Molecular strategies for improving waterlogging tolerance in plants

Waterlogging stress mechanism and membrane transporters in soybean (Glycine max (L.) Merr.)

An excess of water is more harmful to plant growth, root growth and the uniformity of the plant population than a water deficit. Water is a crucial factor in the three basic stages of soybean development: germination, emergence and flowering/seed filling. Waterlogging is one of the biggest constraints to crop production and productivity in India and can occur at any stage in soybean. However, seeds and seedlings are damaged by waterlogging resulting in a significant reduction in grain yield. Seed yield and growth are significantly correlated at the seedling stage. In addition, the plant is under constant pressure due to changing environmental conditions and has difficulty withstanding these harsh, unpredictable and difficult situations. Membrane transporters are essential and play fundamental roles during waterlogging thereby facilitating cellular homeostasis and gaseous exchange, which support plant growth and development. This review highlights the genetic basis and mechanism of waterlogging tolerance in soybean and the role of climate in influencing the genetic makeup of the crop, paving the way for further development of improved soybean varieties. Simultaneously, the article highlights membrane transporters' importance in water-mediated stress in soybeans.

Physiological, molecular, and morphological adjustment to waterlogging stress in ramie and selection of waterlogging-tolerant varieties

Waterlogging stress is a severe abiotic challenge that impedes plant growth and development. Ramie (Boehmeria nivea L.) is a Chinese traditional characteristic economic crop, valued for its fibers and by-products. To investigate the waterlogging tolerance of ramie and provide the scientific basis for selecting waterlogging-tolerant ramie varieties, this study examined the morphological, physiological, biochemical, and molecular responses of 15 ramie germplasms (varieties) under waterlogging stress. The results revealed varied impacts of waterlogging stress across the 15 ramie varieties, characterized by a decrease in SPAD values, net photosynthesis rates, and relative water content of ramie leaves, along with a significant increase in relative conductivity and the activities of antioxidant enzymes such as SOD, POD, CAT, and APX. Additionally, the levels of soluble sugars, soluble proteins, and free proline exhibited varying degrees of increase. Through Principal Component Analysis (PCA), ZZ_2 and ZSZ_1 were identified as relatively tolerant and susceptible varieties. Transcriptome analysis showed that the differential expressed genes between ZZ_2 and ZSZ_1 were significantly enriched in metabolic pathways, ascorbate and aldarate metabolism, and inositol phosphate metabolism, under waterlogging stress. In addition, the expression of hypoxia-responsive genes was higher in ZZ_2 than in ZSZ_1 under waterlogging stress. These differences might account for the varied waterlogging responses between the two varieties. Therefore, this study explored the morpho-physiological responses of ramie under waterlogging stress and identified the molecular mechanisms involved, providing valuable insights for improving ramie varieties and breeding new ones.

The Changes of Amino-Acid Metabolism between Wheat and Rice during Early Growth under Flooding Stress

Floods induce hypoxic stress and reduce wheat growth. On the other hand, rice is a semi-aquatic plant and usually grows even when partially submerged. To clarify the dynamic differences in the cellular mechanism between rice and wheat under flooding stress, morphological and biochemical analyses were performed. Although the growth of wheat in the early stage was significantly suppressed due to flooding stress, rice was hardly affected. Amino-acid analysis revealed significant changes in amino acids involved in the gamma-aminobutyric acid (GABA) shunt and anaerobic/aerobic metabolism. Flood stress significantly increased the contents of GABA and glutamate in wheat compared with rice, though the abundances of glutamate decarboxylase and succinyl semialdehyde dehydrogenase did not change. The abundance of alcohol dehydrogenase and pyruvate carboxylase increased in wheat and rice, respectively. The contents of aspartic acid and pyruvic acid increased in rice root but remained unchanged in wheat; however, the abundance of aspartate aminotransferase increased in wheat root. These results suggest that flooding stress significantly inhibits wheat growth through upregulating amino-acid metabolism and increasing the alcohol-fermentation system compared to rice. When plant growth is inhibited by flooding stress and the aerobic-metabolic system is activated, GABA content increases.

Exogenous Chemicals Used to Alleviate or Salvage Plants under Flooding/Waterlogging Stress: Their Biochemical Effects and Perspectives

Plant flooding/waterlogging stress (FWS) can be a threat to food security worldwide due to climate change. To mitigate its potential devastation, numerous exogenous chemicals (ECs) have been used to demonstrate their effectiveness on alleviating FWS for the last 20 years. This review has summarized the most recent findings on use of various ECs as either nutrients or regulatory substances on crop plants under FWS and their roles involved in improving root respiration of seedlings, optimizing nutritional status, synthesizing osmotic regulators, enhancing the activity of antioxidant enzymes, adjusting phytohormone levels, maintaining photosynthetic systems, and activating flood-tolerance related gene expressions. The effect of ESs on alleviating plants under FWS proves to be beneficial and useful but rather limited unless they are applied on appropriate crops, at the right time, and with optimized methods. Further research should be focused on use of ESs in field settings and on their potential synergetic effect for more FWS tolerance.

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.

Arabidopsis root apical meristem survival during waterlogging is determined by phytoglobin through nitric oxide and auxin

MAIN CONCLUSION

Over-expression of phytoglobin mitigates the degradation of the root apical meristem (RAM) caused by waterlogging through changes in nitric oxide and auxin distribution at the root tip. Plant performance to waterlogging is ameliorated by the over-expression of the Arabidopsis Phytoglobin 1 (Pgb1) which also contributes to the maintenance of a functional RAM. Hypoxia induces accumulation of ROS and damage in roots of wild type plants; these events were preceded by the exhaustion of the RAM resulting from the loss of functionality of the WOX5-expressing quiescent cells (QCs). These phenotypic deviations were exacerbated by suppression of Pgb1 and attenuated when the same gene was up-regulated. Genetic and pharmacological studies demonstrated that degradation of the RAM in hypoxic roots is attributed to a reduction in the auxin maximum at the root tip, necessary for the specification of the QC. This reduction was primarily caused by alterations in PIN-mediated auxin flow but not auxin synthesis. The expression and localization patterns of several PINs, including PIN1, 2, 3 and 4, facilitating the basipetal translocation of auxin and its distribution at the root tip, were altered in hypoxic WT and Pgb1-suppressing roots but mostly unchanged in those over-expressing Pgb1. Disruption of PIN1 and PIN2 signal in hypoxic roots suppressing Pgb1 initiated in the transition zone at 12 h and was specifically associated to the absence of Pgb1 protein in the same region. Exogenous auxin restored a functional RAM, while inhibition of the directional auxin flow exacerbated the degradation of the RAM. The regulation of root behavior by Pgb1 was mediated by nitric oxide (NO) in a model consistent with the recognized function of Pgbs as NO scavengers. Collectively, this study contributes to our understanding of the role of Pgbs in preserving root meristem function and QC niche during conditions of stress, and suggests that the root transition zone is most vulnerable to hypoxia.

Development of a Xanthan Gum Based Superabsorbent and Water Retaining Composites for Agricultural and Forestry Applications

In this work, bio-based hydrogel composites of xanthan gum and cellulose fibers were developed to be used both as soil conditioners and topsoil covers, to promote plant growth and forest protection. The rheological, morphological, and water absorption properties of produced hydrogels were comprehensively investigated, together with the analysis of the effect of hydrogel addition to the soil. Specifically, the moisture absorption capability of these hydrogels was above 1000%, even after multiple dewatering/rehydration cycles. Moreover, the soil treated with 1.8 wt% of these materials increased the water absorption capacity by approximately 60% and reduced the water evaporation rate, due to the formation of a physical network between the soil, xanthan gum and cellulose fibers. Practical experiments on the growth of herbaceous and tomato plants were also performed, showing that the addition of less than 2 wt% of hydrogels into the soil resulted in higher growth rate values than untreated soil. Furthermore, it has been demonstrated that the use of the produced topsoil covers helped promote plant growth. The exceptional water-regulating properties of the investigated materials could allow for the development of a simple, inexpensive and scalable technology to be extensively applied in forestry and/or agricultural applications, to improve plant resilience and face the challenges related to climate change.

