Waterproofing crops: effective flooding survival strategies

Identification of hub genes involved in gibberellin-regulated elongation of coleoptiles of rice seeds germinating under submerged conditions

Rapid elongation of coleoptiles from rice seeds to reach the water surface enables plants to survive submergence stress and therefore plays a crucial role in allowing direct seeding in rice cultivation. Gibberellin (GA) positively influences growth in rice, but the molecular mechanisms underlying its regulation of coleoptile elongation under submerged conditions remain unclear. In this study, we performed a weighted gene co-expression network analysis to conduct a preliminarily examination of the mechanisms. Four key modules were identified with high correlations to the GA regulation of submergence tolerance. The genes within these modules were mainly involved in the Golgi apparatus and carbohydrate metabolic pathways, suggesting their involvement in enhancing submergence tolerance. Further analysis of natural variation revealed that the specific hub genes Os03g0337900, Os03g0355600, and Os07g0638400 exhibited strong correlations with subspecies divergence of the coleoptile elongation phenotype. Consistent with this analysis, mutation of Os07g0638400 resulted in a lower germination potential and a stronger inhibition of coleoptile elongation under submerged conditions. The hub genes identified in this study provide new insights into the molecular mechanisms underlying GA-dependent tolerance to submergence stress in rice, and a potential basis for future modification of rice germplasm to allow for direct seeding.

Transcriptomic Insights into Molecular Response of Butter Lettuce to Different Light Wavelengths

Lettuce is a widely consumed leafy vegetable; it became popular due to its enhanced nutritional content. Recently, lettuce is also regarded as one of the model plants for vegetable production in plant factories. Light and nutrients are essential environmental factors that affect lettuce growth and morphology. To evaluate the impact of light spectra on lettuce, butter lettuce was grown under the light wavelengths of 460, 525, and 660 nm, along with white light as the control. Plant morphology, physiology, nutritional content, and transcriptomic analyses were performed to study the light response mechanisms. The results showed that the leaf fresh weight and length/width were higher when grown at 460 nm and lower when grown at 525 nm compared to the control treatment. When exposed to 460 nm light, the sugar, crude fiber, mineral, and vitamin concentrations were favorably altered; however, these levels decreased when exposed to light with a wavelength of 525 nm. The transcriptomic analysis showed that co-factor and vitamin metabolism- and secondary metabolism-related genes were specifically induced by 460 nm light exposure. Furthermore, the pathway enrichment analysis found that flavonoid biosynthesis- and vitamin B6 metabolism-related genes were significantly upregulated in response to 460 nm light exposure. Additional experiments demonstrated that the vitamin B6 and B2 content was significantly higher in leaves exposed to 460 nm light than those grown under the other conditions. Our findings suggested that the addition of 460 nm light could improve lettuce's biomass and nutritional value and help us to further understand how the light spectrum can be tuned as needed for lettuce production.

Flooding Tolerance of Rice: Regulatory Pathways and Adaptive Mechanisms

Rice is a major food crop for more than half of the world's population, while its production is seriously threatened by flooding, a common environmental stress worldwide. Flooding leads to oxygen deficiency, which is a major problem for submerged plants. Over the past three decades, significant progress has been made in understanding rice adaptation and molecular regulatory mechanisms in response to flooding. At the seed germination and seedling establishment stages, the CIPK15-SnRK1A-MYBS1 signaling cascade plays a central role in determining rice submergence tolerance. However, from seedlings to mature plants for harvesting, SUB1A- and SK1/SK2-regulated pathways represent two principal and opposite regulatory mechanisms in rice. In addition, phytohormones, especially gibberellins, induce adaptive responses to flooding throughout the rice growth period. This review summarizes the significant adaptive traits observed in flooded rice varieties and updates the molecular genetics and mechanisms of submergence tolerance in rice.

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.

Coordination between two cis-elements of WRKY33, bound by the same transcription factor, confers humid adaption in Arabidopsis thaliana

To cope with flooding-induced hypoxia, plants have evolved different strategies. Molecular strategies, such as the N-degron pathway and transcriptional regulation, are known to be crucial for Arabidopsis thaliana's hypoxia response. Our study uncovered a novel molecular strategy that involves a single transcription factor interacting with two identical cis-elements, one located in the promoter region and the other within the intron. This unique double-element adjustment mechanism has seldom been reported in previous studies. In humid areas, WRKY70 plays a crucial role in A. thaliana's adaptation to submergence-induced hypoxia by binding to identical cis-elements in both the promoter and intron regions of WRKY33. This dual binding enhances WRKY33 expression and the activation of hypoxia-related genes. Conversely, in arid regions lacking the promoter cis-element, WRKY70 only binds to the intron cis-element, resulting in limited WRKY33 expression during submergence stress. The presence of a critical promoter cis-element in humid accessions, but not in dry accessions, indicates a coordinated regulation enabling A. thaliana to adapt and thrive in humid habitats.

'Against all floods': plant adaptation to flooding stress and combined abiotic stresses

Current climate change brings with it a higher frequency of environmental stresses, which occur in combination rather than individually leading to massive crop losses worldwide. In addition to, for example, drought stress (low water availability), also flooding (excessive water) can threaten the plant, causing, among others, an energy crisis due to hypoxia, which is responded to by extensive transcriptional, metabolic and growth-related adaptations. While signalling during flooding is relatively well understood, at least in model plants, the molecular mechanisms of combinatorial flooding stress responses, for example, flooding simultaneously with salinity, temperature stress and heavy metal stress or sequentially with drought stress, remain elusive. This represents a significant gap in knowledge due to the fact that dually stressed plants often show unique responses at multiple levels not observed under single stress. In this review, we (i) consider possible effects of stress combinations from a theoretical point of view, (ii) summarize the current state of knowledge on signal transduction under single flooding stress, (iii) describe plant adaptation responses to flooding stress combined with four other abiotic stresses and (iv) propose molecular components of combinatorial flooding (hypoxia) stress adaptation based on their reported dual roles in multiple stresses. This way, more future emphasis may be placed on deciphering molecular mechanisms of combinatorial flooding stress adaptation, thereby potentially stimulating development of molecular tools to improve plant resilience towards multi-stress scenarios.

Root anatomical plasticity contributes to the different adaptive responses of two Phragmites species to water-deficit and low-oxygen conditions

The runner reed (Phragmites japonica ) is the dominant species on riverbanks, whereas the common reed (Phragmites australis ) thrives in continuously flooded areas. Here, we aimed to identify the key root anatomical traits that determine the different adaptative responses of the two Phragmites species to water-deficit and low-oxygen conditions. Growth measurements revealed that P . japonica tolerated high osmotic conditions, whereas P . australis preferred low-oxygen conditions. Root anatomical analysis revealed that the ratios of the cortex to stele area and aerenchyma (gas space) to cortex area in both species increased under low-oxygen conditions. However, a higher ratio of cortex to stele area in P . australis resulted in a higher ratio of aerenchyma to stele, which includes xylem vessels that are essential for water and nutrient uptakes. In contrast, a lower ratio of cortex to stele area in P . japonica could be advantageous for efficient water uptake under high-osmotic conditions. In addition to the ratio of root tissue areas, rigid outer apoplastic barriers composed of a suberised exodermis may contribute to the adaptation of P . japonica and P . australis to water-deficit and low-oxygen conditions, respectively. Our results suggested that root anatomical plasticity is essential for plants to adapt and respond to different soil moisture levels.

Transcriptomic and metabolomic approaches elucidate the systemic response of wheat plants under waterlogging

Extreme weather conditions lead to significant imbalances in crop productivity, which in turn affect food security. Flooding events cause serious problems for many crop species such as wheat. Although metabolic readjustments under flooding are important for plant regeneration, underlying processes remain poorly understood. Here, we investigated the systemic response of wheat to waterlogging using metabolomics and transcriptomics. A 12 d exposure to excess water triggered nutritional imbalances and disruption of metabolite synthesis and translocation, reflected by reductions in plant biomass and growth performance. Metabolic and transcriptomic profiling in roots, xylem sap, and leaves indicated anaerobic fermentation processes as a local response in roots. Differentially expressed genes and ontological categories revealed that carbohydrate metabolism plays an important role in the systemic response. Analysis of the composition of xylem exudates revealed decreased root-to-shoot translocation of nutrients, hormones, and amino acids. Interestingly, among all metabolites measured in xylem exudates, alanine was the most abundant. Immersion of excised leaves derived from waterlogged plants in alanine solution led to increased leaf glucose concentration. Our results suggest an important role of alanine not only as an amino-nitrogen donor but also as a vehicle for carbon skeletons to produce glucose de novo and meet the energy demand during waterlogging.

