Plant waterlogging/flooding stress responses: From seed germination to maturation

Re-watering solution facilitates seed germination and seedling growth of Carex schmidtii: Implication for species re-introduction in degraded semi-arid wetlands

Water deficiency threatens the health and function of wetlands in semi-arid areas. Optimum re-watering is an effective method for close-to-natural restoration to mitigate wetland degradation. Although the ecological importance of optimal re-watering as a nature-based solution for promoting wetland plant growth has been widely recognized, the response mechanisms of seed germination and seedling growth to re-watering are still poorly understood despite their decisive impact on plant life history. To fill this gap, this study compared the characteristics of seed germination and seedling growth in Carex schmidtii under initial water content with three levels (30%, 50%, and 70%) and five re-watering treatments (maintained at constant water content and re-watering to 100% on 7th, 14th, 21st, and 28th day). Moreover, the degree of reserve mobilization during four germination stages (seed suckering, sprouting, 20% germination, and seedling growth) was investigated. The results showed that water deficiency and re-watering treatments significantly affected C. schmidtii seed germination, seedling growth, and reserve mobilization. Compared with the other treatments, 50% moisture content and re-watering to 100% on the 14th day (50%-RT3) treatment significantly improved germination traits (germination rate, daily germination rate, germination index, and vigor index) and seedling growth characteristics (shoot length, root length, shoot biomass, root biomass, and total biomass). Furthermore, the degree of mobilization of starch, soluble protein, fat, and soluble sugar accumulation in C. schmidtii seeds under 50%-RT3 was higher than that in the other treatments. The structural equation model showed that the characteristics of seed germination and seedling growth of C. schmidtii were directly related to water deficiency and re-watering treatments, whereas reserve mobilization indirectly affected seed germination and seedling growth. These findings demonstrated that water deficiency and re-watering treatments have a crucial regulatory effect on seed germination and seedling growth of wetland plant species through a dual mechanism. This study provides information for the formulation of an optimum re-watering strategy for wetland vegetation restoration in semi-arid areas of the world.

Proline Metabolism in Response to Climate Extremes in Hairgrass

Hairgrass (Deschampsia caespitosa), a widely distributed grass species considered promising in the ecological restoration of degraded grassland in the Qinghai-Xizang Plateau, is likely to be subjected to frequent drought and waterlogging stress due to ongoing climate change, further aggravating the degradation of grassland in this region. However, whether it would acclimate to water stresses resulting from extreme climates remains unknown. Proline accumulation is a crucial metabolic response of plants to challenging environmental conditions. This study aims to investigate the changes in proline accumulation and key enzymes in hairgrass shoot and root tissues in response to distinct climate extremes including moderate drought, moderate waterlogging, and dry-wet variations over 28 days using a completely randomized block design. The proline accumulation, contribution of the glutamate and ornithine pathways, and key enzyme activities related to proline metabolism in shoot and root tissues were examined. The results showed that water stress led to proline accumulation in both shoot and root tissues of hairgrass, highlighting the importance of this osmoprotectant in mitigating the effects of environmental challenges. The differential accumulation of proline in shoots compared to roots suggests a strategic allocation of resources by the plant to cope with osmotic stress. Enzymatic activities related to proline metabolism, such as Δ1-pyrroline-5-carboxylate synthetase, ornithine aminotransferase, Δ1-pyrroline-5-carboxylate reductase, Δ1-pyrroline-5-carboxylate dehydrogenase, and proline dehydrogenase, further emphasize the dynamic regulation of proline levels in hairgrass under water stress conditions. These findings support the potential for enhancing the stress resistance of hairgrass through the genetic manipulation of proline biosynthesis and catabolism pathways.

Unraveling Key Factors for Hypoxia Tolerance in Contrasting Varieties of Cotton Rose by Comparative Morpho-physiological and Transcriptome Analysis

The cotton rose (Hibiscus mutabilis) is a plant species commonly found in tropical and subtropical regions. It is remarkably resilient to waterlogging stress; however, the underlying mechanism behind this trait is yet unknown. This study used hypoxia-tolerant "Danbanhong" (DBH) and more hypoxia-sensitive "Yurui" (YR) genotypes and compared their morpho-physiological and transcriptional responses to hypoxic conditions. Notably, DBH had a higher number of adventitious roots (20.3) compared to YR (10.0), with longer adventitious roots in DBH (18.3 cm) than in YR (11.2 cm). Furthermore, the formation of aerenchyma was 3-fold greater in DBH compared to YR. Transcriptomic analysis revealed that DBH had more rapid transcriptional responses to hypoxia than YR. Identification of a greater number of differentially expressed genes (DEGs) for aerenchyma, adventitious root formation and development, and energy metabolism in DBH supported that DBH had better morphological and transcriptional adaptation than YR. DEG functional enrichment analysis indicated the involvement of variety-specific biological processes in adaption to hypoxia. Plant hormone signaling transduction, MAPK signaling pathway and carbon metabolism played more pronounced roles in DBH, whereas the ribosome genes were specifically induced in YR. These results show that effective multilevel coordination of adventitious root development and aerenchyma, in conjunction with plant hormone signaling and carbon metabolism, is required for increased hypoxia tolerance. This study provides new insights into the characterization of morpho-physiological and transcriptional responses to hypoxia in H. mutabilis, shedding light on the molecular mechanisms of its adaptation to hypoxic environments.

Features of the Effect of Quercetin on Different Genotypes of Wheat under Hypoxia

Hypoxia is one of the common abiotic stresses that negatively affects the development and productivity of agricultural crops. Quercetin is used to protect plants from oxidative stress when exposed to environmental stressors. O2 deficiency leads to impaired development and morphometric parameters in wheat varieties Orenburgskaya 22 (Triticum aestivum L.) and varieties Zolotaya (Triticum durum Desf.). Cytological analysis revealed various types of changes in the cytoplasm under conditions of hypoxia and treatment with quercetin. The most critical changes in the cytoplasm occur in the Zolotaya variety during pretreatment with quercetin followed by hypoxia, and in the Orenburgskaya 22 variety during hypoxia. Quercetin has a protective effect only on the Orenburgskaya 22 variety, and also promotes a more effective recovery after exposure to low O2 content. Hypoxia causes an increase in reactive oxygen species and activates the antioxidant system. It has been shown that the most active components of the antioxidant system in the Orenburgskaya 22 variety are MnSOD and Cu/ZnSOD, and in the Zolotaya variety GSH. We have shown that quercetin provides resistance only to the wheat genotype Orenburgskaya 22, as a protective agent against abiotic stress, which indicates the need for a comprehensive study of the effects of exogenous protectors before use in agriculture.

Genetic variations in ZmEREB179 are associated with waterlogging tolerance in maize

Maize (Zea mays) is highly susceptible to waterlogging stress, which reduces both the yield and quality of this important crop. However, the molecular mechanism governing waterlogging tolerance is poorly understood. In this study, we identify a waterlogging- and ethylene-inducible gene ZmEREB179 that encodes an ethylene response factor (ERF) localized in the nucleus. Overexpression of ZmEREB179 in maize increases the sensitivity to waterlogging stress. Conversely, the zmereb179 knockout mutants are more tolerant to waterlogging, suggesting that ZmEREB179 functions as a negative regulator of waterlogging tolerance. A transcriptome analysis of the ZmEREB179-overexpressing plants reveals that the ERF-type transcription factor modulates the expression of various stress-related genes, including ZmEREB180. We find that ZmEREB179 directly targets the ZmEREB180 promoter and represses its expression. Notably, the analysis of a panel of 220 maize inbred lines reveals that genetic variations in the ZmEREB179 promoter (Hap2) are highly associated with waterlogging resistance. The functional association of Hap2 with waterlogging resistance is tightly co-segregated in two F2 segregating populations, highlighting its potential applications in breeding programs. Our findings shed light on the involvement of the transcriptional cascade of ERF genes in regulating plant-waterlogging tolerance.

Morphological and molecular response mechanisms of the root system of different Hemarthria compressa species to submergence stress

Introduction

The severity of flood disasters is increasing due to climate change, resulting in a significant reduction in the yield and quality of forage crops worldwide. This poses a serious threat to the development of agriculture and livestock. Hemarthria compressa is an important high-quality forage grass in southern China. In recent years, frequent flooding has caused varying degrees of impacts on H. compressa and their ecological environment.

Methods

In this study, we evaluated differences in flooding tolerance between the root systems of the experimental materials GY (Guang Yi, flood-tolerant) and N1291 (N201801291, flood-sensitive). We measured their morphological indexes after 7 d, 14 d, and 21 d of submergence stress and sequenced their transcriptomes at 8 h and 24 h, with 0 h as the control.

Results

During submergence stress, the number of adventitious roots and root length of both GY and N1291 tended to increase, but the overall growth of GY was significantly higher than that of N1291. RNA-seq analysis revealed that 6046 and 7493 DEGs were identified in GY-8h and GY-24h, respectively, and 9198 and 4236 DEGs in N1291-8h and N1291-24h, respectively, compared with the control. The GO and KEGG enrichment analysis results indicated the GO terms mainly enriched among the DEGs were oxidation-reduction process, obsolete peroxidase reaction, and other antioxidant-related terms. The KEGG pathways that were most significantly enriched were phenylpropanoid biosynthesis, plant hormone signal transduction etc. The genes of transcription factor families, such as C2H2, bHLH and bZIP, were highly expressed in the H. compressa after submergence, which might be closely related to the submergence adaptive response mechanisms of H. compressa.

