Consequences of waterlogging in cotton and opportunities for mitigation of yield losses

Melatonin promotes the recovery of apple plants after waterlogging by shaping the structure and function of the rhizosphere microbiome

The dynamics of the physiological adaptability of plants and the rhizosphere soil environment after waterlogging remain unclear. Here we investigated the mechanisms regulating plant condition and shaping of the rhizosphere microbiome in a pot experiment. In the experiment, we added melatonin to waterlogged plants, which promoted waterlogging relief. The treatment significantly enhanced photosynthesis and the antioxidant capacity of apple plants, and significantly promoted nitrogen (N) utilization efficiency by upregulating genes related to N transport and metabolism. Multiperiod soil microbiome analysis showed the dynamic effects of melatonin on the diversity of the microbial community during waterlogging recovery. Random forest and linear regression analyses were used to screen for potential beneficial bacteria (e.g., Azoarcus, Pseudomonas and Nocardioides) specifically regulated by melatonin and revealed a positive correlation with soil nutrient levels and plant growth. Furthermore, metagenomic analyses revealed the regulatory effects of melatonin on genes involved in N cycling in soil. Melatonin positively contributed to the accumulation of plant dry weight by upregulating the expression of nifD and nifK (N fixation). In summary, melatonin positively regulates physiological functions in plants and the structure and function of the microbial community; it promoted the recovery of apple plants after waterlogging stress.

Genetic variations in ZmEREB179 are associated with waterlogging tolerance in maize

Maize (Zea mays) is highly susceptible to waterlogging stress, which reduces both the yield and quality of this important crop. However, the molecular mechanism governing waterlogging tolerance is poorly understood. In this study, we identify a waterlogging- and ethylene-inducible gene ZmEREB179 that encodes an ethylene response factor (ERF) localized in the nucleus. Overexpression of ZmEREB179 in maize increases the sensitivity to waterlogging stress. Conversely, the zmereb179 knockout mutants are more tolerant to waterlogging, suggesting that ZmEREB179 functions as a negative regulator of waterlogging tolerance. A transcriptome analysis of the ZmEREB179-overexpressing plants reveals that the ERF-type transcription factor modulates the expression of various stress-related genes, including ZmEREB180. We find that ZmEREB179 directly targets the ZmEREB180 promoter and represses its expression. Notably, the analysis of a panel of 220 maize inbred lines reveals that genetic variations in the ZmEREB179 promoter (Hap2) are highly associated with waterlogging resistance. The functional association of Hap2 with waterlogging resistance is tightly co-segregated in two F2 segregating populations, highlighting its potential applications in breeding programs. Our findings shed light on the involvement of the transcriptional cascade of ERF genes in regulating plant-waterlogging tolerance.

Role of salicylic acid in improving the yield of two mung bean genotypes under waterlogging stress through the modulation of antioxidant defense and osmoprotectant levels

Waterlogging (WL) is a major hindrance to the growth and development of leguminous crops, including mung bean. Here, we explored the effect of salicylic acid (SA) pretreatment on growth and yield output of two elite mung bean genotypes (BU Mung bean-4 and BU Mung bean-6) subjected to WL stress. SA pretreatment significantly improved shoot dry weight, individual leaf area, and photosynthetic pigment contents in both genotypes, while those improvements were higher in BU Mung bean-6 when compared with BU Mung bean-4. We also found that SA pretreatment significantly reduced the reactive oxygen species-induced oxidative burden in both BU Mung bean-6 and BU Mung bean-4 by enhancing peroxidase, glutathione S-transferase, catalase, and ascorbate peroxidase activities, as well as total flavonoid contents. SA pretreatment further improved the accumulation of proline and free amino acids in both genotypes, indicating that SA employed these osmoprotectants to enhance osmotic balance. These results were particularly corroborated with the elevated levels of leaf water status and leaf succulence in BU Mung bean-6. SA-mediated improvement in physiological and biochemical mechanisms led to a greater yield-associated feature in BU Mung bean-6 under WL conditions. Collectively, these findings shed light on the positive roles of SA in alleviating WL stress, contributing to yield improvement in mung bean crop.

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

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

From plant survival to thriving: exploring the miracle of brassinosteroids for boosting abiotic stress resilience in horticultural crops

Abiotic stresses pose significant threat to horticultural crop production worldwide. These stresses adversely affect plant growth, development, and ultimately declined crop growth, yield and quality. In recent years, plant scientists have been actively investigating innovative strategies to enhance abiotic stress resilience in crops, and one promising avenue of research focuses on the use of brassinosteroids (BRs). BRs are a class of plant hormones that play crucial roles in various physiological processes, including cell elongation, differentiation, and stress responses. They have emerged as potent regulators of plant growth and development, and their role in improving abiotic stress tolerance is gaining considerable attention. BRs have been shown to mitigate the negative effects of abiotic stresses by modulating key physiological and biochemical processes, including stomatal regulation, antioxidant defense, osmotic adjustment, and nutrient uptake. Abiotic stresses disrupt numerous physiological functions and lead to undesirable phenotypic traits in plants. The use of BRs as a tool to improve crop resilience offers significant promise for sustainable agriculture in the face of increasing abiotic stresses caused by climate change. By unraveling the phenomenon of BRs, this review emphasizes the potential of BRs as an innovative approach for boosting abiotic stress tolerance and improving the overall productivity and quality of horticultural crops. Further research and field trials are necessary to fully harness the benefits of BRs and translate these findings into practical applications for crop production systems.

