Plant responses to hypoxia--is survival a balancing act?

Hypoxia in tomato (Solanum lycopersicum) fruit during ripening: Biophysical elucidation by a 3D reaction-diffusion model

Respiration provides energy, substrates, and precursors to support physiological changes of the fruit during climacteric ripening. A key substrate of respiration is oxygen that needs to be supplied to the fruit in a passive way by gas transfer from the environment. Oxygen gradients may develop within the fruit due to its bulky size and the dense fruit tissues, potentially creating hypoxia that may have a role in the spatial development of ripening. This study presents a 3D reaction-diffusion model using tomato (Solanum lycopersicum) fruit as a test subject, combining the multiscale fruit geometry generated from magnetic resonance imaging and microcomputed tomography with varying respiration kinetics and contrasting boundary resistances obtained through independent experiments. The model predicted low oxygen levels in locular tissue under atmospheric conditions, and the oxygen level was markedly lower upon scar occlusion, aligning with microsensor profiling results. The locular region was in a hypoxic state, leading to its low aerobic respiration with high CO2 accumulation by fermentative respiration, while the rest of the tissues remained well oxygenated. The model further revealed that the hypoxia is caused by a combination of diffusion resistances and respiration rates of the tissue. Collectively, this study reveals the existence of the respiratory gas gradients and its biophysical causes during tomato fruit ripening, providing richer information for future studies on localized endogenous ethylene biosynthesis and fruit ripening.

Regulation of root growth and elongation in wheat

Currently, the control of rhizosphere selection on farms has been applied to achieve enhancements in phenotype, extending from improvements in single root characteristics to the dynamic nature of entire crop systems. Several specific signals, regulatory elements, and mechanisms that regulate the initiation, morphogenesis, and growth of new lateral or adventitious root species have been identified, but much more work remains. Today, phenotyping technology drives the development of root traits. Available models for simulation can support all phenotyping decisions (root trait improvement). The detection and use of markers for quantitative trait loci (QTLs) are effective for enhancing selection efficiency and increasing reproductive genetic gains. Furthermore, QTLs may help wheat breeders select the appropriate roots for efficient nutrient acquisition. Single-nucleotide polymorphisms (SNPs) or alignment of sequences can only be helpful when they are associated with phenotypic variation for root development and elongation. Here, we focus on major root development processes and detail important new insights recently generated regarding the wheat genome. The first part of this review paper discusses the root morphology, apical meristem, transcriptional control, auxin distribution, phenotyping of the root system, and simulation models. In the second part, the molecular genetics of the wheat root system, SNPs, TFs, and QTLs related to root development as well as genome editing (GE) techniques for the improvement of root traits in wheat are discussed. Finally, we address the effect of omics strategies on root biomass production and summarize existing knowledge of the main molecular mechanisms involved in wheat root development and elongation.

Coping with alpine habitats: genomic insights into the adaptation strategies of Triplostegia glandulifera (Caprifoliaceae)

How plants find a way to thrive in alpine habitats remains largely unknown. Here we present a chromosome-level genome assembly for an alpine medicinal herb, Triplostegia glandulifera (Caprifoliaceae), and 13 transcriptomes from other species of Dipsacales. We detected a whole-genome duplication event in T. glandulifera that occurred prior to the diversification of Dipsacales. Preferential gene retention after whole-genome duplication was found to contribute to increasing cold-related genes in T. glandulifera. A series of genes putatively associated with alpine adaptation (e.g. CBFs, ERF-VIIs, and RAD51C) exhibited higher expression levels in T. glandulifera than in its low-elevation relative, Lonicera japonica. Comparative genomic analysis among five pairs of high- vs low-elevation species, including a comparison of T. glandulifera and L. japonica, indicated that the gene families related to disease resistance experienced a significantly convergent contraction in alpine plants compared with their lowland relatives. The reduction in gene repertory size was largely concentrated in clades of genes for pathogen recognition (e.g. CNLs, prRLPs, and XII RLKs), while the clades for signal transduction and development remained nearly unchanged. This finding reflects an energy-saving strategy for survival in hostile alpine areas, where there is a tradeoff with less challenge from pathogens and limited resources for growth. We also identified candidate genes for alpine adaptation (e.g. RAD1, DMC1, and MSH3) that were under convergent positive selection or that exhibited a convergent acceleration in evolutionary rate in the investigated alpine plants. Overall, our study provides novel insights into the high-elevation adaptation strategies of this and other alpine plants.

Lipids signaling and unsaturation of fatty acids participate in ramie response to submergence stress and hypoxia-responsive gene regulation

Ramie is a valuable crop that produces high-quality fibers and holds promise in ecological management and potential therapeutic properties. The damage of submergence during the fertile period seriously affects the growth of ramie. This study used transcriptomics and UPLC-QTOF/MS-based lipidomics analysis to reveal the lipids remodeling and stress adaptation mechanism in ramie response to submergence. The results of subcellular distribution showed that lipids in ramie leaf cells mostly aggregate in the inter-chloroplast cytoplasm to form lipid droplets under submergence stress. High-performance thin-layer chromatography (HPTLC) and lipidomics analysis showed that the composition and content of lipids in ramie leaves significantly changed under submergence stress, and the content of fatty acids (FAs) gradually accumulated with the extension of the submergence treatment time. Further analysis revealed that the content of 18:3 (n3) Coenzyme A (C18:3-CoA) increased significantly with the prolongation of submergence stress, and the exogenous addition of C18:3-CoA activated the expression of hypoxia-responsive marker genes such as BnADH1, BnPCO2, BnADH1, and BnPDC1. These results suggest that the ramie lipid metabolism pathways were significantly affected under submergence, and the C18:3-CoA may act directly or indirectly on the hypoxia-responsive genes to activate their transcriptional activities, thereby enhancing the tolerance of ramie to submergence stress.

Looking for Resistance to Soft Rot Disease of Potatoes Facing Environmental Hypoxia

Plants are exposed to various stressors, including pathogens, requiring specific environmental conditions to provoke/induce plant disease. This phenomenon is called the "disease triangle" and is directly connected with a particular plant-pathogen interaction. Only a virulent pathogen interacting with a susceptible plant cultivar will lead to disease under specific environmental conditions. This may seem difficult to accomplish, but soft rot Pectobacteriaceae (SRPs) is a group virulent of pathogenic bacteria with a broad host range. Additionally, waterlogging (and, resulting from it, hypoxia), which is becoming a frequent problem in farming, is a favoring condition for this group of pathogens. Waterlogging by itself is an important source of abiotic stress for plants due to lowered gas exchange. Therefore, plants have evolved an ethylene-based system for hypoxia sensing. Plant response is coordinated by hormonal changes which induce metabolic and physiological adjustment to the environmental conditions. Wetland species such as rice (Oryza sativa L.), and bittersweet nightshade (Solanum dulcamara L.) have developed adaptations enabling them to withstand prolonged periods of decreased oxygen availability. On the other hand, potato (Solanum tuberosum L.), although able to sense and response to hypoxia, is sensitive to this environmental stress. This situation is exploited by SRPs which in response to hypoxia induce the production of virulence factors with the use of cyclic diguanylate (c-di-GMP). Potato tubers in turn reduce their defenses to preserve energy to prevent the negative effects of reactive oxygen species and acidification, making them prone to soft rot disease. To reduce the losses caused by the soft rot disease we need sensitive and reliable methods for the detection of the pathogens, to isolate infected plant material. However, due to the high prevalence of SRPs in the environment, we also need to create new potato varieties more resistant to the disease. To reach that goal, we can look to wild potatoes and other Solanum species for mechanisms of resistance to waterlogging. Potato resistance can also be aided by beneficial microorganisms which can induce the plant's natural defenses to bacterial infections but also waterlogging. However, most of the known plant-beneficial microorganisms suffer from hypoxia and can be outcompeted by plant pathogens. Therefore, it is important to look for microorganisms that can withstand hypoxia or alleviate its effects on the plant, e.g., by improving soil structure. Therefore, this review aims to present crucial elements of potato response to hypoxia and SRP infection and future outlooks for the prevention of soft rot disease considering the influence of environmental conditions.

'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.

Group VII ethylene response factors forming distinct regulatory loops mediate submergence responses

Group VII ethylene response factors (ERFVIIs), whose stability is oxygen concentration-dependent, play key roles in regulating hypoxia response genes in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) during submergence. To understand the evolution of flooding tolerance in cereal crops, we evaluated whether Brachypodium distachyon ERFVII genes (BdERFVIIs) are related to submergence tolerance. We found that three BdERFVIIs, BdERF108, BdERF018, and BdERF961, form a feedback regulatory loop to mediate downstream responses. BdERF108 and BdERF018 activated the expression of BdERF961 and PHYTOGLOBIN 1 (PGB1), which promoted nitric oxide turnover and preserved ERFVII protein stability. The activation of PGB1 was subsequently counteracted by increased BdERF961 accumulation through negative feedback regulation. Interestingly, we found that OsERF67, the orthologue of BdERF961 in rice, activated PHYTOGLOBIN (OsHB2) expression and formed distinct regulatory loops during submergence. Overall, the divergent regulatory mechanisms exhibited by orthologs collectively offer perspectives for the development of submergence-tolerant crops.

