Waterlogging of Winter Crops at Early and Late Stages: Impacts on Leaf Physiology, