Flood adaptive traits and processes: an overview

Reciprocal modulation of responses to nitrate starvation and hypoxia in roots and leaves of Arabidopsis thaliana

The flooding of agricultural land leads to hypoxia and nitrate leaching. While understanding the plant's response to these conditions is essential for crop improvement, the effect of extended nitrate limitation on subsequent hypoxia has not been studied in an organ-specific manner. We cultivated Arabidopsis thaliana without nitrate for 1 week before inducing hypoxia by bubbling the hydroponic solution with nitrogen gas for 16 h. In the roots, the transcripts of two transcription factor genes (HRA1, HRE2) and three genes involved in fermentation (SUS4, PDC1, ADH1) were ~10- to 100-fold upregulated by simultaneous hypoxia and nitrate starvation compared to the control condition (replete nitrate and oxygen). In contrast, this hypoxic upregulation was ~5 to 10 times stronger when nitrate was available. The phytoglobin genes PGB1 and PGB2, involved in nitric oxide (NO) scavenging, were massively downregulated by nitrate starvation (~1000-fold and 105-fold, respectively), but only under ambient oxygen levels; this was reflected in a 2.5-fold increase in NO concentration. In the leaves, HRA1, SUS4, and RAP2.3 were upregulated ~20-fold by hypoxia under nitrate starvation, whereas this upregulation was virtually absent in the presence of nitrate. Our results highlight that the plant's responses to nitrate starvation and hypoxia can influence each other.

Hypoxia reshapes Arabidopsis root architecture by integrating ERF-VII factor response and abscisic acid homoeostasis

Oxygen limitation (hypoxia), arising as a key stress factor due to flooding, negatively affects plant development. Consequently, maintaining root growth under such stress is crucial for plant survival, yet we know little about the root system's adaptions to low-oxygen conditions and its regulation by phytohormones. In this study, we examine the impact of hypoxia and, herein, the regulatory role of group VII ETHYLENE-RESPONSE FACTOR (ERFVII) transcription factors on root growth in Arabidopsis. We found lateral root (LR) elongation to be actively maintained by hypoxia via ERFVII factors, as erfVII seedlings possess hypersensitivity towards hypoxia regarding their LR growth. Pharmacological inhibition of abscisic acid (ABA) biosynthesis revealed ERFVII-driven counteraction of hypoxia-induced inhibition of LR formation in an ABA-dependent manner. However, postemergence LR growth under hypoxia mediated by ERFVIIs was independent of ABA. In roots, ERFVIIs mediate, among others, the induction of ABA-degrading ABA 8'-hydroxylases CYP707A1 expression. RAP2.12 could activate the pCYC707A1:LUC reporter gene, indicating, combined with single mutant analyses, that this transcription factor regulates ABA levels through corresponding transcript upregulation. Collectively, hypoxia-induced adaptation of the Arabidopsis root system is shaped by developmental reprogramming, whereby ERFVII-dependent promotion of LR emergence, but not elongation, is partly executed through regulation of ABA degradation.

Effects of drought and moisture stress on the growth and ecophysiological traits of Schima superba seedlings

Changes in rainfall patterns are important environmental factors affecting plant growth, especially when larger precipitation events and prolonged drought periods occur in subtropical regions. There are many studies on how drought reduces plant biomass through drought-sensitive functional traits, but how excess water affects plant growth and ecophysiology is still poorly understood. Therefore, a greenhouse experiment was conducted on Schima superba (Theaceae), a dominant tree species in subtropical forests and commonly used in forestry, in a closed chamber under control (25% soil water content (SWC) as in local forests), drought stress (D, 15% SWC) and moisture stress (W, 35% SWC). Plant growth and ecophysiological traits related to morphology, leaf gas exchange, water potential and structural traits were measured. Compared to control, S. suberba under dry conditions significantly decreased its aboveground biomass, photosynthetic rate (A), leaf water potential and nitrogen use efficiency, but increased intrinsic water use efficiency, root to shoot ratio and specific root length. S. superba under wet conditions also significantly decreased its total biomass, aboveground biomass and specific root length, while W had no effect on A and leaf water potential. Our results indicate that S. superba shows a decrease in carbon gain under drought stress, but less response under wet conditions. This emphasizes the need to consider the strength and frequency of rainfall pattern changes in future studies because rainfall may either alleviate or intensify the effects of drought stress depending on the moisture level, thus suitable water conditions is important for better management of this tree species in subtropical China.

Low-oxygen-induced root bending is altered by phytoglobin1 through mediation of ethylene response factors (ERFs) and auxin signaling

MAIN CONCLUSION

phytoglobin1 positively regulates root bending in hypoxic Arabidopsis roots through regulation of ethylene response factors and auxin transport. Hypoxia-induced root bending is known to be mediated by the redundant activity of the group VII ethylene response factors (ERFVII) RAP2.12 and HRE2, causing changes in polar auxin transport (PAT). Here, we show that phytoglobin1 (Pgb1), implicated in hypoxic adaptation through scavenging of nitric oxide (NO), can alter root direction under low oxygen. Hypoxia-induced bending is exaggerated in roots over-expressing Pgb1 and attenuated in those where the gene is suppressed. These effects were attributed to Pgb1 repressing both RAP2.12 and HRE2. Expression, immunological and genetic data place Pgb1 upstream of RAP2.12 and HRE2 in the regulation of root bending in oxygen-limiting environments. The attenuation of slanting in Pgb1-suppressing roots was associated with depletion of auxin activity at the root tip because of depression in PAT, while exaggeration of root bending in Pgb1-over-expressing roots with the retention of auxin activity. Changes in PIN2 distribution patterns, suggestive of redirection of auxin movement during hypoxia, might contribute to the differential root bending responses of the transgenic lines. In the end, Pgb1, by regulating NO levels, controls the expression of 2 ERFVIIs which, in a cascade, modulate PAT and, therefore, root bending.

Adaptation of the Invasive Plant Sphagneticola trilobata to Flooding Stress by Hybridization with Native Relatives

Hybridization is common between invasive and native species and may produce more adaptive hybrids. The hybrid (Sphagneticola × guangdongensis) of Sphagneticola trilobata (an invasive species) and S. calendulacea (a native species) was found in South China. In this study, S. trilobata, S. calendulacea, and Sphagneticola × guangdongensis were used as research materials to explore their adaptability to flooding stress. Under flooding stress, the ethylene content and the expression of key enzyme genes related to ethylene synthesis in Sphagneticola × guangdongensis and S. calendulacea were significantly higher than those in S. trilobata. A large number of adventitious roots and aerenchyma were generated in Sphagneticola × guangdongensis and S. calendulacea. The contents of reactive oxygen species and malondialdehyde in Sphagneticola × guangdongensis and S. calendulacea were lower than those in S. trilobata, and the leaves of S. trilobata were the most severely damaged under flooding stress. The results indicate that hybridization catalyzed the tolerance of Sphagneticola × guangdongensis to flooding stress, and the responses of Sphagneticola × guangdongensis to flooding stress were more similar to that of its native parent. This suggests that hybridization with native relatives is an important way for invasive species to overcome environmental pressure and achieve invasion.