Discussion

This study provides basic data for analyzing the molecular and morphological mechanisms of H. compressa in response to submergence stress, and also provides theoretical support for the subsequent improvement of submergence tolerance traits of H. compressa.

Genome-wide identification of Avicennia marina aquaporins reveals their role in adaptation to intertidal habitats and their relevance to salt secretion and vivipary

Aquaporins (AQPs) regulate the transport of water and other substrates, aiding plants in adapting to stressful environments. However, the knowledge of AQPs in salt-secreting and viviparous Avicennia marina is limited. In this study, 46 AmAQPs were identified in A. marina genome, and their subcellular localisation and function in transporting H2 O2 and boron were assessed through bioinformatics analysis and yeast transformation. Through analysing their expression patterns via RNAseq and real-time quantitative polymerase chain reaction, we found that most AmAQPs were downregulated in response to salt and tidal flooding. AmPIP (1;1, 1;7, 2;8, 2;9) and AmTIP (1;5, 1;6) as salt-tolerant candidate genes may contribute to salt secretion together with Na+ /H+ antiporters. AmPIP2;1 and AmTIP1;5 were upregulated during tidal flooding and may be regulated by anaerobic-responsive element and ethylene-responsive element cis-elements, aiding in adaptation to tidal inundation. Additionally, we found that the loss of the seed desiccation and dormancy-related TIP3 gene, and the loss of the seed dormancy regulator DOG1 gene, or DOG1 protein lack heme-binding capacity, may be genetic factors contributing to vivipary. Our findings shed light on the role of AQPs in A. marina adaptation to intertidal environments and their relevance to salt secretion and vivipary.

Impacts of the Three Gorges Dam on riparian vegetation in the Yangtze River Basin under climate change

As the largest hydroelectric project in the world, the Three Gorges Dam (TGD) is expected to have significant environmental and ecological impacts on riparian vegetation in the Yangtze River Basin (YRB). However, existing studies have mainly focused on small segments of the YRB. In addition, few studies have quantified the responses of riparian vegetation to both climatic factors and dam construction. In this study, we investigated riparian vegetation dynamics over the entire YRB before, during, and after the construction of TGD from 1982 to 2015 using the normalized difference vegetation index (NDVI). Furthermore, the effects of climatic factors and dam construction on riparian vegetation were quantitatively analyzed using path analysis. The results demonstrate that the YRB has experienced a generally greening trend after TGD construction. The impacts of climate change on riparian vegetation have exhibited notable spatial heterogeneity and temperature is the main climatic factor that affects riparian vegetation growth. Moreover, TGD becomes the major contributor to riparian vegetation dynamics in the YRB after TGD construction. TGD has not only directly enhanced riparian vegetation but also indirectly affected riparian vegetation by regulating the microclimate. This study highlights the significance of anthropogenic interference when evaluating the relationships between riparian vegetation and climatic factors, providing useful insights for the effective management and conservation of large-scale riparian ecosystems.

Waterlogging faced by bulbil expansion improved the growth of Pinellia ternata and its effect reinforced by brassinolide

The bulbil expansion of P. ternata is a key period for its yield formation, and the process of bulbil expansion is often subjected to short-term heavy precipitation. It is not clear whether the short-term waterlogging can affect bulbil expansion. Brassinolide (BR) is widely believed to enhance plant tolerance to abiotic stress. The study investigated the effects of normal water (C), waterlogging (W), waterlogging + BR (W + B), waterlogging + propiconazole (W + P) on P. ternata at the bulbil expansion period in order to assess P. ternata's ability to cope with waterlogging during the bulbil expansion stage and the regulation effects of BR on the process. The biomass of P. ternata was significantly increased after waterlogging. W treatment significantly reduced the H2O2 and MDA contents, the rate of O2⋅- production and the activities of antioxidant enzymes compared with the C group. AsA and GSH contents were significantly reduced by W treatment. However, the ratios of AsA/DHA and GSH/GSSG were slightly affected by W treatment. The rate of O2∙- production and H2O2 content in W + B group were significantly lower than those in W group. The POD, APX, and GR activities, and GSH content in W + B group were evidently increased compared with the W group. Soluble sugar and active ingredients contents were significantly increased after waterlogging, and the enhancement was reinforced by BR. In conclusion, waterlogging reduced oxidative stress in P. ternata under the experimental conditions. BR treatment under waterlogging had a positive effect on P. ternata by enhancing antioxidant capacity and promoting the accumulation of soluble sugars and active ingredients.

The chromosome-level genome of the submerged plant Cryptocoryne crispatula provides insights into the terrestrial-freshwater transition in Araceae

Plant terrestrialization (i.e. the transition to a terrestrial environment) is a significant evolutionary event that has been intensively studied. While certain plant lineages, particularly in angiosperms, have re-adapted to freshwater habitats after colonizing terrene, however, the molecular mechanism of the terrestrial-freshwater (T-F) transition remains limited. Here, the basal monocot Araceae was selected as the study object to explore the T-F transition adaptation mechanism by comparative genomic analysis. Our findings revealed that the substitution rates significantly increased in the lineage of freshwater Araceae, which may promote their adaptation to the freshwater habitat. Additionally, 20 gene sets across all four freshwater species displayed signs of positive selection contributing to tissue development and defense responses in freshwater plants. Comparative synteny analysis showed that genes specific to submerged plants were enriched in cellular respiration and photosynthesis. In contrast, floating plants were involved in regulating gene expression, suggesting that gene and genome duplications may provide the original material for plants to adapt to the freshwater environment. Our study provides valuable insights into the genomic aspects of the transition from terrestrial to aquatic environments in Araceae, laying the groundwork for future research in the angiosperm.

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.

NACs, generalist in plant life

Plant-specific NAC proteins constitute a major transcription factor family that is well-known for its roles in plant growth, development, and responses to abiotic and biotic stresses. In recent years, there has been significant progress in understanding the functions of NAC proteins. NAC proteins have a highly conserved DNA-binding domain; however, their functions are diverse. Previous understanding of the structure of NAC transcription factors can be used as the basis for their functional diversity. NAC transcription factors consist of a target-binding domain at the N-terminus and a highly versatile C-terminal domain that interacts with other proteins. A growing body of research on NAC transcription factors helps us comprehend the intricate signalling network and transcriptional reprogramming facilitated by NAC-mediated complexes. However, most studies of NAC proteins have been limited to a single function. Here, we discuss the upstream regulators, regulatory components and targets of NAC in the context of their prospective roles in plant improvement strategies via biotechnology intervention, highlighting the importance of the NAC transcription factor family in plants and the need for further research.

Mechanisms of Antioxidant Resistance in Different Wheat Genotypes under Salt Stress and Hypoxia

Various stressors lead to an increase in ROS and damage to plant tissues. Plants have a powerful antioxidant system (AOS), which allows them to neutralize excess ROS. We detected an intense fluorescent glow of ROS in the cells of the cap, meristem, and elongation zones in the roots of wheat Triticum aestivum (Orenburgskaya 22 variety) and Triticum durum (Zolotaya variety). An increase in ROS was accompanied by DNA breaks in the nuclei of wheat root cells, the release of cytochrome c from mitochondria into the cytoplasm, and the translocation of phosphatidylserine into the outer layer of the plasma membrane under salt stress and hypoxia. The different resistances of the two wheat varieties to different abiotic stresses were revealed. The soft wheat variety Orenburgskaya 22 showed high resistance to salt stress but sensitivity to hypoxia, and the durum wheat variety Zolotaya showed tolerance to hypoxia but high sensitivity to salt stress. Different activations of AOS components (GSH, MnSOD, Cu/ZnSOD, CAT, PX, GPX, and GST) were revealed in different wheat genotypes. The basis for the tolerance of the Zolotaya variety to hypoxia is the high content of glutathione (GSH) and the activation of glutathione-dependent enzymes. One of the mechanisms of high resistance to salt stress in the Orenburgskaya 22 variety is a decrease in the level of ROS as a result of the increased activity of the MnSOD and Cu/ZnSOD genes. Identifying the mechanisms of plant tolerance to abiotic stress is the most important task for improving breeding varieties of agricultural plants and increasing their yield.