Transcriptomic and metabolomic analyses reveal the potential mechanism of waterlogging resistance in cotton (Gossypium hirsutum L.)

Introduction

Cotton (Gossypium hirsutum L.) is susceptible to long-term waterlogging stress; however, genomic information of cotton response mechanisms toward long days of waterlogging is quite elusive.

Methods

Here, we combined the transcriptome and metabolome expression level changes in cotton roots after 10 and 20 days of waterlogging stress treatment pertaining to potential resistance mechanisms in two cotton genotypes.

Results and discussion

Numerous adventitious roots and hypertrophic lenticels were induced in CJ1831056 and CJ1831072. Transcriptome analysis revealed 101,599 differentially expressed genes in cotton roots with higher gene expression after 20 days of stress. Reactive oxygen species (ROS) generating genes, antioxidant enzyme genes, and transcription factor genes (AP2, MYB, WRKY, and bZIP) were highly responsive to waterlogging stress among the two genotypes. Metabolomics results showed higher expressions of stress-resistant metabolites sinapyl alcohol, L-glutamic acid, galactaric acid, glucose 1-phosphate, L-valine, L-asparagine, and melibiose in CJ1831056 than CJ1831072. Differentially expressed metabolites (adenosine, galactaric acid, sinapyl alcohol, L-valine, L-asparagine, and melibiose) significantly correlated with the differentially expressed PRX52, PER1, PER64, and BGLU11 transcripts. This investigation reveals genes for targeted genetic engineering to improve waterlogging stress resistance to enhance abiotic stress regulatory mechanisms in cotton at the transcript and metabolic levels of study.

Effect of Reproductive Stage-Waterlogging on the Growth and Yield of Upland Cotton (Gossypium hirsutum)

The reproductive stage of cotton (Gossypium sp.) is highly sensitive to waterlogging. The identification of potential elite upland cotton (Gossypium hirsutum) cultivar(s) having higher waterlogging tolerance is crucial to expanding cotton cultivation in the low-lying areas. The present study was designed to investigate the effect of waterlogging on the reproductive development of four elite upland cotton cultivars, namely, Rupali-1, CB-12, CB-13, and DM-3, against four waterlogging durations (e.g., 0, 3, 6, and 9-day). Waterlogging stress significantly impacted morpho-physiological, biochemical, and yield attributes of cotton. Two cotton cultivars, e.g., CB-12 and Rupali-1, showed the lowest reduction in plant height (6 and 9%, respectively) and boll weight (8 and 5%, respectively) at the highest waterlogging duration of 9 days. Physiological and biochemical data revealed that higher leaf chlorophyll, proline, and relative water contents, and lower malondialdehyde contents, particularly in CB-12 and Rupali-1, were positively correlated with yield. Notably, CB-12 and Rupali-1 had higher seed cotton weight (90.34 and 83.10 g, respectively), lint weight (40.12 and 39.32 g, respectively), and seed weight (49.47 and 43.78 g, respectively) per plant than CB-13 and DM-3 in response to the highest duration of waterlogging of 9 days. Moreover, extensive multivariate analyses like Spearman correlation and the principle component analysis revealed that CB-12 and Rupali-1 had greater coefficients in yield and physiological attributes at 9-day waterlogging, whereas CB-13 and DM-3 were sensitive cultivars in response to the same levels of waterlogging. Thus, CB-12 and Rupali-1 might be well adapted to the low-lying waterlogging-prone areas for high and sustained yield.

Physiological, biochemical, and metabolic changes in diploid and triploid watermelon leaves during flooding

BACKGROUND

Flooding is a major stress factor impacting watermelon growth and production globally. Metabolites play a crucial role in coping with both biotic and abiotic stresses.

METHODS

In this study, diploid (2X) and triploid (3X) watermelons were investigated to determine their flooding tolerance mechanisms by examining physiological, biochemical, and metabolic changes at different stages. Metabolite quantification was done using UPLC-ESI-MS/MS and a total of 682 metabolites were detected.

RESULTS

The results showed that 2X watermelon leaves had lower chlorophyll content and fresh weights compared to 3X. The activities of antioxidants, such as superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), were higher in 3X than in 2X. 3X watermelon leaves showed lower O₂ production rates, MDA, and hydrogen peroxide (H₂O₂) levels in response to flooding, while higher ethylene production was observed. 3X had higher levels of dehydrogenase activity (DHA) and ascorbic acid + dehydrogenase (AsA + DHA), but both 2X and 3X showed a significant decline in the AsA/DHA ratio at later stages of flooding. Among them, 4-guanidinobutyric acid (mws0567), an organic acid, may be a candidate metabolite responsible for flooding tolerance in watermelon and had higher expression levels in 3X watermelon, suggesting that triploid watermelon is more tolerant to flooding.

CONCLUSION

This study provides insights into the response of 2X and 3X watermelon to flooding and the physiological, biochemical, and metabolic changes involved. It will serve as a foundation for future in-depth molecular and genetic studies on flooding response in watermelon.