Deciphering Physio-Biochemical Basis of Tolerance Mechanism for Sesame (Sesamum indicum L.) Genotypes under Waterlogging Stress at Early Vegetative Stage

Waterlogging represents a substantial agricultural concern, inducing harmful impacts on crop development and productivity. In the present study, 142 diverse sesame genotypes were examined during the early vegetative phase to assess their response under waterlogging conditions. Based on the severity of symptoms observed, 2 genotypes were classified as highly tolerant, 66 as moderately tolerant, 69 as susceptible, and 5 as highly susceptible. Subsequent investigation focused on four genotypes, i.e., two highly tolerant (JLT-8 and GP-70) and two highly susceptible (R-III-F6 and EC-335003). These genotypes were subjected to incremental stress periods (0 h, 24 h, 48 h, 72 h, and 96 h) to elucidate the biochemical basis of tolerance mechanisms. Each experiment was conducted as a randomized split-plot design with three replications, and the statistical significance of the treatment differences was determined using the one-way analysis of variance (ANOVA) followed by the Fisher least significant difference (LSD) test at p ≤ 0.05. The influence of waterlogging stress on morphological growth was detrimental for both tolerant and susceptible genotypes, with more severe consequences observed in the latter. Although adventitious roots were observed in both sets of genotypes above flooding levels, the tolerant genotypes exhibited a more rapid and vigorous development of these roots after 48 h of stress exposure. Tolerant genotypes displayed higher tolerance coefficients compared to susceptible genotypes. Furthermore, tolerant genotypes maintained elevated antioxidant potential, thereby minimizing oxidative stress. Conversely, susceptible genotypes exhibited higher accumulation of hydrogen peroxide (H2O2) and malondialdehyde content. Photosynthetic efficiency was reduced in all genotypes after 24 h of stress treatment, with a particularly drastic reduction in susceptible genotypes compared to their tolerant counterparts. Tolerant genotypes exhibited significantly higher activities of anaerobic metabolism enzymes, enabling prolonged survival under waterlogging conditions. Increase in proline content was observed in all the genotypes indicating the cellular osmotic balance adjustments in response to stress exposure. Consequently, the robust antioxidant potential and efficient anaerobic metabolism observed in the tolerant genotypes served as key mechanisms enabling their resilience to short-term waterlogging exposure. These findings underscore the promising potential of specific sesame genotypes in enhancing crop resilience against waterlogging stress, offering valuable insights for agricultural practices and breeding programs.

Bicarbonate-Dependent Detoxification by Mitigating Ammonium-Induced Hypoxic Stress in Triticum aestivum Root

Ammonium (NH4+) toxicity is ubiquitous in plants. To investigate the underlying mechanisms of this toxicity and bicarbonate (HCO3-)-dependent alleviation, wheat plants were hydroponically cultivated in half-strength Hoagland nutrient solution containing 7.5 mM NO3- (CK), 7.5 mM NH4+ (SA), or 7.5 mM NH4+ + 3 mM HCO3- (AC). Transcriptomic analysis revealed that compared to CK, SA treatment at 48 h significantly upregulated the expression of genes encoding fermentation enzymes (pyruvate decarboxylase (PDC), alcohol dehydrogenase (ADH), and lactate dehydrogenase (LDH)) and oxygen consumption enzymes (respiratory burst oxidase homologs, dioxygenases, and alternative oxidases), downregulated the expression of genes encoding oxygen transporters (PIP-type aquaporins, non-symbiotic hemoglobins), and those involved in energy metabolism, including tricarboxylic acid (TCA) cycle enzymes and ATP synthases, but upregulated the glycolytic enzymes in the roots and downregulated the expression of genes involved in the cell cycle and elongation. The physiological assay showed that SA treatment significantly increased PDC, ADH, and LDH activity by 36.69%, 43.66%, and 61.60%, respectively; root ethanol concentration by 62.95%; and lactate efflux by 23.20%, and significantly decreased the concentrations of pyruvate and most TCA cycle intermediates, the complex V activity, ATP content, and ATP/ADP ratio. As a consequence, SA significantly inhibited root growth. AC treatment reversed the changes caused by SA and alleviated the inhibition of root growth. In conclusion, NH4+ treatment alone may cause hypoxic stress in the roots, inhibit energy generation, suppress cell division and elongation, and ultimately inhibit root growth, and adding HCO3- remarkably alleviates the NH4+-induced inhibitory effects on root growth largely by attenuating the hypoxic stress.

The Invasive Mechanisms of the Noxious Alien Plant Species Bidens pilosa

Bidens pilosa L. is native to tropical America and has widely naturized from tropical to warm temperate regions in Europe, Africa, Asia, Australia, and North and South America. The species has infested a wide range of habitats such as grasslands, forests, wetlands, streamlines, coastal areas, pasture, plantations, agricultural fields, roadsides, and railway sides and has become a noxious invasive weed species. B. pilosa forms thick monospecific stands, quickly expands, and threatens the indigenous plant species and crop production. It is also involved in pathogen transmission as a vector. The species was reported to have (1) a high growth ability, producing several generations in a year; (2) a high achene production rate; (3) different biotypes of cypselae, differently germinating given the time and condition; (4) a high adaptative ability to various environmental conditions; (5) an ability to alter the microbial community, including mutualism with arbuscular mycorrhizal fungi; and (6) defense functions against natural enemies and allelopathy. The species produces several potential allelochemicals such as palmitic acid, p-coumaric acid, caffeic acid, ferulic acid, p-hydroxybenzoic acid, vanillic acid, salycilic acid, quercetin, α-pinene, and limonene and compounds involved in the defense functions such as 1-phenylhepta-1,3,5-trine, 5-phenyl-2-(1-propynyl)-thiophene, 5-actoxy-2-phenylethinyl-thiophene, and icthyothereol acetate. These characteristics of B. pilosa may contribute to the naturalization and invasiveness of the species in the introduced ranges. This is the first review article focusing on the invasive mechanisms of the species.

Proteomic exploration reveals a metabolic rerouting due to low oxygen during controlled germination of malting barley (Hordeum vulgare L.)

Barley (Hordeum vulgare L.) is used in malt production for brewing applications. Barley malting involves a process of controlled germination that modifies the grain by activating enzymes to solubilize starch and proteins for brewing. Initially, the grain is submerged in water to raise grain moisture, requiring large volumes of water. Achieving grain modification at reduced moisture levels can contribute to the sustainability of malting practices. This study combined proteomics, bioinformatics, and biochemical phenotypic analysis of two malting barley genotypes with observed differences in water uptake and modification efficiency. We sought to reveal the molecular mechanisms at play during controlled germination and explore the roles of protein groups at 24 h intervals across the first 72 h. Overall, 3,485 protein groups were identified with 793 significant differentially abundant (DAP) within and between genotypes, involved in various biological processes, including protein synthesis, carbohydrate metabolism, and hydrolysis. Functional integration into metabolic pathways, such as glycolysis, pyruvate, starch and sucrose metabolism, revealed a metabolic rerouting due to low oxygen enforced by submergence during controlled germination. This SWATH-MS study provides a comprehensive proteome reference, delivering new insights into the molecular mechanisms underlying the impacts of low oxygen during controlled germination. It is concluded that continued efficient modification of malting barley subjected to submergence is largely due to the capacity to reroute energy to maintain vital processes, particularly protein synthesis.