The Metasequoia genome and evolutionary relationships among redwoods

Redwood trees (Sequoioideae), including Metasequoia glyptostroboides (dawn redwood), Sequoiadendron giganteum (giant sequoia), and Sequoia sempervirens (coast redwood), are threatened and widely recognized iconic tree species. Genomic resources for redwood trees could provide clues to their evolutionary relationships. Here, we report the 8-Gb reference genome of M. glyptostroboides and a comparative analysis with two related species. More than 62% of the M. glyptostroboides genome is composed of repetitive sequences. Clade-specific bursts of long terminal repeat retrotransposons may have contributed to genomic differentiation in the three species. The chromosomal synteny between M. glyptostroboides and S. giganteum is extremely high, whereas there has been significant chromosome reorganization in S. sempervirens. Phylogenetic analysis of marker genes indicates that S. sempervirens is an autopolyploid, and more than 48% of the gene trees are incongruent with the species tree. Results of multiple analyses suggest that incomplete lineage sorting (ILS) rather than hybridization explains the inconsistent phylogeny, indicating that genetic variation among redwoods may be due to random retention of polymorphisms in ancestral populations. Functional analysis of ortholog groups indicates that gene families of ion channels, tannin biosynthesis enzymes, and transcription factors for meristem maintenance have expanded in S. giganteum and S. sempervirens, which is consistent with their extreme height. As a wetland-tolerant species, M. glyptostroboides shows a transcriptional response to flooding stress that is conserved with that of analyzed angiosperm species. Our study offers insights into redwood evolution and adaptation and provides genomic resources to aid in their conservation and management.

Plant Adaptation to Flooding Stress under Changing Climate Conditions: Ongoing Breakthroughs and Future Challenges

Climate-change-induced variations in temperature and rainfall patterns are a serious threat across the globe. Flooding is the foremost challenge to agricultural productivity, and it is believed to become more intense under a changing climate. Flooding is a serious form of stress that significantly reduces crop yields, and future climatic anomalies are predicted to make the problem even worse in many areas of the world. To cope with the prevailing flooding stress, plants have developed different morphological and anatomical adaptations in their roots, aerenchyma cells, and leaves. Therefore, researchers are paying more attention to identifying developed and adopted molecular-based plant mechanisms with the objective of obtaining flooding-resistant cultivars. In this review, we discuss the various physiological, anatomical, and morphological adaptations (aerenchyma cells, ROL barriers (redial O2 loss), and adventitious roots) and the phytohormonal regulation in plants under flooding stress. This review comprises ongoing innovations and strategies to mitigate flooding stress, and it also provides new insights into how this knowledge can be used to improve productivity in the scenario of a rapidly changing climate and increasing flood intensity.

Waterlogging increases greenhouse gas release and decreases yield in winter rapeseed (Brassica napus L.) seedlings

A sustainable future depends on increasing agricultural carbon (C) and nitrogen (N) sequestration. Winter rapeseeds are facing severe yield loss after waterlogging due to the effects of extreme rainfall, especially in the seedling stage, where rainfall is most sensitive. Uncertainty exists over the farming greenhouse gas (GHG) release of rapeseed seedlings following the onset of waterlogging. The effect of waterlogging on GHG release and leaf gas exchange in winter rapeseed was examined in a pot experiment. The experiment included waterlogging treatments lasting 7-day and 21-day and normal irrigation as a control treatment. According to our findings, (1) The ecosystem of rapeseed seedlings released methane (CH4) and nitrous oxide (N2O) in a clear up change that was impacted by ongoing waterlogging. Among them, N2O release had a transient rise during the early stages under the effect of seedling fertilizer. (2) The net photosynthetic rate, transpiration rate, stomatal conductance, plant height, soil moisture, and soil oxidation-reduction potential of rapeseed all significantly decreased due to the ongoing waterlogging. However, rapeseed leaves showed a significant increase in intercellular carbon dioxide (CO2) concentration and leaf chlorophyll content values after waterlogging. Additionally, the findings demonstrated an extremely significant increase in the sustained-flux global warming potential of the sum CO2-eq of CH4 and N2O throughout the entire waterlogging stress period. Therefore, continuous waterlogging can increase C and N release from rapeseed seedlings ecosystem and decrease yield. Therefore, we suggest increasing drainage techniques to decrease the release of agricultural GHGs and promote sustainable crop production.

ROS-mediated waterlogging memory, induced by priming, mitigates photosynthesis inhibition in tomato under waterlogging stress

With global climate change, the frequency and intensity of waterlogging events are increasing due to frequent and heavy precipitation. Little is known however about the response of plants to repeated waterlogging stress events. The aim is to clarify physiological regulation mechanisms of tomato plants under repeated waterlogging stress, and whether Trichoderma harzianum can alleviate waterlogging injury. We identified two genotypes of tomato, 'MIX-002' and 'LA4440', as waterlogging tolerant and sensitive genotypes, respectively, based on plant biomass accumulation. The two tomato genotypes were subjected to a waterlogging priming treatment for 2 days (excess water for 1 cm above substrate surface) followed by a recovery stage for 2 days, and then a second waterlogging stress for 5 days (excess water for 1 cm above substrate surface) followed by a second recovery stage for 3 days. Leaf physiological, plant growth parameters, and the expression of five key genes were investigated. We found that the two genotypes responded differently to waterlogging priming and stress in terms of photosynthesis, reactive oxygen species (ROS), and osmotic regulatory mechanisms. Waterlogging stress significantly increased H2O2 content of 'MIX-002', while that of 'LA4440' had no significant change. Under waterlogging stress, photosynthesis of the two genotypes treated with waterlogging priming returned to the control level. However, Trichoderma harzianum treatment during the second recovery stage did not show positive mitigative effects. The plants of 'LA4440' with priming showed lower peroxidase (POD) activity and proline content but higher H2O2 content than that without priming under waterlogging stress. Under waterlogging stress with priming as compared to without priming, SODCC2 was downregulated in two tomatoes, and AGR2 and X92888 were upregulated in 'MIX-002' but downregulated in 'LA4440'. Overall, the two tomato genotypes exhibited distinct photosynthetic, ROS and osmotic regulatory mechanisms responding to the waterlogging stress. Waterlogging priming can induce stress memory by adjusting stomatal conductance, sustaining ROS homeostasis, regulating osmotic regulatory substances and key gene expressions mediated by H2O2, and thus alleviate the damage on tomato photosynthesis when waterlogging reoccurred.

Physiological Mechanism of Waterlogging Stress on Yield of Waxy Maize at the Jointing Stage

In the main agricultural area for waxy maize production in China, waterlogging occurs frequently during the waxy maize jointing stage, and this causes significant yield reduction. It is very important to understand the physiological mechanism of waterlogging stress in waxy maize during the jointing stage to develop strategies against waterlogging stress. Therefore, this study set waterlogging treatments in the field for 0, 2, 4, 6, 8, and 10 days during the waxy maize jointing stage, and were labelled CK, WS2, WS4, WS6, WS8 and WS10, respectively. By analyzing the effect of waterlogging on the source, sink, and transport of photoassimilates, the physiological mechanism of waterlogging stress in the jointing stage was clarified. The results show that PEPC and POD activities and Pro content decreased significantly under WS2 compared to CK. Except for these three indicators, the Pn, GS, leaf area, kernel number, yield, and puncture strength of stems were significantly decreased under the WS4. Under the WS6, the content of MDA began to increase significantly, while almost all other physiological indices decreased significantly. Moreover, the structure of stem epidermal cells and the vascular bundle were deformed after 6 days of waterlogging. Therefore, the threshold value of waterlogging stress occured at 4 to 6 days in the jointing stage of waxy maize. Moreover, waterlogging stress at the jointing stage mainly reduces the yield by reducing the number of kernels; specifically, the kernel number decreased by 6.7-15.5% in 4-10 days of waterlogging, resulting in a decrease of 9.9-20.2% in the final yield. Thus, we have shown that waterlogging stress at the jointing stage results in the decrease of potential waxy maize kernel numbers and yield when the synthesis of sources was limited and the transport of photoassimilates was restricted.

Physiological and transcriptional regulation in Taxodium hybrid 'Zhongshanshan' leaves in acclimation to prolonged partial submergence

MAIN CONCLUSION

Taxodium 703 leaves activate fermentation, amino acids metabolism and ROS detoxification, and reduce TCA cycle and ABA biosynthesis in acclimation to prolonged partial submergence stress. Taxodium hybrid 'Zhongshanshan 703' (T. mucronatum × T. distichum; Taxodium 703) is a highly flooding-tolerant woody plant. To investigate the physiological and transcriptional regulatory mechanisms underlying its leaves in acclimation to long-term flooding, we exposed cuttings of Taxodium 703 to either non-flooding (control) or partial submergence for 2 months. The leaf tissues above (AL) and below (BL) flooding-water were separately harvested. Partial submergence decreased concentrations of chlorophyll (a + b) and dehydroascorbate (DHA) and lactate dehydrogenase (LDH) activity in AL, and reduced biomass, concentrations of succinic acid, fumaric acid and malic acid, and transcript levels of genes involved in tricarboxylic acid (TCA) cycle in BL. Under partial submergence, concentrations of starch, malondialdehyde and abscisic acid (ABA) decreased, and also mRNA levels of nine-cis-epoxycarotenoid dioxygenases that are involved in ABA biosynthesis in AL and BL of Taxodium 703. Partial submergence increased O2- content in AL, and improved concentrations of pyruvate and soluble sugars and activities of LDH and peroxidase in BL. In addition, partial submergence increased concentrations of ethanol, lactate, alanine, γ-aminobutyric acid, total amino acids and ascorbic acid (ASA), and ASA/DHA, activities of alcohol dehydrogenases (ADH) and ascorbate peroxidase, as well as transcript levels of ADH1A, ADH1B and genes involved in alanine biosynthesis and starch degradation in AL and BL of Taxodium 703. Overall, these results suggest that Taxodium 703 leaves activate fermentation, amino acids metabolism and reactive oxygen species detoxification, and maintain a steady supply of sugars, and reduce TCA cycle and ABA biosynthesis in acclimation to prolonged partial submergence stress.