Introducing the halophyte Salicornia europaea to investigate combined impact of salt and tidal submergence conditions

Tolerance mechanisms to single abiotic stress events are being investigated in different plant species, but how plants deal with multiple stress factors occurring simultaneously is still poorly understood. Here, we introduce Salicornia europaea as a species with an extraordinary tolerance level to both flooding and high salt concentrations. Plants exposed to 0.5MNaCl (mimicking sea water concentrations) grew larger than plants not exposed to salt. Adding more salt reduced growth, but concentrations up to 2.5MNaCl were not lethal. Regular tidal flooding with salt water (0.5MNaCl) did not affect growth or chlorophyll fluorescence, whereas continuous flooding stopped growth while plants survived. Quantitative polymerase chain reaction (qPCR) analysis of plants exposed to 1% oxygen in air revealed induction of selected hypoxia responsive genes, but these genes were not induced during tidal flooding, suggesting that S. europaea did not experience hypoxic stress. Indeed, plants were able to transport oxygen into waterlogged soil. Interestingly, sequential exposure to salt and hypoxic air changed the expression of several but not all genes as compared to their expression upon hypoxia only, demonstrating the potential to use S . europaea to investigate signalling-crosstalk between tolerance reactions to multiple environmental perturbations.

Psammophytes Alyssum desertorum Stapf and Secale sylvestre Host Are Sensitive to Soil Flooding

While morphological and functional traits enable hydrophytes to survive under waterlogging and partial or complete submergence, the data on responses of psammophytes-sand plants-to flooding are very limited. We analyzed the effect of 5- and 10-day soil flooding on the photosynthetic apparatus and the synthesis of alcohol dehydrogenase (ADH), heat shock proteins 70 (HSP70), and ethylene in seedlings of psammophytes Alyssum desertorum and Secale sylvestre using electron microscopy, chlorophyll a fluorescence induction, and biochemical methods. It was found that seedlings growing under soil flooding differed from those growing in stationary conditions with such traits as chloroplast ultrastructure, pigment content, chlorophyll fluorescence induction, and the dynamics of ADH, HSP, and ethylene synthesis. Although flooding caused no apparent damage to the photosynthetic apparatus in all the variants, a significant decrease in total photosynthesis efficiency was observed in both studied plants, as indicated by decreased values of φR0 and PIABS,total. More noticeable upregulation of ADH in S. sylvestre, as well as increasing HSP70 level and more intensive ethylene emission in A. desertorum, indicate species-specific differences in these traits in response to short-term soil flooding. Meanwhile, the absence of systemic anaerobic metabolic adaptation to prolonged hypoxia causes plant death.

Comparative analysis of defensive secondary metabolites in wild teosinte and cultivated maize under flooding and herbivory stress

Climate change is driving an alarming increase in the frequency and intensity of abiotic and biotic stress factors, negatively impacting plant development and agricultural productivity. To survive, plants respond by inducing changes in below and aboveground metabolism with concomitant alterations in defensive secondary metabolites. While plant responses to the isolated stresses of flooding and insect herbivory have been extensively studied, much less is known about their response in combination. Wild relatives of cultivated plants with robust stress tolerance traits provide an excellent system for comparing how diverse plant species respond to combinatorial stress, and provide insight into potential germplasms for stress-tolerant hybrids. In this study, we compared the below and aboveground changes in the secondary metabolites of maize (Zea mays) and a flood-tolerant wild relative Nicaraguan teosinte (Zea nicaraguensis) in response to flooding, insect herbivory, and their combination. Root tissue was analyzed for changes in belowground metabolism. Leaf total phenolic content and headspace volatile organic compound emission were analyzed for changes in aboveground secondary metabolism. Results revealed significant differences in the root metabolome profiles of teosinte and maize. Notably, the accumulation of the flavonoids apigenin, naringenin, and luteolin during flooding and herbivory differentiated teosinte from maize. Aboveground, terpenes, including trans-α-bergamotene and (E)-4,8-dimethylnona-1,3,7-triene, shaped compositional differences in their volatile profiles between flooding, herbivory, and their combination. Taken together, these results suggest teosinte may be more tolerant than maize due to dynamic metabolic changes during flooding and herbivory that help relieve stress and influence plant-insect interactions.

Impact of individual, combined and sequential stress on photosynthesis machinery in rice (Oryza sativa L)

Abiotic stresses such as heat, drought and submergence are major threats to global food security. Despite simultaneous or sequential occurrence of these stresses being recurrent under field conditions, crop response to such stress combinations is poorly understood. Rice is a staple food crop for the majority of human beings. Exploitation of existing genetic diversity in rice for combined and/or sequential stress is a useful approach for developing climate-resilient cultivars. We phenotyped ~400 rice accessions under high temperature, drought, or submergence and their combinations. A cumulative performance index revealed Lomello as the best performer across stress and stress combinations at the seedling stage. Lomello showed a remarkable ability to maintain a higher quantum yield of photosystem (PS) II photochemistry. Moreover, the structural integrity of the photosystems, electron flow through both PSI and PSII and the ability to protect photosystems against photoinhibition were identified as the key traits of Lomello across the stress environments. A higher membrane stability and an increased amount of leaf chlorophyll under stress may be due to an efficient management of reactive oxygen species (ROS) at the cellular level. Further, an efficient electron flow through the photosystems and, thus, a higher photosynthetic rate in Lomello is expected to act as a sink for ROS by reducing the rate of electron transport to the high amount of molecular oxygen present in the chloroplast. However, further studies are needed to identify the molecular mechanism(s) involved in the stability of photosynthetic machinery and stress management in Lomello during stress conditions.

Mutation of the gene encoding the PHD-type transcription factor SAB23 confers submergence tolerance in rice

Submergence is a major constraint on rice production in South and Southeast Asia. In this study, we determined that a gene of the Sub1A-binding protein family, SAB23, encodes a plant homeodomain (PHD)-type transcription factor that has a novel function of negatively regulating submergence tolerance in rice. The T-DNA insertion mutant sab23 displayed reduced plant height, delayed seed maturation, and lower percentage seed set. Importantly, this mutant also exhibited enhanced submergence tolerance. In addition, CRISPR/Cas9 knock out of SAB23 resulted in a significant reduction in the content of the gibberellin GA4 and a dramatic increase in the content of GA1 in the plants. SAB23 binds to the promoter of CYTOCHROME P450 714B2 (CYP714B2), which encodes a GA13-oxidase that catalyses the conversion of GA53 to GA19. Disruption of SAB23 function led to increased CYP714B2 transcription, and overexpression of CYP714B2 produced phenotypes similar to those of the SAB23-knockout plants. Taken together, our results reveal that SAB23 negatively regulates rice submergence tolerance by modulating CYP714B2 expression, which has significant potential for use in future breeding.

Role of iron manganese plaque in the safe production of rice (Oryza sativa L.) grains: Field evidence at plot and regional scales in cadmium-contaminated paddy soils

The relationship between iron manganese plaque (IP) and cadmium (Cd) accumulation by rice in the microenvironment of rice rhizosphere at varying field scales needs to be further explored. In this study, we selected different rice varieties and implemented tailored amendments to ensure the safe production of rice grains in heavily Cd-contaminated farmland situated around an E-waste dismantling site. Through regional surveys, we elucidated the role of IP in facilitating safe rice production. The selection of low-Cd accumulating rice varieties and application of appropriate amendments with sufficient dosages allowed for the effective reduction of Cd transport from soil to rice, resulting in a safe concentration of Cd in rice grains. Analysis using a random forest algorithm indicated that iron (Fe) played a more pivotal role than manganese in soil-rice systems in mitigating Cd accumulation in brown rice. The presence of Fe in IP (IP-Fe) at a low loading mass was unfavorable to the Cd-safe production of rice, while at an IP-Fe loading mass of 52 g/kg, the Cd content in brown rice decreased to a safe level. Furthermore, precipitation, coprecipitation, and complexation of surface functional groups contributed to Cd fixation on IP, as indicated by scanning electron microscopy coupled with energy-dispersive X-ray spectroscopy, electron probe microanalysis, and Fourier-transform infrared spectroscopy with attenuated total reflection. Our results highlighted the key role of IP in the production of Cd-safe rice at different field scales.

