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Flooding, as a natural disaster, plays a pivotal role in constraining the growth and development of plants. Flooding stress, including submergence and waterlogging, not only induces oxygen, light, and nutrient deprivation, but also alters soil properties through prolonged inundation, further impeding plant growth and development. However, hypoxia (or anoxia) is the most serious and direct damage to plants caused by flooding. Moreover, flooding disrupts the structural integrity of plant cell walls and compromises endoplasmic reticulum functionality, while hindering nutrient absorption and shifting metabolic processes from normal aerobic respiration to anaerobic respiration. It can be asserted that flooding exerts comprehensive effects on plants encompassing phenotypic changes, transcriptional alterations, protein dynamics, and metabolic shifts. To adapt to flooding environments, plants employ corresponding adaptive mechanisms at the phenotypic level while modulating transcriptomic profiles, proteomic characteristics, and metabolite levels. Hence, this study provides a comprehensive analysis of transcriptomic, proteomic, and metabolomics investigations conducted on flooding stress on model plants and major crops, elucidating their response mechanisms from diverse omics perspectives. [ABSTRACT FROM AUTHOR]

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

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

Carbon (C), nitrogen (N), and phosphorus (P) stoichiometric ratios give valuable insight into ecosystem function. The purpose of the present study is to probe into the C, N, and P stoichiometric characteristics in various organs and their relationships with soil factors of the dominant deciduous conifer plant species (Taxodium ascendens and Taxodium distichum) during afforestation in the riparian zone of Three Gorges Reservoir. The results showed only a small change in the concentration of C in different plant organs and soils. T. ascendens contained mean N and P concentrations of 7.63 and 1.54 g/kg in fine roots, 5.10 and 0.56 g/kg in stems, and 15.48 and 2.30 g/kg in leaves, respectively. Whereas T. distichum had a mean N and P concentration of 7.08 and 1.37 g/kg in fine roots, 4.84 and 0.59 g/kg in stems, and 16.89 and 2.23 g/kg in leaves. The N:P ratios in all organs were below 14, indicating that N may have inhibited tree growth. The fine roots P and N:P of T. distichum were weak plasticity and weak homeostasis, and those of T. ascendens were plasticity and weak plasticity. Their stems and leaves adhere to strict homeostasis. N concentrations were significantly positively related to P concentrations in every tissue (except the stems of T. ascendens), and C concentrations were significantly positively associated with P concentrations in the stems and leaves of T. ascendens and T. distichum (p < 0.05). Likewise, soil P and fine root P were positively associated (p < 0.01). This study contributes to the understanding of deciduous conifer plant stoichiometry. It demonstrates N, P, and N:P stoichiometric homeostasis in T. ascendens and T. distichum, which can withstand flooding and are suitable for vegetation restoration in the hydro-fluctuation zone. [ABSTRACT FROM AUTHOR]

Riparian plants are exposed to harmful stress induced by flooding, which is often accompanied by eutrophication in the Three Gorges Reservoir Region. The phenomenon is mainly caused by domestic sewage discharges, slow water flow, and agricultural fertilizer pollution. Simulating abiotic stress, such as flooding at the initial period, can act as a signal and induce positive responses of plants to subsequent severe stress. In addition, eutrophication supplies nutrients, provides a favorable environment in the early stages of plant, and facilitates good performance in later development. However, whether early flooding (with or without eutrophication) acts as positive cue or as stress on plants at different developmental stages remains unclear. To address this question, seeds of Polygonum hydropiper were collected from low and high elevations in the hydro-fluctuation belt of the Three Gorges Reservoir Region. Plants germinated from these seeds were subjected to shallower and shorter early flooding treatments with or without eutrophication. Subsequently, plants were subjected to deeper and longer flooding treatments with or without eutrophication. Early flooding and eutrophic flooding significantly induced generation of adventitious roots, suggesting morphological adaptation to flooding. Although early flooding and eutrophic flooding treatments did not increase plant biomass in subsequent treatments compared with control, stem length, length and width of the 1st fully expanded leaf, and biomass of plants in the early eutrophic treatment were higher than these of the early flooding treatment plants. These results suggest a negative lag-effect of early flooding, and also indicate that nutrient inputs can alleviate such effects. Similarly, subsequent eutrophic flooding also enhanced plant growth compared with subsequent flooding, showing significantly higher values of leaf traits and adventitious root number. Plants originated from low elevation had significantly higher functional leaf length and stem biomass compared with those from high elevation. These results suggest that nutrient inputs can alleviate negative effects of early and subsequent flooding on growth of P. hydropiper with the generation of adventitious roots. [ABSTRACT FROM AUTHOR]

Hygrophila polysperma is a heterophyllous amphibious plant. The growth of H. polysperma in submerged conditions is challenging due to the low CO2 environment, increased resistance to gas diffusion, and bicarbonate ion (HCO3–) being the dominant dissolved inorganic carbon source. The submerged leaves of H. polysperma have significantly higher rates of underwater photosynthesis compared with the terrestrial leaves. 4,4′-Diisothiocyanatostilbene-2,2′-disulfonate (DIDS), an anion exchanger protein inhibitor, and ethoxyzolamide (EZ), an inhibitor of internal carbonic anhydrase, repressed underwater photosynthesis by the submerged leaves. These results suggested that H. polysperma acclimates to the submerged condition by using HCO3– for photosynthesis. H. polysperma transports HCO3– into the leaf by a DIDS-sensitive HCO3– transporter and converted to CO2 by carbonic anhydrase. Additionally, proteome analysis revealed that submerged leaves accumulated fewer proteins associated with C4 photosynthesis compared with terrestrial leaves. This finding suggested that H. polysperma is capable of C4 and C3 photosynthesis in the terrestrial and submerged leaves, respectively. The ratio of phosphoenol pyruvate carboxylase to ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) in the submerged leaves was less than that in the terrestrial leaves. Upon anatomical observation, the terrestrial leaves exhibited a phenotype similar to the Kranz anatomy found among C4 plants; however, chloroplasts in the bundle sheath cells were not located adjacent to the vascular bundles, and the typical Kranz anatomy was absent in submerged leaves. These results suggest that H. polysperma performs proto-Kranz type photosynthesis in a terrestrial environment and shifts from a proto-Kranz type in terrestrial leaves to a HCO3– use photosynthesis in the submerged environments.

Ethylene positively regulates ABA catabolism and negatively regulates ABA biosynthesis, thereby affecting ABA content. During hypoxia stress, ABA biosynthesis is inhibited, while the catabolism cascade is enhanced, and thus, exogenous ABA can increase the tolerance of plants to hypoxia stress (Dawood et al., [8]; De Ollas et al., [9]). Keywords: ABA; hypoxia; submergence; waterlogging; flooding; ethylene EN ABA hypoxia submergence waterlogging flooding ethylene 1 6 6 06/28/21 20210624 NES 210624 Introduction Hypoxia is one of the major abiotic stresses, primarily caused by numerous flooding events such as waterlogging and submergence (Zhou et al., [56]; Xie et al., [48]), with deleterious effects on plant growth and development (Bailey-Serres et al., [4]; Voesenek and Bailey-Serres, [43]; Xie et al., [48]; Zhou et al., [58]). Abscisic Acid Biosynthesis Under Hypoxia Stress The abscisic acid level in internode meristem and cell elongation zone of submerged plants decreased by 75% in deepwater rice after flooding (Kende, [22]). [Extracted from the article]

Hygrophila polysperma is a heterophyllous amphibious plant. The growth of H. polysperma in submerged conditions is challenging due to the low CO2 environment, increased resistance to gas diffusion, and bicarbonate ion (HCO3–) being the dominant dissolved inorganic carbon source. The submerged leaves of H. polysperma have significantly higher rates of underwater photosynthesis compared with the terrestrial leaves. 4,4′-Diisothiocyanatostilbene-2,2′-disulfonate (DIDS), an anion exchanger protein inhibitor, and ethoxyzolamide (EZ), an inhibitor of internal carbonic anhydrase, repressed underwater photosynthesis by the submerged leaves. These results suggested that H. polysperma acclimates to the submerged condition by using HCO3– for photosynthesis. H. polysperma transports HCO3– into the leaf by a DIDS-sensitive HCO3– transporter and converted to CO2 by carbonic anhydrase. Additionally, proteome analysis revealed that submerged leaves accumulated fewer proteins associated with C4 photosynthesis compared with terrestrial leaves. This finding suggested that H. polysperma is capable of C4 and C3 photosynthesis in the terrestrial and submerged leaves, respectively. The ratio of phosphoenol pyruvate carboxylase to ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) in the submerged leaves was less than that in the terrestrial leaves. Upon anatomical observation, the terrestrial leaves exhibited a phenotype similar to the Kranz anatomy found among C4 plants; however, chloroplasts in the bundle sheath cells were not located adjacent to the vascular bundles, and the typical Kranz anatomy was absent in submerged leaves. These results suggest that H. polysperma performs proto-Kranz type photosynthesis in a terrestrial environment and shifts from a proto-Kranz type in terrestrial leaves to a HCO3– use photosynthesis in the submerged environments. [ABSTRACT FROM AUTHOR]

Soil flooding creates composite and complex stress in plants known as either submergence or waterlogging stress depending on the depth of the water table. In nature, these stresses are important factors dictating the species composition of the ecosystem. On agricultural land, they cause economic damage associated with long-term social consequences. The understanding of the plant molecular responses to these two stresses has benefited from research studying individual components of the stress, in particular low-oxygen stress. To a lesser extent, other associated stresses and plant responses have been incorporated into the molecular framework, such as ion and ROS signaling, pathogen susceptibility, and organ-specific expression and development. In this review, we aim to highlight known or suspected components of submergence/waterlogging stress that have not yet been thoroughly studied at the molecular level in this context, such as miRNA and retrotransposon expression, the influence of light/dark cycles, protein isoforms, root architecture, sugar sensing and signaling, post-stress molecular events, heavy-metal and salinity stress, and mRNA dynamics (splicing, sequestering, and ribosome loading). Finally, we explore biotechnological strategies that have applied this molecular knowledge to develop cultivars resistant to flooding or to offer alternative uses of flooding-prone soils, like bioethanol and biomass production.

Soil flooding creates composite and complex stress in plants known as either submergence or waterlogging stress depending on the depth of the water table. In nature, these stresses are important factors dictating the species composition of the ecosystem. On agricultural land, they cause economic damage associated with long-term social consequences. The understanding of the plant molecular responses to these two stresses has benefited from research studying individual components of the stress, in particular low-oxygen stress. To a lesser extent, other associated stresses and plant responses have been incorporated into the molecular framework, such as ion and ROS signaling, pathogen susceptibility, and organ-specific expression and development. In this review, we aim to highlight known or suspected components of submergence/waterlogging stress that have not yet been thoroughly studied at the molecular level in this context, such as miRNA and retrotransposon expression, the influence of light/dark cycles, protein isoforms, root architecture, sugar sensing and signaling, post-stress molecular events, heavy-metal and salinity stress, and mRNA dynamics (splicing, sequestering, and ribosome loading). Finally, we explore biotechnological strategies that have applied this molecular knowledge to develop cultivars resistant to flooding or to offer alternative uses of flooding-prone soils, like bioethanol and biomass production. [ABSTRACT FROM AUTHOR]

To avoid low oxygen, oxygen deficiency or oxygen deprivation, deepwater rice cultivated in flood planes can develop elongated internodes in response to submergence. Knowledge of the gene regulatory networks underlying rapid internode elongation is important for an understanding of the evolution and adaptation of major crops in response to flooding. To elucidate the genetic and molecular basis controlling their deepwater response we used microarrays and performed expression quantitative trait loci (eQTL) and phenotypic QTL (phQTL) analyses of internode samples of 85 recombinant inbred line (RIL) populations of non-deepwater (Taichung 65)- and deepwater rice (Bhadua). After evaluating the phenotypic response of the RILs exposed to submergence, confirming the genotypes of the populations, and generating 188 genetic markers, we identified 10,047 significant eQTLs comprised of 2,902 cis-eQTLs and 7,145 trans-eQTLs and three significant eQTL hotspots on chromosomes 1, 4, and 12 that affect the expression of many genes. The hotspots on chromosomes 1 and 4 located at different position from phQTLs detected in this study and other previous studies. We then regarded the eQTL hotspots as key regulatory points to infer causal regulatory networks of deepwater response including rapid internode elongation. Our results suggest that the downstream regulation of the eQTL hotspots on chromosomes 1 and 4 is independent, and that the target genes are partially regulated by SNORKEL1 and SNORKEL2 genes (SK1/2), key ethylene response factors. Subsequent bioinformatic analyses, including gene ontology-based annotation and functional enrichment analysis and promoter enrichment analysis, contribute to enhance our understanding of SK1/2-dependent and independent pathways. One remarkable observation is that the functional categories related to photosynthesis and light signaling are significantly over-represented in the candidate target genes of SK1/2. The combined results of these investigations together with genetical genomics approaches using structured populations with a deepwater response are also discussed in the context of current molecular models concerning the rapid internode elongation in deepwater rice. This study provides new insights into the underlying genetic architecture of gene expression regulating the response to flooding in deepwater rice and will be an important community resource for analyses on the genetic basis of deepwater responses.