Potential abiotic stress targets for modern genetic manipulation

Research into crop yield and resilience has underpinned global food security, evident in yields tripling in the past 5 decades. The challenges that global agriculture now faces are not just to feed 10+ billion people within a generation, but to do so under a harsher, more variable, and less predictable climate, and in many cases with less water, more expensive inputs, and declining soil quality. The challenges of climate change are not simply to breed for a "hotter drier climate," but to enable resilience to floods and droughts and frosts and heat waves, possibly even within a single growing season. How well we prepare for the coming decades of climate variability will depend on our ability to modify current practices, innovate with novel breeding methods, and communicate and work with farming communities to ensure viability and profitability. Here we define how future climates will impact farming systems and growing seasons, thereby identifying the traits and practices needed and including exemplars being implemented and developed. Critically, this review will also consider societal perspectives and public engagement about emerging technologies for climate resilience, with participatory approaches presented as the best approach.

Concurrent waterlogging and anthracnose-twister disease in rainy-season onions (Allium cepa): Impact and management

Waterlogging and anthracnose-twister disease are significant obstacles in rainy-season onion cultivation. As a shallow-rooted crop, onions are highly sensitive to waterlogging. Wherever rainy-season onion cultivation has been undertaken, the anthracnose-twister disease complex is also widespread across the world in addition to waterlogging. Waterlogging is the major predisposing factor for anthracnose and other fungal diseases. However, studies on the combined stress impact on onions have been ignored. In the present review, we have presented an overview of the anthracnose-twister disease, the waterlogging effect on host physiology, host-pathogen interaction under waterlogging stress, and appropriate management strategies to mitigate the combined stress effects. Crucial soil and crop management strategies can help cope with the negative impact of concurrent stresses. Raised bed planting with drip irrigation, the use of plant bio-regulators along with nutrient management, and need-based fungicide sprays would be the most reliable and feasible management options. The most comprehensive solution to withstand combined stress impacts would be a genetic improvement of commercial onion cultivars.

Foliar Application of Spermidine Alleviates Waterlogging-Induced Damages to Maize Seedlings by Enhancing Antioxidative Capacity, Modulating Polyamines and Ethylene Biosynthesis

Waterlogging is a major threat to maize production worldwide. The exogenous application of spermidine is well known to enhance plant tolerance to abiotic stresses. The role of exogenous spermidine application in waterlogging tolerance in maize was investigated in this study. Two maize varieties (a waterlogging-tolerant variety: Xundan 20 (XD20) and a waterlogging-sensitive variety: Denghai 662 (DH662)) were subjected to waterlogging stress at the seedling stage, and then foliar spraying of 0.75 mM spermidine or purified water. Findings demonstrated lower chlorophyll content, reduced growth indices, considerable increase in superoxide anion (O₂^-) generation rate, and H₂O₂/malondialdehyde accumulation in the two maize varieties under waterlogging stress compared to the control treatment. However, the tolerance variety performed better than the sensitive one. Foliar application of spermidine significantly increased antioxidant enzyme activities under waterlogging stress. In addition, the application of spermidine increased polyamine levels and led to the reduction of ethylene levels under waterlogging. Consequences of spermidine application were most apparent for the waterlogging-sensitive cultivar DH662 under waterlogging than the waterlogging-tolerant variety XD20.

Modelling Waterlogging Impacts on Crop Growth: A Review of Aeration Stress Definition in Crop Models and Sensitivity Analysis of APSIM

Currently, crop physiological responses to waterlogging are considered only in a few crop models and in a limited way. Here, we examine the process bases of seven contemporary models developed to model crop growth in waterlogged conditions. The representation of plant recovery in these models is over-simplified, while plant adaptation or phenotypic plasticity due to waterlogging is often not considered. Aeration stress conceptualisation varies from the use of simple multipliers in equations describing transpiration and biomass to complex linkages of aeration-deficit factors with root growth, transpiration and nitrogen fixation. We recommend further studies investigating more holistic impacts and multiple stresses caused by plant behaviours driven by soils and climate. A sensitivity analysis using one model (a developer version of APSIM) with default parameters showed that waterlogging has the greatest impact on photosynthesis, followed by phenology and leaf expansion, suggesting a need for improved equations linking waterlogging to carbon assimilation. Future studies should compare the ability of multiple models to simulate real and in situ effects of waterlogging stress on crop growth using consistent experimental data for initialisation, calibration and validation. We conclude that future experimental and modelling studies must focus on improving the extent to which soil porosity, texture, organic carbon and nitrogen and plant-available water affect waterlogging stress, physiological plasticity and the ensuing temporal impacts on phenology, growth and yield.

Post-flowering Soil Waterlogging Curtails Grain Yield Formation by Restricting Assimilates Supplies to Developing Grains