Effects of different water conditions on the cadmium hyperaccumulation efficiency of Rorippa sylvestris (L.) Besser and Rorippa amphibia Besser

Increasing the translocation and accumulation of cadmium (Cd) in Cd hyperaccumulator is an important technology to improve the phytoremediation efficiency of Cd-contaminated soil. In order to investigate the effects of different water conditions on the growth and Cd accumulation ability of Cd hyperaccumulators Rorippa sylvestris (L.) Besser and Rorippa amphibia Besser in Cd-polluted soil, clone seedlings of them were transplanted into pots filled with 50 mg kg^-1 Cd-contaminated soil and cultured with water conditions of soil relative water content (RWC) 35%, 55%, 75%, 95%, and flooding respectively. The results showed the following: with the increase of RWC, the height of R. sylvestris and R. amphibia increased gradually, the dry biomass of shoot and whole plant increased and reached the maximum in 95% and then decreased in flooding; the Cd concentrations in shoots of R. sylvestris and R. amphibia were more than 100 mg kg^-1 except for 35% and flooding; Cd bioconcentration factors (BCFs) of R. amphibia reached the maximum of 3.8870 in 75% and R. sylvestris reached the maximum of 3.2330 in 95%; sufficient water resulted in the decrease of photosynthetic rate due to more Cd accumulation. However, under flooding condition, because of the decrease of Cd bioavailability in soil, the accumulation of Cd in shoots declined and the net photosynthetic rate (P_n) enhanced slightly.

Genotype by Environment Interaction on Tropical Maize Hybrids Under Normal Irrigation and Waterlogging Conditions

Unpredictable rainfall in the tropics often increases the risk of waterlogging or even flooding in agricultural lands, hindering the efforts to fulfill maize demands. Breeding maize for waterlogging tolerance is necessary yet challenging since performing varietal testing on a set of hybrids might be biased toward the presence of genotype and environment interaction (GEI). This study aimed to elucidate the GEI effects on yield and related agronomic traits of tropical maize hybrids under normal irrigation and waterlogging conditions and to assess the adaptability of these hybrids in such conditions using several stability models. Ten hybrids including two commercial checks were evaluated across 14 environments under normal and waterlogging conditions in Indonesia from 2018 to 2020. Waterlogging imposed at the V6 stage for ten consecutive days significantly hampered the plant height and ear height, slightly delayed flowering dates, and reduced yield and yield components. The genotype, location, and genotype by location effects were significant on yield, but the genotype by waterlogging effect was not. Stress tolerance index is highly significantly correlated (p < 0.01) with yield in both normal (r = 0.90) and waterlogging (r = 0.96) conditions. The GGE biplot analysis on yield revealed five sectors, two mega-environments, and five vertex genotypes. This study indicated the possibility of breeding maize hybrids tolerant to waterlogging (G05), as well as high-yielding hybrids under both conditions (G07).

Physiological and comparative transcriptome analyses reveal the mechanisms underlying waterlogging tolerance in a rapeseed anthocyanin-more mutant

BACKGROUND

Rapeseed (Brassica napus) is the second largest oil crop worldwide. It is widely used in food, energy production and the chemical industry, as well as being an ornamental. Consequently, it has a large economic value and developmental potential. Waterlogging is an important abiotic stress that restricts plant growth and development. However, little is known about the molecular mechanisms underlying waterlogging tolerance in B. napus.

RESULTS

In the present study, the physiological changes and transcriptomes of germination-stage rapeseed in response to waterlogging stress were investigated in the B. napus cultivar 'Zhongshuang 11' (ZS11) and its anthocyanin-more (am) mutant, which was identified in our previous study. The mutant showed stronger waterlogging tolerance compared with ZS11, and waterlogging stress significantly increased anthocyanin, soluble sugar and malondialdehyde contents and decreased chlorophyll contents in the mutant after 12 days of waterlogging. An RNA-seq analysis identified 1370 and 2336 differently expressed genes (DEGs) responding to waterlogging stress in ZS11 and am, respectively. An enrichment analysis revealed that the DEGs in ZS11 were predominately involved in carbohydrate metabolism, whereas those in the am mutant were particularly enriched in plant hormone signal transduction and response to endogenous stimulation. In total, 299 DEGs were identified as anthocyanin biosynthesis-related structural genes (24) and regulatory genes encoding transcription factors (275), which may explain the increased anthocyanin content in the am mutant. A total of 110 genes clustered in the plant hormone signal transduction pathway were also identified as DEGs, including 70 involved in auxin and ethylene signal transduction that were significantly changed in the mutant. Furthermore, the expression levels of 16 DEGs with putative roles in anthocyanin accumulation and biotic/abiotic stress responses were validated by quantitative real-time PCR as being consistent with the transcriptome profiles.

CONCLUSION

This study provides new insights into the molecular mechanisms of increased anthocyanin contents in rapeseed in response to waterlogging stress, which should be useful for reducing the damage caused by waterlogging stress and for further breeding new rapeseed varieties with high waterlogging tolerance.

Effects of Waterlogging on Soybean Rhizosphere Bacterial Community Using V4, LoopSeq, and PacBio 16S rRNA Sequence

Waterlogging causes a significant reduction in soil oxygen levels, which in turn negatively affects soil nutrient use efficiency and crop yields. Rhizosphere microbes can help plants to better use nutrients and thus better adapt to this stress, while it is not clear how the plant-associated microbes respond to waterlogging stress. There are also few reports on whether this response is influenced by different sequencing methods and by different soils. In this study, using partial 16S rRNA sequencing targeting the V4 region and two full-length 16S rRNA sequencing approaches targeting the V1 to V9 regions, the effects of waterlogging on soybean rhizosphere bacterial structure in two types of soil were examined. Our results showed that, compared with the partial 16S sequencing, full-length sequencing, both LoopSeq and Pacific Bioscience (PacBio) 16S sequencing, had a higher resolution. On both types of soil, all the sequencing methods showed that waterlogging significantly affected the bacterial community structure of the soybean rhizosphere and increased the relative abundance of Geobacter. Furthermore, modular analysis of the cooccurrence network showed that waterlogging increased the relative abundance of some microorganisms related to nitrogen cycling when using V4 sequencing and increased the microorganisms related to phosphorus cycling when using LoopSeq and PacBio 16S sequencing methods. Core microorganism analysis further revealed that the enriched members of different species might play a central role in maintaining the stability of bacterial community structure and ecological functions. Together, our study explored the role of microorganisms enriched at the rhizosphere under waterlogging in assisting soybeans to resist stress. Furthermore, compared to partial and PacBio 16S sequencing, LoopSeq offers improved accuracy and reduced sequencing prices, respectively, and enables accurate species-level and strain identification from complex environmental microbiome samples. IMPORTANCE Soybeans are important oil-bearing crops, and waterlogging has caused substantial decreases in soybean production all over the world. The microbes associated with the host have shown the ability to promote plant growth, nutrient absorption, and abiotic resistance. High-throughput sequencing of partial 16S rRNA is the most commonly used method to analyze the microbial community. However, partial sequencing cannot provide correct classification information below the genus level, which greatly limits our research on microbial ecology. In this study, the effects of waterlogging on soybean rhizosphere microbial structure in two soil types were explored using partial 16S rRNA and full-length 16S gene sequencing by LoopSeq and Pacific Bioscience (PacBio). The results showed that full-length sequencing had higher classification resolution than partial sequencing. Three sequencing methods all indicated that rhizosphere bacterial community structure was significantly impacted by waterlogging, and the relative abundance of Geobacter was increased in the rhizosphere in both soil types after suffering waterlogging. Moreover, the core microorganisms obtained by different sequencing methods all contain species related to nitrogen cycling. Together, our study not only explored the role of microorganisms enriched at the rhizosphere level under waterlogging in assisting soybean to resist stress but also showed that LoopSeq sequencing is a less expensive and more convenient method for full-length sequencing by comparing different sequencing methods.