Uncovering the effect of waterlogging stress on plant microbiome and disease development: current knowledge and future perspectives

Waterlogging is a constant threat to crop productivity and ecological biodiversity. Plants face multiple challenges during waterlogging stress like metabolic reprogramming, hypoxia, nutritional depletion, reduction in gaseous exchange, pH modifications, microbiome alterations and disease promotion all of which threaten plants survival. Due to global warming and climatic change, the occurrence, frequency and severity of flooding has dramatically increased posing a severe threat to food security. Thus, developing innovative crop management technologies is critical for ensuring food security under changing climatic conditions. At present, the top priority among scientists is to find nature-based solutions to tackle abiotic or biotic stressors in sustainable agriculture in order to reduce climate change hazards to the environment. In this regard, utilizing plant beneficial microbiome is one of the viable nature based remedial tool for mitigating abiotic stressors like waterlogging. Beneficial microbiota provides plants multifaceted benefits which improves their growth and stress resilience. Plants recruit unique microbial communities to shield themselves against the deleterious effects of biotic and abiotic stress. In comparison to other stressors, there has been limited studies on how waterlogging stress affects plant microbiome structure and their functional traits. Therefore, it is important to understand and explore how waterlogging alters plant microbiome structure and its implications on plant survival. Here, we discussed the effect of waterlogging stress in plants and its microbiome. We also highlighted how waterlogging stress promotes pathogen occurrence and disease development in plants. Finally, we highlight the knowledge gaps and areas for future research directions on unwiring how waterlogging affects plant microbiome and its functional traits. This will pave the way for identifying resilient microbiota that can be engineered to promote their positive interactions with plants during waterlogging stress.

Hormonal control of underwater germination in rice

The ability to germinate, develop, and thrive underwater is key to efficient rice cultivation. In this issue of Developmental Cell, Wang et al. (2024) illuminate a hormone synthesis and inactivation cascade that promotes germination of submerged rice seeds and may allow improved germination in the field.

Individual architecture and photosynthetic performance of the submerged form of Drosera intermedia Hayne

Drosera intermedia grows in acidic bogs in parts of valleys that are flooded in winter, and that often dry out in summer. It is also described as the sundew of the most heavily hydrated habitats in peatlands, and it is often found in water and even underwater. This sundew is the only one that can tolerate long periods of submersion, and more importantly produces a typical submerged form that can live in such conditions for many years. Submerged habitats are occupied by D. intermedia relatively frequently. The aim of the study was to determine the environmental conditions and architecture of individuals in the submerged form of D. intermedia. The features of the morphological and anatomical structure and chlorophyll a fluorescence of this form that were measured were compared with analogous ones in individuals that occurred in emerged and peatland habitats. The submerged form occurred to a depth of 20 cm. Compared to the other forms, its habitat had the highest pH (4.71-4.92; Me = 4.71), the highest temperature and substrate hydration, and above all, the lowest photosynthetically active radiation (PAR; 20.4-59.4%). This form differed from the other forms in almost all of the features of the plant's architecture. It is particularly noteworthy that it had the largest main axis height among all of the forms, which exceeded 18 cm. The number of living leaves in a rosette was notable (18.1 ± 8.1), while the number of dead leaves was very low (6.9 ± 3.8). The most significant differences were in the shape of its submerged leaves, in which the length of the leaf blade was the lowest of all of the forms (0.493 ± 0.15 mm; p < 0.001) and usually the widest. The stem cross-sectional area was noticeably smaller in the submerged form than in the other forms, the xylem was less developed and collaterally closed vascular bundles occurred. Our analysis of the parameters of chlorophyll fluorescence in vivo revealed that the maximum quantum yield of the primary photochemistry of photosystem II is the highest for the submerged form (Me = 0.681), the same as the maximum quantum yield of the electron transport (Me φE0 = 0.183). The efficiency of energy use per one active reaction center of photosystem II (RC) was the lowest in the submerged form (Me = 2.978), same as the fraction of energy trapped by one active RC (Me = 1.976) and the non-photochemical energy dissipation (DI0/RC; Me = 0.916). The ET0/RC parameter, associated with the efficiency of the energy utilization for electron transport by one RC, in the submerged plant reached the highest value (Me = 0.489). The submerged form of D. intermedia clearly differed from the emerged and peatland forms in its plant architecture. The submerged plants had a thinner leaf blade and less developed xylem than the other forms, however, their stems were much longer. The relatively high photosynthetic efficiency of the submerged forms suggests that most of the trapped energy is utilized to drive photosynthesis with a minimum energy loss, which may be a mechanism to compensate for the relatively small size of the leaf blade.

Transcriptome and metabolome analyses reveal molecular insights into waterlogging tolerance in Barley

Waterlogging stress is one of the major abiotic stresses affecting the productivity and quality of many crops worldwide. However, the mechanisms of waterlogging tolerance are still elusive in barley. In this study, we identify key differentially expressed genes (DEGs) and differential metabolites (DM) that mediate distinct waterlogging tolerance strategies in leaf and root of two barley varieties with contrasting waterlogging tolerance under different waterlogging treatments. Transcriptome profiling revealed that the response of roots was more distinct than that of leaves in both varieties, in which the number of downregulated genes in roots was 7.41-fold higher than that in leaves of waterlogging sensitive variety after 72 h of waterlogging stress. We also found the number of waterlogging stress-induced upregulated DEGs in the waterlogging tolerant variety was higher than that of the waterlogging sensitive variety in both leaves and roots in 1 h and 72 h treatment. This suggested the waterlogging tolerant variety may respond more quickly to waterlogging stress. Meanwhile, phenylpropanoid biosynthesis pathway was identified to play critical roles in waterlogging tolerant variety by improving cell wall biogenesis and peroxidase activity through DEGs such as Peroxidase (PERs) and Cinnamoyl-CoA reductases (CCRs) to improve resistance to waterlogging. Based on metabolomic and transcriptomic analysis, we found the waterlogging tolerant variety can better alleviate the energy deficiency via higher sugar content, reduced lactate accumulation, and improved ethanol fermentation activity compared to the waterlogging sensitive variety. In summary, our results provide waterlogging tolerance strategies in barley to guide the development of elite genetic resources towards waterlogging-tolerant crop varieties.

Adventitious rooting in response to long-term cold: a possible mechanism of clonal growth in alpine perennials

Arctic alpine species experience extended periods of cold and unpredictable conditions during flowering. Thus, often, alpine plants use both sexual and asexual means of reproduction to maximize fitness and ensure reproductive success. We used the arctic alpine perennial Arabis alpina to explore the role of prolonged cold exposure on adventitious rooting. We exposed plants to 4°C for different durations and scored the presence of adventitious roots on the main stem and axillary branches. Our physiological studies demonstrated the presence of adventitious roots after 21 weeks at 4°C saturating the effect of cold on this process. Notably, adventitious roots on the main stem developing in specific internodes allowed us to identify the gene regulatory network involved in the formation of adventitious roots in cold using transcriptomics. These data and histological studies indicated that adventitious roots in A. alpina stems initiate during cold exposure and emerge after plants experience growth promoting conditions. While the initiation of adventitious root was not associated with changes of DR5 auxin response and free endogenous auxin level in the stems, the emergence of the adventitious root primordia was. Using the transcriptomic data, we discerned the sequential hormone responses occurring in various stages of adventitious root formation and identified supplementary pathways putatively involved in adventitious root emergence, such as glucosinolate metabolism. Together, our results highlight the role of low temperature during clonal growth in alpine plants and provide insights on the molecular mechanisms involved at distinct stages of adventitious rooting.

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.