Soil waterlogging is among the major factors limiting the grain yield of winter wheat crops in many parts of the world, including the middle and lower reaches of the Yangtze River China. In a field study, we investigated the relationship between leaf physiology and grain development under a varying duration of post-flowering waterlogging. A winter wheat cultivar Ningmai 13 was exposed to soil waterlogging for 0 (W0), 3 (W3), 6 (W6), and 9 d (W9) at anthesis. Increasing waterlogging duration significantly reduced flag leaf SPAD (soil plant analysis development) values and net photosynthetic rate (Pn). There was a linear reduction in flag leaf Pn and SPAD as plant growth progressed under all treatments; however, the speed of damage was greater in the waterlogged leaves. For example, compared with their respective control (W0), flag leaves of W9 treatment have experienced 46% more reduction in Pn at 21 d after anthesis (DAA) than at 7 DAA. Increasing waterlogging duration also induced oxidative damage in flag leaves, measured as malondialdehyde (MDA) contents. The capacity to overcome this oxidative damage was limited by the poor performance of antioxidant enzymes in wheat leaves. Inhibited leaf Pn and capacity to sustain assimilate synthesis under waterlogged environments reduced grain development. Compared with W0, W6 and W9 plants experienced a 20 and 22% reduction in thousand grain weight (TGW) in response to W6 and W9, respectively at 7 DAA and 11 and 19%, respectively at 28 DAA. Sustained waterlogging also significantly reduced grain number per spike and final grain yield. Averaged across two years of study, W9 plants produced 28% lesser final grain yield than W0 plants. Our study suggested that wheat crops are highly sensitive to soil waterlogging during reproductive and grain filling phases due to their poor capacity to recover from oxidative injury to photosynthesis. Management strategies such as planting time, fertilization and genotype selection should be considered for the areas experiencing frequent waterlogging problems.

Effects of Hypoxia Stress on Growth, Root Respiration, and Metabolism of Phyllostachys praecox

Hypoxia affects plant growth, hormone content, various enzyme activities, cell structure, peroxide production, and metabolic level, therefore reducing crop yield. This study assessed the physiological, biochemical, and metabolic characteristics of Phyllostachys praecox. Results revealed that hypoxia stress treatment significantly inhibited plant growth. Leaf chlorophyll contents was initially improved and then reduced with plant growth time. Under hypoxia stress, the root activity significantly was reduced, leading to the decrease in the nutrient absorption and transport. Yet, with low oxygen concentration, the contents of ethanol, acetaldehyde, and lactic acid were improved. With hypoxia stress, phospholipids and amino acids were the main metabolites of Phyllostachys praecox. Glycosphospholipid metabolism is the key pathway in responding to hypoxia stress significantly (p < 0.05), and lysophosphatidlycholine (lysoPC) and phosphatidylcholines (PC) in the metabolites of this metabolic pathway were significantly enhanced. Our study reveals the mechanism of Phyllostachys praecox cell membrane responding to hypoxia stress based on molecular level. This is conducive to finding targeted solutions to improve the productivity of Phyllostachys praecox to better optimize a mulching approach in the bamboo forest.

Waterlogged Conditions Influence the Nitrogen, Phosphorus, Potassium, and Sugar Distribution in Sago Palm (Metroxylon sagu Rottb.) at Seedling Stages

Sago palm (Metroxylon sagu Rottb.) grows in well-drained mineral soil and in peatland with high groundwater levels until complete submersion. However, the published information on nutrient uptake and carbohydrate content in sago palms growing under waterlogging remains unreported. This experiment observed sago palm growth performance under normal soil conditions (non-submerged conditions) as a control plot and extended waterlogged conditions. Several parameters were analyzed: Plant morphological growth traits, nitrogen, phosphorus, potassium, and sugar concentration in the plant organ, including sucrose, glucose, starch, and non-structural carbohydrate. The analysis found that sago palm morphological growth traits were not significantly affected by extended waterlogging. However, waterlogging reduced carbohydrate levels in the upper part of the sago palm, especially the petiole, and increased sugar levels, especially glucose, in roots. Waterlogging also reduced N concentration in roots and leaflets and P in petioles. The K level was independent of waterlogging as the sago palm maintained a sufficient level in all of the plant organs. Long duration waterlogging may reduce the plant’s economic value as the starch level in the trunk decreases, although sago palm can grow while waterlogged.

Cytokinin and gibberellic acid-mediated waterlogging tolerance of mungbean (Vigna radiata L. Wilczek)

BACKGROUND

Mungbean (Vigna radiata L. Wilczek) is one of the most important pulse crops, well-known for its protein-rich seeds. Growth and productivity are severely undermined by waterlogging.

METHODS

In this study, we aim to evaluate how two promising phytohormones, namely cytokinin (CK) and gibberellic acid (GA₃), can improve waterlogging tolerance in mungbean by investigating key morphological, physiological, biochemical, and yield-related attributes.

RESULTS

Our results showed that foliar application of CK and GA₃ under 5-day of waterlogged conditions improved mungbean growth and biomass, which was associated with increased levels of photosynthetic rate and pigments. Waterlogged-induced accumulation of reactive oxygen species and the consequently elevated levels of malondialdehyde were considerably reduced by CK and GA₃ treatments. Mungbean plants sprayed with either CK or GA₃ suffered less oxidative stress due to the enhancement of total phenolics and flavonoids levels. Improvement in the contents of proline and total soluble sugars indicated a better osmotic adjustment following CK and GA₃ treatments in waterlogged-exposed plants. Most fundamentally, CK or GA₃-sprayed waterlogged-stressed mungbean plants demonstrated better performance in the aforementioned parameters after the 15-day recovery period as compared to water-sprayed waterlogged-exposed plants. Our results also revealed that CK and GA₃ treatments increased yield-associated features in the waterlogged-stressed plant. Here, both phytohormones are efficient in improving mungbean resistance to waterlogging. However, CK was found to be more effective. Overall, our findings suggested that CK or GA₃ could be used for managing waterlogging-induced damage to mungbean and perhaps in other cash crops.

Screening of Onion (Allium cepa L.) Genotypes for Waterlogging Tolerance

Onion production is severely affected by waterlogging conditions, which are created due to heavy rainfall. Hence, the identification of waterlogging-tolerant onion genotypes is crucial for increasing onion production. In the present study, 100 distinct onion genotypes were screened for waterlogging tolerance under artificial conditions by using the phenotypic approach in the monsoon season of 2017. Based on plant survival and recovery and changes in bulb weight, we identified 19 tolerant, 27 intermediate tolerant, and 54 highly sensitive onion genotypes. The tolerant genotypes exhibited higher plant survival and better recovery and bulb size, whereas sensitive genotypes exhibited higher plant mortality, poor recovery, and small bulb size under waterlogging conditions. Furthermore, a subset of 12 contrasting genotypes was selected for field trials during monsoon seasons 2018 and 2019. Results revealed that considerable variation in the morphological, physiological, and yield characteristics were observed across the genotypes under stress conditions. Waterlogging-tolerant genotypes, namely, Acc. 1666, Acc. 1622, W-355, W-208, KH-M-2, and RGP-5, exhibited higher plant height, leaf number, leaf area, leaf length, chlorophyll content, membrane stability index (MSI), pyruvic acid, antioxidant content, and bulb yield than sensitive genotypes under stress conditions. Furthermore, the principal component analysis biplot revealed a strong association of leaf number, leaf area, chlorophyll content, MSI, and bulb yield with tolerant genotypes under stress conditions. The study indicates that the waterlogging-tolerant onion genotypes with promising stress-adaptive traits can be used in plant breeding programs for developing waterlogging-tolerant onion varieties.

Nitrogen use efficiency in cotton: Challenges and opportunities against environmental constraints

Nitrogen is a vital nutrient for agricultural, and a defieciency of it causes stagnate cotton growth and yield penalty. Farmers rely heavily on N over-application to boost cotton output, which can result in decreased lint yield, quality, and N use efficiency (NUE). Therefore, improving NUE in cotton is most crucial for reducing environmental nitrate pollution and increasing farm profitability. Well-defined management practices, such as the type of sources, N-rate, application time, application method, crop growth stages, and genotypes, have a notable impact on NUE. Different N formulations, such as slow and controlled released fertilizers, have been shown to improve N uptake and, NUE. Increasing N rates are said to boost cotton yield, although high rates may potentially impair the yield depending on the soil and environmental conditions. This study comprehensively reviews various factors including agronomic and environmental constraints that influence N uptake, transport, accumulation, and ultimately NUE in cotton. Furthermore, we explore several agronomic and molecular approaches to enhance efficiency for better N uptake and utilization in cotton. Finally, this objective of this review to highlight a comprehensive view on enhancement of NUE in cotton and could be useful for understanding the physiological, biochemical and molecular mechanism of N in cotton.

Aerenchyma formation in the root of leaf-vegetable sweet potato: Programmed cell death initiated by ethylene-mediated H2 O2 accumulation

Sweet potato, commonly planted in Southeast Asia and South America with abundant rainfall, often suffers from waterlogging. The aerenchyma formation in roots is an effective way for plants to facilitate gas exchange. In the present study, tolerant and sensitive varieties, respectively, designated NC1 and C211, were evaluated under water oxygen content at 2.0 mg·L^-1 (hypoxia treatment) and 8.0 mg·L^-1 (control). The results showed that NC1 variety has a relatively higher root growth rate under low oxygen condition. In NC1 plants, aerenchyma was observed in the mid-section of the main adventitious root and spread to the proximal and distal ends, forming a complete channel in the cortex. However, in C211 plants, the aerenchyma occurred relatively later and could not turn into a whole channel. Ethylene synthesis-related (ACS1, ACS4, ACS5, etc.) and signal transduction-related (ETR1, ERS1, EIN2, etc.) genes were upregulated in the NC1 plants and led to changes in the reactive oxygen species-related genes (RBOHA, SOD, CAT, etc.) and enzyme activities. It was found that programmed cell death was induced by H₂ O₂ accumulation. A regulatory model of lysigenous aerenchyma formation in the root of sweet potato was constructed. Our study enriches the understanding of the mechanisms of the aerenchyma formation in plants.

Assessing the impacts of irrigation termination periods on cotton productivity under strategic deficit irrigation regimes

Determining optimum irrigation termination periods for cotton (Gossypium hirsutum L.) is crucial for efficient utilization and conservation of finite groundwater resources of the Ogallala Aquifer in the Texas High Plains (THP) region. The goal of this study was to suggest optimum irrigation termination periods for different Evapotranspiration (ET) replacement-based irrigation strategies to optimize cotton yield and irrigation water use efficiency (IWUE) using the CROPGRO-Cotton model. We re-evaluated a previously evaluated CROPGRO-Cotton model using updated yield and in-season physiological data from 2017 to 2019 growing seasons from an IWUE experiment at Halfway, TX. The re-evaluated model was then used to study the effects of combinations of irrigation termination periods (between August 15 and September 30) and deficit/excess irrigation strategies (55%-115% ET-replacement) under dry, normal and wet years using weather data from 1978 to 2019. The 85% ET-replacement strategy was found ideal for optimizing irrigation water use and cotton yield, and the optimum irrigation termination period for this strategy was found to be the first week of September during dry and normal years, and the last week of August during wet years. Irrigation termination periods suggested in this study are useful for optimizing cotton production and IWUE under different levels of irrigation water availability.