Uncovering the roles of hemoglobins in soybean facing water stress

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

Calcium peroxide alleviates the waterlogging stress of rapeseed by improving root growth status in a rice-rape rotation field

Waterlogging stress has a negative influence on agricultural production, particularly for rapeseed yield in a rice-rape rotation field. To alleviate the profound impacts of waterlogging stress on rapeseed production, a new fertilization with calcium peroxide (CaO₂) was proposed. In this field experiment, with the conventional rape (Brassica napus L.) variety fengyou958 (FY958) and early maturing rape variety xiangyou420 (XY420) as materials, waterlogging was imposed from the bud to flowering stage, and three supplies of CaO₂ (0, C1 for the 594 kg hm^-2 and C2 for the 864 kg hm^-2) were added as basal fertilizer. The results showed that CaO₂ significantly reduced the accumulation of fermentation products in roots and alleviated the peroxidation of leaves. The reduced waterlogging stress promoted the root vigor and agronomic characters, such as branches, plant height and stem diameter, accelerated dry matter and nutrients accumulation, and resulting in 22.7% (C1) to 232.8% (C2) higher grain yields in XY420, and 112.4% (C1) to 291.8% (C2) higher grain yields in FY958, respectively. In conclusion, 594 kg hm^-2 to 864 kg hm^-2 CaO₂ application restored the growth of waterlogged rapeseed leaves, and reduced the anaerobic intensity of root, which enhanced the resistance of plants to waterlogging, and improved crop productivity. In a certain range, the higher CaO₂ application, the more the yield. This study provides a valid method to prevent damage from flooding in crop fields.

Effect of different waterlogging periods on biochemistry, growth, and chlorophyll a fluorescence of Arachis hypogaea L

Peanut is among the main oil crops in India with huge economic importance. The unpredictable rainy season during the growing time of peanuts causes waterlogging in peanut fields. Waterlogging triggers major environmental limitations that negatively affect the growth, physiology, and development of peanuts. Thus, the export and production of peanuts are severely affected by waterlogging. Therefore, the understanding of metabolic mechanisms under waterlogging is important to future water-stress tolerance breeding in peanuts. This study aimed to evaluate how peanuts responded to various waterlogging conditions in terms of their development, metabolic processes, and chlorophyll fluorescence characteristics. The evaluations were carried out at different stages of peanut variety DH-86 treated with waterlogging. The peanut plants were subjected to different waterlogging periods of 20, 40, 60, 80, and 100 days. The growth parameters including total dry mass, total leaf area, and total leaves number were calculated in all treatments. The phenomenological and specific energy fluxes and maximum photosystem II efficiency (F_V/Fm) were also determined. The measurements were done statistically using PCA, G-Means clustering, and correlation analysis to explore the interaction between different physiological parameters. The waterlogging for 100 days caused a significant reduction in the total number of leaves, dry mass, and total leaf area. The most sensitive parameters are specific and phenomenological energy fluxes and Fv/Fm, which notably decreased as waterlogging duration increased. The results indicated the growth and physiological performance of the peanut cv. DH-86 was affected significantly due to waterlogging and the interaction between all these parameters in waterlogging. This research focused on how peanuts respond to waterlogging stress and provides the basis for future plant breeding efforts to improve peanut waterlogging tolerance, especially in rainy regions. This will improve the sustainability of the entire peanut industry.

Quantitative Proteomics and Relative Enzymatic Activities Reveal Different Mechanisms in Two Peanut Cultivars (Arachis hypogaea L.) Under Waterlogging Conditions

Peanut is an important oil and economic crop in China. The rainy season (April-June) in the downstream Yangtze River in China always leads to waterlogging, which seriously affects plant growth and development. Therefore, understanding the metabolic mechanisms under waterlogging stress is important for future waterlogging tolerance breeding in peanut. In this study, waterlogging treatment was carried out in two different peanut cultivars [Zhonghua 4 (ZH4) and Xianghua08 (XH08)] with different waterlogging tolerance. The data-independent acquisition (DIA) technique was used to quantitatively identify the differentially accumulated proteins (DAPs) between two different cultivars. Meanwhile, the functions of DAPs were predicted, and the interactions between the hub DAPs were analyzed. As a result, a total of 6,441 DAPs were identified in ZH4 and its control, of which 49 and 88 DAPs were upregulated and downregulated under waterlogging stress, respectively, while in XH08, a total of 6,285 DAPs were identified, including 123 upregulated and 114 downregulated proteins, respectively. The hub DAPs unique to the waterlogging-tolerant cultivar XH08 were related to malate metabolism and synthesis, and the utilization of the glyoxylic acid cycle, such as L-lactate dehydrogenase, NAD+-dependent malic enzyme, aspartate aminotransferase, and glutamate dehydrogenase. In agreement with the DIA results, the alcohol dehydrogenase and malate dehydrogenase activities in XH08 were more active than ZH4 under waterlogging stress, and lactate dehydrogenase activity in XH08 was prolonged, suggesting that XH08 could better tolerate waterlogging stress by using various carbon sources to obtain energy, such as enhancing the activity of anaerobic respiration enzymes, catalyzing malate metabolism and the glyoxylic acid cycle, and thus alleviating the accumulation of toxic substances. This study provides insight into the mechanisms in response to waterlogging stress in peanuts and lays a foundation for future molecular breeding targeting in the improvement of peanut waterlogging tolerance, especially in rainy area, and will enhance the sustainable development in the entire peanut industry.

Towards Monitoring Waterlogging with Remote Sensing for Sustainable Irrigated Agriculture

Waterlogging is an increasingly important issue in irrigated agriculture that has a detrimental impact on crop productivity. The above-ground effect of waterlogging on crops is hard to distinguish from water deficit stress with remote sensing, as responses such as stomatal closure and leaf wilting occur in both situations. Currently, waterlogging as a source of crop stress is not considered in remote sensing-based evaporation algorithms and this may therefore lead to erroneous interpretation for irrigation scheduling. Monitoring waterlogging can improve evaporation models to assist irrigation management. In addition, frequent spatial information on waterlogging will provide agriculturalists information on land trafficability, assist drainage design, and crop choice. This article provides a scientific perspective on the topic of waterlogging by consulting literature in the disciplines of agronomy, hydrology, and remote sensing. We find the solution to monitor waterlogging lies in a multi-sensor approach. Future scientific routes should focus on monitoring waterlogging by combining remote sensing and ancillary data. Here, drainage parameters deduced from high spatial resolution Digital Elevation Models (DEMs) can play a crucial role. The proposed approaches may provide a solution to monitor and prevent waterlogging in irrigated agriculture.

Novel Insights Into Genetic Responses for Waterlogging Stress in Two Local Wheat Cultivars in Yangtze River Basin

Wheat (Triticum aestivum L.), the most widely cultivated crop, is affected by waterlogging that limited the wheat production. Given the incompleteness of its genome annotation, PacBio SMRT plus Illumina short-read sequencing strategy provided an efficient approach to investigate the genetic regulation of waterlogging stress in wheat. A total of 947,505 full-length non-chimetric (FLNC) sequences were obtained with two wheat cultivars (XM55 and YM158) with PacBio sequencing. Of these, 5,309 long-non-coding RNAs, 1,574 fusion genes and 739 transcription factors were identified with the FLNC sequences. These full-length transcripts were derived from 49,368 genes, including 47.28% of the genes annotated in IWGSC RefSeq v1.0 and 40.86% genes encoded two or more isoforms, while 27.31% genes in the genome annotation of IWGSC RefSeq v1.0 were multiple-exon genes encoding two or more isoforms. Meanwhile, the individuals with waterlogging treatments (WL) and control group (CK) were selected for Illumina sequencing. Totally, 6,829 differentially expressed genes (DEGs) were detected from four pairwise comparisons. Notably, 942 DEGs were overlapped in the two comparisons (i.e., XM55-WL vs. YM158-WL and YM158-WL vs. YM158-CK). Undoubtedly, the genes involved in photosynthesis were downregulated after waterlogging treatment in two cultivars. Notably, the genes related to steroid biosynthesis, steroid hormone biosynthesis, and downstream plant hormone signal transduction were significantly upregulated after the waterlogging treatment, and the YM158 variety revealed different genetic regulation patterns compared with XM55. The findings provided valuable insights into unveiling regulation mechanisms of waterlogging stress in wheat at anthesis and contributed to molecular selective breeding of new wheat cultivars in future.

