, activating or suppressing senescence. Moreover, posttranslational regulation through ubiquitin-proteasome degradation and autophagy modulates senescence, with the proteasome accelerating it and autophagy delaying it through selective protein turnover. This review comprehensively explores the transcriptional regulation of leaf senescence under drought and submergence stresses, along with epigenetic and posttranslational regulation, and emphasizes the role of key transcription factor families. Understanding the molecular and physiological mechanisms regulating leaf senescence under these contrasting water stresses is critical for developing stress-resilient crops and enhancing agricultural sustainability in the face of climate change.

Trihelix transcription factors (TTF) are a class of light-responsive proteins with a typical triple-helix structure (helix-loop-helix-loop-helix). Members of this gene family play an important role in plant growth and development, especially in various abiotic stress responses. Salix matsudana Koidz is an allotetraploid ornamental forest tree that is widely planted for its excellent resistance to stress, but no studies on its Trihelix gene family have been reported. In this study, the Trihelix gene family was analyzed at the genome-wide level in S. matsudana . A total of 78 S. matsudana Trihelix transcription factors ( SmTTFs ) were identified, distributed on 29 chromosomes, and classified into four subfamilies (GT-1, GT-2, SH4, SIP1) based on their structural features. The gene structures and conserved functional domains of these Trihelix genes are similar in the same subfamily and differ between subfamilies. The presence of multiple stress-responsive cis-elements on the promoter of the S. matsudana Trihelix gene suggests that the S. matsudana Trihelix gene may respond to abiotic stresses. Expression pattern analysis revealed that Trihelix genes have different functions during flooding stress, salt stress, drought stress and low temperature stress in S. matsudana . Given that SmTTF30 , as a differentially expressed gene, has a faster response to flooding stress, we selected SmTTF30 for functional studies. Overexpression of SmTTF30 in Arabidopsis thaliana (Arabidopsis) enhances its tolerance to flooding stress. Under flooding stress, the leaf cell activity and peroxidase activity (POD) of the overexpression strain were significantly higher than the leaf cell activity and POD of the wild type, and the malondialdehyde (MDA) content was significantly lower than the MDA content of the wild type. Thus, these results suggest that SmTTF30 enhances plant flooding tolerance and plays a positive regulatory role in plant flooding tolerance.

Background Seed flooding stress is one of the threatening environmental stressors that adversely limits soybean at the germination stage across the globe. The knowledge on the genetic basis underlying seed-flooding tolerance is limited. Therefore, we performed a genome-wide association study (GWAS) using 34,718 single nucleotide polymorphism (SNPs) in a panel of 243 worldwide soybean collections to identify genetic loci linked to soybean seed flooding tolerance at the germination stage. Results In the present study, GWAS was performed with two contrasting models, Mixed Linear Model (MLM) and Multi-Locus Random-SNP-Effect Mixed Linear Model (mrMLM) to identify significant SNPs associated with electrical conductivity (EC), germination rate (GR), shoot length (ShL), and root length (RL) traits at germination stage in soybean. With MLM, a total of 20, 40, 4, and 9 SNPs associated with EC, GR, ShL and RL, respectively, whereas in the same order mrMLM detected 27, 17, 13, and 18 SNPs. Among these SNPs, two major SNPs, Gm_08_11971416, and Gm_08_46239716 were found to be consistently connected with seed-flooding tolerance related traits, namely EC and GR across two environments. We also detected two SNPs, Gm_05_1000479 and Gm_01_53535790 linked to ShL and RL, respectively. Based on Gene Ontology enrichment analysis, gene functional annotations, and protein-protein interaction network analysis, we predicted eight candidate genes and three hub genes within the regions of the four SNPs with Cis- elements in promoter regions which may be involved in seed-flooding tolerance in soybeans and these warrant further screening and functional validation. Conclusions Our findings demonstrate that GWAS based on high-density SNP markers is an efficient approach to dissect the genetic basis of complex traits and identify candidate genes in soybean. The trait associated SNPs could be used for genetic improvement in soybean breeding programs. The candidate genes could help researchers better understand the molecular mechanisms underlying seed-flooding stress tolerance in soybean.

Submergence, a major abiotic stress in hydrologically dynamic ecosystems, poses severe challenges to plant survival and growth. Existing studies have demonstrated that plants employ a suite of adaptive strategies to tolerate submergence. These divergent adaptive responses are endogenously regulated by phytohormones; yet, the underlying mechanisms that connect hormonal regulation, anatomical plasticity, and growth adaptation in the context of submergence remain insufficiently elucidated. Alternanthera philoxeroides (Mart.) Griseb. is widely distributed in disturbed, flood-prone habitats and exhibits exceptional adaptability to hydrological fluctuations, making it a suitable species for exploring submergence stress responses. This study investigated A. philoxeroides’ responses to three hydrological conditions (non-submergence, partial submergence, complete submergence), focusing on stem growth and its anatomical and hormonal regulatory drivers. Results revealed an unexpected growth pattern: complete submergence induced significantly faster stem elongation than partial submergence, with this growth-promoting effect most pronounced in immature stems—particularly the basal parts of immature internodes. This elongation correlated positively with enlarged pith cavities and elevated gibberellin (GA 4 ), while it was significantly negatively correlated with abscisic acid (ABA). GA 4 content and pith cavity area were also highly positively correlated. These findings unravel a critical adaptation mechanism in A. philoxeroides : coordinated hormonal adjustments (GA 4 up, ABA down, higher GA 4 /ABA) and morphological remodeling (pith cavity enlargement) that synergistically support enhanced growth under severe submergence. This work advances understanding of plant adaptive strategies under climate-driven hydrological stress, enriches insights into abiotic stress response mechanisms, and provides valuable references for wetland ecosystem conservation and the improvement of crop submergence tolerance.