Extracellular nitric oxide sustains root surface redox activity and growth under sudden flooding-induced hypoxic conditions in barley root tips

MAIN CONCLUSION

Nitric oxide sustains root tip surface redox activity and restricts lipid peroxidation-triggered cell death in the root tips. In order to gain more insight into the involvement of nitric oxide (NO) in plant response to sudden flooding-induced hypoxic stress, we studied the effect of two NO donors, sodium nitroprusside and S-nitroso-L-glutathione, on short-term partial submergence-induced root growth inhibition, alteration in root surface redox activity, lipid peroxidation and cell death in two barley cultivars (cv.) at their early seedling stage. The short-term hypoxic stress induces root growth arrest in cv. Karmel, accompanied by increased lipid peroxidation and cell death. By contrast, in cv. Slaven, short-term hypoxic conditions cause only reduced root growth rate, associated with elevated extracellular NO level in the root tips. The root tip surface redox activity decreases with the increasing timespan of hypoxic conditions in both cultivars; however, this decrease in redox activity started earlier and was greater in the cv. Karmel in comparison with cv. Slaven. Application of NO donors during hypoxic stress sustains the root redox activity and eliminates the hypoxia-induced lipid peroxidation, accompanied by a partial restoration of root growth after short-term hypoxic stress. These results suggest that extracellular NO plays a key role in maintaining the root tip surface redox activity and in the restriction of lipid peroxidation and cell death under short-term hypoxic stress in the root tips of barley seedlings.

Plant Life with and without Oxygen: A Metabolomics Approach

Oxygen deficiency is an environmental challenge which affects plant growth, the development and distribution in land and aquatic ecosystems, as well as crop yield losses worldwide. The capacity to exist in the conditions of deficiency or the complete lack of oxygen depends on a number of anatomic, developmental and molecular adaptations. The lack of molecular oxygen leads to an inhibition of aerobic respiration, which causes energy starvation and the acceleration of glycolysis passing into fermentations. We focus on systemic metabolic alterations revealed with the different approaches of metabolomics. Oxygen deprivation stimulates the accumulation of glucose, pyruvate and lactate, indicating the acceleration of the sugar metabolism, glycolysis and lactic fermentation, respectively. Among the Krebs-cycle metabolites, only the succinate level increases. Amino acids related to glycolysis, including the phosphoglycerate family (Ser and Gly), shikimate family (Phe, Tyr and Trp) and pyruvate family (Ala, Leu and Val), are greatly elevated. Members of the Asp family (Asn, Lys, Met, Thr and Ile), as well as the Glu family (Glu, Pro, Arg and GABA), accumulate as well. These metabolites are important members of the metabolic signature of oxygen deficiency in plants, linking glycolysis with an altered Krebs cycle and allowing alternative pathways of NAD(P)H reoxidation to avoid the excessive accumulation of toxic fermentation products (lactate, acetaldehyde, ethanol). Reoxygenation induces the downregulation of the levels of major anaerobically induced metabolites, including lactate, succinate and amino acids, especially members of the pyruvate family (Ala, Leu and Val), Tyr and Glu family (GABA and Glu) and Asp family (Asn, Met, Thr and Ile). The metabolic profiles during native and environmental hypoxia are rather similar, consisting in the accumulation of fermentation products, succinate, fumarate and amino acids, particularly Ala, Gly and GABA. The most intriguing fact is that metabolic alterations during oxidative stress are very much similar, with plant response to oxygen deprivation but not to reoxygenation.

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.

Genotypic differences in systemic root responses to mechanical obstacles

As roots grow through the soil to forage for water and nutrients, they encounter mechanical obstacles such as patches of dense soil and stones that locally impede root growth. Here, we investigated hitherto poorly understood systemic responses of roots to localised root impedance. Seedlings of two wheat genotypes were grown in hydroponics and exposed to impenetrable obstacles constraining the vertical growth of the primary or a single seminal root. We deployed high-resolution in vivo imaging to quantify temporal dynamics of root elongation rate, helical root movement, and root growth direction. The two genotypes exhibited distinctly different patterns of systemic responses to localised root impedance, suggesting different strategies to cope with obstacles, namely stress avoidance and stress tolerance. Shallower growth of unconstrained seminal roots and more pronounced helical movement of unconstrained primary and seminal roots upon localised root impedance characterised the avoidance strategy shown by one genotype. Stress tolerance to localised root impedance, as exhibited by the other genotype, was indicated by relatively fast elongation of primary roots and steeper seminal root growth. These different strategies highlight that the effects of mechanical obstacles on spatiotemporal root growth patterns can differ within species, which may have major implications for resource acquisition and whole-plant growth.

Genetic and molecular exploration of maize environmental stress resilience: Toward sustainable agriculture

Global climate change exacerbates the effects of environmental stressors, such as drought, flooding, extreme temperatures, salinity, and alkalinity, on crop growth and grain yield, threatening the sustainability of the food supply. Maize (Zea mays) is one of the most widely cultivated crops and the most abundant grain crop in production worldwide. However, the stability of maize yield is highly dependent on environmental conditions. Recently, great progress has been made in understanding the molecular mechanisms underlying maize responses to environmental stresses and in developing stress-resilient varieties due to advances in high-throughput sequencing technologies, multi-omics analysis platforms, and automated phenotyping facilities. In this review, we summarize recent advances in dissecting the genetic factors and networks that contribute to maize abiotic stress tolerance through diverse strategies. We also discuss future challenges and opportunities for the development of climate-resilient maize varieties.

Nano hydroxyapatite pre-treatment effectively reduces Cd accumulation in rice (Oryza sativa L.) and its impact on paddy microbial communities

Cadmium (Cd) contamination in paddy soil has become a worldwide concern and severely endangered human health. Nano hydroxyapatite (n-HAP) is a practical material to manage paddy Cd pollution, but its dosage should not be excessive. Based on previous studies, we validated the effect of n-HAP pre-treatment on rice Cd uptake in pot and field experiments. The results indicated that n-HAP pre-treatment effectively restricted Cd translocation in the soil-rice system. In pot experiment, when soil n-HAP concentration was 5000 mg/kg, the Cd content in the grains of n-HAP pre-treated rice was 0.171 mg/kg, decreased by 29.3% compared with normal rice (0.242 mg/kg). In field experiment, when soil n-HAP concentration was 20,000 mg/kg, the Cd content in the grains of n-HAP pre-treated rice was 0.156 mg/kg, decreased by 35.3% compared with normal rice (0.241 mg/kg). The primary mechanism was that n-HAP pre-treatment altered the formation and composition of iron plaque and therefore enhanced the Cd binding ability of iron plaque. The available N and P content and urease activity in paddy field were increased. We further investigated the impact of n-HAP on the diversity and structure of paddy microbial communities. The Chao1 and Shannon diversity indices showed no significant difference. The relative abundance of Actinobacteria and Proteobacteria was significantly decreased by n-HAP, indicating that Cd pollution might be alleviated. Desulfobacterota, Gemmatimonadota, and Geobacteraceae were significantly enriched by n-HAP. The declining relative abundance of Basidiomycota and the increasing relative abundance of other fungal taxa also suggested that n-HAP could alleviate Cd toxicity in soil.

ERFVII transcription factors and their role in the adaptation to hypoxia in Arabidopsis and crops

In this review, we focus on ethylene transcription factors (ERFs), which are a crucial family of transcription factors that regulate plant development and stress responses. ERFVII transcription factors have been identified and studied in several crop species, including rice, wheat, maize, barley, and soybean. These transcription factors are known to be involved in regulating the plant's response to low oxygen stress-hypoxia and could thus improve crop yields under suboptimal growing conditions. In rice (Oryza sativa) several ERFVII genes have been identified and characterized, including SUBMERGENCE 1A (SUB1A), which enables rice to tolerate submergence. The SUB1A gene was used in the development of SUB1 rice varieties, which are now widely grown in flood-prone areas and have been shown to improve yields and farmer livelihoods. The oxygen sensor in plants was discovered using the model plant Arabidopsis. The mechanism is based on the destabilization of ERFVII protein via the N-degron pathway under aerobic conditions. During hypoxia, the stabilized ERFVIIs translocate to the nucleus where they activate the transcription of hypoxia-responsive genes (HRGs). In summary, the identification and characterization of ERFVII transcription factors and their mechanism of action could lead to the development of new crop varieties with improved tolerance to low oxygen stress, which could have important implications for global food security.

Transcriptional analysis in multiple barley varieties identifies signatures of waterlogging response

Waterlogging leads to major crop losses globally, particularly for waterlogging-sensitive crops such as barley. Waterlogging reduces oxygen availability and results in additional stresses, leading to the activation of hypoxia and stress response pathways that promote plant survival. Although certain barley varieties have been shown to be more tolerant to waterlogging than others and some tolerance-related quantitative trait loci have been identified, the molecular mechanisms underlying this trait are mostly unknown. Transcriptomics approaches can provide very valuable information for our understanding of waterlogging tolerance. Here, we surveyed 21 barley varieties for the differential transcriptional activation of conserved hypoxia-response genes under waterlogging and selected five varieties with different levels of induction of core hypoxia-response genes. We further characterized their phenotypic response to waterlogging in terms of shoot and root traits. RNA sequencing to evaluate the genome-wide transcriptional responses to waterlogging of these selected varieties led to the identification of a set of 98 waterlogging-response genes common to the different datasets. Many of these genes are orthologs of the so-called "core hypoxia response genes," thus highlighting the conservation of plant responses to waterlogging. Hierarchical clustering analysis also identified groups of genes with intrinsic differential expression between varieties prior to waterlogging stress. These genes could constitute interesting candidates to study "predisposition" to waterlogging tolerance or sensitivity in barley.

Developing functional relationships between waterlogging and cotton growth and physiology-towards waterlogging modeling

Cotton crop is known to be poorly adapted to waterlogging, especially during the early growth stages. Developing functional relationships between crop growth and development parameters and the duration of waterlogging is essential to develop or improve existing cotton crop models for simulating the impact of waterlogging. However, there are only limited experimental studies conducted on cotton specifically aimed at developing the necessary functional relationships required for waterlogging modeling. Further research is needed to understand the effects of waterlogging on cotton crops and improve modeling capabilities in this area. The current study aimed to conduct waterlogging experiments and develop functional relationships between waterlogging and cotton growth and physiology. The experiments were conducted in pots, and the waterlogging was initiated by plugging the drain hole at the bottom of the pot using a wooden peg. In the experiments, eight waterlogging treatments, including the control treatment, were imposed at the vegetative growth stage (15 days after sowing). Control treatment had zero days of water-logged condition; other treatments had 2, 4, 6, 8, 10, 12, and 14 days of waterlogging. It took five days to reach zero oxygen levels and one to two days to return to control after the treatment. After a total treatment duration of 14 days (30 days after sowing), the growth, physiological, reproductive, and nutrient analysis was conducted. All physiological parameters decreased with the number of days of waterlogging. Flavonoid and anthocyanin index increased with increased duration of waterlogging. Photosynthesis and whole plant dry weight in continuously waterlogged conditions were 75% and 78% less compared to 0, and 2-day water-logged plants. Plant height, stem diameter, number of main stem leaves, leaf area, and leaf length also decreased with waterlogging duration. When waterlogging duration increased, leaf, stem, and root macronutrients decreased, while micronutrients showed mixed trends. Based on the experimental study, functional relationships (linear, quadratic, and exponential decay) and waterlogging stress response indices are developed between growth and development parameters and the duration of waterlogging. This can serve as a base for developing or improving process-based cotton models to simulate the impact of waterlogging.

Genomic landscape of the OsTPP7 gene in its haplotype diversity and association with anaerobic germination tolerance in rice

Early season flooding is a major constraint in direct-seeded rice, as rice genotypes vary in their coleoptile length during anoxia. Trehalose-6-phosphate phosphatase 7 (OsTPP7, Os09g0369400) has been identified as the genetic determinant for anaerobic germination (AG) and coleoptile elongation during flooding. We evaluated the coleoptile length of a diverse rice panel under normal and flooded conditions and investigated the Korean rice collection of 475 accessions to understand its genetic variation, population genetics, evolutionary relationships, and haplotypes in the OsTPP7 gene. Most accessions displayed enhanced flooded coleoptile lengths, with the temperate japonica ecotype exhibiting the highest average values for normal and flooded conditions. Positive Tajima's D values in indica, admixture, and tropical japonica ecotypes suggested balancing selection or population expansion. Haplotype analysis revealed 18 haplotypes, with three in cultivated accessions, 13 in the wild type, and two in both. Hap_1 was found mostly in japonica, while Hap-2 and Hap_3 were more prevalent in indica accessions. Further phenotypic performance of major haplotypes showed significant differences in flooded coleoptile length, flooding tolerance index, and shoot length between Hap_1 and Hap_2/3. These findings could be valuable for future selective rice breeding and the development of efficient haplotype-based breeding strategies for improving flood tolerance.

iTRAQ-Based Quantitative Proteomics Unveils Protein Dynamics in the Root of Solanum melongena L. under Waterlogging Stress Conditions

Waterlogging poses significant abiotic stress that endangers the survival of plants, including crops. In response, plants dramatically change their physiology to enhance their tolerance to waterlogging, such as proteome reconfiguration. Here, we utilized isobaric tags for the relative and absolute quantitation (iTRAQ)-based protein labeling technique to examine the proteomic changes induced by waterlogging in the roots of Solanum melongena L., a solanaceous plant. The plants were subjected to 6, 12, and 24 h of waterlogging stress at the flowering stage. Of the 4074 identified proteins, compared to the control, the abundance of the proteins increased and decreased in 165 and 78 proteins, respectively, in 6 h of treatments; 219 and 89 proteins, respectively, in 12 h of treatments; and 126 and 127 proteins, respectively, in 24 h of treatments. The majority of these differentially regulated proteins participated in processes such as energy metabolism, amino acid biosynthesis, signal transduction, and nitrogen metabolism. Fructose-bisphosphate aldolase and three alcohol dehydrogenase genes, in particular, were up- or down-regulated in waterlogging-treated Solanum melongena roots, suggesting that some proteins related to anaerobic metabolism (glycolysis and fermentation) may play vital roles in protecting its roots from waterlogging stress to enable long-term survival. Overall, this research not only offers a comprehensive dataset of protein alterations in waterlogged Solanum melongena roots but also insights into the mechanisms by which solanaceous plants adapt to waterlogging stress.

Comparative Physiological and Transcriptome Analysis Reveals Potential Pathways and Specific Genes Involved in Waterlogging Tolerance in Apple Rootstocks

Apple (Malus × domestica Borkh.) is one of the most cultivated fruit crops in China. Apple trees frequently encounter waterlogging stress, mainly due to excess rainfall, soil compaction, or poor soil drainage, results in yellowing leaves and declined fruit quality and yield in some regions. However, the mechanism underlying the response to waterlogging has not been well elucidated. Therefore, we performed a physiological and transcriptomic analysis to examine the differential responses of two apple rootstocks (waterlogging-tolerant M. hupehensis and waterlogging-sensitive M. toringoides) to waterlogging stress. The results showed that M. toringoides displayed more severe leaf chlorosis during the waterlogging treatment than M. hupehensis. Compared with M. hupehensis, the more severe leaf chlorosis induced by waterlogging stress in M. toringoides was highly correlated with increased electrolyte leakage and superoxide radicals, hydrogen peroxide accumulation, and increased stomata closure. Interestingly, M. toringoides also conveyed a higher ethylene production under waterlogging stress. Furthermore, RNA-seq revealed that a total of 13,913 common differentially expressed genes (DEGs) were differentially regulated between M. hupehensis and M. toringoides under waterlogging stress, especially those DEGs involved in the biosynthesis of flavonoids and hormone signaling. This suggests a possible link of flavonoids and hormone signaling to waterlogging tolerance. Taken together, our data provide the targeted genes for further investigation of the functions, as well as for future molecular breeding of waterlogging-tolerant apple rootstocks.

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.

Submergence Stress Alters the Expression of Clock Genes and Configures New Zeniths and Expression of Outputs in Brachypodium distachyon

Plant networks of oscillating genes coordinate internal processes with external cues, contributing to increased fitness. We hypothesized that the response to submergence stress may dynamically change during different times of the day. In this work, we determined the transcriptome (RNA sequencing) of the model monocotyledonous plant, Brachypodium distachyon, during a day of submergence stress, low light, and normal growth. Two ecotypes of differential tolerance, Bd21 (sensitive) and Bd21-3 (tolerant), were included. We submerged 15-day-old plants under a long-day diurnal cycle (16 h light/8 h dark) and collected samples after 8 h of submergence at ZT0 (dawn), ZT8 (midday), ZT16 (dusk), ZT20 (midnight), and ZT24 (dawn). Rhythmic processes were enriched both with up- and down-regulated genes, and clustering highlighted that the morning and daytime oscillator components (PRRs) show peak expression in the night, and a decrease in the amplitude of the clock genes (GI, LHY, RVE) was observed. Outputs included photosynthesis-related genes losing their known rhythmic expression. Up-regulated genes included oscillating suppressors of growth, hormone-related genes with new late zeniths (e.g., JAZ1, ZEP), and mitochondrial and carbohydrate signaling genes with shifted zeniths. The results highlighted genes up-regulated in the tolerant ecotype such as METALLOTHIONEIN3 and ATPase INHIBITOR FACTOR. Finally, we show by luciferase assays that Arabidopsis thaliana clock genes are also altered by submergence changing their amplitude and phase. This study can guide the research of chronocultural strategies and diurnal-associated tolerance mechanisms.

A quantitative trait locus conferring flood tolerance to deepwater rice regulates the formation of two distinct types of aquatic adventitious roots

A key trait conferring flood tolerance is the ability to grow adventitious roots as a response to submergence. The genetic traits of deepwater rice determining the development and characteristics of aquatic adventitious roots (AAR) had not been evaluated. We used near-isogenic lines introgressed to test the hypothesis that the impressive shoot elongation ability of deepwater rice linked to quantitative trait loci 1 and 12 also promote the development of AAR. The deepwater rice genotype NIL-12 possessed expanded regions at the stem nodes where numerous AAR developed as a response to submergence. Two types (AR1 and AR2) of roots with distinct timing of emergence and large differences in morphological and anatomical traits formed within 3 (AR1) to 7 (AR2) d of submergence. The mechanical impedance provided by the leaf sheath caused AR2 to emerge later promoting thicker roots, higher elongation capacity and higher desiccation tolerance. Upregulation of key genes suggests a joint contribution in activating the meristem in AAR enhancing the development of these in response to submergence. The morphological and anatomical traits suggested that AR2 is better adapted to long-term flooding than AR1. We therefore propose that AR2 in deepwater rice functions as an evolutionary defence strategy to tackle periodic submergence.

Above- and belowground linkages during extreme moisture excess: leveraging knowledge from natural ecosystems to better understand implications for row-crop agroecosystems

Above- and belowground linkages are responsible for some of the most important ecosystem processes in unmanaged terrestrial systems including net primary production, decomposition, and carbon sequestration. Global change biology is currently altering above- and belowground interactions, reducing ecosystem services provided by natural systems. Less is known regarding how above- and belowground linkages impact climate resilience, especially in intentionally managed cropping systems. Waterlogged or flooded conditions will continue to increase across the Midwestern USA due to climate change. The objective of this paper is to explore what is currently known regarding above- and belowground linkages and how they impact biological, biochemical, and physiological processes in systems experiencing waterlogged conditions. We also identify key above- and belowground processes that are critical for climate resilience in Midwestern cropping systems by exploring various interactions that occur within unmanaged landscapes. Above- and belowground interactions that support plant growth and development, foster multi-trophic-level interactions, and stimulate balanced nutrient cycling are critical for crops experiencing waterlogged conditions. Moreover, incorporating ecological principles such as increasing plant diversity by incorporating crop rotations and adaptive management via delayed planting dates and adjustments in nutrient management will be critical for fostering climate resilience in row-crop agriculture moving forward.

UDP-glucosyltransferase OsUGT75A promotes submergence tolerance during rice seed germination

Submergence stress represents a major obstacle limiting the application of direct seeding in rice cultivation. Under flooding conditions, coleoptile elongation can function as an escape strategy that contributes to submergence tolerance during seed germination in rice; however, the underlying molecular bases have yet to be fully determined. Herein, we report that natural variation of rice coleoptile length subjected to submergence is determined by the glucosyltransferase encoding gene OsUGT75A. OsUGT75A regulates coleoptile length via decreasing free abscisic acid (ABA) and jasmonic acid (JA) levels by promoting glycosylation of these two phytohormones under submergence. Moreover, we find that OsUGT75A accelerates coleoptile length through mediating the interactions between JASMONATE ZIMDOMAIN (OsJAZ) and ABSCISIC ACID-INSENSITIVE (OsABI) proteins. Last, we reveal the origin of the haplotype that contributes to coleoptile length in response to submergence and transferring this haplotype to indica rice can enhance coleoptile length in submergence conditions. Thus, we propose that OsUGT75A is a useful target in breeding of rice varieties suitable for direct seeding cultivation.

Oxygenation alleviates waterlogging-caused damages to cherry rootstocks

Waterlogging has occurred more frequently in recent years due to climate change, so it is a huge threat to crop yield and quality. Sweet cherry, a fruit tree with a high economic value, is sensitive to waterlogging stress. One of the most effective methods for enhancing the waterlogging tolerance of sweet cherries is to select waterlogging-tolerant rootstocks. However, the waterlogging tolerance of different cherry rootstocks, and the underlying mechanism remains uncharacterized. Thus, we first evaluated the waterlogging resistance of five sweet cherry rootstocks planted in China. The data showed that 'Gisela 12' and 'Colt' were the most waterlogging-sensitive and -tolerant among the five tested varieties, respectively. Oxygenation effectively alleviated the adverse impacts of waterlogging stress on cherry rootstocks. Moreover, we found that the waterlogging group had lower relative water content, Fv/Fm value, net photosynthetic rate, and higher antioxidant enzyme activities, whereas the oxygenated group performed better in all these parameters. RNA-Seq analysis revealed that numerous DEGs were involved in energy production, antioxidant metabolism, hormone metabolism pathways, and stress-related transcription factors. These findings will help provide management strategies to enhance the waterlogging tolerance of cherry rootstocks and thereby achieve higher yield and better quality of cherries.

In situ mapping of ion distribution profiles and gene expression reveals interactions between hypoxia and Mn2+/Fe2+ availability in barley roots

Flooding stress affects soil properties thus altering the availability, uptake, and transport of mineral nutrients in plant roots. Flooding stress also increases the amount of soluble Mn²⁺ and Fe²⁺ in the soil and their uptake by plants, causing elemental toxicity. However, as oxygen profiles in plant roots are not uniform, it is still unclear how soil flooding will affect Mn²⁺/Fe²⁺ absorption and distribution in different cell types and tissues. In this study, waterlogging sensitive barley variety NasoNijo (NN) and tolerant variety TX9425 (TX) were exposed to hypoxia, metal (Mn²⁺ and Fe²⁺), and combined hypoxia + metal treatment to map the in situ ion profiles at different regions of barley root. We found that combined hypoxia and metal stress causes significantly more reduction in plant biomass compared with the single submergence or metal stress. Despite this, more Fe and Mn were accumulated under metal stress condition than those under combined stress, regardless of variety. Cultivar NN absorbed more Fe and Mn than TX in the cortical cells of the root meristem and in the mature zone under metal stress which was also verified by histochemical detection. In the mature zone, the expressions of Fe and Mn transporter genes including HvADPRibase-Mn (Manganese-dependent ADP-ribose), HvZIP1 (zinc-regulated transporter /Fe-regulated transporter-like protein 1), HvYS1 (yellow stripe 1), HvNRAMP5 (Natural Resistance-Associated Macrophage Protein 5) were significantly downregulated under all three treatments in both barley varieties except HvADPRibase-Mn HvZIP1 cortex of TX were unchanged under metal stress. Interestingly, the transcripts of HvMTP1 (metal tolerance protein 1) were significantly downregulated by metal and combined stress in stele and upregulated by hypoxia and metal stress in cortex of TX, but not affected in NN. It is concluded that Fe and Mn absorption involving HvMTP1is associated with the extent of waterlogging tolerance in barley.