Deficiency in alcohol dehydrogenase 2 reduces arsenic in rice grains by suppressing silicate transporters

Paddy fields are anaerobic and facilitate arsenite (As(III)) elution from the soil. Paddy-field rice accumulates arsenic (As) in its grains because silicate transporters actively assimilate As(III) during the reproductive stage. Reducing the As level in rice grains is an important challenge for agriculture. Using a forward genetic approach, we isolated a rice (Oryza sativa) mutant, low arsenic line 3 (las3), whose As levels were decreased in aerial tissues, including grains. The low-As phenotype was not observed in young plants before heading (emergence of the panicle). Genetic analyses revealed that a deficiency in alcohol dehydrogenase (ADH) 2 by mutation is responsible for the phenotype. Among the three rice ADH paralogues, ADH2 was the most efficiently produced in root tissue under anaerobic conditions. In wild-type (WT), silicon and As concentrations in aerial tissues increased with growth. However, the increase was suppressed in las3 during the reproductive stage. Accordingly, the gene expression of two silicate transporters, Lsi1 and Lsi2, was increased in WT around the time of heading, whereas the increase was suppressed in las3. These results indicate that the low-As phenotype in las3 is due to silicate transporter suppression. Measurement of intracellular pH by 31P-nuclear magnetic resonance revealed intracellular acidification of las3 roots under hypoxia, suggesting that silicate transporter suppression in las3 might arise from an intracellular pH decrease, which is known to be facilitated by a deficiency in ADH activity under anaerobic conditions. This study provides valuable insight into reducing As levels in rice grains.

Sorghum mitigates climate variability and change on crop yield and quality

Global food insecurity concerns due to climate change, emphasizes the need to focus on the sensitivity of sorghum to climate change and potential crop improvement strategies available, which is discussed in the current review to promote climate-smart agriculture. Climate change effects immensely disturb the global agricultural systems by reducing crop production. Changes in extreme weather and climate events such as high-temperature episodes and extreme rainfalls events, droughts, flooding adversely affect the production of staple food crops, posing threat to ecosystem resilience. The resulting crop losses lead to food insecurity and poverty and question the sustainable livelihoods of small farmer communities, particularly in developing countries. In view of this, it is essential to focus and adapt climate-resilient food crops which need lower inputs and produce sustainable yields through various biotic and abiotic stress-tolerant traits. Sorghum, "the camel of cereals", is one such climate-resilient food crop that is less sensitive to climate change vulnerabilities and also an important staple food in many parts of Asia and Africa. It is a rainfed crop and provides many essential nutrients. Understanding sorghum's sensitivity to climate change provides scope for improvement of the crop both in terms of quantity and quality and alleviates food and feed security in future climate change scenarios. Thus, the current review focused on understanding the sensitivity of sorghum crop to various stress events due to climate change and throws light on different crop improvement strategies available to pave the way for climate-smart agriculture.

Harnessing the potential of plant transcription factors in developing climate resilient crops to improve global food security: Current and future perspectives

Crop plants should be resilient to climatic factors in order to feed ever-increasing populations. Plants have developed stress-responsive mechanisms by changing their metabolic pathways and switching the stress-responsive genes. The discovery of plant transcriptional factors (TFs), as key regulators of different biotic and abiotic stresses, has opened up new horizons for plant scientists. TFs perceive the signal and switch certain stress-responsive genes on and off by binding to different cis-regulatory elements. More than 50 families of plant TFs have been reported in nature. Among them, DREB, bZIP, MYB, NAC, Zinc-finger, HSF, Dof, WRKY, and NF-Y are important with respect to biotic and abiotic stresses, but the potential of many TFs in the improvement of crops is untapped. In this review, we summarize the role of different stress-responsive TFs with respect to biotic and abiotic stresses. Further, challenges and future opportunities linked with TFs for developing climate-resilient crops are also elaborated.

Elucidating the morpho-physiological adaptations and molecular responses under long-term waterlogging stress in maize through gene expression analysis

Waterlogging stress in maize is one of the emerging abiotic stresses in the current climate change scenario. To gain insights in transcriptional reprogramming during late hours of waterlogging stress under field conditions, we aimed to elucidate the transcriptional and anatomical changes in two contrasting maize inbreds viz. I110 (susceptible) and I172 (tolerant). Waterlogging stress reduced dry matter translocations from leaves and stems to ears, resulting in a lack of sink capacity and inadequate grain filling in I110, thus decreased the grain yield drastically. The development of aerenchyma cells within 48 h in I172 enabled hypoxia tolerance. The upregulation of alanine aminotransferase, ubiquitin activating enzyme E1, putative mitogen activated protein kinase and pyruvate kinase in I172 suggested that genes involved in protein degradation, signal transduction and carbon metabolism provided adaptive mechanisms during waterlogging. Overexpression of alcohol dehydrogenase, sucrose synthase, aspartate aminotransferase, NADP dependent malic enzyme and many miRNA targets in I110 indicated that more oxygen and energy consumption might have shortened plant survival during long-term waterlogging exposure. To the best of our knowledge, this is the first report of transcript profiling at late stage (24-96 h) of waterlogging stress under field conditions and provides new visions to understand the molecular basis of waterlogging tolerance in maize.

Genome-wide analysis of HSP90 gene family in the Mediterranean olive (Olea europaea subsp. europaea) provides insight into structural patterns, evolution and functional diversity

Plants regularly experience multiple abiotic and biotic pressures affecting their normal development. The 90-kDa heat shock protein (HSP90) plays a dynamic role in countering abiotic and biotic stresses via a plethora of functional mechanisms. The HSP90 has been investigated in many plant species. However, there is little information available about this gene family in the cultivated Mediterranean olive tree, Olea europaea subsp. europaea var. europaea. In the current study, we systematically performed genome-wide identification and characterization of the HSP90 gene family in O. europaea var. europaea (OeHSP90s). Twelve regular OeHSP90s were identified, which were phylogenetically grouped into two major clusters and four sub-clusters, showing five paralogous gene pairs evolving under purifying selection. All of the 12 proteins contained a Histidine kinase-like ATPase (HATPase_c) domain, justifying the role played by HSP90 proteins in ATP binding and hydrolysis. The predicted 3D structure of OeHSP90 proteins provided information to understand their functions at the biochemical level. Consistent with their phylogenetic relationships, OeHSP90 members were predicted to be localized in different cellular compartments, suggesting their involvement in various subcellular processes. In consonance with their spatial organization, olive HSP90 family members were found to share similar motif arrangements and similar number of exons. We found that OeHSP90 promoters contained various cis-acting elements associated with light responsiveness, hormone signaling pathways and reaction to various stress conditions. In addition, expression sequence tags (ESTs) analysis offered a view of OeHSP90 tissue- and developmental stage specific pattern of expression. Proteins interacting with OeHSP90s were predicted and their potential roles were discussed. Overall, our results offer premises for further investigation of the implication of HSP90 genes in the physiological processes of the olive and its adaptation to stresses.

Selection of flooding stress tolerant sweetpotato cultivars based on biochemical and phenotypic characterization

Sweetpotato [Ipomoea batatas (L.) Lam] serves as a sustainable food source and ensures nutrition security in the face of climate change. Recently, farmers have developed increased interest in replacing rice with sweetpotato in paddy fields for higher income. However, sweetpotato is more susceptible to flooding stress than other abiotic stresses including drought and salinity. Here, we selected flooding tolerant sweetpotato cultivars based on biochemical characterization. Young seedlings of 33 sweetpotato cultivars were subjected to flooding stress for 20 days, and Yeonjami (YJM) was identified as the most flooding tolerant sweetpotato cultivar. Plant growth and biochemical characteristics of YJM were compared with those of Jeonmi (JM), a flooding sensitive sweetpotato cultivar. Under flooding stress, YJM showed higher content of chlorophyll and lower inhibition of plant height and fibrous root length than JM. Biochemical characterization revealed that although malondialdehyde and hydrogen peroxide contents were increased in fibrous roots of both cultivars, the amount of increase was 4-fold lower in YJM than in JM. Additionally, leaves of YJM showed higher ascorbate peroxidase activity than those of JM under flooding stress. Our results suggest that high membrane stability and antioxidant capacity are important flooding tolerance factors in sweetpotato. Furthermore, several flooding tolerance-related genes involved in starch and sucrose metabolism, fermentation, and cell wall loosening showed earlier induction and higher transcript levels in YJM leaves and fibrous roots than in JM tissues under flooding stress. Thus, phenotypic and biochemical characterization suggests that YJM could be used as a flooding tolerant sweetpotato cultivar.