Molecular Interplay between Non-Host Resistance, Pathogens and Basal Immunity as a Background for Fatal Yellowing in Oil Palm (Elaeis guineensis Jacq.) Plants

An oil palm (Elaeis guineensis Jacq.) bud rod disorder of unknown etiology, named Fatal Yellowing (FY) disease, is regarded as one of the top constraints with respect to the growth of the palm oil industry in Brazil. FY etiology has been a challenge embraced by several research groups in plant pathology throughout the last 50 years in Brazil, with no success in completing Koch's postulates. Most recently, the hypothesis of having an abiotic stressor as the initial cause of FY has gained ground, and oxygen deficiency (hypoxia) damaging the root system has become a candidate for stress. Here, a comprehensive, large-scale, single- and multi-omics integration analysis of the metabolome and transcriptome profiles on the leaves of oil palm plants contrasting in terms of FY symptomatology-asymptomatic and symptomatic-and collected in two distinct seasons-dry and rainy-is reported. The changes observed in the physicochemical attributes of the soil and the chemical attributes and metabolome profiles of the leaves did not allow the discrimination of plants which were asymptomatic or symptomatic for this disease, not even in the rainy season, when the soil became waterlogged. However, the multi-omics integration analysis of enzymes and metabolites differentially expressed in asymptomatic and/or symptomatic plants in the rainy season compared to the dry season allowed the identification of the metabolic pathways most affected by the changes in the environment, opening an opportunity for additional characterization of the role of hypoxia in FY symptom intensification. Finally, the initial analysis of a set of 56 proteins/genes differentially expressed in symptomatic plants compared to the asymptomatic ones, independent of the season, has presented pieces of evidence suggesting that breaks in the non-host resistance to non-adapted pathogens and the basal immunity to adapted pathogens, caused by the anaerobic conditions experienced by the plants, might be linked to the onset of this disease. This set of genes might offer the opportunity to develop biomarkers for selecting oil palm plants resistant to this disease and to help pave the way to employing strategies to keep the safety barriers raised and strong.

Physiological responses and Ethylene-Response AP2/ERF Factor expression in Indica rice seedlings subjected to submergence and osmotic stress

BACKGROUND

The increased frequency of heavy rains in recent years has led to submergence stress in rice paddies, severely affecting rice production. Submergence causes not only hypoxic stress from excess water in the surrounding environment but also osmotic stress in plant cells. We assessed physiological responses and Ethylene-Response AP2/ERF Factor regulation under submergence conditions alone and with ionic or nonionic osmotic stress in submergence-sensitive IR64 and submergence-tolerant IR64-Sub1 Indica rice cultivars.

RESULTS

Our results indicate that both IR64 and IR64-Sub1 exhibited shorter plant heights and root lengths under submergence with nonionic osmotic stress than normal condition and submergence alone. IR64-Sub1 seedlings exhibited a significantly lower plant height under submergence conditions alone and with ionic or nonionic osmotic stress than IR64 cultivars. IR64-Sub1 seedlings also presented lower malondialdehyde (MDA) concentration and higher survival rates than did IR64 seedlings after submergence with ionic or nonionic osmotic stress treatment. Sub1A-1 affects reactive oxygen species (ROS) accumulation and antioxidant enzyme activity in rice. The results also show that hypoxia-inducible ethylene response factors (ERF)-VII group and alcohol dehydrogenase 1 (ADH1) and lactate dehydrogenase 1 (LDH1) genes exhibited different expression levels under nonionic or ionic osmotic stress during submergence on rice.

CONCLUSIONS

Together, these results demonstrate that complex regulatory mechanisms are involved in responses to the aforementioned forms of stress and offer new insights into the effects of submergence and osmotic stress on rice.

Dim artificial light at night alters gene expression rhythms and growth in a key seagrass species (Posidonia oceanica)

Artificial light at night (ALAN) is a globally spreading anthropogenic stressor, affecting more than 20% of coastal habitats. The alteration of the natural light/darkness cycle is expected to impact the physiology of organisms by acting on the complex circuits termed as circadian rhythms. Our understanding of the impact of ALAN on marine organisms is lagging behind that of terrestrial ones, and effects on marine primary producers are almost unexplored. Here, we investigated the molecular and physiological response of the Mediterranean seagrass, Posidonia oceanica (L.) Delile, as model to evaluate the effect of ALAN on seagrass populations established in shallow waters, by taking advantage of a decreasing gradient of dim nocturnal light intensity (from < 0.01 to 4 lx) along the NW Mediterranean coastline. We first monitored the fluctuations of putative circadian-clock genes over a period of 24 h along the ALAN gradient. We then investigated whether key physiological processes, known to be synchronized with day length by the circadian rhythm, were also affected by ALAN. ALAN influenced the light signalling at dusk/night in P. oceanica, including that of shorter blue wavelengths, through the ELF3-LUX1-ZTL regulatory network, and suggested that the daily perturbation of internal clock orthologs in seagrass might have caused the recruitment of PoSEND33 and PoPSBS genes to mitigate the repercussions of a nocturnal stress on photosynthesis during the day. A long-lasting impairment of gene fluctuations in sites characterised by ALAN could explain the reduced growth of the seagrass leaves when these were transferred into controlled conditions and without lighting during the night. Our results highlight the potential contribution of ALAN to the global loss of seagrass meadows, posing questions about key interactions with a variety of other human-related stressors in urban areas, in order to develop more efficient strategies to globally preserve these coastal foundation species.

Relationship between pepper (Capsicum annuum L.) root morphology, inter-root soil bacterial community structure and diversity under water-air intercropping conditions

The combination of water and gas at an aeration rate of 15 mg/L and irrigation amount of 0.8 Ep significantly promoted the root morphology, inter-root soil bacterial community structure and diversity of pepper, enhanced the structure of molecular symbiotic network, and stimulated the potential ecosystem function. Poor aeration adversely affects the root morphology of pepper (Capsicum annuum L.) and bacterial community. It is critical to understand the effects of water-air interactions on root morphology and bacterial community structure and diversity. A randomized block experiment was conducted under the two aeration rates of dissolved oxygen mass concentrations, including A: 15 mg/L, O: 40 mg/L, and C: non-aeration as control treatment, and two irrigation rates of W₁ and W₂ (0.8 Ep and 1.0 Ep). The results showed that aerated irrigation had a significant effect on the root morphology of pepper. Compared with treatment CW₁, treatment AW₁ increased root dry weight, root length, root volume, and root surface area by 13.63%, 11.09%, 59.47%, and 61.67%, respectively (P < 0.05). Aerated irrigation significantly increased the relative abundance of Actinobacteria, Gemmatimonadetes, Alphaproteobacteria, Gemmatimonas, Sphingomonas, and KD4-96 aerobic beneficial bacteria. It decreased the relative abundance of Proteobacteria, Monomycetes, Bacteroidetes, Corynebacterium, Gammaproteobacteria, Anaerolineae, Subgroup_6, MND1, Haliangium, and Thiobacillus. The Pielou_e, Shannon and Simpson indexes of treatment AW₁ were significantly higher than treatments OW₁ and CW₁. The results of the β-diversity of bacterial communities showed that the structure of soil bacterial communities differed significantly among treatments. Actinobacteria was a key phylum affecting root morphology, and AW₁ treatment was highly correlated with Actinobacteria. Molecular ecological network analysis showed a relatively high number of bacterial network nodes and more complex relationships among species under the aeration of level 15 mg/L and 0.8 Ep, as well as the emergence of new phylum-level beneficial species: Dependentiae, BRC1, Cyanobacteria, Deinococcus-Thermus, Firmicutes, and Planctomycetes. Therefore, the aeration of 15 mg/L and 0.8 times crop-evaporation coefficient can increase root morphology, inter-root soil bacterial community diversity and bacterial network structure, and enhance potential ecosystem functions in the rhizosphere.

Genomic convergence underlying high-altitude adaptation in alpine plants

Evolutionary convergence is one of the most striking examples of adaptation driven by natural selection. However, genomic evidence for convergent adaptation to extreme environments remains scarce. Here, we assembled reference genomes of two alpine plants, Saussurea obvallata (Asteraceae) and Rheum alexandrae (Polygonaceae), with 37,938 and 61,463 annotated protein-coding genes. By integrating an additional five alpine genomes, we elucidated genomic convergence underlying high-altitude adaptation in alpine plants. Our results detected convergent contractions of disease-resistance genes in alpine genomes, which might be an energy-saving strategy for surviving in hostile environments with only a few pathogens present. We identified signatures of positive selection on a set of genes involved in reproduction and respiration (e.g., MMD1, NBS1, and HPR), and revealed signatures of molecular convergence on genes involved in self-incompatibility, cell wall modification, DNA repair and stress resistance, which may underlie adaptation to extreme cold, high ultraviolet radiation and hypoxia environments. Incorporating transcriptomic data, we further demonstrated that genes associated with cuticular wax and flavonoid biosynthetic pathways exhibit higher expression levels in leafy bracts, shedding light on the genetic mechanisms of the adaptive "greenhouse" morphology. Our integrative data provide novel insights into convergent evolution at a high-taxonomic level, aiding in a deep understanding of genetic adaptation to complex environments.