Mitochondrial alternative NADH dehydrogenases NDA1 and NDA2 promote survival of reoxygenation stress in Arabidopsis by safeguarding photosynthesis and limiting ROS generation

Plant submergence stress is a growing problem for global agriculture. During desubmergence, rising O₂ concentrations meet a highly reduced mitochondrial electron transport chain (mETC) in the cells. This combination favors the generation of reactive oxygen species (ROS) by the mitochondria, which at excess can cause damage. The cellular mechanisms underpinning the management of reoxygenation stress are not fully understood. We investigated the role of alternative NADH dehydrogenases (NDs), as components of the alternative mETC in Arabidopsis, in anoxia-reoxygenation stress management. Simultaneous loss of the matrix-facing NDs, NDA1 and NDA2, decreased seedling survival after reoxygenation, while overexpression increased survival. The absence of NDAs led to reduced maximum potential quantum efficiency of photosystem II linking the alternative mETC to photosynthetic function in the chloroplast. NDA1 and NDA2 were induced upon reoxygenation, and transcriptional activation of NDA1 was controlled by the transcription factors ANAC016 and ANAC017 that bind to the mitochondrial dysfunction motif (MDM) in the NDA1 promoter. The absence of NDA1 and NDA2 did not alter recovery of cytosolic ATP levels and NADH : NAD⁺ ratio at reoxygenation. Rather, the absence of NDAs led to elevated ROS production, while their overexpression limited ROS. Our observations indicate that the control of ROS formation by the alternative mETC is important for photosynthetic recovery and for seedling survival of anoxia-reoxygenation stress.

Morphology, photosynthetic physiology and biochemistry of nine herbaceous plants under water stress

Global climate warming and shifts in rainfall patterns are expected to trigger increases in the frequency and magnitude of drought and/or waterlogging stress in plants. To cope with water stress, plants develop diverse tactics. However, the adoption capability and mechanism vary depending upon the plant species identity as well as stress duration and intensity. The objectives of this study were to evaluate the species-dependent responses of alpine herbaceous species to water stress. Nine herbaceous species were subjected to different water stresses (including moderate drought and moderate waterlogging) in pot culture using a randomized complete block design with three replications for each treatment. We hypothesized that water stress would negatively impact plant growth and metabolism. We found considerable interspecies differences in morphological, physiological, and biochemical responses when plants were exposed to the same water regime. In addition, we observed pronounced interactive effects of water regime and plant species identity on plant height, root length, root/shoot ratio, biomass, and contents of chlorophyll a, chlorophyll b, chlorophyll (a+b), carotenoids, malondialdehyde, soluble sugar, betaine, soluble protein and proline, implying that plants respond to water regime differently. Our findings may cast new light on the ecological restoration of grasslands and wetlands in the Qinghai-Tibetan Plateau by helping to select stress-tolerant plant species.

Responses of key root traits in the genus Oryza to soil flooding mimicked by stagnant, deoxygenated nutrient solution

Excess water can induce flooding stress resulting in yield loss, even in wetland crops such as rice (Oryza). However, traits from species of wild Oryza have already been used to improve tolerance to abiotic stress in cultivated rice. This study aimed to establish root responses to sudden soil flooding among eight wild relatives of rice with different habitat preferences benchmarked against three genotypes of O. sativa. Plants were raised hydroponically, mimicking drained or flooded soils, to assess the plasticity of adventitious roots. Traits included were apparent permeance (PA) to O2 of the outer part of the roots, radial water loss, tissue porosity, apoplastic barriers in the exodermis, and root anatomical traits. These were analysed using a plasticity index and hierarchical clustering based on principal component analysis. For example, O. brachyantha, a wetland species, possessed very low tissue porosity compared with other wetland species, whereas dryland species O. latifolia and O. granulata exhibited significantly lower plasticity compared with wetland species and clustered in their own group. Most species clustered according to growing conditions based on PA, radial water loss, root porosity, and key anatomical traits, indicating strong anatomical and physiological responses to sudden soil flooding.

Iron plaque formation, characteristics, and its role as a barrier and/or facilitator to heavy metal uptake in hydrophyte rice (Oryza sativa L.)

The persistent bioavailability of toxic metal(oids) (TM) is undeniably the leading source of serious environmental problems. Through the transfer of these contaminants into food networks, sediments and the aquatic environmental pollution by TM serve as key routes for potential risks to soil and human health. The formation of iron oxyhydroxide plaque (IP) on the root surface of hydrophytes, particularly rice, has been linked to the impact of various abiotic and biotic factors. Radial oxygen loss has been identified as a key driver for the oxidation of rhizosphere ferrous iron (Fe²⁺) and its subsequent precipitation as low-to-high crystalline and/or amorphous Fe minerals on root surfaces as IP. Considering that each plant species has its unique capability of creating an oxidised rhizosphere under anaerobic conditions, the abundance of rhizosphere Fe²⁺, functional groups from organic matter decomposition and variations in binding capacities of Fe oxides, thus, impacting the mobility and interaction of several contaminants as well as toxic/non-toxic metals on the specific surface areas of the IP. More insight from wet extraction and advanced synchrotron-based analytical techniques has provided further evidence on how IP formation could significantly affect the fate of plant physiology and biomass production, particularly in contaminated settings. Collectively, this information sets the stage for the possible implementation of IP and related analytical protocols as a strategic framework for the management of rice and other hydrophytes, particularly in contaminated sceneries. Other confounding variables involved in IP formation, as well as operational issues related to some advanced analytical processes, should be considered.

Multi-stress resilience in plants recovering from submergence

Submergence limits plants' access to oxygen and light, causing massive changes in metabolism; after submergence, plants experience additional stresses, including reoxygenation, dehydration, photoinhibition and accelerated senescence. Plant responses to waterlogging and partial or complete submergence have been well studied, but our understanding of plant responses during post-submergence recovery remains limited. During post-submergence recovery, whether a plant can repair the damage caused by submergence and reoxygenation and re-activate key processes to continue to grow, determines whether the plant survives. Here, we summarize the challenges plants face when recovering from submergence, primarily focusing on studies of Arabidopsis thaliana and rice (Oryza sativa). We also highlight recent progress in elucidating the interplay among various regulatory pathways, compare post-hypoxia reoxygenation between plants and animals and provide new perspectives for future studies.

Genome-wide association study reveals novel genetic loci involved in anaerobic germination tolerance in Indica rice

Increasing numbers of rice farmers are adopting methods of direct seeding in flooded paddy fields to save costs associated with labor and transplanting. Successful seedling establishment under anoxic conditions requires rapid coleoptile growth to access oxygen near the water surface. It is important to identify relevant genetic loci for coleoptile growth in rice. In this study, the coleoptile length (CL), coleoptile surface area (CSA), coleoptile volume (CV), and coleoptile diameter (CD) of a germplasm collection consisting of 200 cultivars growing in a low-oxygen environment for 6 days varied extensively. A genome-wide association study (GWAS) was performed using 161,657 high-quality single nucleotide polymorphisms (SNPs), which were obtained via genotyping by sequencing (GBS). A total of 96 target trait-associated loci were detected, of which 14 were detected repeatedly in both the wet and dry seasons. For these 14 loci, 384 genes were located within a 200-kb genomic region (± 100 kb from the peak SNP). In addition, 12,084 differentially expressed genes (DEGs) were identified using transcriptome expression profiling. Based on the GWAS and expression profiling, we further narrowed the candidate genes down to 111. Among the 111 candidate DEGs, Os02g0285300, Os02g0639300, Os04g0671300, Os06g0702600, Os06g0707300, and Os12g0145700 were the most promising candidates associated with anaerobic germination. In addition, we performed a detailed analysis of OsTPP7 sequences from 29 samples in our panel containing 200 diverse germplasms. A total of 11 mutation sites were identified, and four haplotypes were obtained. We found that 7 varieties with the OsTPP7-1 haplotype had higher phenotypic values. This work broadens our understanding of the genetic control of germination tolerance of anaerobic conditions. This study also provides a material basis for breeding superior direct-seeded rice varieties.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-022-01345-1.