Melatonin-Induced Water Stress Tolerance in Plants: Recent Advances

Water stress (drought and waterlogging) is severe abiotic stress to plant growth and development. Melatonin, a bioactive plant hormone, has been widely tested in drought situations in diverse plant species, while few studies on the role of melatonin in waterlogging stress conditions have been published. In the current review, we analyze the biostimulatory functions of melatonin on plants under both drought and waterlogging stresses. Melatonin controls the levels of reactive oxygen and nitrogen species and positively changes the molecular defense to improve plant tolerance against water stress. Moreover, the crosstalk of melatonin and other phytohormones is a key element of plant survival under drought stress, while this relationship needs further investigation under waterlogging stress. In this review, we draw the complete story of water stress on both sides-drought and waterlogging-through discussing the previous critical studies under both conditions. Moreover, we suggest several research directions, especially for waterlogging, which remains a big and vague piece of the melatonin and water stress puzzle.

Melatonin-Induced Water Stress Tolerance in Plants: Recent Advances

Water stress (drought and waterlogging) is severe abiotic stress to plant growth and development. Melatonin, a bioactive plant hormone, has been widely tested in drought situations in diverse plant species, while few studies on the role of melatonin in waterlogging stress conditions have been published. In the current review, we analyze the biostimulatory functions of melatonin on plants under both drought and waterlogging stresses. Melatonin controls the levels of reactive oxygen and nitrogen species and positively changes the molecular defense to improve plant tolerance against water stress. Moreover, the crosstalk of melatonin and other phytohormones is a key element of plant survival under drought stress, while this relationship needs further investigation under waterlogging stress. In this review, we draw the complete story of water stress on both sides-drought and waterlogging-through discussing the previous critical studies under both conditions. Moreover, we suggest several research directions, especially for waterlogging, which remains a big and vague piece of the melatonin and water stress puzzle.

Transcriptome analysis on responses of orchardgrass (Dactylis glomerata L.) leaves to a short term flooding

BACKGROUND

Orchardgrass (Dactylis glomerata L.) is a popular cool-season perennial grass with a high production value, and orchardgrass seed is the fourth top-selling forage grass seed in the world. However, its yield and quality are often affected by flooding. To date, the molecular responses of orchardgrass to flooding were poorly understood.

RESULTS

Here, we performed mRNA-seq to explore the transcriptomic responses of orchardgrass to a short term flooding (8 h and 24 h). There were 1454 and 565 differentially expressed genes identified in the 8 h and 24 h of flooding, respectively, compared to well control. GO functional enrichment analysis showed that oxidoreductase activity and oxidation-reduction process were highly present, suggesting that flooding induced the response to oxygen stress. Pathways enrichment analysis highlights the importance of glutathione metabolism, peroxidase, glycolysis and plant hormone signal transduction in response to flooding acclimation. Besides, the ROS clearance system is activated by significantly expressed glutathione S-transferase and genes encoding SOD and CAT (CAT1 and CDS2). The significant positive correlation between RNA sequencing data and a qPCR analysis indicated that the identified genes were credible.

CONCLUSION

In the process of orchardgrass response to flooding stress, multiple differential genes and biological processes have participated in its acclimation to flooding, especially the biological processes involved in the removal of ROS. These results provide a basis for further research on the adaptation mechanism of orchardgrass to flood tolerance.

Genome-Wide Analysis of Gene Expression Provides New Insights into Waterlogging Responses in Barley (Hordeum vulgare L.)

Waterlogging is a major abiotic stress causing oxygen depletion and carbon dioxide accumulation in the rhizosphere. Barley is more susceptible to waterlogging stress than other cereals. To gain a better understanding, the genome-wide gene expression responses in roots of waterlogged barley seedlings of Yerong and Deder2 were analyzed by RNA-Sequencing. A total of 6736, 5482, and 4538 differentially expressed genes (DEGs) were identified in waterlogged roots of Yerong at 72 h and Deder2 at 72 and 120 h, respectively, compared with the non-waterlogged control. Gene Ontology (GO) enrichment analyses showed that the most significant changes in GO terms, resulted from these DEGs observed under waterlogging stress, were related to primary and secondary metabolism, regulation, and oxygen carrier activity. In addition, more than 297 transcription factors, including members of MYB, AP2/EREBP, NAC, WRKY, bHLH, bZIP, and G2-like families, were identified as waterlogging responsive. Tentative important contributors to waterlogging tolerance in Deder2 might be the highest up-regulated DEGs: Trichome birefringence, α/β-Hydrolases, Xylanase inhibitor, MATE efflux, serine carboxypeptidase, and SAUR-like auxin-responsive protein. The study provides insights into the molecular mechanisms underlying the response to waterlogging in barley, which will be of benefit for future studies of molecular responses to waterlogging and will greatly assist barley genetic research and breeding.

Indoleacetic Acid Levels in Wheat and Rice Seedlings under Oxygen Deficiency and Subsequent Reoxygenation

The lack of oxygen and post-anoxic reactions cause significant alterations of plant growth and metabolism. Plant hormones are active participants in these alterations. This study focuses on auxin-a phytohormone with a wide spectrum of effects on plant growth and stress tolerance. The indoleacetic acid (IAA) content in plants was measured by ELISA. The obtained data revealed anoxia-induced accumulation of IAA in wheat and rice seedlings related to their tolerance of oxygen deprivation. The highest IAA accumulation was detected in rice roots. Subsequent reoxygenation was accompanied with a fast auxin reduction to the control level. A major difference was reported for shoots: wheat seedlings contained less than one-third of normoxic level of auxin during post-anoxia, while IAA level in rice seedlings rapidly recovered to normoxic level. It is likely that the mechanisms of auxin dynamics resulted from oxygen-induced shift in auxin degradation and transport. Exogenous IAA treatment enhanced plant survival under anoxia by decreased electrolyte leakage, production of hydrogen peroxide and lipid peroxidation. The positive effect of external IAA application coincided with improvement of tolerance to oxygen deprivation in the 35S:iaaM × 35S:iaaH lines of transgene tobacco due to its IAA overproduction.

Immunoprofiling of Cell Wall Carbohydrate Modifications During Flooding-Induced Aerenchyma Formation in Fabaceae Roots

Understanding plant adaptation mechanisms to prolonged water immersion provides options for genetic modification of existing crops to create cultivars more tolerant of periodic flooding. An important advancement in understanding flooding adaptation would be to elucidate mechanisms, such as aerenchyma air-space formation induced by hypoxic conditions, consistent with prolonged immersion. Lysigenous aerenchyma formation occurs through programmed cell death (PCD), which may entail the chemical modification of polysaccharides in root tissue cell walls. We investigated if a relationship exists between modification of pectic polysaccharides through de-methyl esterification (DME) and the formation of root aerenchyma in select Fabaceae species. To test this hypothesis, we first characterized the progression of aerenchyma formation within the vascular stele of three different legumes-Pisum sativum, Cicer arietinum, and Phaseolus coccineus-through traditional light microscopy histological staining and scanning electron microscopy. We assessed alterations in stele morphology, cavity dimensions, and cell wall chemistry. Then we conducted an immunolabeling protocol to detect specific degrees of DME among species during a 48-hour flooding time series. Additionally, we performed an enzymatic pretreatment to remove select cell wall polymers prior to immunolabeling for DME pectins. We were able to determine that all species possessed similar aerenchyma formation mechanisms that begin with degradation of root vascular stele metaxylem cells. Immunolabeling results demonstrated DME occurs prior to aerenchyma formation and prepares vascular tissues for the beginning of cavity formation in flooded roots. Furthermore, enzymatic pretreatment demonstrated that removal of cellulose and select hemicellulosic carbohydrates unmasks additional antigen binding sites for DME pectin antibodies. These results suggest that additional carbohydrate modification may be required to permit DME and subsequent enzyme activity to form aerenchyma. By providing a greater understanding of cell wall pectin remodeling among legume species, we encourage further investigation into the mechanism of carbohydrate modifications during aerenchyma formation and possible avenues for flood-tolerance improvement of legume crops.