Elucidating the molecular responses to waterlogging stress in onion (Allium cepa L.) leaf by comparative transcriptome profiling

Introduction

Waterlogging is a major stress that severely affects onion cultivation worldwide, and developing stress-tolerant varieties could be a valuable measure for overcoming its adverse effects. Gathering information regarding the molecular mechanisms and gene expression patterns of waterlogging-tolerant and sensitive genotypes is an effective method for improving stress tolerance in onions. To date, the waterlogging tolerance-governing molecular mechanism in onions is unknown.

Methods

This study identified the differentially expressed genes (DEGs) through transcriptome analysis in leaf tissue of two onion genotypes (Acc. 1666; tolerant and W-344; sensitive) presenting contrasting responses to waterlogging stress.

Results

Differential gene expression analysis revealed that in Acc. 1666, 1629 and 3271 genes were upregulated and downregulated, respectively. In W-344, 2134 and 1909 genes were upregulated and downregulated, respectively, under waterlogging stress. The proteins coded by these DEGs regulate several key biological processes to overcome waterlogging stress such as phytohormone production, antioxidant enzymes, programmed cell death, and energy production. The clusters of orthologous group pathway analysis revealed that DEGs contributed to the post-translational modification, energy production, and carbohydrate metabolism-related pathways under waterlogging stress. The enzyme assay demonstrated higher activity of antioxidant enzymes in Acc. 1666 than in W-344. The differential expression of waterlogging tolerance related genes, such as those related to antioxidant enzymes, phytohormone biosynthesis, carbohydrate metabolism, and transcriptional factors, suggested that significant fine reprogramming of gene expression occurs in response to waterlogging stress in onion. A few genes such as ADH, PDC, PEP carboxylase, WRKY22, and Respiratory burst oxidase D were exclusively upregulated in Acc. 1666.

Discussion

The molecular information about DEGs identified in the present study would be valuable for improving stress tolerance and for developing waterlogging tolerant onion varieties.

Plant transcriptional memory and associated mechanism of abiotic stress tolerance

Plants face various adverse environmental conditions, particularly with the ongoing changes in global climate, which drastically affect the growth, development and productivity of crops. To cope with these stresses, plants have evolved complex mechanisms, and one of the crucial ways is to develop transcriptional memories from stress exposure. This induced learning enables plants to better and more strongly restart the response and adaptation mechanism to stress when similar or dissimilar stresses reoccur. Understanding the molecular mechanism behind plant transcriptional memory of stress can provide a theoretical basis for breeding stress-tolerant crops with resilience to future climates. Here we review the recent research progress on the transcriptional memory of plants under various stresses and the applications of underlying mechanisms for sustainable agricultural production. We propose that a thorough understanding of plant transcriptional memory is crucial for both agronomic management and resistant breeding, and thus may help to improve agricultural yield and quality under changing climatic conditions.

Biochemical Alterations in Triticale Seedlings Pretreated with Selective Herbicide and Subjected to Drought or Waterlogging Stress

Waterlogging and drought disrupt crop development and productivity. Triticale is known to be relatively tolerant to different stress factors. In natural conditions, plants are rather subjected to multiple environmental factors. Serrate® (Syngenta) is a systemic selective herbicide suitable for cereal crops such as triticale and wheat to restrain annual grass and broadleaf weeds. Triticale (×Triticosecale Wittm., cv. Rozhen) was grown as soil culture under controlled conditions. Seventeen-day-old plantlets were leaf sprayed with Serrate®. The water stress (drought or waterlogging) was applied after 72 h for 7 days, and then the seedlings were left for recovery. The herbicide does not provoke sharp alterations in the antioxidant state (stress markers level, and antioxidant and xenobiotic-detoxifying enzymes activity). The water stresses and combined treatments enhanced significantly the content of stress markers (malondialdehyde, proline, hydrogen peroxide), non-enzymatic (total phenolics and thiol groups-containing compounds), and enzymatic (activities of superoxide dismutase, catalase, guaiacol peroxidase, glutathione reductase) antioxidants, and xenobiotic-detoxifying enzymes (activities of glutathione S-transferase, NADPH:cytochrome P450 reductase, NADH:cytochrome b5 reductase). These effects were more severely expressed after the drought stress, suggesting that this cultivar is more tolerant to waterlogging than to drought stress.

Phenological phase affects carrot seed production sensitivity to climate change - A panel data analysis

New Zealand is a major producer of carrot seeds globally. Carrots are an important nutritional crop for human consumption. Since the growth and development of carrot seed crops mainly depend on climatic factors, seed yield is extremely susceptible to climate change. This modeling study was undertaken using a panel data approach to determine the impact of the atmospheric conditions (proxied by maximum and minimum temperature) and precipitation during the critical growth stages for seed production in carrot, viz., juvenile phase, vernalization phase, floral development phase, and flowering and seed development phase on carrot seed yield. The panel dataset was created using cross-sections from 28 locations within the Canterbury and Hawke's Bay regions of New Zealand that cultivate carrot seed crops and time series from 2005 to 2022. Pre-diagnostic tests were performed to test the model assumptions, and a fixed effect model was selected subsequently. There was significant (p < 0.01) variability in temperature and rainfall throughout different growing phases, except for precipitation at the vernalization phase. The highest rate of changes in maximum temperature, minimum temperature, and precipitation were recorded during the vernalization phase (+0.254 °C per year), floral development phase (+0.18 °C per year), and juvenile phase (-6.508 mm per year), respectively. Based on marginal effect analysis, the highest significant influence of minimum (187.724 kg/ha of seed yield decrease for each 1 °C increment) and maximum temperature (1 °C rise increases seed yield by 132.728 kg/ha), and precipitation (1 mm increment of rainfall decreases the seed yield by 1.745 kg/ha) on carrot seed yield were reported at vernalization, and flowering and seed development, respectively. The minimum and maximum temperatures have a higher marginal effect on carrot seed production. Analysis of the panel data demonstrates that the production of carrot seeds will be vulnerable to climatic change.

Peroxynitrite is essential for aerenchyma formation in rice roots under waterlogging conditions

MAIN CONCLUSION

In this study, we report that peroxynitrite is necessary for ethylene-mediated aerenchyma formation in rice roots under waterlogging conditions. Plants under waterlogging stress face anoxygenic conditions which reduce their metabolism and induce several adaptations. The formation of aerenchyma is of paramount importance for the survival of plants under waterlogging conditions. Though some studies have shown the involvement of ethylene in aerenchyma formation under waterlogging conditions, the implication of peroxynitrite (ONOO-) in such a developmental process remains elusive. Here, we report an increase in aerenchyma formation in rice roots exposed to waterlogging conditions under which the number of aerenchyma cells and their size was further enhanced in response to exogenous ethephon (a donor of ethylene) or SNP (a donor of nitric oxide) treatment. Application of epicatechin (a peroxynitrite scavenger) to waterlogged plants inhibited the aerenchyma formation, signifying that ONOO- might have a role in aerenchyma formation. Interestingly, epicatechin and ethephon co-treated waterlogged plants were unable to form aerenchyma, indicating the necessity of ONOO- in ethylene-mediated aerenchyma formation under waterlogging conditions. Taken together, our results highlight the role of ONOO- in ethylene-mediated aerenchyma formation in rice and could be used in the future to develop waterlogging stress-tolerant varieties of rice.

Beneficial Microorganisms Improve Agricultural Sustainability under Climatic Extremes

The challenging alterations in climate in the last decades have had direct and indirect influences on biotic and abiotic stresses that have led to devastating implications on agricultural crop production and food security. Extreme environmental conditions, such as abiotic stresses, offer great opportunities to study the influence of different microorganisms in plant development and agricultural productivity. The focus of this review is to highlight the mechanisms of plant growth-promoting microorganisms (especially bacteria and fungi) adapted to environmental induced stresses such as drought, salinity, heavy metals, flooding, extreme temperatures, and intense light. The present state of knowledge focuses on the potential, prospective, and biotechnological approaches of plant growth-promoting bacteria and fungi to improve plant nutrition, physio-biochemical attributes, and the fitness of plants under environmental stresses. The current review focuses on the importance of the microbial community in improving sustainable crop production under changing climatic scenarios.