Physiological and comparative transcriptome analysis of the response and adaptation mechanism of the photosynthetic function of mulberry (Morus alba L.) leaves to flooding stress

Flooding has become one of the major abiotic stresses that seriously affects plant growth and development owing to changes in the global precipitation pattern. Mulberry (Morus alba L.) is a desirable tree spePhysocarpus amurensis Maxim andcies with high ecological and economic benefits. To reveal the response and adaptive mechanisms of the photosynthetic functions of mulberry leaves to flooding stress, chlorophyll synthesis, photosynthetic electron transfer and the Calvin cycle were investigated by physiological studies combined with an analysis of the transcriptome. Flooding stress inhibited the synthesis of chlorophyll (Chl) and decreased its content in mulberry leaves. The sensitivity of Chl a to flooding stress was higher than that of Chl b owing to the changes of CHLG (LOC21385082) and CAO (LOC21408165) that encode genes during chlorophyll synthesis. The levels of expression of Chl b reductase NYC (LOC112094996) and NYC (LOC21385774), which are involved in Chl b degradation, were upregulated on the fifteenth day of flooding, which accelerated the transformation of Chl b to Chl a, and upregulated the expression of PPH (LOC21385040) and PAO (LOC21395013). This accelerated the degradation of chlorophyll. Flooding stress significantly inhibited the photosynthetic function of mulberry leaves. A Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of differentially expressed genes under different days of flooding stress indicated significant enrichment in Photosynthesis-antenna proteins (map00196), Photosynthesis (map00195) and Carbon fixation in photosynthetic organisms (map00710). On the fifth day of flooding, 7 and 5 genes that encode antenna proteins were identified on LHCII and LHCI, respectively. They were significantly downregulated, and the degree of downregulation increased as the trees were flooded longer. Therefore, the power of the leaves to capture solar energy and transfer this energy to the reaction center was reduced. The chlorophyll fluorescence parameters and related changes in the expression of genes in the transcriptome indicated that the PSII and PSI of mulberry leaves were damaged, and their activities decreased under flooding stress. On the fifth day of flooding, electron transfer on the PSII acceptor side of mulberry leaves was blocked, and the oxygen-evolving complex (OEC) on the donor side was damaged. On the tenth day of flooding, the thylakoid membranes of mulberry leaves were damaged. Five of the six coding genes that mapped to the OEC were significantly downregulated. Simultaneously, other coding genes located at the PSII reaction center and those located at the PSI reaction center, including Cytb6/f, PC, Fd, FNR and ATP, were also significantly downregulated. In addition, the gas exchange parameters (P_n, G_s, T_r, and C_i) of the leaves decreased after 10 days of flooding stress primarily owing to the stomatal factor. However, on the fifteenth day of flooding, the value for the intracellular concentration of CO₂ was significantly higher than that on the tenth day of flooding. In addition, the differentially expressed genes identified in the Calvin cycle were significantly downregulated, suggesting that in addition to stomatal factors, non-stomatal factors were also important factors that mediated the decrease in the photosynthetic capacity of mulberry leaves. In conclusion, the inhibition of growth of mulberry plants caused by flooding stress was primarily related to the inhibition of chlorophyll synthesis, antenna proteins, photosynthetic electron transfer and the Calvin cycle. The results of this study provide a theoretical basis for the response and mechanism of adaptation of the photosynthetic function of mulberry to flooding stress.

The Effects of Submergence on Selected Malaysian Rice Varieties

Various varieties have been developed in Malaysia, mainly to improve rice response to environmental changes, pests, and diseases, as well as to increase rice productivity under stressful conditions. Despite being semi-aquatic plants, rice is intolerant to complete submergence for a long period. This study was conducted to evaluate the response of seven Malaysian rice varieties at the vegetative stage under submergence stress. Two-week-old rice seedlings were submerged for 14 days, and the changes in plant height, chlorophyll content, and soluble sugar content were determined. The survival percentage of these varieties was observed after 14 days of de-submergence, where UKMRC2 and MR220CL possessed high survivability (90% & 60%, respectively). After submergence, all varieties showed height increment and reduced chlorophyll and soluble sugar contents. Based on our analyses, UKMRC2 performed better than other varieties, although slightly less than IR64-Sub1. It was confirmed that UKMRC2 is the submergence-tolerant variety, and its response to underwater germination was also determined. Our result showed that UKMRC2 might possess tolerance to anaerobic germination conditions, and more studies are needed to understand its molecular mechanism for submergence. In conclusion, many varieties used were susceptible to submergence, and the development of more submergence-tolerant varieties is crucial for Malaysia’s food security sustainability.

Exogenous ABA and IAA modulate physiological and hormonal adaptation strategies in Cleistocalyx operculatus and Syzygium jambos under long-term waterlogging conditions

BACKGROUND

The mechanisms of abscisic acid (ABA) and auxin (IAA) in inducing adventitious root (AR) formation, biomass accumulation, and plant development under long-term waterlogging (LT-WL) conditions are largely unexplored. This study aimed to determine the roles of exogenous application of ABA and IAA in two woody plants (Cleistocalyx operculatus and Syzygium jambos) under LT-WL conditions. A pot experiment was conducted using a complete randomized design with two factors: (i) LT-WL and (ii) application of exogenous phytohormones (ABA and IAA) for 120 d.

RESULTS

Results revealed that exogenous ABA and IAA promoted LT-WL tolerance in both species. In C. operculatus and S. jambos, plant height, the number of blades, leaf area, and fresh shoot weight were increased by exogenous IAA under LT-WL. However, exogenous ABA affected more the adventitious and primary root in C. operculatus compared to S. jambos. LT-WL decreased drastically the photosynthetic activities in both species, but adding moderate amounts of exogenous ABA or IAA protected the photosynthesis apparatus under LT-WL. Exogenous phytohormones at certain levels decreased the superoxide anion level and malondialdehyde accumulation in plants under LT-WL. Also, the increase of the peroxidases and superoxide dismutase activities by exogenous phytohormones was more marked in C. operculatus compared to S. jambos. Meanwhile, the catalase activity was down-regulated in both species by exogenous phytohormones. Exogenous ABA or IAA positively regulated the jasmonic acid content in ARs under LT-WL. Moderate application of exogenous ABA or IAA in plants under LT-WL decreased the ABA content in the leaves. Lower accumulation of IAA and ABA in the leaves of C. operculatus under LT-WL was positively correlated with a decrease in antioxidant activity.

CONCLUSIONS

Lastly, C. operculatus which has greater morphology indexes was more tolerant to waterlogging than S. jambos. Moreover, the adaptive strategies via exogenous ABA were more built around the below-ground biomass indexes particularly in C. operculatus, while exogenous IAA backed the above-ground biomass in both species. Overall, the exogenous hormones applied (spraying or watering) influenced differentially the plant's responses to LT-WL. The phytohormonal profile of plants exposed to waterlogging stress varied depending on the species' tolerance level.

Root cell types as an interface for biotic interactions

Root responses to environmental stresses show a high level of cell type and developmental stage specificity. Interactions with beneficial and pathogenic organisms - including microbes and parasites - elicit a set of transcriptional responses unique to each root cell type, often dependent on their differentiation state. Localized changes to the cell wall and to the integrity of root cell types can serve as a physical barrier for a range of pests. Conversely, certain microorganisms weaken existing barriers within root cell types. Interactions with microorganisms vary between roots of different developmental origins and cellular architectures. Here we provide an overview of the molecular, architectural, and structural properties of root cell types crucial to both maintaining beneficial interactions and protecting from pathogens.

Seed priming with protein hydrolysate promotes seed germination via reserve mobilization, osmolyte accumulation and antioxidant systems under PEG-induced drought stress

Seed priming with pig blood protein hydrolysate improves tomato seed germination and seedling growth via regulation of reserve mobilization, osmotic adjustment, and antioxidant mechanism under drought conditions. Protein hydrolysates obtained from agro-industrial byproducts are widely recognized because of their positive roles in regulating plant responses to environmental stresses. However, little is known regarding the roles of animal protein hydrolysates in mediating seed drought tolerance and its underlying mechanisms. This study investigated the potential effects of seed priming on tomato seed germination and seedling growth under PEG-induced drought stress using protein hydrolysates derived from pig blood (PP). PP priming effectively alleviated the drought-induced reduction in seed germination traits, resulting in improved tomato seedling growth. PP priming enhanced the gene expressions and activities of amylase and sucrose synthase and soluble sugar, soluble protein, and free amino acid levels, thereby promoting reserve mobilization in seeds. PP priming also reduced osmotic toxicity through increased accumulations of proline, soluble protein, and soluble sugar. Drought stress substantially enhanced reactive oxygen species production and the subsequent increases in malondialdehyde levels and Evans blue solution uptake, which were substantially alleviated after PP priming via the improved activities of enzymatic and non-enzymatic antioxidants. Moreover, the increased DPPH free radical scavenging capacity and ferric reducing antioxidant power indicated that PP-treated tomato seedings had high antioxidant activities under drought stress. Therefore, PP priming is a novel, promising, and practicable method for improving tomato seed germination and seedling growth under drought stress.