Proteomic Analysis of Irradiation with Millimeter Waves on Soybean Growth under Flooding Conditions

Improving soybean growth and tolerance under environmental stress is crucial for sustainable development. Millimeter waves are a radio-frequency band with a wavelength range of 1-10 mm that has dynamic effects on organisms. To investigate the potential effects of millimeter-waves irradiation on soybean seedlings, morphological and proteomic analyses were performed. Millimeter-waves irradiation improved the growth of roots/hypocotyl and the tolerance of soybean to flooding stress. Proteomic analysis indicated that the irradiated soybean seedlings recovered under oxidative stress during growth, whereas proteins related to glycolysis and ascorbate/glutathione metabolism were not affected. Immunoblot analysis confirmed the promotive effect of millimeter waves to glycolysis- and redox-related pathways under flooding conditions. Sugar metabolism was suppressed under flooding in unirradiated soybean seedlings, whereas it was activated in the irradiated ones, especially trehalose synthesis. These results suggest that millimeter-waves irradiation on soybean seeds promotes the recovery of soybean seedlings under oxidative stress, which positively regulates soybean growth through the regulation of glycolysis and redox related pathways.

A heuristic classification of woody plants based on contrasting shade and drought strategies

Woody plants vary in their adaptations to drought and shade. For a better prediction of vegetation responses to drought and shade within dynamic global vegetation models, it is critical to group species into functional types with similar adaptations. One of the key challenges is that the adaptations are generally determined by a large number of plant traits that may not be available for a large number of species. In this study, we present two heuristic woody plant groups that were separated using cluster analysis in a three-dimensional trait-environment space based on three key metrics for each species: mean xylem embolism resistance, shade tolerance and habitat aridity. The two heuristic groups separate these species into tolerators and avoiders. The tolerators either rely on their high embolism resistance to tolerate drought in arid habitats (e.g., Juniperus and Prunus) or rely on high shade tolerance to withstand shaded conditions in wet habitats (e.g., Picea, Abies and Acer). In contrast, all avoiders have low embolism resistance and low shade tolerance. In arid habitats, avoiders tend to minimize catastrophic embolism (e.g., most Pinus species) while in wet habitats, they may survive despite low shade tolerance (e.g., Betula, Populus, Alnus and Salix). Because our approach links traits to the environmental conditions, we expect it could be a promising framework for predicting changes in species composition, and therefore ecosystem function, under changing environmental conditions.

Identification and validation of reference genes for real-time quantitative RT-PCR analysis in jute

BACKGROUND

With the availability of genome sequences, gene expression analysis of jute has drawn considerable attention for understanding the regulatory mechanisms of fiber development and improving fiber quality. Gene expression profiles of a target gene can provide valuable clues towards the understanding of its biological function. Reverse transcription quantitative real-time PCR (qRT-PCR) is the best method for targeted gene expression analysis due to its sensitivity and reproducibility. However, calculating relative expression requires reference genes, which must be stable across various biological conditions. For this purposes, 11 prospective genes namely, 28S RNA, ACT7, CYP, EF1A, EF2, ETIF3E, GAPDH, PP2Ac, PTB, UBC2 and UBI1 were evaluated for their potential use as reference genes in jute.

RESULTS

The expression stabilities of eleven prospective genes were analyzed in various jute plant tissues, such as the root, stick, bark, leaf, flower, seed and fiber, as well as under abiotic (waterlogged, drought and salinity) and biotic stress (infestation with Macrophomina phaseolina) conditions with different time points. All 11 genes were variably expressed in different tissues and stress conditions. To find suitable reference genes in different sample sets, a comprehensive approach based on four statistical algorithms such as GeNorm, BestKeeper, NormFinder the ΔCt was used. The PP2Ac and EF2 genes were the most stably expressed across the different tissues. ACT7 and UBC2 were suitable reference genes under drought stress, and CYP and PP2Ac were the most appropriate after inoculation with Macrophomina phaseolina. Under salinity stress, PP2Ac and UBC2 were the best genes, and ACT7 and PP2Ac were the most suitable under waterlogged conditions.

CONCLUSION

Expression stability of reference genes from jute varied in different tissues and selected experimental conditions. Our results provide a valuable resource for the accurate normalization of gene expression experiments in fiber research for important bast fiber crops.

Comprehensive metabolomic and proteomic analysis in biochemical metabolic pathways of rice spikes under drought and submergence stress

Drought and submergence are the main adverse factors affecting plant growth and yield formation in parts of China, especially in the Yangtze River region. In this study, T1 (drought duration: 10 d), T2 (submergence duration: 8 d) and CK (control) treatments were applied. This work aimed to study the changes in metabolic pathways of rice under drought and submergence stress during the panicle differentiation stage. The identification and analysis of differential metabolites and differentially expressed proteins functions indicate that drought and submergence mainly promoted the energy metabolism pathway, carbon fixation in photosynthetic organism pathway, carbohydrate metabolic process, and reactive oxygen species (ROS) metabolic process functions. Under drought stress, the inhibition of photosynthetic rate is mainly through stomatal conductance restriction, and flavonoid pathway regulates the metabolic process of ROS. Under submergence stress, the electron transfer chain was destroyed to inhibit the photosynthetic rate, and the antioxidant system was activated to regulate the metabolism of ROS. The changes in related enzymes or proteins in metabolic regulatory networks are analyzed, which will be conducive to understanding the response mechanism of rice drought and submergence more deeply and provide a scientific basis for rice drought and submergence prevention and mitigation, and the breeding of drought- and submergence-resistant varieties.

PhERF2, an ethylene-responsive element binding factor, plays an essential role in waterlogging tolerance of petunia

Ethylene-responsive element binding factors (ERFs) are involved in regulation of various stress responses in plants, but their biological functions in waterlogging stress are largely unclear. In this study, we identified a petunia (Petunia × hybrida) ERF gene, PhERF2, that was significantly induced by waterlogging in wild-type (WT). To study the regulatory role of PhERF2 in waterlogging responses, transgenic petunia plants with RNAi silencing and overexpression of PhERF2 were generated. Compared with WT plants, PhERF2 silencing compromised the tolerance of petunia seedlings to waterlogging, shown as 96% mortality after 4 days waterlogging and 14 days recovery, while overexpression of PhERF2 improved the survival of seedlings subjected to waterlogging. PhERF2-RNAi lines exhibited earlier and more severe leaf chlorosis and necrosis than WT, whereas plants overexpressing PhERF2 showed promoted growth vigor under waterlogging. Chlorophyll content was dramatically lower in PhERF2-silenced plants than WT or overexpression plants. Typical characteristics of programmed cell death (PCD), DNA condensation, and moon-shaped nuclei were only observed in PhERF2-overexpressing lines but not in PhERF2-RNAi or control lines. Furthermore, transcript abundances of the alcoholic fermentation-related genes ADH1-1, ADH1-2, ADH1-3, PDC1, and PDC2 were reduced in PhERF2-silenced plants, but increased in PhERF2-overexpressing plants following exposure to 12-h waterlogging. In contrast, expression of the lactate fermentation-related gene LDH was up-regulated in PhERF2-silenced plants, but down-regulated in its overexpressing plants. Moreover, PhERF2 was observed to directly bind to the ADH1-2 promoter bearing ATCTA motifs. Our results demonstrate that PhERF2 contributes to petunia waterlogging tolerance through modulation of PCD and alcoholic fermentation system.

Preformed and induced mechanisms underlies the differential responses of Prunus rootstock to hypoxia

Analysis of the transcriptomic changes produced in response to hypoxia in root tissues from two rootstock Prunus genotypes differing in their sensitivity to waterlogging: resistant Myrobalan 'P.2175' (P. cerasifera Erhr.), and sensitive 'Felinem' hybrid [P. amygdalus Batsch × P. persica (L.) Batsch] revealed alterations in both metabolism and regulatory processes. Early hypoxia response in both genotypes is characterized by a molecular program aimed to adapt the cell metabolism to the new conditions. Upon hypoxia conditions, tolerant Myrobalan represses first secondary metabolism gene expression as a strategy to prevent the waste of resources/energy, and by the up-regulation of protein degradation genes probably leading to structural adaptations to long-term response to hypoxia. In response to the same conditions, sensitive 'Felinem' up-regulates a core of signal transduction and transcription factor genes. A combination of PLS-DA and qRT-PCR approaches revealed a set of transcription factors and signalling molecules as differentially regulated in the sensitive and tolerant genotypes including the peach orthologs for oxygen sensors. Apart from providing insights into the molecular processes underlying the differential response to waterlogging of two Prunus rootstocks, our approach reveals a set of candidate genes to be used expression biomarkers for biotech or breeding approaches to waterlogging tolerance.