Comparative transcriptome analysis provides molecular insights into heterosis of waterlogging tolerance in Chrysanthemum indicum

BACKGROUND

Heterosis breeding is one of the most important breeding methods for chrysanthemum. To date, the genetic mechanisms of heterosis for waterlogging tolerance in chrysanthemum are still unclear. This study aims to analyze the expression profiles and potential heterosis-related genes of two hybrid lines and their parents with extreme differences in waterlogging tolerance under control and waterlogging stress conditions by RNA-seq.

RESULTS

A population of 140 F1 progeny derived from Chrysanthemum indicum (Nanchang) (waterlogging-tolerant) and Chrysanthemum indicum (Nanjing) (waterlogging-sensitive) was used to characterize the extent of genetic variation in terms of seven waterlogging tolerance-related traits across two years. Lines 98 and 95, respectively displaying positive and negative overdominance heterosis for the waterlogging tolerance traits together with their parents under control and waterlogging stress conditions, were used for RNA-seq. In consequence, the maximal number of differentially expressed genes (DEGs) occurred in line 98. Gene ontology (GO) enrichment analysis revealed multiple stress-related biological processes for the common up-regulated genes. Line 98 had a significant increase in non-additive genes under waterlogging stress, with transgressive up-regulation and paternal-expression dominant patterns being the major gene expression profiles. Further, GO analysis identified 55 and 95 transgressive up-regulation genes that overlapped with the up-regulated genes shared by two parents in terms of responses to stress and stimulus, respectively. 6,640 genes in total displaying maternal-expression dominance patterns were observed in line 95. In addition, 16 key candidate genes, including SAP12, DOX1, and ERF017 which might be of significant importance for the formation of waterlogging tolerance heterosis in line 98, were highlighted.

CONCLUSION

The current study provides a comprehensive overview of the root transcriptomes among F1 hybrids and their parents under waterlogging stress. These findings lay the foundation for further studies on molecular mechanisms underlying chrysanthemum heterosis on waterlogging tolerance.

Integrated meta-analysis and transcriptomics pinpoint genomic loci and novel candidate genes associated with submergence tolerance in rice

BACKGROUND

Due to rising costs, water shortages, and labour shortages, farmers across the globe now prefer a direct seeding approach. However, submergence stress remains a major bottleneck limiting the success of this approach in rice cultivation. The merger of accumulated rice genetic resources provides an opportunity to detect key genomic loci and candidate genes that influence the flooding tolerance of rice.

RESULTS

In the present study, a whole-genome meta-analysis was conducted on 120 quantitative trait loci (QTL) obtained from 16 independent QTL studies reported from 2004 to 2023. These QTL were confined to 18 meta-QTL (MQTL), and ten MQTL were successfully validated by independent genome-wide association studies from diverse natural populations. The mean confidence interval (CI) of the identified MQTL was 3.44 times narrower than the mean CI of the initial QTL. Moreover, four core MQTL loci with genetic distance less than 2 cM were obtained. By combining differentially expressed genes (DEG) from two transcriptome datasets with 858 candidate genes identified in the core MQTL regions, we found 38 common differentially expressed candidate genes (DECGs). In silico expression analysis of these DECGs led to the identification of 21 genes with high expression in embryo and coleoptile under submerged conditions. These DECGs encode proteins with known functions involved in submergence tolerance including WRKY, F-box, zinc fingers, glycosyltransferase, protein kinase, cytochrome P450, PP2C, hypoxia-responsive family, and DUF domain. By haplotype analysis, the 21 DECGs demonstrated distinct genetic differentiation and substantial genetic distance mainly between indica and japonica subspecies. Further, the MQTL7.1 was successfully validated using flanked marker S2329 on a set of genotypes with phenotypic variation.

CONCLUSION

This study provides a new perspective on understanding the genetic basis of submergence tolerance in rice. The identified MQTL and novel candidate genes lay the foundation for marker-assisted breeding/engineering of flooding-tolerant cultivars conducive to direct seeding.

Transcriptome analysis of waterlogging-induced adventitious root and control taproot of Mentha arvensis

KEY MESSAGE

The present study reports differentially expressed transcripts in the waterlogging-induced adventitious root (AR) of Mentha arvensis; the identified transcripts will help to understand AR development and improve waterlogging stress response. Waterlogging notably hampers plant growth in areas facing waterlogged soil conditions. In our previous findings, Mentha arvensis was shown to adapt better in waterlogging conditions by initiating the early onset of adventitious root development. In the present study, we compared the transcriptome analysis of adventitious root induced after the waterlogging treatment with the control taproot. The biochemical parameters of total carbohydrate, total protein content, nitric oxide (NO) scavenging activity and antioxidant enzymes, such as catalase activity (CAT) and superoxide dismutase (SOD) activity, were enhanced in the adventitious root compared with control taproot. Analysis of differentially expressed genes (DEGs) in adventitious root compared with the control taproot were grouped into four functional categories, i.e., carbohydrate metabolism, antioxidant activity, hormonal regulation, and transcription factors that could be majorly involved in the development of adventitious roots. Differential expression of the upregulated and uniquely expressing thirty-five transcripts in adventitious roots was validated using qRT-PCR. This study has generated the resource of differentially and uniquely expressing transcripts in the waterlogging-induced adventitious roots. Further functional characterization of these transcripts will be helpful to understand the development of adventitious roots, leading to the resistance towards waterlogging stress in Mentha arvensis.

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.

Callus proliferation-induced hypoxic microenvironment decreases shoot regeneration competence in Arabidopsis

Plants are aerobic organisms that rely on molecular oxygen for respiratory energy production. Hypoxic conditions, with oxygen levels ranging between 1% and 5%, usually limit aerobic respiration and affect plant growth and development. Here, we demonstrate that the hypoxic microenvironment induced by active cell proliferation during the two-step plant regeneration process intrinsically represses the regeneration competence of the callus in Arabidopsis thaliana. We showed that hypoxia-repressed plant regeneration is mediated by the RELATED TO APETALA 2.12 (RAP2.12) protein, a member of the Ethylene Response Factor VII (ERF-VII) family. We found that the hypoxia-activated RAP2.12 protein promotes salicylic acid (SA) biosynthesis and defense responses, thereby inhibiting pluripotency acquisition and de novo shoot regeneration in calli. Molecular and genetic analyses revealed that RAP2.12 could bind directly to the SALICYLIC ACID INDUCTION DEFICIENT 2 (SID2) gene promoter and activate SA biosynthesis, repressing plant regeneration possibly via a PLETHORA (PLT)-dependent pathway. Consistently, the rap2.12 mutant calli exhibits enhanced shoot regeneration, which is impaired by SA treatment. Taken together, these findings uncover that the cell proliferation-dependent hypoxic microenvironment reduces cellular pluripotency and plant regeneration through the RAP2.12-SID2 module.

Molecular mechanisms underlying coordinated responses of plants to shade and environmental stresses

Shade avoidance syndrome (SAS) is triggered by a low ratio of red (R) to far-red (FR) light (R/FR ratio), which is caused by neighbor detection and/or canopy shade. In order to compete for the limited light, plants elongate hypocotyls and petioles by deactivating phytochrome B (phyB), a major R light photoreceptor, thus releasing its inhibition of the growth-promoting transcription factors PHYTOCHROME-INTERACTING FACTORs. Under natural conditions, plants must cope with abiotic stresses such as drought, soil salinity, and extreme temperatures, and biotic stresses such as pathogens and pests. Plants have evolved sophisticated mechanisms to simultaneously deal with multiple environmental stresses. In this review, we will summarize recent major advances in our understanding of how plants coordinately respond to shade and environmental stresses, and will also discuss the important questions for future research. A deep understanding of how plants synergistically respond to shade together with abiotic and biotic stresses will facilitate the design and breeding of new crop varieties with enhanced tolerance to high-density planting and environmental stresses.