Effects of drought, subsequent waterlogging and redrying on growth, physiology and metabolism of wheat

With climate change, longer periods without precipitation but also heavy rains will become more frequent. Thus, understanding and predicting the implications of drought-waterlogging-redrying cycles for plants is essential. We examined the effects of such events on wheat (Triticum aestivum). We measured the impacts of subsequent water treatments (drought-waterlogging-redrying) on plant shoot and root biomass, photosynthesis and transpiration, as well as on primary metabolites and transcripts of leaves. Drought and drought followed by waterlogging severely reduced shoot and root biomass. Chlorophyll fluorescence parameters and the CO2 assimilation rate per unit leaf area were not affected by the treatments but, after the redrying phase, plants grown under the stress treatments showed a higher transpiration rate per unit leaf area and a lower instantaneous water use efficiency. Many organic acids of the citrate cycle were less concentrated in leaves of stressed plants, while most amino acids were more concentrated. Transcript analysis of genes involved in signalling and metabolism revealed different expression patterns. While some genes responded only to drought or drought followed by waterlogging, several genes were induced upon both treatments and some were still upregulated at the end of the redrying phase. We provide insights into how wheat responds to changes in water regimes, with some of the changes probably allowing the plants to cope with these stressors, at least to a certain degree.

Growth performance of different forestry species irrigated with moderately saline wastewater

A seven month, pot study was conducted to evaluate the impact of moderately saline wastewater on the growth potential of six forestry plant species viz., Eucalyptus calmaldulensis, Dendrocalamus strictus, Casurina equisetfolia, Cassia fistula, Melia dubia, and Bambusa arundinacea under different drainage conditions namely, well-drained saline (WDS) condition and poor-drained saline condition (PDS) and the control with well-drained non-saline condition. WDS treatment resulted in no mortality whereas PDS treatment resulted in mortality in the range of 33-66%. The plant height and root dry biomass increased in the range of 145% to 221.6% and 4.3-37.1 g respectively in WDS treatment, however, 23.60% to 173.4% and 4.1-10.1 g in PDS treatment. Among all, Eucalyptus camaldulensis and Dendrocalamus strictus showed high Na+ accumulation in roots (2.16 ± 0.02% and 1.13 ± 0.01%), shoots (1.98 ± 0.01% and 0.74 ± 0.01%) and leaves (1.27 ± 0.02% and 0.86 ± 0.01%) in WDS treatment and in case of PDS treatment root (1.01 ± 0.01% and 0.23 ± 0.01%), shoot (1.12 ± 0.02% and 0.11 ± 0.01%), and leaf (0.07 ± 0.01% and 0.1 ± 0.02). The overall performance of both Eucalyptus camaldulensis and Dendrocalamus strictus was highest in WDS treatment. Therefore, it was concluded, that both plants had better performance than other plant species, a proper drainage system defines the overall productivity and treatment efficiency.

Impact of climate perturbations on seeds and seed quality for global agriculture

In agriculture, seeds are the most basic and vital input on which croplands productivity depends. These implies a good starting material, good production lines and good storage options. High-quality seed lots must be free of pests and pathogens and contain a required degree of genetic purity. Seeds need also to be stored in good condition between harvest and later sowing, to insure later on the field a good plant density and higher crop yield. In general, these parameters are already widely accepted and considered in many countries where advanced technologies evaluate them. However, the more and more frequently devastating climate changes observed around the world has put seed quality under threat, and current seeds may not be adapted to hazardous and unpredictable conditions. Climate-related factors such as temperature and water availability directly affect seed development and later germination. For these reasons, investigating seed quality in response to climate changes is a step to propose new crop varieties and practices that will bring solutions for our future.

Comparative transcriptomic analysis of the gene expression and underlying molecular mechanism of submergence stress response in orchardgrass roots

INTRODUCTION

Submergence stress creates a hypoxic environment. Roots are the first plant organ to face these low-oxygen conditions, which causes damage and affects the plant growth and yield. Orchardgrass (Dactylis glomerata L.) is one of the most important cold-season forage grasses globally. However, their submergence stress-induced gene expression and the underlying molecular mechanisms of orchardgrass roots are still unknown.

METHODS

Using the submergence-tolerant 'Dianbei' and submergence-sensitive 'Anba', the transcriptomic analysis of orchardgrass roots at different time points of submergence stress (0 h, 8 h, and 24 h) was performed.

RESULTS

We obtained 118.82Gb clean data by RNA-Seq. As compared with the control, a total of 6663 and 9857 differentially expressed genes (DEGs) were detected in Dianbei, while 7894 and 11215 DEGs were detected in Anba at 8 h and 24 h post-submergence-stress, respectively. Gene Ontology (GO) enrichment analysis obtained 986 terms, while Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis obtained 123 pathways. Among them, the DEGs in plant hormones, mitogen-activated protein kinase (MAPK) and Ca²⁺ signal transduction were significantly differentially expressed in Dianbei, but not in Anba.

DISCUSSION

This study was the first to molecularly elucidate the submergence stress tolerance in the roots of two orchardgrass cultivars. These findings not only enhanced our understanding of the orchardgrass submergence tolerance, but also provided a theoretical basis 36 for the cultivation of submergence-tolerant forage varieties.

TMT proteomics analysis of a pseudocereal crop, quinoa (Chenopodium quinoa Willd.), during seed maturation

Quinoa (Chenopodium quinoa Willd.), an Andean native crop, is increasingly popular around the world due to its high nutritional content and stress tolerance. The production and the popularity of this strategic global food are greatly restricted by many limiting factors, such as seed pre-harvest sprouting, bitter saponin, etc. To solve these problems, the underlying mechanism of seed maturation in quinoa needs to be investigated. In this study, based on the investigation of morphological characteristics, a quantitative analysis of its global proteome was conducted using the combinational proteomics of tandem mass tag (TMT) labeling and parallel reaction monitoring (PRM). The proteome changes related to quinoa seed maturation conversion were monitored to aid its genetic improvement. Typical changes of morphological characteristics were discovered during seed maturation, including mean grain diameter, mean grain thickness, mean hundred-grain weight, palea, episperm color, etc. With TMT proteomics analysis, 581 differentially accumulated proteins (DAPs) were identified. Functional classification analysis and Gene Ontology enrichment analysis showed that most DAPs involved in photosynthesis were downregulated, indicating low levels of photosynthesis. DAPs that participated in glycolysis, such as glyceraldehyde-3-phosphate dehydrogenase, pyruvate decarboxylase, and alcohol dehydrogenase, were upregulated to fulfill the increasing requirement of energy consumption during maturation conversion. The storage proteins, such as globulins, legumins, vicilins, and oleosin, were also increased significantly during maturation conversion. Protein-protein interaction analysis and function annotation revealed that the upregulation of oleosin, oil body-associated proteins, and acyl-coenzyme A oxidase 2 resulted in the accumulation of oil in quinoa seeds. The downregulation of β-amyrin 28-oxidase was observed, indicating the decreasing saponin content, during maturation, which makes the quinoa "sweet". By the PRM and qRT-PCR analysis, the expression patterns of most selected DAPs were consistent with the result of TMT proteomics. Our study enhanced the understanding of the maturation conversion in quinoa. This might be the first and most important step toward the genetic improvement of quinoa.

Effects of hydrogen peroxide priming on yield, photosynthetic capacity and chlorophyll fluorescence of waterlogged summer maize

Extreme rainfall events during the summer maize growth and development periods, which have induced losses in summer maize production. There was a completely randomized block experiment being designed with four treatments: waterlogging for 6 days at the V3 stage (C-W), H₂O₂-priming + non-waterlogging (H-CK), H₂O₂-priming + waterlogging for 6 days at the V3 stage (H-W) and control (C-CK). This study investigated the effects of H₂O₂ priming on yield and photosynthetic parameters of (Zea mays. L) summer maize hybrid DengHai605 (DH605) by measuring the leaf area index (LAI), soil and plant analyzer development (SPAD) value, stomatal morphology, gas exchange parameters, and chlorophyll fluorescence parameters. The results showed that the net photosynthetic rate (Pn) was decreased after waterlogging through the stomatal limitation of CO₂ supply and reduction of PSII photochemical efficiency, which led to the decrease in dry matter accumulation and grain yield. H₂O₂ priming increased the number of opening stomas, the stomatal length, and width, thus increasing Ci by 12.1%, which enhanced the Pn by 37.5%. Additionally, H₂O₂ priming could improve the energy of dark reaction carbohydrates by increasing the light energy absorption and utilization, alleviating the function of PSII reaction centers, protecting the PSII receptor and donor side, and the electron transport chain. The φEo, φPo, φRo, and Ψo of H-W were increased by 89.9%, 16.2%, 55.4%, and 63.9% respectively, and the φDo was decreased by 23.5%, compared with C-W. Therefore, H₂O₂ priming significantly enhanced the PSII photochemical efficiency, and increased the CO₂ supply in dark reactions to promote carbon assimilation, alleviating the waterlogging-induced damage to maize plant growth and grain yield.