Subsurface aeration mitigates organic material mulching-induced anaerobic stress via regulating hormone signaling in Phyllostachys praecox roots

Organic material mulching has been used extensively to allow Phyllostachys praecox to promote growth and development of shoots. However, the bamboo forest always showed a significant degradation, probably due to anaerobic damage caused by the mulching after several years. Therefore, we have innovatively proposed an improvement measure to aerate the underground pipes for the first time. We investigated the role of subsurface pipe aeration in regulating root hypoxia to reduce the stress and to identify the degradation mechanism. Results showed that aeration increased oxygen concentration, shoot yield and root growth compared with mulching, and the aeration enhanced the concentration of indole-3-acetic acid (IAA) and the expression of Aux/IAAs (Aux1, Aux2, Aux3, and Aux4). Aeration reduced gibberellin (GA), ethylene (ETH), and abscisic acid (ABA) contents as well as anaerobic enzyme activities (alanine transaminase, AlaAT; alcohol dehydrogenase, ADH; pyruvate decarboxylase, PDC; and lactate dehydrogenase, LDH), which alleviated root damage in anoxic conditions. Furthermore, correlation showed that the activities of ADH, LDH, PDC, and AlaAT showed significant linear correlations with soil oxygen levels. RDA analyses showed that ABA, IAA, and ETH were found as the key driving hormones of Aux/IAAs in the root of the forest mulched with organic material. Here we show that subsurface aeration increases soil oxygen concentration, shoot yield, root growth and regulates phytohormone concentrations and Aux/IAAs expression, which reduces anaerobic enzyme activities. Consequently, subsurface pipe aeration is an effective measure to mitigate the degradation of bamboo forests caused by soil hypoxia that results from organic material mulching.

Differences in physiological and biochemical responses to short-term flooding among the three avocado (Persea americana Mill.) races

Avocado (P. americana Mill.) trees are classified into three botanical races, Mexican (M), Guatemalan (G), and West Indian (WI), each distinguished by their geographical centers of origin. While avocados are considered highly sensitive to flooding stress, comparative responses of the different races to short-term flooding are not known. This study assessed the differences in physiological and biochemical responses among clonal, non-grafted avocado cultivars of each race to short-term (2-3 days) flooding. In two separate experiments, each with different cultivars of each race, container-grown trees were divided into two treatments: 1) flooded and 2) non-flooded. Net CO₂ assimilation (A), stomatal conductance (g_s), and transpiration (Tr) were measured periodically over time beginning the day before treatments were imposed, through the flooding period, and during a recovery period (after unflooding). At the end of the experiments, concentrations of sugars in leaves, stems, and roots, and reactive oxygen species (ROS), antioxidants, and osmolytes in leaves and roots were determined. Guatemalan trees were more sensitive to short-term flooding than M or WI trees based on decreased A, g_s, and Tr and survival of flooded trees. Guatemalan trees generally had less partitioning of sugars, particularly mannoheptulose, to the roots of flooded compared to non-flooded trees. Principal component analysis showed distinct clustering of flooded trees by race based on ROS and antioxidant profiles. Thus, differential partitioning of sugars and ROS and antioxidant responses to flooding among races may explain the greater flooding sensitivity of G trees compared to M and WI trees.

Plant translational reprogramming for stress resilience

Organisms regulate gene expression to produce essential proteins for numerous biological processes, from growth and development to stress responses. Transcription and translation are the major processes of gene expression. Plants evolved various transcription factors and transcriptome reprogramming mechanisms to dramatically modulate transcription in response to environmental cues. However, even the genome-wide modulation of a gene's transcripts will not have a meaningful effect if the transcripts are not properly biosynthesized into proteins. Therefore, protein translation must also be carefully controlled. Biotic and abiotic stresses threaten global crop production, and these stresses are seriously deteriorating due to climate change. Several studies have demonstrated improved plant resistance to various stresses through modulation of protein translation regulation, which requires a deep understanding of translational control in response to environmental stresses. Here, we highlight the translation mechanisms modulated by biotic, hypoxia, heat, and drought stresses, which are becoming more serious due to climate change. This review provides a strategy to improve stress tolerance in crops by modulating translational regulation.

ADH Gene Cloning and Identification of Flooding-Responsive Genes in Taxodium distichum (L.) Rich

As a flooding-tolerant tree species, Taxodium distichum has been utilized in afforestation projects and proven to have important value in flooding areas. Alcohol dehydrogenase (ADH), which participates in ethanol fermentation, is essential for tolerance to the anaerobic conditions caused by flooding. In a comprehensive analysis of the ADH gene family in T. distichum, TdADHs were cloned on the basis of whole-genome sequencing, and then bioinformatic analysis, subcellular localization, and gene expression level analysis under flooding were conducted. The results show that the putative protein sequences of 15 cloned genes contained seven TdADHs and eight TdADH-like genes (one Class III ADH included) that were divided into five clades. All the sequences had an ADH_N domain, and except for TdADH-likeE2, all the other genes had an ADH_zinc_N domain. Moreover, the TdADHs in clades A, B, C, and D had a similar motif composition. Additionally, the number of TdADH amino acids ranged from 277 to 403, with an average of 370.13. Subcellular localization showed that, except for TdADH-likeD3, which was not expressed in the nucleus, the other genes were predominantly expressed in both the nucleus and cytosol. TdADH-likeC2 was significantly upregulated in all three organs (roots, stems, and leaves), and TdADHA3 was also highly upregulated under 24 h flooding treatment; the two genes might play key roles in ethanol fermentation and flooding tolerance. These findings offer a comprehensive understanding of TdADHs and could provide a foundation for the molecular breeding of T. distichum and current research on the molecular mechanisms driving flooding tolerance.

Complexity of Abiotic Stress Stimuli: Mimicking Hypoxic Conditions Experimentally on the Basis of Naturally Occurring Environments

Plants require oxygen to respire and produce energy. Plant cells are exposed to low oxygen levels (hypoxia) in different contexts and have evolved conserved molecular responses to hypoxia. Both environmental and developmental factors can influence intracellular oxygen concentrations. In nature, plants can experience hypoxic conditions when the soil becomes saturated with water following heavy precipitation (i.e., waterlogging). Hypoxia can also arise in specific tissues that have poor gas exchange with atmospheric oxygen. In this case, hypoxic niches that are physiologically and developmentally relevant may form. To dissect the molecular mechanisms underlying the regulation of hypoxia response in plants, a wide range of hypoxia-inducing methods have been used in the laboratory setting. Yet, the different characteristics, pros and cons of each of these hypoxia treatments are seldom compared between methods, and with natural forms of hypoxia. In this chapter, we present both environmental and developmental forms of hypoxia that plants encounter in the wild, as well as the different experimental hypoxia treatments used to mimic them in the laboratory setting, with the aim of informing on what experimental approaches might be most appropriate to the questions addressed, including stress signaling and regulation.

Changing winter climate and snow conditions induce various transcriptional stress responses in Scots pine seedlings

In northern boreal forests the warming winter climate leads to more frequent snowmelt, rain-on-snow events and freeze-thaw cycles. This may be harmful or even lethal for tree seedlings that spend even a half of the year under snow. We conducted a snow cover manipulation experiment in a natural forest to find out how changing snow conditions affect young Scots pine (Pinus sylvestris L.) seedlings. The ice encasement (IE), absence of snow (NoSNOW) and snow compaction (COMP) treatments affected ground level temperature, ground frost and subnivean gas concentrations compared to the ambient snow cover (AMB) and led to the increased physical damage and mortality of seedlings. The expression responses of 28 genes related to circadian clock, aerobic and anaerobic energy metabolism, carbohydrate metabolism and stress protection revealed that seedlings were exposed to different stresses in a complex way depending on the thickness and quality of the snow cover. The IE treatment caused hypoxic stress and probably affected roots which resulted in reduced water uptake in the beginning of the growing season. Without protective snowpack in NoSNOW seedlings suffered from cold and drought stresses. The combination of hypoxic and cold stresses in COMP evoked unique transcriptional responses including oxidative stress. Snow cover manipulation induced changes in the expression of several circadian clock related genes suggested that photoreceptors and the circadian clock system play an essential role in the adaptation of Scots pine seedlings to stresses under different snow conditions. Our findings show that warming winter climate alters snow conditions and consequently causes Scots pine seedlings various abiotic stresses, whose effects extend from overwintering to the following growing season.

Exogenous treatment with melatonin enhances waterlogging tolerance of kiwifruit plants

Waterlogging stress has an enormous negative impact on the kiwifruit yield and quality. The protective role of exogenous melatonin on water stress has been widely studied, especially in drought stress. However, the research on melatonin-induced waterlogging tolerance is scarce. Here, we found that treatment with exogenous melatonin could effectively alleviate the damage on kiwifruit plants in response to waterlogging treatment. This was accompanied by higher antioxidant activity and lower ROS accumulation in kiwifruit roots during stress period. The detection of changes in amino acid levels of kiwifruit roots during waterlogging stress showed a possible interaction between melatonin and amino acid metabolism, which promoted the tolerance of kiwifruit plants to waterlogging. The higher levels of GABA and Pro in the roots of melatonin-treated kiwifruit plants partly contributed to their improved waterlogging tolerance. In addition, some plant hormones were also involved in the melatonin-mediated waterlogging tolerance, such as the enhancement of ACC accumulation. This study discussed the melatonin-mediated water stress tolerance of plants from the perspective of amino acid metabolism for the first time.