Plant water transport and aquaporins in oxygen-deprived environments

Oxygen deprivation commonly affects plants exposed to flooding and soil compaction. The resulting root hypoxia has an immediate effect on plant water relations and upsets water balance. Hypoxia inhibits root water transport and triggers stomatal closure. The processes contributing to the inhibition of root hydraulic conductivity and conductance (hydraulic conductivity of the whole root system) are complex and involve changes in root morphology and the functions of aquaporins. Aquaporins (AQPs) comprise a group of membrane intrinsic proteins that are responsible for the transport of water, as well as some small neutral solutes and ions. They respond to a wide range of environmental stresses including O₂ deprivation, but the underlying functional mechanisms are still elusive. The aquaporin-mediated water transport is affected by the acidification of the cytoplasm and depletion of ATP that is required for aquaporin phosphorylation and membrane functions. Cytoplasmic pH, phosphorylation, and intracellular Ca²⁺ concentration directly control AQP gating, all of which are related to O₂ deprivation. This review addresses the structural determinants that are essential for pore conformational changes in AQPs, to highlight the underlying mechanisms triggered by O₂ deprivation stress. Gene expression of AQPs is modified in hypoxic plants, which may constitute an important, yet little explored, mechanism of hypoxia tolerance. In addition to water transport, AQPs may contribute to hypoxia tolerance by transporting O₂, H₂O₂, and lactic acid. Responses of plants to O₂ deprivation, and especially those that contribute to maintenance of water transport, are highly complex and entail the signals originating in roots and shoots that lead to and follow the stomatal closure. These complex responses may involve ethylene, abscisic acid, and possibly other hormonal factors and signaling molecules in ways that remain to be elucidated.

Functional Characterization of Waterlogging and Heat Stresses Tolerance Gene Pyruvate decarboxylase 2 from Actinidia deliciosa

A previous report showed that both Pyruvatedecarboxylase (PDC) genes were significantly upregulated in kiwifruit after waterlogging treatment using Illumina sequencing technology, and that the kiwifruit AdPDC1 gene was required during waterlogging, but might not be required during other environmental stresses. Here, the function of another PDC gene, named AdPDC2, was analyzed. The expression of the AdPDC2 gene was determined using qRT-PCR, and the results showed that the expression levels of AdPDC2 in the reproductive organs were much higher than those in the nutritive organs. Waterlogging, NaCl, and heat could induce the expression of AdPDC2. Overexpression of kiwifruit AdPDC2 in transgenic Arabidopsis enhanced resistance to waterlogging and heat stresses in five-week-old seedlings, but could not enhance resistance to NaCl and mannitol stresses at the seed germination stage and in early seedlings. These results suggested that the kiwifruit AdPDC2 gene may play an important role in waterlogging resistance and heat stresses in kiwifruit.

Improvement in Submergence Tolerance of Cherry Through Regulation of Carbohydrate Metabolism and Plant Growth by PsERF and PsCIPK

Cherry is an important fruit tree with delicious taste and high economic value, which have been planted worldwide. However, this species cannot withstand the presence of excessive amount of water; submergence injury sometimes occurs during cultivation of cherry and results in severe economic losses. By using a submergence-tolerant germplasm Prunus serrulata "Yimeng" and a submergence-sensitive germplasm Prunus pseudocerasus "Aihua" as test materials, this study cloned PsERF and PsCIPK, which are related to submergence tolerance in cherry, and analyzed the expression of PsERF and PsCIPK in submergence-tolerant and submergence-sensitive germplasms under submergence stress; moreover, the consistency and correlation of such expression with carbohydrate metabolism and plant growth-related genes (PsPDC, PsSUS, PsRAMY, and PsEXP) were analyzed. The results showed that PsERF and PsCIPK influence the expression of PsPDC, PsSUS, PsRAMY, and PsEXP at different extents under submergence and during recovery to systematically improve the submergence resistance of P. serrulata "Yimeng". This study lays the important theoretical and practical foundation for molecular improvement and germplasm innovation in submergence tolerance in cherry through genetic engineering.

Overexpression of Actinidia deliciosa pyruvate decarboxylase 1 gene enhances waterlogging stress in transgenic Arabidopsis thaliana

Ethanolic fermentation is classically associated with waterlogging tolerance when plant cells switch from respiration to anaerobic fermentation. Pyruvate decarboxylase (PDC), which catalyzes the first step in this pathway, is thought to be the main regulatory enzyme. Here, we cloned a full-length PDC cDNA sequence from kiwifruit, named AdPDC1. We determined the expression of the AdPDC1 gene in kiwifruit under different environmental stresses using qRT-PCR, and the results showed that the increase of AdPDC1 expression during waterlogging stress was much higher than that during salt, cold, heat and drought stresses. Overexpression of kiwifruit AdPDC1 in transgenic Arabidopsis enhanced the resistance to waterlogging stress but could not enhance resistance to cold stress at five weeks old seedlings. Overexpression of kiwifruit AdPDC1 in transgenic Arabidopsis could not enhance resistance to NaCl and mannitol stresses at the stage of seed germination and in early seedlings. These results suggested that the kiwifruit AdPDC1 gene is required during waterlogging but might not be required during other environmental stresses. Expression of the AdPDC1 gene was down-regulated by abscisic acid (ABA) in kiwifruit, and overexpression of the AdPDC1 gene in Arabidopsis inhibited seed germination and root length under ABA treatment, indicating that ABA might negatively regulate the AdPDC1 gene under waterlogging stress.

Effect of Waterlogging on Carbohydrate Metabolism and the Quality of Fiber in Cotton (Gossypium hirsutum L.)

Transient waterlogging occurs frequently in the Yangtze River and adversely affects cotton fiber quality. However, the carbohydrate metabolic mechanism that affects fiber quality after waterlogging remains undescribed. Here, the effects of five waterlogging levels (0, 3, 6, 9, and 12 days) were assessed during flowering and boll formation to characterize the carbohydrates, enzymes and genes that affect the fiber quality of cotton after waterlogging. The cellulose and sucrose contents of cotton fibers were significantly decreased after waterlogging for 6 (WL6), 9 (WL9), and 12 d (WL12), although these properties were unaffected after 3 (WL3) and 6 days at the fruiting branch 14-15 (FB14-15). Sucrose phosphate synthase (SPS) was the most sensitive to waterlogging among the enzymes tested. SPS activity was decreased by waterlogging at FB6-7, whereas it was significantly enhanced under WL3-6 at FB10-15. Waterlogging down-regulated the expression of fiber invertase at 10 days post anthesis (DPA), whereas that of expansin, β-1,4-glucanase and endoxyloglucan transferase (XET) was up-regulated with increasing waterlogging time. Increased mRNA levels and activities of fiber SuSy at each fruiting branch indicated that SuSy was the main enzyme responsible for sucrose degradation because it was markedly induced by waterlogging and was active even when waterlogging was discontinued. We therefore concluded that the reduction in fiber sucrose and down-regulation of invertase at 10 DPA led to a markedly shorter fiber length under conditions WL6-12. Significantly decreased fiber strength at FB6-11 for WL6-12 was the result of the inhibition of cellulose synthesis and the up-regulation of expansin, β-1,4-glucanase and XET, whereas fiber strength increased under WL3-6 at FB14-15 due to the increased cellulose content of the fibers. Most of the indictors tested revealed that WL6 resulted in the best compensatory performance, whereas exposure to waterlogged conditions for more than 6 days led to an irreversible limitation in fiber development.