Physiological Responses of Wheat Seedlings to Soil Waterlogging Applied after Treatment with Selective Herbicide

Waterlogging impairs crop development and considerably affects plant productivity worldwide. Wheat is sensitive to waterlogging. Serrate^® (Syngenta) is a selective herbicide controlling annual grass and broadleaf weeds for use in wheat. To extend the existing information about the physiological effects of selective herbicides (Serrate^® in particular) and subsequent waterlogging in wheat, we monitored phenotype alterations and examined key enzymatic and non-enzymatic antioxidant defense systems together with typical oxidative stress biomarkers. Seventeen-day-old wheat (Triticum asetivum L., cv. Sadovo-1) plants were sprayed with Serrate^®; 72 h later, waterlogging was applied for 7 days, and then seedlings were left to recover for 96 h. The herbicide did not alter plant phenotype and increased antioxidant defense, along with H₂O₂ content, confirming the wheat’s tolerance to Serrate^®. Evident yellowing and wilting of the leaves were observed at 96 h of recovery in waterlogged wheat, which were stronger in plants subjected to Serrate^® + waterlogging. Waterlogging alone and herbicide + waterlogging gradually enhanced the content of stress markers (malondialdehyde, proline, and H₂O₂), non-enzymatic antioxidants (low-molecular thiols and total phenolics), and the activity of superoxide dismutase, guaiacol peroxidase, and glutathione reductase. The effects of herbicide + waterlogging were stronger than those of waterlogging alone even during recovery, suggesting that Serrate^® interacted synergistically with the subsequently applied flooding.

How Does the Waterlogging Regime Affect Crop Yield? A Global Meta-Analysis

Waterlogging, an abiotic stress, severely restricts crop yield in various parts of the world. Thus, we conducted a meta-analysis of 2,419 comparisons from 115 studies to comprehensively evaluate the overall change in crop yield induced by waterlogging in the global region. The results suggested that waterlogging obviously decreased crop yield by 32.9% on average, compared with no waterlogging, which was a result of a reduced 1,000-grain weight (13.67%), biomass (28.89%), plant height (10.68%), net photosynthetic rate (P n , 39.04%), and leaf area index (LAI, 22.89%). The overall effect of a waterlogging regime on crop yield is related to the crop type; the crop yield reduction varied between wheat (25.53%) and cotton (59.95%), with an overall average value of 36.81% under field conditions. In addition, we also found that compared with no waterlogging, waterlogging in the reproductive growth stage (41.90%) caused a greater yield reduction than in the vegetative growth stage (34.75%). Furthermore, decreases in crop yield were observed with an extension in the waterlogging duration; the greatest decreases in crop yield occurred at 15 < D ≤ 28 (53.19 and 55.96%) under field and potted conditions, respectively. Overall, the results of this meta-analysis showed that waterlogging can decrease crop yield and was mainly affected by crop type, growth stage, and experimental duration.

Maintenance of photosynthetic capacity in flooded tomato plants with reduced ethylene sensitivity

Ethylene is considered one of the most important plant hormones orchestrating plant responses to flooding stress. However, ethylene may induce deleterious effects on plants, especially when produced at high rates in response to stress. In this paper, we explored the effect of attenuated ethylene sensitivity in the Never ripe (Nr) mutant on leaf photosynthetic capacity of flooded tomato plants. We found out that reduced ethylene perception in Nr plants was associated with a more efficient photochemical and non-photochemical radiative energy dissipation capability in response to flooding. The data correlated with the retention of chlorophyll and carotenoids content in flooded Nr leaves. Moreover, leaf area and specific leaf area were higher in Nr, indicating that ethylene would exert a negative role in leaf growth and expansion under flooded conditions. Although stomatal conductance was hampered in flooded Nr plants, carboxylation activity was not affected by flooding in the mutant, suggesting that ethylene is responsible for inducing non-stomatal limitations to photosynthetic CO₂ uptake. Upregulation of several cysteine protease genes and high protease activity led to Rubisco protein loss in response to ethylene under flooding. Reduction of Rubisco content would, at least in part, account for the reduction of its carboxylation efficiency in response to ethylene in flooded plants. Therefore, besides its role as a trigger of many adaptive responses, perception of ethylene entails limitations in light and dark photosynthetic reactions by speeding up the senescence process that leads to a progressive disassembly of the photosynthetic machinery in leaves of flooded tomato plants.

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.

Soil and Crop Management Practices to Minimize the Impact of Waterlogging on Crop Productivity

Waterlogging remains a significant constraint to cereal production across the globe in areas with high rainfall and/or poor drainage. Improving tolerance of plants to waterlogging is the most economical way of tackling the problem. However, under severe waterlogging combined agronomic, engineering and genetic solutions will be more effective. A wide range of agronomic and engineering solutions are currently being used by grain growers to reduce losses from waterlogging. In this scoping study, we reviewed the effects of waterlogging on plant growth, and advantages and disadvantages of various agronomic and engineering solutions which are used to mitigate waterlogging damage. Further research should be focused on: cost/benefit analyses of different drainage strategies; understanding the mechanisms of nutrient loss during waterlogging and quantifying the benefits of nutrient application; increasing soil profile de-watering through soil improvement and agronomic strategies; revealing specificity of the interaction between different management practices and environment as well as among management practices; and more importantly, combined genetic, agronomic and engineering strategies for varying environments.