Dominant and Priming Role of Waterlogging in Tomato at e[CO2] by Multivariate Analysis

The frequency of waterlogging episodes has increased due to unpredictable and intense rainfalls. However, less is known about waterlogging memory and its interaction with other climate change events, such as elevated CO₂ concentration (e[CO₂]). This study investigated the combined effects of e[CO₂] and two rounds of waterlogging stress on the growth of cultivated tomato (Solanum lycopersicum) and wild tomato (S. pimpinellifolium). The aim is to elucidate the interaction between genotypes and environmental factors and thereby to improve crop resilience to climate change. We found that two rounds of treatments appeared to induce different acclimation strategies of the two tomato genotypes. S. pimpinellifolium responded more negatively to the first-time waterlogging than S. lycopersicum, as indicated by decreased photosynthesis and biomass loss. Nevertheless, the two genotypes respond similarly when waterlogging stress recurred, showing that they could maintain a higher leaf photosynthesis compared to single stress, especially for the wild genotype. This showed that waterlogging priming played a positive role in stress memory in both tomato genotypes. Multivariate analysis showed that waterlogging played a dominant role when combined with [CO₂] for both the cultivated and wild tomato genotypes. This work will benefit agricultural production strategies by pinpointing the positive effects of e[CO₂] and waterlogging memory.

Nitrate–Nitrite–Nitric Oxide Pathway: A Mechanism of Hypoxia and Anoxia Tolerance in Plants

Oxygen (O₂) is the most crucial substrate for numerous biochemical processes in plants. Its deprivation is a critical factor that affects plant growth and may lead to death if it lasts for a long time. However, various biotic and abiotic factors cause O₂ deprivation, leading to hypoxia and anoxia in plant tissues. To survive under hypoxia and/or anoxia, plants deploy various mechanisms such as fermentation paths, reactive oxygen species (ROS), reactive nitrogen species (RNS), antioxidant enzymes, aerenchyma, and adventitious root formation, while nitrate (NO₃⁻), nitrite (NO₂⁻), and nitric oxide (NO) have shown numerous beneficial roles through modulating these mechanisms. Therefore, in this review, we highlight the role of reductive pathways of NO formation which lessen the deleterious effects of oxidative damages and increase the adaptation capacity of plants during hypoxia and anoxia. Meanwhile, the overproduction of NO through reductive pathways during hypoxia and anoxia leads to cellular dysfunction and cell death. Thus, its scavenging or inhibition is equally important for plant survival. As plants are also reported to produce a potent greenhouse gas nitrous oxide (N₂O) when supplied with NO₃⁻ and NO₂⁻, resembling bacterial denitrification, its role during hypoxia and anoxia tolerance is discussed here. We point out that NO reduction to N₂O along with the phytoglobin-NO cycle could be the most important NO-scavenging mechanism that would reduce nitro-oxidative stress, thus enhancing plants’ survival during O₂-limited conditions. Hence, understanding the molecular mechanisms involved in reducing NO toxicity would not only provide insight into its role in plant physiology, but also address the uncertainties seen in the global N₂O budget.

Application of RNAi technology: a novel approach to navigate abiotic stresses

BACKGROUND

Due to the rising population globally, and the demand for food, it is critical to significantly increase crop production by 2050. However, climate change estimates show that droughts and heatwaves will become more prevalent in many parts of the world, posing a severe danger to food output.

METHODS

Selective breeding based on genetic diversity is falling short of meeting the expanding need for food and feed. However, the advent of modern plant genetic engineering, genome editing, and synthetic biology provides precise techniques for producing crops capable of sustaining yield under stress situations.

RESULTS

As a result, crop varieties with built-in genetic tolerance to environmental challenges are desperately needed. In the recent years, small RNA (sRNA) data has progressed to become one of the most effective approaches for the improvement of crops. So many sRNAs (18-30nt) have been found with the use of hi-tech bioinformatics and sequencing techniques which are involved in the regulation of sequence specific gene noncoding RNAs (short ncRNAs) i.e., microRNA (miRNA) and small interfering RNA (siRNA). Such research outcomes may advance our understanding of the genetic basis of adaptability of plants to various environmental challenges and the genetic variation of plant's tolerance to a number of abiotic stresses.

CONCLUSION

The review article highlights current trends and advances in sRNAs' critical role in responses of plants to drought, heat, cold, and salinity, and also the potential technology that identifies the abiotic stress-regulated sRNAs, and techniques for analyzing and validating the target genes.

Phenotyping for waterlogging tolerance in crops: current trends and future prospects

Yield losses to waterlogging are expected to become an increasingly costly and frequent issue in some regions of the world. Despite the extensive work that has been carried out examining the molecular and physiological responses to waterlogging, phenotyping for waterlogging tolerance has proven difficult. This difficulty is largely due to the high variability of waterlogging conditions such as duration, temperature, soil type, and growth stage of the crop. In this review, we highlight use of phenotyping to assess and improve waterlogging tolerance in temperate crop species. We start by outlining the experimental methods that have been utilized to impose waterlogging stress, ranging from highly controlled conditions of hydroponic systems to large-scale screenings in the field. We also describe the phenotyping traits used to assess tolerance ranging from survival rates and visual scoring to precise photosynthetic measurements. Finally, we present an overview of the challenges faced in attempting to improve waterlogging tolerance, the trade-offs associated with phenotyping in controlled conditions, limitations of classic phenotyping methods, and future trends using plant-imaging methods. If effectively utilized to increase crop resilience to changing climates, crop phenotyping has a major role to play in global food security.

Exogenous spermidine regulates the anaerobic enzyme system through hormone concentrations and related-gene expression in Phyllostachys praecox roots under flooding stress

PURPOSE

Acclimation to hypoxia and anoxia is important in various ecological systems, especially flooded soil. Phyllostachys pracecox is sensitive to flooding, and therefore, it is important to explore ways of alleviating hypoxia stress in the roots. In this study, we investigated the regulatory effect of spermidine (Spd) on flooded P. praecox seedlings.

METHODS

A batch experiment was carried out in roots treated with Spd under flooding for eight days. The following factors were subsequently measured: growth, survival rate, root respiratory activity, soluble protein and anaerobic respiration enzyme contents (pyruvate decarboxylase, PDC; alcohol dehydrogenase, ADH; lactate dehydrogenase, LDH; alanine aminotransferase, AlaAT), S-adenosylmethionine decarboxylase (SAMDC), nitrate reductase (NR), ACC oxidase (ACO) and ACC synthetase (ACS) activities, free Spd, spermine (Spm) and the diamine precursor putrescine (Put) content, indole-3-acetic acid (IAA) and abscisic acid (ABA) content, ethylene emissions and expression of hormone-related genes.

RESULTS

Application of Spd promoted root growth (root length, volume, surface and dry weight) and root respiratory inhibition, improved the soluble protein content, and reduced the O₂^·- production rate, H₂O₂ and MDA content to alleviate the damage of roots under flooding. A significant increase in SAMDC activity, and ABA and IAA contents were also observed, along with a reduction in ethylene emissions, NR, ACO and ACS activities (p < 0.05). Exogenous Spd increased the free Spd and Spm contents in the P. praecox roots, but decreased the free Put content. Taken together, these findings suggest that hypoxia stress was alleviated. Moreover, exogenous Spd up-regulated the expression of auxin-related genes ARF1, AUX1, AUX2, AUX3 and AUX4, and down-regulated the expression of ethylene-related ACO and ACS genes during flooding. In addition, correlation and RDA analysis showed that ARF1, ACO and ACS significantly promoted the expression of auxin, ACO and ACS enzyme activities, respectively (p < 0.05), while ADH, NR, AlaAT, ethylene emissions, Put, Spd, ACS and ACO were significantly correlated with ACS, ACO, and auxin-related gene expression (p < 0.05). Overall, ethylene emissions, ACS and ACO were identified as the main drivers of ethylene and auxin-related gene structure.

CONCLUSIONS

These results suggest that Spd regulated hormone concentrations, the content of Spd, Spm and Put, and related gene expression, in turn regulating physiological changes such as anaerobic enzyme activity, mitigating flooding stress in the roots and improving overall growth. Spd therefore has the potential to improve the adaptability of P. praecox to flooding stress.

Phenotypic variation from waterlogging in multiple perennial ryegrass varieties under climate change conditions

Identifying how various components of climate change will influence ecosystems and vegetation subsistence will be fundamental to mitigate negative effects. Climate change-induced waterlogging is understudied in comparison to temperature and CO2. Grasslands are especially vulnerable through the connection with global food security, with perennial ryegrass dominating many flood-prone pasturelands in North-western Europe. We investigated the effect of long-term waterlogging on phenotypic responses of perennial ryegrass using four common varieties (one diploid and three tetraploid) grown in atmospherically controlled growth chambers during two months of peak growth. The climate treatments compare ambient climatological conditions in North-western Europe to the RCP8.5 climate change scenario in 2050 (+2°C and 550 ppm CO2). At the end of each month multiple phenotypic plant measurements were made, the plants were harvested and then allowed to grow back. Using image analysis and principal component analysis (PCA) methodologies, we assessed how multiple predictors (phenotypic, environmental, genotypic, and temporal) influenced overall plant performance, productivity and phenotypic responses. Long-term waterlogging was found to reduce leaf-color intensity, with younger plants having purple hues indicative of anthocyanins. Plant performance and yield was lower in waterlogged plants, with tetraploid varieties coping better than the diploid one. The climate change treatment was found to reduce color intensities further. Flooding was found to reduce plant productivity via reductions in color pigments and root proliferation. These effects will have negative consequences for global food security brought on by increased frequency of extreme weather events and flooding. Our imaging analysis approach to estimate effects of waterlogging can be incorporated into plant health diagnostics tools via remote sensing and drone-technology.