To avoid low oxygen, oxygen deficiency or oxygen deprivation, deepwater rice cultivated in flood planes can develop elongated internodes in response to submergence. Knowledge of the gene regulatory networks underlying rapid internode elongation is important for an understanding of the evolution and adaptation of major crops in response to flooding. To elucidate the genetic and molecular basis controlling their deepwater response we used microarrays and performed expression quantitative trait loci (eQTL) and phenotypic QTL (phQTL) analyses of internode samples of 85 recombinant inbred line (RIL) populations of non-deepwater (Taichung 65)- and deepwater rice (Bhadua). After evaluating the phenotypic response of the RILs exposed to submergence, confirming the genotypes of the populations, and generating 188 genetic markers, we identified 10,047 significant eQTLs comprised of 2,902 cis-eQTLs and 7,145 trans-eQTLs and three significant eQTL hotspots on chromosomes 1, 4, and 12 that affect the expression of many genes. The hotspots on chromosomes 1 and 4 located at different position from phQTLs detected in this study and other previous studies. We then regarded the eQTL hotspots as key regulatory points to infer causal regulatory networks of deepwater response including rapid internode elongation. Our results suggest that the downstream regulation of the eQTL hotspots on chromosomes 1 and 4 is independent, and that the target genes are partially regulated by SNORKEL1 and SNORKEL2 genes (SK1/2), key ethylene response factors. Subsequent bioinformatic analyses, including gene ontology-based annotation and functional enrichment analysis and promoter enrichment analysis, contribute to enhance our understanding of SK1/2-dependent and independent pathways. One remarkable observation is that the functional categories related to photosynthesis and light signaling are significantly over-represented in the candidate target genes of SK1/2. The combined results of these investigations together with genetical genomics approaches using structured populations with a deepwater response are also discussed in the context of current molecular models concerning the rapid internode elongation in deepwater rice. This study provides new insights into the underlying genetic architecture of gene expression regulating the response to flooding in deepwater rice and will be an important community resource for analyses on the genetic basis of deepwater responses. [ABSTRACT FROM AUTHOR]

Perennial ryegrass is a popular cool-season grass species due to its high quality for forage and turf. The objective of this study was to identify associations of candidate genes with growth and physiological traits to submergence stress and recovery after de-submergence in a global collection of 94 perennial ryegrass accessions. Accessions varied largely in leaf color, plant height (HT), leaf fresh weight (LFW), leaf dry weight (LDW), and chlorophyll fluorescence (Fv/Fm) at 7 days of submergence and in HT, LFW and LDW at 7 days of recovery in two experiments. Among 26 candidate genes tested by various models, single nucleotide polymorphisms (SNPs) in 10 genes showed significant associations with traits including 16 associations for control, 10 for submergence, and 8 for recovery. Under submergence, Lp1-SST encoding sucrose:sucrose 1-fructosyltransferase and LpGA20ox encoding gibberellin 20-oxidase were associated with LFW and LDW, and LpACO1 encoding 1-aminocyclopropane-1-carboxylic acid oxidase was associated with LFW. Associations between Lp1-SST and HT, Lp6G-FFT encoding fructan:fructan 6G-fructosyltransferase and Fv/Fm, LpCAT encoding catalase and HT were also detected under submergence stress. Upon de-submergence, Lp1-SST, Lp6G-FFT, and LpPIP1 encoding plasma membrane intrinsic protein type 1 were associated with LFW or LDW, while LpCBF1b encoding C-repeat binding factor were associated with HT. Nine significant SNPs in Lp1-SST, Lp6G-FFT, LpCAT, and LpACO1 resulted in amino acid changes with five substitutions found in Lp1-SST under submergence or recovery. The results indicated that allelic diversity in genes involved in carbohydrate and antioxidant metabolism, ethylene and gibberellin biosynthesis, and transcript factor could contribute to growth variations in perennial ryegrass under submergence stress and recovery after de-submergence.