UAV Image-Based Crop Growth Analysis of 3D-Reconstructed Crop Canopies

Plant growth rate is an essential phenotypic parameter for quantifying potential crop productivity. Under field conditions, manual measurement of plant growth rate is less accurate in most cases. Image-based high-throughput platforms offer great potential for rapid, non-destructive, and objective estimation of plant growth parameters. The aim of this study was to assess the potential for quantifying plant growth rate using UAV-based (unoccupied aerial vehicle) imagery collected multiple times throughout the growing season. In this study, six diverse lines of lentils were grown in three replicates of 1 m² microplots with six biomass collection time-points throughout the growing season over five site-years. Aerial imagery was collected simultaneously with each manual measurement of the above-ground biomass time-point and was used to produce two-dimensional orthomosaics and three-dimensional point clouds. Non-linear logistic models were fit to multiple data collection points throughout the growing season. Overall, remotely detected vegetation area and crop volume were found to produce trends comparable to the accumulation of dry weight biomass throughout the growing season. The growth rate and G50 (days to 50% of maximum growth) parameters of the model effectively quantified lentil growth rate indicating significant potential for image-based tools to be used in plant breeding programs. Comparing image-based groundcover and vegetation volume estimates with manually measured above-ground biomass suggested strong correlations. Vegetation area measured from a UAV has utility in quantifying lentil biomass and is indicative of leaf area early in the growing season. For mid- to late-season biomass estimation, plot volume was determined to be a better estimator. Apart from traditional traits, the estimation and analysis of plant parameters not typically collected in traditional breeding programs are possible with image-based methods, and this can create new opportunities to improve breeding efficiency mainly by offering new phenotypes and affecting selection intensity.

Differences in the metabolic and functional mechanisms used to tolerate flooding in Guazuma ulmifolia (Lam.) from flood-prone Amazonian and dry Cerrado savanna populations

Flood tolerance is crucial to the survival of tree species subject to long periods of flooding, such as those present in the Amazonian várzea. Tolerance can be mediated by adjustments of metabolism, physiology and morphology, reinforcing the need to investigate the physiological and biochemical mechanisms used by tropical tree species to survive this stress. Moreover, such mechanisms may vary between populations that are subjected to differences in the frequency of flooding events. Here, we aimed to identify the mechanisms used by two populations of the tropical tree Guazuma ulmifolia (Lam.) to tolerate flooding: an Amazonian population frequently exposed to flooding and a Cerrado population, adapted to a dry environment. Young plants were subjected to a flooding of the roots and lower stem for 32 days, followed by 17 days of recovery. Amazonian plants exhibited greater increases in shoot length and higher maximum photosynthetic rate (Amax) compared with non-flooded plants from 7 days of flooding onwards, whereas increased Amax occurred later in flooded Cerrado plants and was not accompanied by increased shoot length. Lactate accumulated in roots of Cerrado plants after 24 h flooding, together with transcripts coding for lactate dehydrogenase in roots of both Cerrado and Amazonian plants. After 7 days of flooding, lactate decreased and alcohol dehydrogenase activity increased transiently, together with concentrations of alanine, γ-aminobutyric acid and succinate, indicating activation of metabolic processes associated with low oxygen availability. Other amino acids also increased in flooded Cerrado plants, revealing more extensive metabolic changes than in Amazonian plants. Wetland and dryland populations of G. ulmifolia revealed the great capacity to tolerate flooding stress through a suite of alterations in photosynthetic gas exchange and metabolism. However, the integrated physiological, biochemical and molecular analyses realized here indicated that wetland plants acclimatized more efficiently with increased shoot elongation and more rapid restoration of normal metabolism.

Identification of Functional Genetic Variations Underlying Flooding Tolerance in Brazilian Soybean Genotypes

Flooding is a frequent environmental stress that reduces soybean (Glycine max) growth and grain yield in many producing areas in the world, such as, e.g., in the United States, Southeast Asia and Southern Brazil. In these regions, soybean is frequently cultivated in lowland areas by rotating with rice (Oryza sativa), which provides numerous technical, economic and environmental benefits. Given these realities, this work aimed to characterize physiological responses, identify genes differentially expressed under flooding stress in Brazilian soybean genotypes with contrasting flooding tolerance, and select SNPs with potential use for marker-assisted selection. Soybean cultivars TECIRGA 6070 (flooding tolerant) and FUNDACEP 62 (flooding sensitive) were grown up to the V6 growth stage and then flooding stress was imposed. Total RNA was extracted from leaves 24 h after the stress was imposed and sequenced. In total, 421 induced and 291 repressed genes were identified in both genotypes. TECIRGA 6070 presented 284 and 460 genes up- and down-regulated, respectively, under flooding conditions. Of those, 100 and 148 genes were exclusively up- and down-regulated, respectively, in the tolerant genotype. Based on the RNA sequencing data, SNPs in differentially expressed genes in response to flooding stress were identified. Finally, 38 SNPs, located in genes with functional annotation for response to abiotic stresses, were found in TECIRGA 6070 and absent in FUNDACEP 62. To validate them, 22 SNPs were selected for designing KASP assays that were used to genotype a panel of 11 contrasting genotypes with known phenotypes. In addition, the phenotypic and grain yield impacts were analyzed in four field experiments using a panel of 166 Brazilian soybean genotypes. Five SNPs possibly related to flooding tolerance in Brazilian soybean genotypes were identified. The information generated from this research will be useful to develop soybean genotypes adapted to poorly drained soils or areas subject to flooding.

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

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

Plant hormone signals regulate trehalose accumulation against osmotic stress in watermelon cells

Trehalose, one of the most chemically stable sugars, can effectively improve the tolerance of various plants against abiotic stress by protecting and stabilizing protein and cell membranes. However, the signaling pathway in trehalose biosynthesis triggered by abiotic stresses is still unclear. In the study, it can be shown that exogenous trehalose can alleviate the inhibitory effect of osmotic stress on cell growth, suppress extracellular alkalization, ROS burst, and maintain the integrity of the microtubular cytoskeleton. Trehalose-6-phosphate synthase (TPS) is the key limiting enzyme for trehalose synthesis and is encoded by 7 ClTPS genes, located in 7 different chromosomes of the watermelon genome. Expression analysis by qRT-PCR indicated that osmotic stress could upregulate the expression of all the family members of ClTPS and promote the accumulation of trehalose in watermelon cells accordingly. Exogenous methyl jasmonate (MeJA), ethephon (ETH), abscisic acid (ABA), or salicylic acid (SA) induced trehalose accumulation, with MeJA being the most effective treatment. When fluridone (FL), an ABA biosynthesis inhibitor, was pre-perfused into the cells before osmotic stress, trehalose accumulation and packed cell volume were suppressed significantly, whereas inhibition of ethylene biosynthesis could even restore cell growth. Moreover, inhibition of trehalose hydrolysis could also increase the tolerance against osmotic stress. This study shows that trehalose biosynthesis is phytohormone-dependent and the hydrolysis of trehalose is involved in osmotic tolerance regulation.

Genome-Wide Identification of DUF26 Domain-Containing Genes in Dongxiang Wild Rice and Analysis of Their Expression Responses under Submergence

The DUF26 domain-containing protein is an extracellular structural protein, which plays an important role in signal transduction. Dongxiang wild rice (Oryza rufipogon Griff.) is the northern-most common wild rice in China. Using domain analysis, 85 DUF26 domain-containing genes were identified in Dongxiang wild rice (DXWR) and further divided into four categories. The DUF26 domain-containing genes were unevenly distributed on chromosomes, and there were 18 pairs of tandem repeats. Gene sequence analysis showed that there were significant differences in the gene structure and motif distribution of the DUF26 domain in different categories. Motifs 3, 8, 9, 13, 14, 16, and 18 were highly conserved in all categories. It was also found that there were eight plasmodesmata localization proteins (PDLPs) with a unique motif 19. Collinearity analysis showed that DXWR had a large number of orthologous genes with wheat, maize, sorghum and zizania, of which 17 DUF26 domain-containing genes were conserved in five gramineous crops. Under the stress of anaerobic germination and seedling submergence treatment, 33 DUF26 domain-containing genes were differentially expressed in varying degrees. Further correlation analysis with the expression of known submergence tolerance genes showed that these DUF26 domain-containing genes may jointly regulate the submergence tolerance process with these known submergence tolerance genes in DXWR.