Modelling Waterlogging Impacts on Crop Growth: A Review of Aeration Stress Definition in Crop Models and Sensitivity Analysis of APSIM

Currently, crop physiological responses to waterlogging are considered only in a few crop models and in a limited way. Here, we examine the process bases of seven contemporary models developed to model crop growth in waterlogged conditions. The representation of plant recovery in these models is over-simplified, while plant adaptation or phenotypic plasticity due to waterlogging is often not considered. Aeration stress conceptualisation varies from the use of simple multipliers in equations describing transpiration and biomass to complex linkages of aeration-deficit factors with root growth, transpiration and nitrogen fixation. We recommend further studies investigating more holistic impacts and multiple stresses caused by plant behaviours driven by soils and climate. A sensitivity analysis using one model (a developer version of APSIM) with default parameters showed that waterlogging has the greatest impact on photosynthesis, followed by phenology and leaf expansion, suggesting a need for improved equations linking waterlogging to carbon assimilation. Future studies should compare the ability of multiple models to simulate real and in situ effects of waterlogging stress on crop growth using consistent experimental data for initialisation, calibration and validation. We conclude that future experimental and modelling studies must focus on improving the extent to which soil porosity, texture, organic carbon and nitrogen and plant-available water affect waterlogging stress, physiological plasticity and the ensuing temporal impacts on phenology, growth and yield.

Physiological and phenotypic characterization of diverse Camelina sativa lines in response to waterlogging

Waterlogging is a serious threat to agriculture that is expected to become more common due to climate change. It is well established that many plants are susceptible to waterlogging, including crops such as rapeseed. To investigate the responses and tolerance to waterlogging of the re-emerging oilseed crop camelina (Camelina sativa), camelina lines of different geographical origins were subjected to waterlogging. Camelina was very sensitive to waterlogging at vegetative growth stages, with a relatively short treatment of 4 days proving lethal for the plants. A treatment duration of 2 days resulted in growth inhibition and lower yields and was used to study the response of 8 different camelina lines to waterlogging at two different vegetative growth stages before bolting. Generally, younger plants (7-9 leaves) were more sensitive than older plants (15-16 leaves). In addition to morphological and agronomic traits, plants were phenotyped for physiological parameters such as chlorophyll content index and total antioxidant capacity of the leaves, which showed significant age-dependent changes due to waterlogging. These results underpin that waterlogging during the vegetative phase is a serious threat to camelina, which needs to be addressed by identifying and establishing tolerance to excess water to harness camelina's potential as a climate-smart crop.

Priming crops for the future: rewiring stress memory

The agricultural sector must produce resilient and climate-smart crops to meet the increasing needs of global food production. Recent advancements in elucidating the mechanistic basis of plant stress memory have provided new opportunities for crop improvement. Stress memory-coordinated changes at the organismal, cellular, and various omics levels prepare plants to be more responsive to reoccurring stress within or across generation(s). The exposure to a primary stress, or stress priming, can also elicit a beneficial impact when encountering a secondary abiotic or biotic stress through the convergence of synergistic signalling pathways, referred to as cross-stress tolerance. 'Rewired plants' with stress memory provide a new means to stimulate adaptable stress responses, safeguard crop reproduction, and engineer climate-smart crops for the future.

Identification and Prediction of Crop Waterlogging Risk Areas under the Impact of Climate Change

Waterlogging refers to the damage to plants by water stress due to excess soil water in the crop’s root zone that exceeds the maximum water holding capacity of the field. It is one of the major disasters affecting agricultural production. This study aims to add a crop waterlogging identification module to the coupled SWAT (Soil and Water Assessment Tools)-MODFLOW (Modular Finite Difference Groundwater Flow Model) model and to accurately identify and predict crop waterlogging risk areas under the CMIP6 (Coupled Model Intercomparison Project 6) climate scenarios. The result showed that: (1) The SWAT-MODFLOW model, which coupled with a crop waterlogging identification module, had good simulation results for LAI (Leaf Area Index), ET (Evapotranspiration), spring wheat yield, and groundwater level in the middle and lower reaches of the Bayin River; (2) The precipitation showed an overall increasing trend in the Bayin River watersheds over the next 80 years under the SSP1-2.6, SSP2-4.5 and SSP5-8.5 scenarios. The temperature showed a clear increasing trend over the next 80 years under the SSP2-4.5 and SSP5-8.5 scenarios; (3) Under the SSP1-2.6 scenario, the mountain runoff from the upper reaches of the Bayin River was substantially higher than in other scenarios after 2041. The mountain runoff in the next 80 years will decrease substantially under the SSP2-4.5 scenario. The mountain runoff over the next 80 years showed an initial decrease and then an increasing trend under the SSP5-8.5 scenario; (4) During the historical period, the crop waterlogging risk area was 10.9 km2. In the next 80 years, the maximum crop waterlogging area will occur in 2055 under the SSP1-2.6 scenario. The minimum crop waterlogging area, 9.49 km2, occurred in 2042 under the SSP2-4.5 scenario. The changes in the area at risk of crop waterlogging under each scenario are mainly influenced by the mountain runoff from the upper reaches of the Bayin River.

Post-flowering Soil Waterlogging Curtails Grain Yield Formation by Restricting Assimilates Supplies to Developing Grains

Soil waterlogging is among the major factors limiting the grain yield of winter wheat crops in many parts of the world, including the middle and lower reaches of the Yangtze River China. In a field study, we investigated the relationship between leaf physiology and grain development under a varying duration of post-flowering waterlogging. A winter wheat cultivar Ningmai 13 was exposed to soil waterlogging for 0 (W0), 3 (W3), 6 (W6), and 9 d (W9) at anthesis. Increasing waterlogging duration significantly reduced flag leaf SPAD (soil plant analysis development) values and net photosynthetic rate (Pn). There was a linear reduction in flag leaf Pn and SPAD as plant growth progressed under all treatments; however, the speed of damage was greater in the waterlogged leaves. For example, compared with their respective control (W0), flag leaves of W9 treatment have experienced 46% more reduction in Pn at 21 d after anthesis (DAA) than at 7 DAA. Increasing waterlogging duration also induced oxidative damage in flag leaves, measured as malondialdehyde (MDA) contents. The capacity to overcome this oxidative damage was limited by the poor performance of antioxidant enzymes in wheat leaves. Inhibited leaf Pn and capacity to sustain assimilate synthesis under waterlogged environments reduced grain development. Compared with W0, W6 and W9 plants experienced a 20 and 22% reduction in thousand grain weight (TGW) in response to W6 and W9, respectively at 7 DAA and 11 and 19%, respectively at 28 DAA. Sustained waterlogging also significantly reduced grain number per spike and final grain yield. Averaged across two years of study, W9 plants produced 28% lesser final grain yield than W0 plants. Our study suggested that wheat crops are highly sensitive to soil waterlogging during reproductive and grain filling phases due to their poor capacity to recover from oxidative injury to photosynthesis. Management strategies such as planting time, fertilization and genotype selection should be considered for the areas experiencing frequent waterlogging problems.

Effects of Hypoxia Stress on Growth, Root Respiration, and Metabolism of Phyllostachys praecox

Hypoxia affects plant growth, hormone content, various enzyme activities, cell structure, peroxide production, and metabolic level, therefore reducing crop yield. This study assessed the physiological, biochemical, and metabolic characteristics of Phyllostachys praecox. Results revealed that hypoxia stress treatment significantly inhibited plant growth. Leaf chlorophyll contents was initially improved and then reduced with plant growth time. Under hypoxia stress, the root activity significantly was reduced, leading to the decrease in the nutrient absorption and transport. Yet, with low oxygen concentration, the contents of ethanol, acetaldehyde, and lactic acid were improved. With hypoxia stress, phospholipids and amino acids were the main metabolites of Phyllostachys praecox. Glycosphospholipid metabolism is the key pathway in responding to hypoxia stress significantly (p < 0.05), and lysophosphatidlycholine (lysoPC) and phosphatidylcholines (PC) in the metabolites of this metabolic pathway were significantly enhanced. Our study reveals the mechanism of Phyllostachys praecox cell membrane responding to hypoxia stress based on molecular level. This is conducive to finding targeted solutions to improve the productivity of Phyllostachys praecox to better optimize a mulching approach in the bamboo forest.