'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.

A group VIIIa ethylene-responsive factor, CmERF4, negatively regulates waterlogging tolerance in chrysanthemum

Ethylene-responsive factors (ERF) play an important role in plant responses to waterlogging stress. However, the function and mechanism of action of ERFVIII in response to waterlogging stress remain poorly understood. In this study, we found that expression of the ERF VIIIa gene CmERF4 in chrysanthemum was induced by waterlogging stress. CmERF4 localized to the nucleus when expressed in tobacco leaves. Yeast two-hybrid and luciferase assays showed that CmERF4 is a transcriptional inhibitor. CmERF4 overexpression in chrysanthemum reduced plant waterlogging tolerance, whereas overexpression of the chimeric activator CmERF4-VP64 reversed its transcriptional activity, promoting higher waterlogging tolerance than that observed in wild-type plants, indicating that CmERF4 negatively regulates waterlogging tolerance. Transcriptome profiling showed that energy metabolism and reactive oxygen species (ROS) pathway-associated genes were differentially expressed between CmERF4-VP64 and wild-type plants. RT-qPCR analysis of selected energy metabolism and reactive oxygen species-related genes showed that the gene expression patterns were consistent with the expression levels obtained from RNA-seq analysis. Overall, we identified new functions of CmERF4 in negatively regulating chrysanthemum waterlogging tolerance by modulating energy metabolism and ROS pathway genes.

Identification and Regulation of Hypoxia-Tolerant and Germination-Related Genes in Rice

In direct seeding, hypoxia is a major stress faced by rice plants. Therefore, dissecting the response mechanism of rice to hypoxia stress and the molecular regulatory network is critical to the development of hypoxia-tolerant rice varieties and direct seeding of rice. This review summarizes the morphological, physiological, and ecological changes in rice under hypoxia stress, the discovery of hypoxia-tolerant and germination-related genes/QTLs, and the latest research on candidate genes, and explores the linkage of hypoxia tolerance genes and their distribution in indica and japonica rice through population variance analysis and haplotype network analysis. Among the candidate genes, OsMAP1 is a typical gene located on the MAPK cascade reaction for indica-japonica divergence; MHZ6 is involved in both the MAPK signaling and phytohormone transduction pathway. MHZ6 has three major haplotypes and one rare haplotype, with Hap3 being dominated by indica rice varieties, and promotes internode elongation in deep-water rice by activating the SD1 gene. OsAmy3D and Adh1 have similar indica-japonica varietal differentiation, and are mainly present in indica varieties. There are three high-frequency haplotypes of OsTPP7, namely Hap1 (n = 1109), Hap2 (n = 1349), and Hap3 (n = 217); Hap2 is more frequent in japonica, and the genetic background of OsTPP7 was derived from the japonica rice subpopulation. Further artificial selection, natural domestication, and other means to identify more resistance mechanisms of this gene may facilitate future research to breed superior rice cultivars. Finally, this study discusses the application of rice hypoxia-tolerant germplasm in future breeding research.

CiAP2/ERF65 and CiAP2/ERF106, a pair of homologous genes in pecan (Carya illinoensis), regulate plant responses during submergence in transgenic Arabidopsis thaliana

When plants are entirely submerged, photosynthesis and respiration are severely restricted, affecting plant growth and potentially even causing plant death. The AP2/ERF superfamily has been widely reported to play a vital role in plant growth, development and resistance to biotic and abiotic stresses. However, no relevant studies exist on flooding stress in pecan. In this investigation, we observed that CiAP2/ERF65 positively modulated the hypoxia response during submergence, whereas CiAP2/ERF106 was sensitive to submergence. The levels of physiological and biochemical indicators, such as POD, CAT and among others, in CiAP2/ERF65-OE lines were significantly higher than those in wild-type Arabidopsis thaliana, indicating that the antioxidant capacity of CiAP2/ERF65-OE lines was enhanced under submergence. The RNA-seq results revealed that the maintenance of the expression levels of the antenna protein gene, different signaling pathways for regulation, as well as the storage and consumption of ATP, might account for the opposite phenotypes of CiAP2/ERF65 and CiAP2/ERF106. Furthermore, the expression of some stress-related genes was altered during submergence and reoxygenation. Overall, these findings enhance our understanding of submergence stress in pecan, providing important candidate genes for the molecular design and breeding of hypoxia resistant in plants.

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.

Nitrogen availability affects the responses of marsh grass and sedge plants (Phragmites australis and Bolboschoenus planiculmis) to flooding time

Flooding time and external nitrogen (N) input have been projected to be the main threats to marsh ecosystems in the scenario of more intense flooding events and N deposition. How flooding and N addition experienced at different growth stages interact in determining phenotypic change remains scarce. We established a controlled experiment (3 flooding time treatments x 5 N addition levels) using two herbaceous marsh species (Phragmites australis and Bolboschoenus planiculmis) to assess the responses of six key traits to environmental changes and the indication of plant performance. Early flooding reduced plant height and aboveground biomass of P. australis and below/aboveground biomass ratio of B. planiculmis and increased below/aboveground biomass ratio of P. australis and root biomass of B. planiculmis, whereas late flooding reduced root biomass of P. australis and ramet number and aboveground biomass of B. planiculmis. The combination of flooding and high N (16 and 32 g N m-2) exerted negative effects on ramet number of both plant species. The interaction of early flooding and low-medium N (8 and 16 g N m-2) inhibited clonal/belowground biomass ratio of both plant species. The combination of early flooding and low N (0, 4 and 8 g N m-2) promoted root biomass and below/aboveground biomass ratio of P. australis. Ramet number, plant height, and root biomass explained 80-90 % of aboveground biomass variation of both plant species, and the contribution of ramet number was greater than that of the other two traits. These results highlight that the influence of flooding time and external N input on the performance of marsh plants depends on species identity. Meanwhile, the ramet number-plant height-root biomass (RHR) strategy is supposed to be the adaptation strategy of wetland clonal plants to environmental changes, and clonal reproductive traits should be incorporated into vegetation dynamics models for marsh plants.

Characterization and transformation of the CabHLH18 gene from hot pepper to enhance waterlogging tolerance

Basic helix-loop-helix (bHLH) proteins are important in abiotic stress control. Here, a specific bHLH transcription factor gene, CabHLH18, from a strong waterlogging-tolerant pepper cultivar, 'ZHC2', was successfully cloned. The CabHLH18 gene presented a coding sequence length of 1,056 bp, encoding 352 amino acids, and the protein was the closest to Capsicum annuum XM016694561.2 protein. The CabHLH18 protein was located in the nucleus. The transformation of the CabHLH18 overexpression vector into the plumules of hot peppers, 'DFZJ' and 'ZHC1', exhibited 21.37% and 22.20% efficiency, respectively. The root length, plant height, and fresh weight of the 'DFZJ' overexpression lines were greater than those of wild-type (WT) plants under waterlogging conditions. Compared with the WT plants, the overexpression lines generally showed greater contents of water, the amino acid, proline, soluble sugar, root viability, and superoxide dismutase activity, but lower malondialdehyde content under waterlogging conditions. Plant fresh weight, amino acids, proline, and soluble sugar levels of the overexpression lines were 39.17%, 45.03%, 60.67%, and 120.18% greater, respectively, compared with the WT plants at 24 h after waterlogging stress. Therefore, the CabHLH18 gene could be implicated in conferring waterlogging tolerance in hot peppers and holds promise for enhancing their overall waterlogging tolerance.