Transcriptomic Analysis of Distal Parts of Roots Reveals Potentially Important Mechanisms Contributing to Limited Flooding Tolerance of Canola (Brassica napus) Plants

Since most of the root metabolic activities as well as root elongation and the uptake of water and mineral nutrients take place in the distal parts of roots, we aimed to gain insight into the physiological and transcriptional changes induced by root hypoxia in the distal parts of roots in canola (Brassica napus) plants, which are relatively sensitive to flooding conditions. Plants were subject to three days of root hypoxia via lowering oxygen content in hydroponic medium, and various physiological and anatomical features were examined to characterize plant responses. Untargeted transcriptomic profiling approaches were also applied to investigate changes in gene expression that took place in the distal root tissues in response to hypoxia. Plants responded to three days of root hypoxia by reducing growth and gas exchange rates. These changes were accompanied by decreases in leaf water potential (Ψ_leaf) and root hydraulic conductivity (L_pr). Increased deposition of lignin and suberin was also observed in the root tissues of hypoxic plants. The transcriptomic data demonstrated that the effect of hypoxia on plant water relations involved downregulation of most BnPIPs in the root tissues with the exception of BnPIP1;3 and BnPIP2;7, which were upregulated. Since some members of the PIP1 subfamily of aquaporins are known to transport oxygen, the increase in BnPIP1;3 may represent an important hypoxia tolerance strategy in plants. The results also demonstrated substantial rearrangements of different signaling pathways and transcription factors (TFs), which resulted in alterations of genes involved in the regulation of L_pr, TCA (tricarboxylic acid) cycle-related enzymes, antioxidant enzymes, and cell wall modifications. An integration of these data enabled us to draft a comprehensive model of the molecular pathways involved in the responses of distal parts of roots in B. napus. The model highlights systematic transcriptomic reprogramming aimed at explaining the relative sensitivity of Brassica napus to root hypoxia.

Comparative genomic analysis of the aldehyde dehydrogenase gene superfamily in Arabidopsis thaliana - searching for the functional key to hypoxia tolerance

Flooding entails different stressful conditions leading to low oxygen availability for respiration and as a result plants experience hypoxia. Stress imposed by hypoxia affects cellular metabolism, including the formation of toxic metabolites that dramatically reduce crop productivity. Aldehyde dehydrogenases (ALDHs) are a group of enzymes participating in various aspects of plant growth, development and stress responses. Although we have knowledge concerning the multiple functionalities of ALDHs in tolerance to various stresses, the engagement of ALDH in plant metabolism adjustment to hypoxia is poorly recognized. Therefore, we explored the ALDH gene superfamily in the model plant Arabidopsis thaliana. Genome-wide analyses revealed that 16 AtALDH genes are organized into ten families and distributed irregularly across Arabidopsis 5 chromosomes. According to evolutionary relationship studies from different plant species, the ALDH gene superfamily is highly conserved. AtALDH2 and ALDH3 are the most numerous families in plants, while ALDH18 was found to be the most distantly related. The analysis of cis-acting elements in promoters of AtALDHs indicated that AtALDHs participate in responses to light, phytohormones and abiotic stresses. Expression profile analysis derived from qRT-PCR showed the AtALDH2B7, AtALDH3H1 and AtALDH5F1 genes as the most responsive to hypoxia stress. In addition, the expression of AtALDH18B1, AtALDH18B2, AtALDH2B4, and AtALDH10A8 was highly altered during the post-hypoxia-reoxygenation phase. Taken together, we provide comprehensive functional information on the ALDH gene superfamily in Arabidopsis during hypoxia stress and highlight ALDHs as a functional element of hypoxic systemic responses. These findings might help develop a framework for application in the genetic improvement of crop plants.

Waterlogging priming alleviates the oxidative damage, carbohydrate consumption, and yield loss in soybean (Glycine max) plants exposed to waterlogging

In this study, we tested whether waterlogging priming at the vegetative stage would mitigate a subsequent waterlogging event at the reproductive stage in soybean [Glycine max (L.) Merr.]. Plants (V3 stage) were subjected to priming for 7days and then exposed to waterlogging stress for 5days (R2 stage) with non-primed plants. Roots and leaves were sampled on the fifth day of waterlogging and the second and fifth days of reoxygenation. Overall, priming decreased the H2 O2 concentration and lipid peroxidation in roots and leaves during waterlogging and reoxygenation. Priming also decreased the activity of antioxidative enzymes in roots and leaves and increased the foliar concentration of phenols and photosynthetic pigments. Additionally, priming decreased fermentation and alanine aminotransferase activity during waterlogging and reoxygenation. Finally, priming increased the concentration of amino acids, sucrose, and total soluble sugars in roots and leaves during waterlogging and reoxygenation. Thus, primed plants were higher and more productive than non-primed plants. Our study shows that priming alleviates oxidative stress, fermentation, and carbohydrate consumption in parallel to increase the yield of soybean plants exposed to waterlogging and reoxygenation.

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.

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

Waterlogging induces growth and developmental changes in sensitive crops such as cucumber (Cucumis sativus L.) during early plant development. However, information on the physiological mechanisms underpinning the response of cucumber plants to waterlogging conditions is limited. Here, we investigated the effects of 10-day waterlogging stress on the morphology, photosynthesis, and chlorophyll fluorescence parameters in two cultivars of cucumber seedlings. Waterlogging stress hampered cultivars' growth, biomass accumulation, and photosynthetic capacity. Both cultivars also developed adventitious roots (ARs) after 10 days of waterlogging (DOW). We observed differential responses in the light- and carbon-dependent reactions of photosynthesis, with an increase in light-dependent reactions. At the same time, carbon assimilation was considerably inhibited by waterlogging. Specifically, the CO₂ assimilation rate (A) in leaves was significantly reduced and was caused by a corresponding decrease in stomatal conductance (g_s). The downregulation of the maximum rate of Rubisco efficiency (V_cmax) and the maximum rate of photosynthetic electron transport (J_max) were non-stomatal limiting factors contributing to A reduction. Exposure of cucumber to 10 DOW affected the PSII photochemistry by downregulating the PSII quantum yield (Φ_PSII). The redox state of the primary quinone acceptor in the lake model (1-qL), a measure of the regulatory balance of the light reactions, became more oxidized after 10 DOW, indicating enhanced electron sink capacity despite a reduced A. Overall, the results suggest that waterlogging induces alterations in the photochemical apparatus efficiency of cucumber. Thus, developing cultivars that resist inhibition of PSII photochemistry while maintaining carbon metabolism is a potential approach for increasing crops' tolerance to waterlogged environments.

Stone Wool Substrate Cover Incision Impacts on the Root-Zone Water Content, Temperature, and Yield of Tomato Cultures

Standardized cultivation systems are crucial for establishing reproducible agronomic techniques. Especially stone wool-based cultivation is governed by standardized specifications and provides a controllable root-zone environment. However, the effects of stone wool cover incision on root-zone variability have rarely been studied. Therefore, in this study, we focused on the effect of the stone wool cover incision method on environmental variations and their subsequent effects on tomato plant productivity. Stone wool slab plastic covers represent a core component of this substrate system that can potentially affect the performance of water control techniques. We designed a cover incision method to create four different levels of drainage performances that were tested by cultivating tomato plants (Solanum lycopersicum "Dafnis"). The water content, root-zone temperature, and dissolved oxygen were measured and analyzed relative to the tomato yield. We found that the incision level with the lowest drainage performance showed a lower air-root zone temperature correlation slope than those of slabs with favorable drainage conditions. Furthermore, these slabs had low dissolved oxygen levels (3.2 mg/L); nevertheless, the tomatoes grown in the slabs with incision level showing the lowest drainage performance had greater fruit yield (6,748 g/plant) than those in the slabs with favorable drainage conditions (6,160 g/plant). Furthermore, the normalized yield separation timing between treatments coincided with the hotter air temperature (27°C average) periods. We noted that manipulating the cover incision process consequently entailed variations in the correlation slope between the air temperature and root-zone temperature in the substrate. Our results reveal another trade-off relationship in the conventional perspective on the drainage performance effects and provide insights into further optimization of crop production and water use in the stone wool-based system.