The genome of hibiscus hamabo reveals its adaptation to saline and waterlogged habitat

Hibiscus hamabo is a semi-mangrove species with strong tolerance to salt and waterlogging stress. However, the molecular basis and mechanisms that underlie this strong adaptability to harsh environments remain poorly understood. Here, we assembled a high-quality, chromosome-level genome of this semi-mangrove plant and analyzed its transcriptome under different stress treatments to reveal regulatory responses and mechanisms. Our analyses suggested that H. hamabo has undergone two recent successive polyploidy events, a whole-genome duplication followed by a whole-genome triplication, resulting in an unusually large gene number (107 309 genes). Comparison of the H. hamabo genome with that of its close relative Hibiscus cannabinus, which has not experienced a recent WGT, indicated that genes associated with high stress resistance have been preferentially preserved in the H. hamabo genome, suggesting an underlying association between polyploidy and stronger stress resistance. Transcriptomic data indicated that genes in the roots and leaves responded differently to stress. In roots, genes that regulate ion channels involved in biosynthetic and metabolic processes responded quickly to adjust the ion concentration and provide metabolic products to protect root cells, whereas no such rapid response was observed from genes in leaves. Using co-expression networks, potential stress resistance genes were identified for use in future functional investigations. The genome sequence, along with several transcriptome datasets, provide insights into genome evolution and the mechanism of salt and waterlogging tolerance in H. hamabo, suggesting the importance of polyploidization for environmental adaptation.

Genotypic Diversity Improves Photosynthetic Traits of Hydrocotyle vulgaris and Alters Soil Organic Matter and N2O Emissions of Wetland Microecosystems

In plant communities, genotypic diversity can impact the plant community structure and ecosystem functions, but related research has focused on native plants. Therefore, whether genotypic diversity affects the growth of invasive plants and then changes the wetland microecosystem remains unresolved. In this study, six different genotypes of Hydrocotyle vulgaris, a common invasive plant in China, were selected to construct populations with three different genotypic diversity levels (one, three, and six genotype combinations, respectively) to explore the effects of different genotypic diversity levels on the growth and physiological traits of H. vulgaris, and soil nutrients and greenhouse gas emissions of the wetland microecosystem under flooding conditions. We found that genotypic diversity improved the leaf area, root to shoot ratio and photosynthetic physiological traits of H. vulgaris, especially under flooding. Moreover, genotypic diversity increased soil organic matter (SOM) contents in the wetland microecosystem, while it reduced the cumulative nitrous oxide emissions under flooding conditions. Overall, genotype diversity improved photosynthetic traits of H. vulgaris, further increased SOM, and reduced the N2O emissions of the wetland microecosystem. The results of this study can provide a theoretical basis for exploring how genotypic diversity levels affect the invasiveness of invasive plants and ecosystems in wetland microecosystems.

Iron toxicity increases oxidative stress and impairs mineral accumulation and leaf gas exchange in soybean plants during hypoxia

Iron toxicity is a major challenge faced by plants in hypoxic soils; however, the consequences of such combined stress for soybean (Glycine max) remain to be determined. Here we assessed the physiological responses of soybean plants exposed to hypoxia and a high concentration of iron. Soil-grown plants cultivated in a greenhouse until the vegetative stage were transferred to a hydroponic system containing nutrient solution and subjected to two oxygen conditions (normoxia (6.2 mg L-1) and hypoxia (0.33 mg L-1)) and two iron concentrations (Fe-EDTA) (0.09 and 1.8 mM) for 72 h. During hypoxia, high concentrations of iron in the nutrient solution resulted in increased iron accumulation in roots and leaves. Under this condition, the concentrations of zinc, nitrogen, potassium, and calcium decreased in the roots, while the concentration of nitrogen and magnesium decreased in the leaves. Additionally, during hypoxia, the higher concentration of iron led to an increase in the activity of the antioxidant enzymes in roots and leaves, while decreased the levels of the photosynthetic pigments, leaf gas exchange, and plant growth. In conclusion, high iron concentration in the root medium results in a considerably more severe damage condition to soybean plants under hypoxia compared to plants grown under low iron availability.

Transcriptome analysis of gibberellins and abscisic acid during the flooding response in Fokienia hodginsii

Flooding is one of the main abiotic stresses suffered by plants. Plants respond to flooding stress through regulating their morphological structure, endogenous hormone biosynthesis, and genetic signaling transduction. We previously found that Fokienia hodginsii varieties originating from Gutian exhibited typical flooding tolerance traits compared to three other provenances (Yongzhou, Sanming, Nanping), expressed as increased height, longer diameter at breast height (DBH), and smaller branch angle. Herein, the changes in endogenous gibberellins (GA) and abscisic acid (ABA) contents were measured under flooding stress in F. hodginsii, and ABA was found to decrease, whereas GA increased with time. Furthermore, the GA and ABA contents of the varieties originating from Gutian and the three other provenances were measured, and the results indicated that F. hodginsii from Gutian could respond more rapidly to flooding stress. The transcriptomes of the varieties originating from Gutian and the other three provenances were compared using RNA sequencing to explore the underlying genetic mechanisms of the flood-resistant phenotypes in F. hodginsii. The results indicated that two flood-stress response genes (TRINITY_DN142_c0_g2 and TRINITY_DN7657_c0_g1) were highly related to both the ABA and GA response in F. hodginsii.

Poplar's Waterlogging Resistance Modeling and Evaluating: Exploring and Perfecting the Feasibility of Machine Learning Methods in Plant Science

Floods, as one of the most common disasters in the natural environment, have caused huge losses to human life and property. Predicting the flood resistance of poplar can effectively help researchers select seedlings scientifically and resist floods precisely. Using machine learning algorithms, models of poplar's waterlogging tolerance were established and evaluated. First of all, the evaluation indexes of poplar's waterlogging tolerance were analyzed and determined. Then, significance testing, correlation analysis, and three feature selection algorithms (Hierarchical clustering, Lasso, and Stepwise regression) were used to screen photosynthesis, chlorophyll fluorescence, and environmental parameters. Based on this, four machine learning methods, BP neural network regression (BPR), extreme learning machine regression (ELMR), support vector regression (SVR), and random forest regression (RFR) were used to predict the flood resistance of poplar. The results show that random forest regression (RFR) and support vector regression (SVR) have high precision. On the test set, the coefficient of determination (R²) is 0.8351 and 0.6864, the root mean square error (RMSE) is 0.2016 and 0.2780, and the mean absolute error (MAE) is 0.1782 and 0.2031, respectively. Therefore, random forest regression (RFR) and support vector regression (SVR) can be given priority to predict poplar flood resistance.

Cytokinin and gibberellic acid-mediated waterlogging tolerance of mungbean (Vigna radiata L. Wilczek)

BACKGROUND

Mungbean (Vigna radiata L. Wilczek) is one of the most important pulse crops, well-known for its protein-rich seeds. Growth and productivity are severely undermined by waterlogging.

METHODS

In this study, we aim to evaluate how two promising phytohormones, namely cytokinin (CK) and gibberellic acid (GA₃), can improve waterlogging tolerance in mungbean by investigating key morphological, physiological, biochemical, and yield-related attributes.

RESULTS

Our results showed that foliar application of CK and GA₃ under 5-day of waterlogged conditions improved mungbean growth and biomass, which was associated with increased levels of photosynthetic rate and pigments. Waterlogged-induced accumulation of reactive oxygen species and the consequently elevated levels of malondialdehyde were considerably reduced by CK and GA₃ treatments. Mungbean plants sprayed with either CK or GA₃ suffered less oxidative stress due to the enhancement of total phenolics and flavonoids levels. Improvement in the contents of proline and total soluble sugars indicated a better osmotic adjustment following CK and GA₃ treatments in waterlogged-exposed plants. Most fundamentally, CK or GA₃-sprayed waterlogged-stressed mungbean plants demonstrated better performance in the aforementioned parameters after the 15-day recovery period as compared to water-sprayed waterlogged-exposed plants. Our results also revealed that CK and GA₃ treatments increased yield-associated features in the waterlogged-stressed plant. Here, both phytohormones are efficient in improving mungbean resistance to waterlogging. However, CK was found to be more effective. Overall, our findings suggested that CK or GA₃ could be used for managing waterlogging-induced damage to mungbean and perhaps in other cash crops.

Effects of Flooding and Endogenous Hormone on the Formation of Knee Roots in Taxodium ascendens

Taxodium ascendens is a typical tree species with high flood tolerance, and it can generate knee roots in the wetlands. This study investigated the number and size of knee roots and the soil flooding conditions. Furthermore, we also measured physiology, biochemical responses, and the anatomical structure of knee roots and underground roots at different developmental stages. This study aimed to understand the adaptation mechanism of T. ascendens to flooding stress and the formation mechanism of the knee roots. The results showed that the formation of knee roots was significantly affected by the soil water table (P < 0.05). The middle water table was more conducive to the formation of knee roots. In the middle water table, the 1-aminocyclopropane-1-carboxylic acid (ACC) content and ACC synthase activity were significantly lower in the knee roots than in the underground roots. The knee roots at the young-aged stage showed the highest ACC oxidase activity among the development stages of the knee roots. The ethylene release rate was significantly higher in the knee roots than in the underground roots (P < 0.05). Indole-3-acetic acid (IAA) content first increased, then decreased with knee root development. The periderm cells at the apex of the knee roots were dead and had many intercellular spaces, which was beneficial for the growth of T. ascendens. In conclusion, the middle water table induced the ethylene and IAA production, which promoted the formation of knee roots, which improved roots ventilation and flooding tolerance of T. ascendens. The results obtained can provide information about mechanisms of knee roots formation and provide scientific evidence for the afforestation and management under wetland conditions.