How plant roots respond to waterlogging

Plant submergence is a major abiotic stress that impairs plant performance. Under water, reduced gas diffusion exposes submerged plant cells to an environment that is enriched in gaseous ethylene and is limited in oxygen (O2) availability (hypoxia). The capacity for plant roots to avoid and/or sustain critical hypoxia damage is essential for plants to survive waterlogging. Plants use spatiotemporal ethylene and O2 dynamics as instrumental flooding signals to modulate potential adaptive root growth and hypoxia stress acclimation responses. However, how non-adapted plant species modulate root growth behaviour during actual waterlogged conditions to overcome flooding stress has hardly been investigated. Here we discuss how changes in the root growth rate, lateral root formation, density, and growth angle of non-flood adapted plant species (mainly Arabidopsis) could contribute to avoiding and enduring critical hypoxic conditions. In addition, we discuss current molecular understanding of how ethylene and hypoxia signalling control these adaptive root growth responses. We propose that future research would benefit from less artificial experimental designs to better understand how plant roots respond to and survive waterlogging. This acquired knowledge would be instrumental to guide targeted breeding of flood-tolerant crops with more resilient root systems.

Identification and characterization of waterlogging-responsive genes in the parental line of maize hybrid An'nong 876

Waterlogging stress is an important abiotic stress that adversely affects maize growth and yield. The mechanism regulating the early stage of the maize response to waterlogging stress is largely unknown. In this study, CM37 and cmh15 seedlings were treated with waterlogging stress and then examined in terms of their physiological changes. The results indicated that inbred line cmh15 is more tolerant to waterlogging stress and less susceptible to peroxide-based damages than CM37. The RNA sequencing analysis identified 1,359 down-regulated genes and 830 up-regulated genes in the waterlogging-treated cmh15 plants (relative to the corresponding control levels). According to the Gene Ontology analysis for the differentially expressed genes (DEGs), some important terms were identified which may play important roles in the response to waterlogging stress. Moreover, enriched Kyoto Encyclopedia of Genes and Genomes pathways were also identified for the DEGs. Furthermore, the substantial changes in the expression of 36 key transcription factors may be closely related to the maize in response to waterlogging stress. This study offers important insights into the mechanism in regulating maize tolerance to waterlogging stress, with important foundations for future research.

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.

Seed bacterial microbiota in post-submergence tolerant and sensitive barley genotypes

Flooding is a predominant abiotic stress for cultivated plants, including barley. This cereal crop shows a large adaptability to different environmental conditions, suggesting the presence of key traits to tolerate adverse conditions. During germination, genetic variations account for dissimilarities in flooding tolerance. However, differences in the seed microbiota may also contribute to tolerance/sensitivity during seedling establishment. This work investigated differences in microbiome among the grains of barley accessions. Two barley phenotypes were compared, each either tolerant or sensitive to a short submergence period followed by a recovery. The study used a metataxonomic analysis based on 16S ribosomal RNA gene sequencing and subsequent functional prediction. Our results support the hypothesis that bacterial microbiota inhabiting the barley seeds are different between sensitive and tolerant barley accessions, which harbour specific bacterial phyla and families. Finally, bacteria detected in tolerant barley accessions show a peculiar functional enrichment that suggests a possible connection with successful germination and seedling establishment.

ZmB12D, a target of transcription factor ZmWRKY70, enhances the tolerance of Arabidopsis to submergence

Submergence stress represents a serious threat to the yield and quality of maize because it can lead to oxygen deficiency and the accumulation of toxic metabolites. However, the mechanisms by which maize resists the adverse effects of submergence stress have yet to be fully elucidated. Here, we cloned a gene from maize Balem (Barley aleurone and embryo), ZmB12D, which was expressed at significant levels in seed embryos during imbibition and in leaves under submergence stress. Subcellular localization analysis indicated that the ZmB12D protein was localized in the mitochondria. The overexpression of ZmB12D in increased the tolerance of Arabidopsis to submergence stress, probably due to a reduction in the levels of malonaldehyde (MDA), the increased activity of antioxidant enzymes (SOD, POD and CAT), enhanced electron transport by coordinating the expression of non-symbiotic hemoglobin-2 (AHb2) and Fe transport-related (AtNAS3) genes (mediating Fe and oxygen availability) and also modulated the anaerobic respiration rates through upregulated the AtPDC1, AtADH1, AtSUS4 genes under submergence. Yeast one-hybrid (Y1H) and transient transactivation assays demonstrated that ZmWRKY70 bound to the ZmB12D promoter and activated ZmB12D. Collectively, out findings indicate that ZmB12D plays an important role in the tolerance of maize to submergence stress. This research provides new insights into the genetic improvement of maize with regards to submergence tolerance.

Flooding-adaptive root and shoot traits in rice

Wetland plants, including rice (Oryza spp.), have developed multiple functional adaptive traits to survive soil flooding, partial submergence or even complete submergence. In waterlogged soils and under water, diffusion of O2 and CO2 is extremely slow with severe impacts on photosynthesis and respiration. As a response to shallow floods or rising floodwater, several rice varieties, including deepwater rice, elongate their stems to keep their leaves above the water surface so that photosynthesis can occur unhindered during partial submergence. In stark contrast, some other varieties hardly elongate even if they become completely submerged. Instead, their metabolism is reduced to an absolute minimum so that carbohydrates are conserved enabling fast regrowth once the floodwater recedes. This review focuses on the fascinating functional adaptive traits conferring tolerance to soil flooding, partial or complete submergence. We provide a general analysis of these traits focusing on molecular, anatomical and morphological, physiological and ecological levels. Some of these key traits have already been introgressed into modern high-yielding genotypes improving flood tolerance of several cultivars used by millions of farmers in Asia. However, with the ongoing changes in climate, we propose that even more emphasis should be placed on improving flood tolerance of rice by breeding for rice that can tolerate longer periods of complete submergence or stagnant flooding. Such tolerance could be achieved via additional tissues; i.e. aquatic adventitious roots relevant during partial submergence, and leaves with higher underwater photosynthesis caused by a longer gas film retention time.