The Intersection of Non-Coding RNAs Contributes to Forest Trees' Response to Abiotic Stress

Non-coding RNAs (ncRNAs) play essential roles in plants by modulating the expression of genes at the transcriptional or post-transcriptional level. In recent years, ncRNAs have been recognized as crucial regulators for growth and development in forest trees, and ncRNAs that respond to various abiotic stresses are now under intense study. In this review, we summarized recent advances in the understanding of abiotic stress-responsive microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) in forest trees. Furthermore, we analyzed the intersection of miRNAs, and epigenetic modified ncRNAs of forest trees in response to abiotic stress. In particular, the abiotic stress-related lncRNA/circRNA-miRNA-mRNA regulatory network of forest trees was explored.

The Role of Phytohormones in Plant Response to Flooding

Climatic variations influence the morphological, physiological, biological, and biochemical states of plants. Plant responses to abiotic stress include biochemical adjustments, regulation of proteins, molecular mechanisms, and alteration of post-translational modifications, as well as signal transduction. Among the various abiotic stresses, flooding stress adversely affects the growth of plants, including various economically important crops. Biochemical and biological techniques, including proteomic techniques, provide a thorough understanding of the molecular mechanisms during flooding conditions. In particular, plants can cope with flooding conditions by embracing an orchestrated set of morphological adaptations and physiological adjustments that are regulated by an elaborate hormonal signaling network. With the help of these findings, the main objective is to identify plant responses to flooding and utilize that information for the development of flood-tolerant plants. This review provides an insight into the role of phytohormones in plant response mechanisms to flooding stress, as well as different mitigation strategies that can be successfully administered to improve plant growth during stress exposure. Ultimately, this review will expedite marker-assisted genetic enhancement studies in crops for developing high-yield lines or varieties with flood tolerance.

Crosstalk between H2 S and NO: an emerging signalling pathway during waterlogging stress in legume crops

In legumes, waterlogging is a major detrimental factor leading to huge yield losses. Generally, legumes lack tolerance to submergence, and conventional breeding to develop tolerant varieties are limited due to the lack of tolerant germplasm and potential target genes. Moreover, our understanding of the various signalling cascades, their interactions and key pathways induced during waterlogging is limited. Here, we focus on the role of two important plant signalling molecules, viz. hydrogen sulphide (H₂ S) and nitric oxide (NO), during waterlogging stress in legumes. Plants and soil microbes produce these signalling molecules both endogenously and exogenously under various stresses, including waterlogging. NO and H₂ S are known to regulate key physiological pathways, such as stomatal closure, leaf senescence and regulation of numerous stress signalling pathways, while NO plays a pivotal role in adventitious root formation during waterlogging. The crosstalk between H₂ S and NO is synergistic because of the resemblance of their physiological effects and proteomic functions, which mainly operate through cysteine-dependent post-translational modifications via S-nitrosation and persulfidation. Such knowledge has provided novel platforms for researchers to unravel the complexity associated with H₂ S-NO signalling and interactions with plant stress hormones. This review provides an overall summary on H₂ S and NO, including biosynthesis, biological importance, crosstalk, transporter regulation as well as understanding their role during waterlogging using 'multi-omics' approach. Understanding H₂ S and NO signalling will help in deciphering the metabolic interactions and identifying key regulatory genes that could be used for developing waterlogging tolerance in legumes.

Photoperiod Stress in Arabidopsis thaliana Induces a Transcriptional Response Resembling That of Pathogen Infection

Plants are exposed to regular diurnal rhythms of light and dark. Changes in the photoperiod by the prolongation of the light period cause photoperiod stress in short day-adapted Arabidopsis thaliana. Here, we report on the transcriptional response to photoperiod stress of wild-type A. thaliana and photoperiod stress-sensitive cytokinin signaling and clock mutants and identify a core set of photoperiod stress-responsive genes. Photoperiod stress caused altered expression of numerous reactive oxygen species (ROS)-related genes. Photoperiod stress-sensitive mutants displayed similar, but stronger transcriptomic changes than wild-type plants. The alterations showed a strong overlap with those occurring in response to ozone stress, pathogen attack and flagellin peptide (flg22)-induced PAMP triggered immunity (PTI), which have in common the induction of an apoplastic oxidative burst. Interestingly, photoperiod stress triggers transcriptional changes in jasmonic acid (JA) and salicylic acid (SA) biosynthesis and signaling and results in increased JA, SA and camalexin levels. These responses are typically observed after pathogen infections. Consequently, photoperiod stress increased the resistance of Arabidopsis plants to a subsequent infection by Pseudomonas syringae pv. tomato DC3000. In summary, we show that photoperiod stress causes transcriptional reprogramming resembling plant pathogen defense responses and induces systemic acquired resistance (SAR) in the absence of a pathogen.

Full-Length Transcriptome and RNA-Seq Analyses Reveal the Mechanisms Underlying Waterlogging Tolerance in Kiwifruit (Actinidia valvata)

Actinidia valvata possesses waterlogging tolerance; however, the mechanisms underlying this trait are poorly characterized. Here, we performed a transcriptome analysis by combining single-molecule real-time (SMRT) sequencing and Illumina RNA sequencing and investigated the physiological responses of the roots of KR5 (A. valvata, a tolerant genotype) after 0, 12, 24 and 72 h of waterlogging stress. KR5 roots responded to waterlogging stress mainly via carbohydrate and free amino acids metabolism and reactive oxygen species (ROS) scavenging pathways. Trehalose-6-phosphate synthase (TPS) activity, alcohol dehydrogenase (ADH) activity and the total free amino acid content increased significantly under waterlogging stress. The nicotinamide adenine dinucleotide-dependent glutamate synthase/alanine aminotransferase (NADH-GOGAT/AlaAT) cycle was correlated with alanine accumulation. Levels of genes encoding peroxidase (POD) and catalase (CAT) decreased and enzyme activity increased under waterlogging stress. Members of the LATERAL ORGAN BOUNDARIES (LOB), AP2/ERF-ERF, Trihelix and C3H transcription factor families were identified as potential regulators of the transcriptional response. Several hub genes were identified as key factors in the response to waterlogging stress by a weighted gene co-expression network analysis (WGCNA). Our results provide insights into the factors contributing to waterlogging tolerance in kiwifruit, providing a basis for further studies of interspecific differences in an important plant trait and for molecular breeding.

Time-course analysis and transcriptomic identification of key response strategies to complete submergence in Nelumbo nucifera

Water submergence is an environmental stress with detrimental effects on plant growth and survival. As a wetland plant species, lotus (Nelumbo nucifera) is widely cultivated in flood-prone lowlands throughout Asian countries, but little is known about its endurance and acclimation mechanisms to complete submergence. Here, we combined a time-course submergence experiment and an RNA-sequencing transcriptome analysis on two lotus varieties of "Qiuxing" and "China Antique". Both varieties showed a low submergence tolerance, with a median lethal time of around 10 days. Differentially expressed gene (DEG) analysis and weighted gene co-expression network analysis (WGCNA) identified a number of key genes putatively involved in lotus submergence responses. Lotus plants under complete submergence developed thinned leaves and elongated petioles containing high density of aerenchyma. All four lotus submergence responsive ERF-VII genes and gene sets corresponding to the low oxygen "escape" strategy (LOES) were elevated. In addition, a number of lotus innate immunity genes were rapidly induced by submergence, likely to confer resistance to possible pathogen infections. Our data also reveals the likely involvement of jasmonic acid in modulating lotus submergence responses, but to a lesser extent than the gaseous ethylene hormone. These results suggest that lotus plants primarily take the LOES strategy in coping with submergence-induced complex stresses, and will be valuable for people understanding the molecular basis underlying the plant submergence acclimations.

Uncovering the roles of hemoglobins in soybean facing water stress

Water stress drastically hinders crop yield, including soybean - one of the world's most relevant feeding crops - threatening the food security of an ever-growing global population. Hemoglobins (GLBs) are involved in water stress tolerance; however, the role they effectively play in soybean remains underexplored. In this study, in silico and in vivo analyses were performed to identify soybean GLBs, capture their transcriptional profile under water stress, and overexpress promising members to assess how soybean cope with waterlogging. Seven GLBs were found, two GLB1 (non-symbiotic) and five GLB2 (symbiotic or leghemoglobins). Three out of the seven GLBs were differentially expressed in soybean RNA-seq libraries of water stress and were evaluated by real-time PCR. Consistently, GmGLB1-1 and GmGLB1-2 were moderately and highly expressed under waterlogging, respectively. Composite plants with roots overexpressing GmGLB1-1 or GmGLB1-2 (mostly) showed higher transcript abundance of stress-defensive genes involved in anaerobic, nitrogen, carbon, and antioxidant metabolism when subjected to waterlogging. In addition, soybean bearing p35S:GmGLB1-2 had lower H2O2 root content, a reactive oxygen species (ROS), under water excess compared with the control condition. Altogether these results suggest that GmGLB1-2 is a strong candidate for soybean genetic engineering to generate waterlogging-tolerant soybean cultivars.