Plant Growth Promotion Under Water: Decrease of Waterlogging-Induced ACC and Ethylene Levels by ACC Deaminase-Producing Bacteria

Some plant growth-promoting bacteria encode for 1-aminocyclopropane-1-carboxylate (ACC) deaminase, which facilitates plant growth and development by lowering the level of stress ethylene under waterlogged conditions. The substrate ACC is the immediate precursor for ethylene synthesis in plants; while bacterial ACC deaminase hydrolyzes this compound into α-ketobutyrate and ammonia to mitigate the adverse effects of the stress caused by ethylene exposure. Here, the structure and function of ACC deaminase, ethylene biosynthesis and waterlogging response, waterlogging and its consequences, role of bacterial ACC deaminase under waterlogged conditions, and effect of this enzyme on terrestrial and riparian plants are discussed.

Hormone dependent survival mechanisms of plants during post-waterlogging stress

Waterlogging stress has two phases like waterlogging phase and post-waterlogging phase where both are injurious to plants. Susceptible plants normally die at post-waterlogging phase due to damaged root system, sudden rexoygenation, dehydration and photoinhibition of the desubmerged tissues. Formation of reactive oxygen species (ROS) is the main result of reoxygenation stress that can cause oxidative damage of the functional tissues responsible for normal physiological activities. There are almost all types of hormones responsible to recover plants from these destructive phenomenons. Among these hormones ethylene and abscisic acid (ABA) are the main regulators to overcome the reoxygenation and drought like stresses in plants at post-waterlogging condition. The balanced crosstalk among the hormones is highly important for the survival of plants at these stresses. So this paper is completely a precise summary of hormonal homeostasis of post-waterlogged plants through physiological, biochemical and signaling pathways.

Global gene expression in cotton (Gossypium hirsutum L.) leaves to waterlogging stress

Cotton is sensitive to waterlogging stress, which usually results in stunted growth and yield loss. To date, the molecular mechanisms underlying the responses to waterlogging in cotton remain elusive. Cotton was grown in a rain-shelter and subjected to 0 (control)-, 10-, 15- and 20-d waterlogging at flowering stage. The fourth-leaves on the main-stem from the top were sampled and immediately frozen in liquid nitrogen for physiological measurement. Global gene transcription in the leaves of 15-d waterlogged plants was analyzed by RNA-Seq. Seven hundred and ninety four genes were up-regulated and 1018 genes were down-regulated in waterlogged cotton leaves compared with non-waterlogged control. The differentially expressed genes were mainly related to photosynthesis, nitrogen metabolism, starch and sucrose metabolism, glycolysis and plant hormone signal transduction. KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis indicated that most genes related to flavonoid biosynthesis, oxidative phosphorylation, amino acid metabolism and biosynthesis as well as circadian rhythm pathways were differently expressed. Waterlogging increased the expression of anaerobic fermentation related genes, such as alcohol dehydrogenase (ADH), but decreased the leaf chlorophyll concentration and photosynthesis by down-regulating the expression of photosynthesis related genes. Many genes related to plant hormones and transcription factors were differently expressed under waterlogging stress. Most of the ethylene related genes and ethylene-responsive factor-type transcription factors were up-regulated under water-logging stress, suggesting that ethylene may play key roles in the survival of cotton under waterlogging stress.

Identification and Characterization of miRNA Transcriptome in Asiatic Cotton (Gossypium arboreum) Using High Throughput Sequencing

MicroRNAs (miRNAs) are small 20-24nt molecules that have been well studied over the past decade due to their important regulatory roles in different cellular processes. The mature sequences are more conserved across vast phylogenetic scales than their precursors and some are conserved within entire kingdoms, hence, their loci and function can be predicted by homology searches. Different studies have been performed to elucidate miRNAs using de novo prediction methods but due to complex regulatory mechanisms or false positive in silico predictions, not all of them express in reality and sometimes computationally predicted mature transcripts differ from the actual expressed ones. With the availability of a complete genome sequence of Gossypium arboreum, it is important to annotate the genome for both coding and non-coding regions using high confidence transcript evidence, for this cotton species that is highly resistant to various biotic and abiotic stresses. Here we have analyzed the small RNA transcriptome of G. arboreum leaves and provided genome annotation of miRNAs with evidence from miRNA/miRNA∗ transcripts. A total of 446 miRNAs clustered into 224 miRNA families were found, among which 48 families are conserved in other plants and 176 are novel. Four short RNA libraries were used to shortlist best predictions based on high reads per million. The size, origin, copy numbers and transcript depth of all miRNAs along with their isoforms and targets has been reported. The highest gene copy number was observed for gar-miR7504 followed by gar-miR166, gar-miR8771, gar-miR156, and gar-miR7484. Altogether, 1274 target genes were found in G. arboreum that are enriched for 216 KEGG pathways. The resultant genomic annotations are provided in UCSC, BED format.