Understanding plant responses to saline waterlogging: insights from halophytes and implications for crop tolerance

MAIN CONCLUSION

Saline and wet environments stress most plants, reducing growth and yield. Halophytes adapt with ion regulation, energy maintenance, and antioxidants. Understanding these mechanisms aids in breeding resilient crops for climate change. Waterlogging and salinity are two abiotic stresses that have a major negative impact on crop growth and yield. These conditions cause osmotic, ionic, and oxidative stress, as well as energy deprivation, thus impairing plant growth and development. Although few crop species can tolerate the combination of salinity and waterlogging, halophytes are plant species that exhibit high tolerance to these conditions due to their morphological, anatomical, and metabolic adaptations. In this review, we discuss the main mechanisms employed by plants exposed to saline waterlogging, intending to understand the mechanistic basis of their ion homeostasis. We summarize the knowledge of transporters and channels involved in ion accumulation and exclusion, and how they are modulated to prevent cytosolic toxicity. In addition, we discuss how reactive oxygen species production and cell signaling enhance ion transport and aerenchyma formation, and how plants exposed to saline waterlogging can control oxidative stress. We also address the morphological and anatomical modifications that plants undergo in response to combined stress, including aerenchyma formation, root porosity, and other traits that help to mitigate stress. Furthermore, we discuss the peculiarities of halophyte plants and their features that can be leveraged to improve crop yields in areas prone to saline waterlogging. This review provides valuable insights into the mechanisms of plant adaptation to saline waterlogging thus paving the path for future research on crop breeding and management strategies.

The vacuolar Ca2+ transporter CATION EXCHANGER 2 regulates cytosolic calcium homeostasis, hypoxic signaling, and response to flooding in Arabidopsis thaliana

Flooding represents a major threat to global agricultural productivity and food security, but plants are capable of deploying a suite of adaptive responses that can lead to short- or longer-term survival to this stress. One cellular pathway thought to help coordinate these responses is via flooding-triggered Ca2+ signaling. We have mined publicly available transcriptomic data from Arabidopsis subjected to flooding or low oxygen stress to identify rapidly upregulated, Ca2+ -related transcripts. We then focused on transporters likely to modulate Ca2+ signals. Candidates emerging from this analysis included AUTOINHIBITED Ca2+ ATPASE 1 and CATION EXCHANGER 2. We therefore assayed mutants in these genes for flooding sensitivity at levels from growth to patterns of gene expression and the kinetics of flooding-related Ca2+ changes. Knockout mutants in CAX2 especially showed enhanced survival to soil waterlogging coupled with suppressed induction of many marker genes for hypoxic response and constitutive activation of others. CAX2 mutants also generated larger and more sustained Ca2+ signals in response to both flooding and hypoxic challenges. CAX2 is a Ca2+ transporter located on the tonoplast, and so these results are consistent with an important role for vacuolar Ca2+ transport in the signaling systems that trigger flooding response.

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

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

Identification of Genomic Regions for Deep-Water Resistance in Rice for Efficient Weed Control with Reduced Herbicide Use

Deep-water (DW) management in rice fields is a promising technique for efficient control of paddy weeds with reduced herbicide use. Maintaining a water depth of 10-20 cm for several weeks can largely suppress the weed growth, though it also inhibits rice growth because the DW management is usually initiated immediately after transplanting. Improving the DW resistance of rice during the initial growth stage is essential to avoid suppressing growth. In this study, we demonstrate a large genetic variation in the above-ground biomass (AGB) after the end of DW management among 165 temperate japonica varieties developed in Japan. Because the AGB closely correlated with plant length (PL) and tiller number (TN) at the early growth stage, we analyzed genomic regions associated with PL and TN by conducting a genome-wide association study. For PL, a major peak was detected on chromosome 3 (qPL3), which includes a gene encoding gibberellin biosynthesis, OsGA20ox1. The rice varieties with increased PL had a higher expression level of OsGA20ox1 as reported previously. For TN, a major peak was detected on chromosome 4 (qTN4), which includes NAL1 gene associated with leaf morphological development and panicle number. Although there was less difference in the expression level of NAL1 between genotypes, our findings suggest that an amino acid substitution in the exon region is responsible for the phenotypic changes. We also found that the rice varieties having alternative alleles of qPL3 and qTN4 showed significantly higher AGB than the varieties with the reference alleles. Our results suggest that OsGA20ox1 and NAL1 are promising genes for improving DW resistance in rice.

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.

Physiological and transcriptomic analysis of the mangrove species Kandelia obovata in response to flooding stress

Flooding stress on mangroves is growing continually with rising sea level. In this study, the physiology and transcriptome of the mangrove species Kandelia obovata under flooding stress were analyzed. With increasing inundation time, malondialdehyde (MDA), superoxide dismutase (SOD), glutathione (GSH), soluble sugar (SS), soluble protein (SP), and proline (Pro) content declined, while peroxidase (POD) and ascorbate peroxidase (APX) activity rose significantly. According to the KEGG pathway enrichment analysis, upregulated differentially expressed genes (DEGs) were enriched in the plant hormone signaling pathway. Furthermore, MYB44 and MYB108 genes from the MYB transcription factor family and RAP2.12, DREB2B, and ERF4 genes from the AP2/ERF family were up-regulated under flooding conditions. A strong correlation was established between the expression levels of 12 DEGs under flooding stress and RNA sequencing data and was verified by qRT-PCR. These results provide new insights into the molecular mechanism of K. obovata in response to flooding stress.

Enhanced meristem development, tolerance to oxidative stress and hyposensitivity to nitric oxide in the hypermorphic vq10-H mutant in AtVQ10 gene

Nitric oxide (NO) and reactive oxygen are common factors in multiple plant responses to stress, and their involvement in hypoxia-triggered responses is key to ensure growth under adverse environmental conditions. Here, we analyse the regulatory functions exerted by hypoxia-, NO- and oxidative stress-inducible Arabidopsis gene coding for the VQ motif-containing protein 10 (VQ10). A hypermorphic vq10-H mutant allowed identifying VQ10-exerted regulation on root and shoot development as well as its role in regulating responses to NO and oxidative stress. Enhanced VQ10 expression in vq10-H plants led to enhanced elongation of the primary root, and increased root cell division and meristem size during early postgermination development. In shoots, VQ10 activation of cell division was counteracted by WRKY33-exerted repression, thus leading to a dwarf bushy phenotype in plants with enhanced VQ10 expression in a wrky33 knock-out background. Low number of differentially expressed genes were identified when vq10-H versus Col-0 plants were compared either under normoxia or hypoxia. vq10-H and VQ10ox plants displayed less tolerance to submergence but, in turn, were more tolerant to oxidative stress and less sensitive to NO than wild-type plants. VQ10 could be a node integrating redox-related regulation on development and stress responses.

Transcriptome Analysis Reveals the Molecular Mechanism and Responsive Genes of Waterlogging Stress in Actinidia deliciosa Planch Kiwifruit Plants

Waterlogging stress is one of the major natural issues resulting in stunted growth and loss of agricultural productivity. Cultivated kiwifruits are popular for their rich vitamin C content and unique flavor among consumers, while commonly sensitive to waterlogging stress. The wild kiwifruit plants are usually obliged to survive in harsh environments. Here, we carried out a transcriptome analysis by high-throughput RNA sequencing using the root tissues of Actinidia deliciosa (a wild resource with stress-tolerant phenotype) after waterlogging for 0 d, 3 d, and 7 d. Based on the RNA sequencing data, a high number of differentially expressed genes (DEGs) were identified in roots under waterlogging treatment, which were significantly enriched into four biological processes, including stress response, metabolic processes, molecular transport, and mitotic organization, by gene ontology (GO) simplify enrichment analysis. Among these DEGs, the hypoxia-related genes AdADH1 and AdADH2 were correlated well with the contents of acetaldehyde and ethanol, and three transcription factors Acc26216, Acc08443, and Acc16908 were highly correlated with both AdADH1/2 genes and contents of acetaldehyde and ethanol. In addition, we found that there might be an evident difference among the promoter sequences of ADH genes from A. deliciosa and A. chinensis. Taken together, our results provide additional information on the waterlogging response in wild kiwifruit plants.