Cation transporters in cell fate determination and plant adaptive responses to a low-oxygen environment

Soil flooding creates low-oxygen environments in root zones and thus severely affects plant growth and productivity. Plants adapt to low-oxygen environments by a suite of orchestrated metabolic and anatomical alterations. Of these, formation of aerenchyma and development of adventitious roots are considered very critical to enable plant performance in waterlogged soils. Both traits have been firmly associated with stress-induced increases in ethylene levels in root tissues that operate upstream of signalling pathways. Recently, we used a bioinformatic approach to demonstrate that several Ca2+ and K+ -permeable channels from KCO, AKT, and TPC families could also operate in low oxygen sensing in Arabidopsis. Here we argue that low-oxygen-induced changes to cellular ion homeostasis and operation of membrane transporters may be critical for cell fate determination and formation of the lysigenous aerenchyma in plant roots and shaping the root architecture and adventitious root development in grasses. We summarize the existing evidence for a causal link between tissue-specific changes in oxygen concentration, intracellular Ca2+ and K+ homeostasis, and reactive oxygen species levels, and their role in conferring those two major traits enabling plant adaptation to a low-oxygen environment. We conclude that, for efficient operation, plants may rely on several complementary signalling pathway mechanisms that operate in concert and 'fine-tune' each other. A better understanding of this interaction may create additional and previously unexplored opportunities to crop breeders to improve cereal crop yield losses to soil flooding.

Transcriptomic profiling suggests candidate molecular responses to waterlogging in cassava

Owing to climate change impacts, waterlogging is a serious abiotic stress that affects crops, resulting in stunted growth and loss of productivity. Cassava (Manihot esculenta Grantz) is usually grown in areas that experience high amounts of rainfall; however, little research has been done on the waterlogging tolerance mechanism of this species. Therefore, we investigated the physiological responses of cassava plants to waterlogging stress and analyzed global gene transcription responses in the leaves and roots of waterlogged cassava plants. The results showed that waterlogging stress significantly decreased the leaf chlorophyll content, caused premature senescence, and increased the activities of superoxide dismutase (SOD), catalase (CAT) and peroxidase (POD) in the leaves and roots. In total, 2538 differentially expressed genes (DEGs) were detected in the leaves and 13364 in the roots, with 1523 genes shared between the two tissues. Comparative analysis revealed that the DEGs were related mainly to photosynthesis, amino metabolism, RNA transport and degradation. We also summarized the functions of the pathways that respond to waterlogging and are involved in photosynthesis, glycolysis and galactose metabolism. Additionally, many transcription factors (TFs), such as MYBs, AP2/ERFs, WRKYs and NACs, were identified, suggesting that they potentially function in the waterlogging response in cassava. The expression of 12 randomly selected genes evaluated via both quantitative real-time PCR (qRT-PCR) and RNA sequencing (RNA-seq) was highly correlated (R2 = 0.9077), validating the reliability of the RNA-seq results. The potential waterlogging stress-related transcripts identified in this study are representatives of candidate genes and molecular resources for further understanding the molecular mechanisms underlying the waterlogging response in cassava.

Try or Die: Dynamics of Plant Respiration and How to Survive Low Oxygen Conditions

Fluctuations in oxygen (O₂) availability occur as a result of flooding, which is periodically encountered by terrestrial plants. Plant respiration and mitochondrial energy generation rely on O₂ availability. Therefore, decreased O₂ concentrations severely affect mitochondrial function. Low O₂ concentrations (hypoxia) induce cellular stress due to decreased ATP production, depletion of energy reserves and accumulation of metabolic intermediates. In addition, the transition from low to high O₂ in combination with light changes-as experienced during re-oxygenation-leads to the excess formation of reactive oxygen species (ROS). In this review, we will update our current knowledge about the mechanisms enabling plants to adapt to low-O₂ environments, and how to survive re-oxygenation. New insights into the role of mitochondrial retrograde signaling, chromatin modification, as well as moonlighting proteins and mitochondrial alternative electron transport pathways (and their contribution to low O₂ tolerance and survival of re-oxygenation), are presented.

Reference-Guided De Novo Genome Assembly to Dissect a QTL Region for Submergence Tolerance Derived from Ciherang-Sub1

Global climate change has increased the number of severe flooding events that affect agriculture, including rice production in the U.S. and internationally. Heavy rainfall can cause rice plants to be completely submerged, which can significantly affect grain yield or completely destroy the plants. Recently, a major effect submergence tolerance QTL during the vegetative stage, qSub8.1, which originated from Ciherang-Sub1, was identified in a mapping population derived from a cross between Ciherang-Sub1 and IR10F365. Ciherang-Sub1 was, in turn, derived from a cross between Ciherang and IR64-Sub1. Here, we characterize the qSub8.1 region by analyzing the sequence information of Ciherang-Sub1 and its two parents (Ciherang and IR64-Sub1) and compare the whole genome profile of these varieties with the Nipponbare and Minghui 63 (MH63) reference genomes. The three rice varieties were sequenced with 150 bp pair-end whole-genome shotgun sequencing (Illumina HiSeq4000), followed by performing the Trimmomatic-SOAPdenovo2-MUMmer3 pipeline for genome assembly, resulting in approximate genome sizes of 354.4, 343.7, and 344.7 Mb, with N50 values of 25.1, 25.4, and 26.1 kb, respectively. The results showed that the Ciherang-Sub1 genome is composed of 59–63% Ciherang, 22–24% of IR64-Sub1, and 15–17% of unknown sources. The genome profile revealed a more detailed genomic composition than previous marker-assisted breeding and showed that the qSub8.1 region is mostly from Ciherang, with some introgressed segments from IR64-Sub1 and currently unknown source(s).

Physiological Responses of Two Contrasting Kiwifruit (Actinidia spp.) Rootstocks against Waterlogging Stress

Rootstocks from Actinidia valvata are much more tolerant to waterlogging stress than those from Actinidia deliciosa, which are commonly used in kiwifruit production. To date, the tolerance mechanism of A. valvata rootstocks' adaptation to waterlogging stress has not been well explored. In this study, the responses of KR5 (A. valvata) and 'Hayward' (A. deliciosa) to waterlogging stress were compared. Results showed that KR5 plants performed much better than 'Hayward' during waterlogging by exhibiting higher net photosynthetic rates in leaves, more rapid formation of adventitious roots at the base of stems, and less severe damage to the main root system. In addition to morphological adaptations, metabolic responses of roots including sufficient sucrose reserves, modulated adjustment of fermentative enzymes, avoidance of excess lactic acid and ethanol accumulation, and promoted accumulation of total amino acids all possibly rendered KR5 plants more tolerant to waterlogging stress compared to 'Hayward' plants. Lysine contents of roots under waterlogging stress were increased in 'Hayward' and decreased in KR5 compared with their corresponding controls. Overall, our results revealed the morphological and metabolic adaptations of two kiwifruit rootstocks to waterlogging stress, which may be responsible for their genotypic difference in waterlogging tolerance.

Transient Waterlogging Events Impair Shoot and Root Physiology and Reduce Grain Yield of Durum Wheat Cultivars

Durum wheat (Triticum turgidum L. subsp. durum (Desf.) Husn) is a staple crop of the Mediterranean countries, where more frequent waterlogging events are predicted due to climate change. However, few investigations have been conducted on the physiological and agronomic responses of this crop to waterlogging. The present study provides a comprehensive evaluation of the effects of two waterlogging durations (i.e., 14 and 35 days) on two durum wheat cultivars (i.e., Svevo and Emilio Lepido). An integrated analysis of an array of physiological, biochemical, biometric, and yield parameters was performed at the end of the waterlogging events, during recovery, and at physiological maturity. Results established that effects on durum wheat varied depending on waterlogging duration. This stress imposed at tillering impaired photosynthetic activity of leaves and determined oxidative injury of the roots. The physiological damages could not be fully recovered, subsequently slowing down tiller formation and crop growth, and depressing the final grain yield. Furthermore, differences in waterlogging tolerance between cultivars were discovered. Our results demonstrate that in durum wheat, the energy maintenance, the cytosolic ion homeostasis, and the ROS control and detoxification can be useful physiological and biochemical parameters to consider for the waterlogging tolerance of genotypes, with regard to sustaining biomass production and grain yield.

Understanding a Mechanistic Basis of ABA Involvement in Plant Adaptation to Soil Flooding: The Current Standing

Soil flooding severely impairs agricultural crop production. Plants can cope with flooding conditions by embracing an orchestrated set of morphological adaptations and physiological adjustments that are regulated by the elaborated hormonal signaling network. The most prominent of these hormones is ethylene, which has been firmly established as a critical signal in flooding tolerance. ABA (abscisic acid) is also known as a “stress hormone” that modulates various responses to abiotic stresses; however, its role in flooding tolerance remains much less established. Here, we discuss the progress made in the elucidation of morphological adaptations regulated by ABA and its crosstalk with other phytohormones under flooding conditions in model plants and agriculturally important crops.