Nitrogen fertility and abiotic stresses management in cotton crop: a review

This review outlines nitrogen (N) responses in crop production and potential management decisions to ameliorate abiotic stresses for better crop production. N is a primary constituent of the nucleotides and proteins that are essential for life. Production and application of N fertilizers consume huge amounts of energy, and excess is detrimental to the environment. Therefore, increasing plant N use efficiency (NUE) is important for the development of sustainable agriculture. NUE has a key role in crop yield and can be enhanced by controlling loss of fertilizers by application of humic acid and natural polymers (hydrogels), having high water-holding capacity which can improve plant performance under field conditions. Abiotic stresses such as waterlogging, drought, heat, and salinity are the major limitations for successful crop production. Therefore, integrated management approaches such as addition of aminoethoxyvinylglycine (AVG), the film antitranspirant (di-1-p-menthene and pinolene) nutrients, hydrogels, and phytohormones may provide novel approaches to improve plant tolerance against abiotic stress-induced damage. Moreover, for plant breeders and molecular biologists, it is a challenge to develop cotton cultivars that can tolerate plant abiotic stresses while having high potential NUE for the future.

Combined elevated temperature and soil waterlogging stresses inhibit cell elongation by altering osmolyte composition of the developing cotton (Gossypium hirsutum L.) fiber

Soil waterlogging events and high temperature conditions occur frequently in the Yangtze River Valley, yet the effects of these co-occurring stresses on fiber elongation have received little attention. In the current study, the combined effect of elevated temperature (ET) and soil waterlogging (SW) more negatively affected final fiber length (reduced by 5.4%-11.3%) than either stress alone by altering the composition of osmotically active solutes (sucrose, malate, and K⁺), where SW had the most pronounced effect. High temperature accelerated early fiber development, but limited the duration of elongation, thereby limiting final fiber length. Treatment of ET alone altered fiber sucrose content mainly through decreased source strength and the expression of the sucrose transporter gene GhSUT-1, making sucrose availability the primary determinant of final fiber length under ET. Waterlogging stress alone decreased source strength, down-regulated GhSUT-1 expression and enhanced SuSy catalytic activity for sucrose reduction. Waterlogging treatment alone also limited fiber malate production by down-regulating GhPEPC-1 & -2. However, combined elevated temperature and waterlogging limited primary cell wall synthesis by affecting GhCESAs genes and showed a negative impact on all three major osmotic solutes through the regulation of GhSUT-1, GhPEPC-1 & -2 and GhKT-1 expression and altered SuSy activity, which functioned together to produce a shorter fiber length.

Effect of Waterlogging Duration at Different Growth Stages on the Growth, Yield and Quality of Cotton

In this study, a soil culture experiment was set up in barrels to investigate the effect of waterlogging duration at different growth stages on the growth, yield, and quality of cotton in the Huang-Huai Region of China during summer. The experiment was conducted at four growth stages of cotton (seedling, squaring, flowering, and boll opening), and the waterlogging duration at each stage was set to five levels (2, 4, 6, 8, and 10 d) and the waterlogging depth was 5cm. Twenty different treatment combinations were established, and one group without waterlogging throughout the whole growth period was used as the control (CK). The results showed that the waterlogging treatments at the different growth stages reduced the morphological and yield parameters of the cotton plants as well as the physiological parameters of the cotton leaves, and the extent of the reduction in these parameters increased with the extension of the waterlogging duration. The effect of waterlogging at different growth stages on the cotton decreased in the order of the flowering, squaring, seedling, and boll-opening stages, and the highest yield reduction rates for the four stages were 38.8%, 27.9%, 18.3%, and 7.6% respectively. Additionally, waterlogging decreased the quality parameters of cotton such as the upper-half mean length, uniformity index, micronaire value, elongation, yellowness, and lint percentage at the squaring, flowering, and boll-opening stages. Furthermore, at the seedling stage waterlogging for no more than 6 d allowed the morphological and yield parameters to recover in the boll-opening stage upon timely drainage, and these parameters showed no significant decreases compared with the CK level. The critical duration of waterlogging at the squaring stage was 4 d. However, at the flowering stage, even 2 d of waterlogging could lead to the stagnation of morphological development and prevent the recovery of the cotton yield to the CK level. Therefore, when waterlogging disasters occur in cotton fields, the implementation of appropriate surface and subsurface drainage schemes for the different growth stages is needed as soon as possible to mitigate the damage.

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.

Introduction to the Special Issue: Electrons, water and rice fields: plant response and adaptation to flooding and submergence stress

Flooding and submergence impose widespread and unpredictable environmental stresses on plants and depress the yield of most food crops. The problem is increasing, as is the need for greater food production from an expanding human population. The incompatibility of these opposing trends creates an urgent need to improve crop resilience to flooding in its multifarious forms. This Special Issue brings together research findings from diverse plant species to address the challenge of enhancing adaptation to flooding in major crops and learning from tactics of wetland plants. Here we provide an overview of the articles, with attempts to summarize how recent research results are being used to produce varieties of crop plants with greater flooding tolerance, notably in rice. The progress is considerable and based firmly on molecular and physiological research findings. The article also sets out how next-generation improvements in crop tolerance are likely to be achieved and highlights some of the new research that is guiding the development of improved varieties. The potential for non-model species from the indigenous riparian flora to uncover and explain novel adaptive mechanisms of flooding tolerance that may be introduced into crop species is also explored. The article begins by considering how, despite the essential role of water in sustaining plant life, floodwater can threaten its existence unless appropriate adaptations are present. Central to resolving the contradiction is the distinction between the essential role of cellular water as the source of electrons and protons used to build and operate the plant after combining with CO2 and O2 and the damaging role of extracellular water that, in excess, interferes with the union of these gases with photosynthetic or respiratory electrons and protons.