Rapid systemic responses of Arabidopsis to waterlogging stress

Waterlogging stress (WLS) negatively impacts the growth and yield of crops resulting in heavy losses to agricultural production. Previous studies have revealed that WLS induces a systemic response in shoots that is partially dependent on the plant hormones ethylene and abscisic acid. However, the role of rapid cell-to-cell signaling pathways, such as the reactive oxygen species (ROS) and calcium waves, in systemic responses of plants to WLS is unknown at present. Here, we reveal that an abrupt WLS treatment of Arabidopsis (Arabidopsis thaliana) plants growing in peat moss triggers systemic ROS and calcium wave responses and that the WLS-triggered ROS wave response of Arabidopsis is dependent on the ROS-generating RESPIRATORY BURST OXIDASE HOMOLOG D (RBOHD), calcium-permeable channels GLUTAMATE-LIKE RECEPTOR 3.3 and 3.6 (GLR3.3 and GLR3.6), and aquaporin PLASMA MEMBRANE INTRINSIC PROTEIN 2;1 (PIP2;1) proteins. We further show that WLS is accompanied by a rapid systemic transcriptomic response that is evident as early as 10 min following waterlogging initiation, includes many hypoxia-response transcripts, and is partially dependent on RBOHD. Interestingly, the abrupt WLS of Arabidopsis resulted in the triggering of a rapid hydraulic wave response and the transient opening of stomata on leaves. In addition, it induced in plants a heightened state of tolerance to a subsequent submergence stress. Taken together, our findings reveal that the initiation of WLS in plants is accompanied by rapid systemic physiological and transcriptomic responses that involve the ROS, calcium, and hydraulic waves, as well as the induction of hypoxia acclimation mechanisms in systemic tissues.

Fine-tuned nitric oxide and hormone interface in plant root development and regeneration

Plant root growth and developmental capacities reside in a few stem cells of the root apical meristem (RAM). Maintenance of these stem cells requires regenerative divisions of the initial stem cell niche (SCN) cells, self-maintenance, and proliferative divisions of the daughter cells. This ensures sufficient cell diversity to guarantee the development of complex root tissues in the plant. Damage in the root during growth involves the formation of a new post-embryonic root, a process known as regeneration. Post-embryonic root development and organogenesis processes include primary root development and SCN maintenance, plant regeneration, and the development of adventitious and lateral roots. These developmental processes require a fine-tuned balance between cell proliferation and maintenance. An important regulator during root development and regeneration is the gasotransmitter nitric oxide (NO). In this review we have sought to compile how NO regulates cell rate proliferation, cell differentiation, and quiescence of SCNs, usually through interaction with phytohormones, or other molecular mechanisms involved in cellular redox homeostasis. NO exerts a role on molecular components of the auxin and cytokinin signaling pathways in primary roots that affects cell proliferation and maintenance of the RAM. During root regeneration, a peak of auxin and cytokinin triggers specific molecular programs. Moreover, NO participates in adventitious root formation through its interaction with players of the brassinosteroid and cytokinin signaling cascade. Lately, NO has been implicated in root regeneration under hypoxia conditions by regulating stem cell specification through phytoglobins.

Morphological and transcriptomic responses/acclimations of erect-type submerged macrophyte Hydrilla verticillata both at low-light exposure and light recovery phases

Light intensity is a determinant for submerged macrophytes. Little is known about their molecular responses to low-light exposure, despite more informative and responsive than morphological traits. For erect-type submerged macrophytes, the stem is more crucial relative to the leaf in acclimation to low-light stress, but receives less attention. We determined morphological and stem transcriptomic responses/acclimations of Hydrilla verticillata to extremely and mildly low light (7.2 and 36 μmol photons m-2 s-1, respectively), that is, EL and ML, with the radiation intensity of 180 μmol photons m-2 s-1 as the control. Low-light exposure continued for 9 days, followed by a 7-day recovery phase (180 μmol photons m-2 s-1). At the exposure phase, the low-light treatments, in particular the EL, decreased the relative growth ratio, but induced greater height and longer stem internode distance and epidermal cell. Such responses/acclimations continued into the recovery phase, despite more or less changes in the magnitude. Transcriptome showed that the photosynthetic system was inhibited at the exposure phase, but the macrophyte adjusted hormone synthesis relating to cell division and elongation. Moreover, the EL activated cell stress responses such as DNA repair. Following light recovery, the macrophyte exhibited a strong-light response, although energy metabolism enhanced. Especially, the EL enriched the pathways relating to anthocyanin synthesis at such phase, indicating an activation of photoprotective mechanism. Our findings suggest that negative influences of low light occur at both low-light exposure and recovery phases, but submerged macrophytes would acclimate to light environments. Transcriptome can show molecular basis of plant responses/acclimations, including but not limited to morphology. This study establishes a bridge connecting morphological and molecular responses/acclimations.

Waterlogging Tolerance of Actinidia valvata Dunn Is Associated with High Activities of Pyruvate Decarboxylase, Alcohol Dehydrogenase and Antioxidant Enzymes

Kiwifruit (Actinidia spp.) is susceptible to waterlogging stress. Although abundant wild germplasm resources exist among Actinidia plants for improving the waterlogging tolerance of kiwifruit cultivars, the underlying mechanisms remain largely unknown. Here, a comparative study was undertaken using one wild germplasm, Maorenshen (A. valvata Dunn, MRS), and one cultivar, Miliang-1 (A. chinensis var. deliciosa (A.Chev.) A.Chev. cv. Miliang-1, ML). Under stress, the ML plantlets were seriously damaged with wilted chlorotic leaves and blackened rotten roots, whereas the symptoms of injury in the MRS plantlets were much fewer, along with higher photosynthetic rates, chlorophyll fluorescence characteristics and root activity under stress conditions. However, neither aerenchyma in the root nor adventitious roots appeared in both germplasms upon stress exposure. The activities of pyruvate decarboxylase (PDC) and alcohol dehydrogenase (ADH), as well as their transcript levels, were constitutively higher in MRS than those in ML under both normal and stress conditions. Waterlogging stress significantly enhanced the PDC and ADH enzyme activities in both germplasms, which were 60.8% and 22.4% higher in the MRS roots than those in the ML roots under waterlogging stress, respectively. Moreover, MRS displayed higher activities of antioxidant enzymes, including SOD, CAT, and APX, as well as DPPH-radical scavenging ability, and decreased H2O2 and MDA accumulation under both normal and stress conditions. Our findings suggest that the waterlogging tolerance of the wild A. valvata germplasm was associated with high PDC and ADH, as well as antioxidant ability.

Ethylene enhanced waterlogging tolerance by changing root architecture and inducing aerenchyma formation in maize seedlings

Waterlogging negatively affects maize growth and yield. In this study, we found that ethylene played a vital role in plant adaptation to waterlogging. ET promotes better growth in seedlings under waterlogging conditions by altering root architecture and increasing lateral root formation by 42.1%. What's more, plants with high endogenous ethylene levels exhibited reduced sensitivity to waterlogging stress. ET also induced the formation of aerenchyma, a specialized tissue that facilitates gas exchange, in a different pattern compared to aerenchyma formed under waterlogging. Aerenchyma induced by ET was mainly located in the medial cortex of the roots and was not prone to decay. ethylene inhibited root elongation under normal conditions, but this inhibition was not alleviated under waterlogging stress. Upon activation of the ET signaling pathway, the transcription factor EREB90 promoted aerenchyma formation by enhancing the programmed cell death process. Overexpression of EREB90 resulted in increased waterlogging tolerance compared to wild type plants. Our findings suggest that pre-treatment of maize seedlings with ET before waterlogging stress can trigger the programmed cell death process and induce aerenchyma formation, thus improving waterlogging resistance.