Carbohydrate saving or biomass maintenance: which is the main determinant of the plant's long-term submergence tolerance?

It is hypothesized that plant submergence tolerance could be assessed from the decline of plant biomass due to submergence, as biomass integrates all eco-physiological processes leading to fitness. An alternative hypothesis stated that the consumption rate of carbohydrate is essential in differing tolerance to submergence. In the present study, the responses of biomass, biomass allocation, and carbohydrate content to simulated long-term winter submergence were assessed in four tolerant and four sensitive perennials. The four tolerant perennials occur in a newly established riparian ecosystem created by The Three Gorges Dam, China. They had 100% survival after 120 days' simulated submergence, and had full photosynthesis recovery after 30 days' re-aeration, and the photosynthetic rate was positively related to the growth during the recovery period. Tolerant perennials were characterized by higher carbohydrate levels, compared with the four sensitive perennials (0% survival) at the end of submergence. Additionally, by using a method which simulates posterior estimates, and bootstraps the confidence interval for the difference between strata means, it was found that the biomass response to post-hypoxia, rather than that to submergence, could be a reliable indicator to assess submergence tolerance. Interestingly, the differences of changes in carbohydrate content between tolerant and sensitive perennials during submergence were significant, which were distinct from the biomass response, supporting the hypothesis that tolerant perennials could sacrifice non-vital components of biomass to prioritize the saving of carbohydrates for later recovery. Our study provides some insight into the underlying mechanism(s) of perennials' tolerance to submergence in ecosystems such as temperate wetland and reservoir riparian.

Opportunities for Improving Waterlogging Tolerance in Cereal Crops-Physiological Traits and Genetic Mechanisms

Waterlogging occurs when soil is saturated with water, leading to anaerobic conditions in the root zone of plants. Climate change is increasing the frequency of waterlogging events, resulting in considerable crop losses. Plants respond to waterlogging stress by adventitious root growth, aerenchyma formation, energy metabolism, and phytohormone signalling. Genotypes differ in biomass reduction, photosynthesis rate, adventitious roots development, and aerenchyma formation in response to waterlogging. We reviewed the detrimental effects of waterlogging on physiological and genetic mechanisms in four major cereal crops (rice, maize, wheat, and barley). The review covers current knowledge on waterlogging tolerance mechanism, genes, and quantitative trait loci (QTL) associated with waterlogging tolerance-related traits, the conventional and modern breeding methods used in developing waterlogging tolerant germplasm. Lastly, we describe candidate genes controlling waterlogging tolerance identified in model plants Arabidopsis and rice to identify homologous genes in the less waterlogging-tolerant maize, wheat, and barley.

EGY3 mediates chloroplastic ROS homeostasis and promotes retrograde signaling in response to salt stress in Arabidopsis

The chloroplast is the main organelle for stress-induced production of reactive oxygen species (ROS). However, how chloroplastic ROS homeostasis is maintained under salt stress is largely unknown. We show that EGY3, a gene encoding a chloroplast-localized protein, is induced by salt and oxidative stresses. The loss of EGY3 function causes stress hypersensitivity while EGY3 overexpression increases the tolerance to both salt and chloroplastic oxidative stresses. EGY3 interacts with chloroplastic Cu/Zn-SOD2 (CSD2) and promotes CSD2 stability under stress conditions. In egy3-1 mutant plants, the stress-induced CSD2 degradation limits H2O2 production in chloroplasts and impairs H2O2-mediated retrograde signaling, as indicated by the decreased expression of retrograde-signal-responsive genes required for stress tolerance. Both exogenous application of H2O2 (or APX inhibitor) and CSD2 overexpression can rescue the salt-stress hypersensitivity of egy3-1 mutants. Our findings reveal that EGY3 enhances the tolerance to salt stress by promoting the CSD2 stability and H2O2-mediated chloroplastic retrograde signaling.

Antagonism between abscisic acid and gibberellin regulates starch synthesis and corm development in Gladiolus hybridus

Understanding corm development in flower bulbs is of importance for securing the quality of cut flowers and propagation of commercial stocks. Gladiolus is one of the most popular bulb plants worldwide. Its corm development is characterized by starch accumulation. Previous research has shown that phytohormones (especially gibberellin (GA)) are involved in tuber development. However, the relationship between abscisic acid (ABA)/GA and starch during corm development remains unclear. To gain deeper insights into the biological process of corm development, we performed a detailed anatomical characterization of different stages of corm development and analyzed phytohormone levels. Our study showed that corm development is linked to hormones (ABA and GA) and carbohydrates (sucrose and starch). Exogenous hormone treatment and silencing of endogenous hormone biosynthesis genes indicated that ABA positively regulates corm development, while GA acts as an antagonist of ABA function. A sucrose synthase gene (GhSUS2) was shown to be involved in the antagonism between ABA and GA. GhSUS2 was upregulated by ABA and downregulated by GA. The increase in the transcript level of GhSUS2 coincided with the development of corm/cormels. Silencing of GhSUS2 repressed corm development and starch accumulation. In conclusion, we propose that GhSUS2, an essential enzyme in sucrose degradation, is differentially regulated by ABA and GA and controls corm development in Gladiolus.

Overlapping and stress-specific transcriptomic and hormonal responses to flooding and drought in soybean

Flooding and drought are serious constraints that reduce crop productivity worldwide. Previous studies identified genes conferring tolerance to both water extremes in various plants. However, overlapping responses to flooding and drought at the genome-scale remain obscure. Here, we defined overlapping and stress-specific transcriptomic and hormonal responses to submergence, drought and recovery from these stresses in soybean (Glycine max). We performed comparative RNA-sequencing and hormone profiling, identifying genes, hormones and biological processes that are differentially regulated in an overlapping or stress-specific manner. Overlapping responses included positive regulation of trehalose and sucrose metabolism and negative regulation of cellulose, tubulin, photosystem II and I, and chlorophyll biosynthesis, facilitating the economization of energy reserves under both submergence and drought. Additional energy-consuming pathways were restricted in a stress-specific manner. Downregulation of distinct pathways for energy saving under each stress suggests energy-consuming processes that are relatively unnecessary for each stress adaptation are turned down. Our newly developed transcriptomic-response analysis revealed that abscisic acid and ethylene responses were activated in common under both stresses, whereas stimulated auxin response was submergence-specific. The energy-saving strategy is the key overlapping mechanism that underpins adaptation to both submergence and drought in soybean. Abscisic acid and ethylene are candidate hormones that coordinate transcriptomic energy-saving processes under both stresses. Auxin may be a signaling component that distinguishes submergence-specific regulation of the stress response.

Redox imbalance impedes photosynthetic activity in rice by disrupting cellular membrane integrity and induces programmed cell death under submergence

Climate change negatively impacts the global hydrological resources leading to detrimental flood events. Submergence impedes the cellular membrane integrity, consequently affecting the membrane fluidity. Different abiotic stresses influence membrane lipid composition. Therefore, the remodeling of membrane lipids plays a major role in stress adaptation. Submergence-induced membrane lipid peroxidation is well established in plants. However, dynamic changes in lipid composition for regulating submergence tolerance in rice remain so far unexplored. The present study explored the effect of submergence on the lipidomic profile of the Sub1 near-isogenic lines (NILs) of rice, viz. Swarna, and Swarna Sub1 with contrasting submergence tolerance. The study also examined the association of lipidomic alteration with the membrane integrity and submergence tolerance. Submergence caused increased accumulation of reactive oxygen species (ROS), which was significantly higher in Swarna than Swarna Sub1. The lipid profile was also considerably altered under submergence. Following submergence, Swarna exhibited a significant decrease in phospholipid content accompanied by increased lipid peroxidation and electrolyte leakage. Furthermore, the disintegration of the thylakoid membrane resulted in a significant decrease in the chlorophyll content and photosynthesis rate under submergence. Submergence-induced hypoxic condition also promoted starch depletion to fulfill the energy requirement. In contrast, submergence acclimation in Swarna Sub1 was associated with the shift to anaerobic respiration mediated by increased alcohol dehydrogenase (ADH) activity. Effective ROS detoxification in Swarna Sub1 facilitated by increased antioxidant enzyme activities contributed to the submergence tolerance by maintaining membrane integrity and photosynthetic activity. The present study established the direct association of lipid remodeling with membrane integrity, cell viability, and photosynthesis and also devised a crop model to reveal the molecular background of submergence tolerance in plants.