MicroRNAs (miRNAs) are endogenous non-coding RNAs with important regulatory functions in plant development and stress responses. However, their population abundance in lotus (Nelumbo nucifera Gaertn) has so far been poorly described, particularly in response to stresses. In this work, submergence-related miRNAs and their target genes were systematically identified, compared, and validated at the transcriptome-wide level using high-throughput sequencing data of small RNA, Mrna, and the degradome. A total of 128 known and 20 novel miRNAs were differentially expressed upon submergence. We identified 629 target transcripts for these submergence-responsive miRNAs. Based on the miRNA expression profiles and GO and KEGG annotation of miRNA target genes, we suggest possible molecular responses and physiological changes of lotus in response to submergence. Several metabolic, physiological and morphological adaptations-related miRNAs, i.e., NNU_far-miR159, NNU_gma-miR393h, and NNU_aly-miR319c-3p, were found to play important regulatory roles in lotus response to submergence. This work will contribute to a better understanding of miRNA-regulated adaption responses of lotus to submergence stress. [ABSTRACT FROM AUTHOR]

Plants possess two types of phosphofructokinase proteins for phosphorylation of fructose-6-phosphate, the ATP-dependent phosphofructokinase (PFK) and the pyrophosphate-(PPi) dependent pyrophosphate-fructose-6-phosphate-phosphotransferase (PFP). During oxygen deficiency ATP levels in rice seedlings are severely reduced, and it is hypothesized that PPi is used as an alternative energy source for the phosphorylation of fructose-6-phosphate during glycolysis. In this study, we analyzed the expression of 15 phosphofructokinase-encoding genes in roots and aerial tissues of anoxia-tolerant rice seedlings in response to anoxic stress and compared our data with transcript profiles obtained from microarray analyses. Furthermore, the intracellular localization of rice PFK proteins was determined, and the PFK and PFP isoforms were grouped in a phylogenetic tree. Two PFK and two PFP transcripts accumulated during anoxic stress, whereas mRNA levels of four PFK and three PFP genes were decreased. The total specific activity of both PFK and PFP changed only slightly during a 24 h anoxia treatment. It is assumed that expression of different isoforms and their catalytic properties differ during normoxic and anoxic conditions and contribute to balanced glycolytic activity during the low oxygen stress. These characterizations of phosphofructokinase genes and the comparison to other plant species allowed us to suggest candidate rice genes for adaptation to anoxic stress.

Plants possess two types of phosphofructokinase proteins for phosphorylation of fructose- 6-phosphate, the ATP-dependent phosphofructokinase (PFK) and the pyrophosphate-(PPi) dependent pyrophosphate-fructose-6-phosphate-phosphotransferase (PFP). During oxygen deficiency ATP levels in rice seedlings are severely reduced, and it is hypothesized that PPi is used as an alternative energy source for the phosphorylation of fructose-6-phosphate during glycolysis. In this study, we analyzed the expression of 15 phosphofructokinaseencoding genes in roots and aerial tissues of anoxia-tolerant rice seedlings in response to anoxic stress and compared our data with transcript profiles obtained from microarray analyses. Furthermore, the intracellular localization of rice PFK proteins was determined, and the PFK and PFP isoforms were grouped in a phylogenetic tree. Two PFK and two PFP transcripts accumulated during anoxic stress, whereas mRNA levels of four PFK and three PFP genes were decreased. The total specific activity of both PFK and PFP changed only slightly during a 24-h anoxia treatment. It is assumed that expression of different isoforms and their catalytic properties differ during normoxic and anoxic conditions and contribute to balanced glycolytic activity during the low-oxygen stress. These characterizations of phosphofructokinase genes and the comparison to other plant species allowed us to suggest candidate rice genes for adaptation to anoxic stress. [ABSTRACT FROM AUTHOR]

The authors reflect on the responses of plants to flooding. They note the significance of understanding various elements that define flooding stress and of identifying how plants sense and respond to them for flood resilience generation. They also pointed out the relevance of studying flood adaptive strategies in stress-tolerant crop variety development.