Parallels between drought and flooding: An integrated framework for plant eco-physiological responses to water stress

Drought and flooding occur at opposite ends of the soil moisture spectrum yet their resulting stress responses in plants share many similarities. Drought limits root water uptake to which plants respond with stomatal closure and reduced leaf gas exchange. Flooding limits root metabolism due to soil oxygen deficiency, which also limits root water uptake and leaf gas exchange. As drought and flooding can occur consecutively in the same system and resulting plant stress responses share similar mechanisms, a single theoretical framework that integrates plant responses over a continuum of soil water conditions from drought to flooding is attractive. Based on a review of recent literature, we integrated the main plant eco-physiological mechanisms in a single theoretical framework with a focus on plant water transport, plant oxygen dynamics, and leaf gas exchange. We used theory from the soil-plant-atmosphere continuum modeling as "backbone" for our framework, and subsequently incorporated interactions between processes that regulate plant water and oxygen status, abscisic acid and ethylene levels, and the resulting acclimation strategies in response to drought, waterlogging, and complete submergence. Our theoretical framework provides a basis for the development of mathematical models to describe plant responses to the soil moisture continuum from drought to flooding.

ZmWRKY70 activates the expression of hypoxic responsive genes in maize and enhances tolerance to submergence in Arabidopsis

Hypoxic stress due to submergence is a serious threat to the growth and development of maize. WRKY transcription factors are significant regulators of plant responses to various abiotic and biotic stresses. Nevertheless, their function and regulatory mechanisms in the resistance of maize to submergence stress remain unclear. Here we report the cloning of a maize WRKY transcription factor gene, ZmWRKY70, transcripts of which accumulate under submergence stress in maize seedlings. Subcellular localization analysis and yeast transcriptional activation assay indicated that ZmWRKY70 was localized in the nucleus and had transcriptional activation activity. Heterologous overexpression of ZmWRKY70 in Arabidopsis increased the tolerance of seeds and seedlings to submergence stress by upregulating the transcripts of several key genes involved in anaerobic respiration, such as group VII ethylene-responsive factor (ERFVII) (AtRAP2.2), alcohol dehydrogenase (AtADH1), pyruvate decarboxylase (AtPDC1/2), and sucrose synthase (AtSUS4), under submergence conditions. Moreover, the overexpression of ZmWRKY70 in maize mesophyll protoplasts enhanced the expression of ZmERFVII members (ZmERF148, ZmERF179, and ZmERF193), ZmADH1, ZmPDC2/3, and ZmSUS1. Yeast one-hybrid and dual-luciferase activity assays further confirmed that ZmWRKY70 enhanced the expression of ZmERF148 by binding to the W box motif located in the promoter region of ZmERF148. Together, these results indicate that ZmWRKY70 plays a significant role in tolerance of submergence stress. This work provides a theoretical basis, and suggests excellent genes, for biotechnological breeding to improve the tolerance of maize to submergence through the regulation of ZmWRKY genes.

A meta-analysis of plant tissue O2 dynamics

Adequate tissue O2 supply is crucial for plant function. We aimed to identify the environmental conditions and plant characteristics that affect plant tissue O2 status. We extracted data and performed meta-analysis on >1500 published tissue O2 measurements from 112 species. Tissue O2 status ranged from anoxic conditions in roots to >53kPa in submerged, photosynthesising shoots. Using information-theoretic model selection, we identified 'submergence', 'light', 'tissue type' as well as 'light×submergence' interaction as significant drivers of tissue O2 status. Median O2 status were especially low (Solanum tuberosum ) tubers and root nodules. Mean shoot and root O2 were ~25% higher in light than in dark when shoots had atmospheric contact. However, light showed a significant interaction with submergence on plant O2 , with a submergence-induced 44% increase in light, compared with a 42% decline in dark, relative to plants with atmospheric contact. During submergence, ambient water column O2 and shoot tissue O2 correlated stronger in darkness than in light conditions. Although use of miniaturised Clark-type O2 electrodes has enhanced understanding of plant O2 dynamics, application of non-invasive methods in plants is still lacking behind its widespread use in mammalian tissues.

Functional responses to multiple sequential abiotic stress (waterlogging-drought) in three woody taxa with different root systems and stress tolerance

There is generally a trade-off in the resistance to drought and to waterlogging. However, several species are sequentially subjected to both stressors in many environments. We evaluated the ecophysiological strategies to cope with multiple sequential stress of waterlogging and drought (W + D) of three taxa differing in stress resistance and root morphology: the phreatophic Eucalyptus camaldulensis (Ec) and two shallow-rooted willow clones: Salix matsudana x Salix alba (SmxSa) and Salix nigra (Sn4). Individuals of the three taxa were grown in pots and assigned to either of four treatments: Control (well-watered plants), well-watered followed by drought (C + D); waterlogged for 15 days followed by drought (W15d + D) and waterlogged for 30 days followed by drought (W30d + D). Biomass allocation, growth (diameter, height, length of leaves, and roots), specific leaf area, stomatal conductance, water potential, hydraulic conductivity of roots and branches, leaf C13 and root cortical aerenchyma formation were determined at different stages of the experiment. Ec growth was not affected by W + D, developing tolerance strategies at leaf and whole plant levels. Differential effects of W + D were observed in both Salix clones depending on the time of waterlogging. In Sn4 and SmxSa, the root biomass was affected in W15d + D treatment, but a root tolerance response (aerenchyma and adventitious root formation) was observed in W30d + D. In the three taxa, and contrary to expectations, the previous exposure to a waterlogging period did not increase the susceptibility of the plants to a subsequent drought event. On the contrary, we found tolerance, which depended on the time of waterlogging exposure.

STOP1 and STOP1-like proteins, key transcription factors to cope with acid soil syndrome

Acid soil syndrome leads to severe yield reductions in various crops worldwide. In addition to low pH and proton stress, this syndrome includes deficiencies of essential salt-based ions, enrichment of toxic metals such as manganese (Mn) and aluminum (Al), and consequent phosphorus (P) fixation. Plants have evolved mechanisms to cope with soil acidity. In particular, STOP1 (Sensitive to proton rhizotoxicity 1) and its homologs are master transcription factors that have been intensively studied in low pH and Al resistance. Recent studies have identified additional functions of STOP1 in coping with other acid soil barriers: STOP1 regulates plant growth under phosphate (Pi) or potassium (K) limitation, promotes nitrate (NO₃ ^-) uptake, confers anoxic tolerance during flooding, and inhibits drought tolerance, suggesting that STOP1 functions as a node for multiple signaling pathways. STOP1 is evolutionarily conserved in a wide range of plant species. This review summarizes the central role of STOP1 and STOP1-like proteins in regulating coexisting stresses in acid soils, outlines the advances in the regulation of STOP1, and highlights the potential of STOP1 and STOP1-like proteins to improve crop production on acid soils.