Identification of microRNAs and their targets in Paulownia fortunei plants free from phytoplasma pathogen after methyl methane sulfonate treatment

MicroRNAs (miRNAs) play major roles in plant responses to various biotic and abiotic stresses by regulating gene expression at the transcriptional and post-transcriptional levels. Paulownia witches' broom (PaWB) disease caused by phytoplasmas reduces Paulownia production worldwide. In this study, we investigated the miRNA-mediated plant response to PaWB phytoplasma by Illumina sequencing and degradome analysis of Paulownia fortunei small RNAs (sRNAs). The sRNA and degradome libraries were constructed from healthy and diseased P. fortunei plants and the plants free from phytoplasma pathogen after 60 mg L(-1) methyl methane sulfonate treatment. A total of 96 P. fortunei-conserved miRNAs and 83 putative novel miRNAs were identified. Among them, 37 miRNAs (17 conserved, 20 novel) were found to be differentially expressed in response to PaWB phytoplasma infection. In addition, 114 target genes for 18 of the conserved miRNA families and 33 target genes for 15 of the novel miRNAs in P. fortunei were detected. The expression patterns of 14 of the PaWB phytoplasma-responsive miRNAs and 12 target genes were determined by quantitative real-time polymerase chain reaction (qPCR) experiments. A functional analysis of the miRNA targets indicated that these targeted genes may regulate transcription, stress response, nitrogen metabolism, and various other activities. Our results will help identify the potential roles of miRNAs involved in protecting P. fortunei from diseases.

Differential root transcriptomics in a polyploid non-model crop: the importance of respiration during osmotic stress

To explore the transcriptomic global response to osmotic stress in roots, 18 mRNA-seq libraries were generated from three triploid banana genotypes grown under mild osmotic stress (5% PEG) and control conditions. Illumina sequencing produced 568 million high quality reads, of which 70-84% were mapped to the banana diploid reference genome. Using different uni- and multivariate statistics, 92 genes were commonly identified as differentially expressed in the three genotypes. Using our in house workflow to analyze GO enriched and underlying biochemical pathways, we present the general processes affected by mild osmotic stress in the root and focus subsequently on the most significantly overrepresented classes associated with: respiration, glycolysis and fermentation. We hypothesize that in fast growing and oxygen demanding tissues, mild osmotic stress leads to a lower energy level, which induces a metabolic shift towards (i) a higher oxidative respiration, (ii) alternative respiration and (iii) fermentation. To confirm the mRNA-seq results, a subset of twenty up-regulated transcripts were further analysed by RT-qPCR in an independent experiment at three different time points. The identification and annotation of this set of genes provides a valuable resource to understand the importance of energy sensing during mild osmotic stress.

The sunflower transcription factor HaHB11 improves yield, biomass and tolerance to flooding in transgenic Arabidopsis plants

HaHB11 is a member of the sunflower homeodomain-leucine zipper I subfamily of transcription factors. The analysis of a sunflower microarray hybridized with RNA from HaHB11-transformed leaf-disks indicated the regulation of many genes encoding enzymes from glycolisis and fermentative pathways. A 1300bp promoter sequence, fused to the GUS reporter gene, was used to transform Arabidopsis plants showing an induction of expression after flooding treatments, concurrently with HaHB11 regulation by submergence in sunflower. Arabidopsis transgenic plants expressing HaHB11 under the control of the CaMV 35S promoter and its own promoter were obtained and these plants exhibited significant increases in rosette and stem biomass. All the lines produced more seeds than controls and particularly, those of high expression level doubled seeds yield. Transgenic plants also showed tolerance to flooding stress, both to submergence and waterlogging. Carbohydrates contents were higher in the transgenics compared to wild type and decreased less after submergence treatments. Finally, transcript levels of selected genes involved in glycolisis and fermentative pathways as well as the corresponding enzymatic activities were assessed both, in sunflower and transgenic Arabidopsis plants, before and after submergence. Altogether, the present work leads us to propose HaHB11 as a biotechnological tool to improve crops yield, biomass and flooding tolerance.

Proteins involved in biophoton emission and flooding-stress responses in soybean under light and dark conditions

To know the molecular systems basically flooding conditions in soybean, biophoton emission measurements and proteomic analyses were carried out for flooding-stressed roots under light and dark conditions. Photon emission was analyzed using a photon counter. Gel-free quantitative proteomics were performed to identify significant changes proteins using the nano LC-MS along with SIEVE software. Biophoton emissions were significantly increased in both light and dark conditions after flooding stress, but gradually decreased with continued flooding exposure compared to the control plants. Among the 120 significantly identified proteins in the roots of soybean plants, 73 and 19 proteins were decreased and increased in the light condition, respectively, and 4 and 24 proteins were increased and decreased, respectively, in the dark condition. The proteins were mainly functionally grouped into cell organization, protein degradation/synthesis, and glycolysis. The highly abundant lactate/malate dehydrogenase proteins were decreased in flooding-stressed roots exposed to light, whereas the lysine ketoglutarate reductase/saccharopine dehydrogenase bifunctional enzyme was increased in both light and dark conditions. Notably, however, specific enzyme assays revealed that the activities of these enzymes and biophoton emission were sharply increased after 3 days of flooding stress. This finding suggests that the source of biophoton emission in roots might involve the chemical excitation of electron or proton through enzymatic or non-enzymatic oxidation and reduction reactions. Moreover, the lysine ketoglutarate reductase/saccharopine dehydrogenase bifunctional enzyme may play important roles in responses in flooding stress of soybean under the light condition and as a contributing factor to biophoton emission.

ALA Pretreatment Improves Waterlogging Tolerance of Fig Plants

5-aminolevulinic acid (ALA), a natural and environmentally friendly plant growth regulator, can improve plant tolerance to various environmental stresses. However, whether ALA can improve plant waterlogging tolerance is unknown. Here, we investigated the effects of ALA pretreatment on the waterlogging-induced damage of fig (Ficus carica Linn.) plants, which often suffer from waterlogging stress. ALA pretreatment significantly alleviated stress-induced morphological damage, increased leaf relative water content (RWC), and reduced leaf superoxide anion ([Formula: see text]) production rate and malonaldehyde (MDA) content in fig leaves, indicating ALA mitigates waterlogging stress of fig plants. We further demonstrated that ALA pretreatment largely promoted leaf chlorophyll content, photosynthetic electron transfer ability, and photosynthetic performance index, indicating ALA significantly improves plant photosynthetic efficiency under waterlogging stress. Moreover, ALA pretreatment significantly increased activities of leaf superoxide dismutase (SOD) and peroxidase (POD), root vigor, and activities of root alcohol dehydrogenase (ADH), and lactate dehydrogenase (LDH), indicating ALA also significantly improves antioxidant ability and root function of fig plants under waterlogging stress. Taken together, ALA pretreatment improves waterlogging tolerance of fig plants significantly, and the promoted root respiration, leaf photosynthesis, and antioxidant ability may contribute greatly to this improvement. Our data firstly shows that ALA can improve plant waterlogging tolerance.

Efecto del Anegamiento en la Actividad de la Enzima Alcohol Deshidrogenasa en Raíces de Maracuyá Amarillo Passiflora Edulis var. Flavicarpa

<p><strong>Título en ingles: Effect of Waterlogging on the Alcohol Dehydrogenase Activity in yellow Passion Fruit Roots <em>Passiflora Edulis</em> var. <em>Flavicarpa</em></strong></p><p>Bajo entornos naturales, las plantas de maracuyá amarillo frecuentemente se enfrentan a condiciones de anegamiento, un factor limitante para la producción generalizada de su cultivo, especialmente en tierras bajas inundables. El presente estudio se encargó de identificar la activación de la enzima alcohol deshidrogenasa (ADH) durante la inundación, como un posible mecanismo de sobrevivencia de plántulas de maracuyá amarillo. Se evaluó la actividad de la enzima ADH durante 0, 1, 3, 7, 9 y 14 días de tratamiento con inundación y sin inundación, en raíces de plántulas de maracuyá amarillo de tres meses y medio de germinadas. En las raíces de plántulas de maracuyá amarillo en condiciones de inundación, la actividad de la enzima ADH presentó un aumento significativo respecto a las plántulas en condiciones normales de riego (sin inundación). Esto sugiere que la actividad de la enzima alcohol deshidrogenasa, implicada en el metabolismo anaeróbico, es un posible mecanismo de supervivencia al anegamiento de plántulas de maracuyá amarillo en periodos cortos de inundación.</p>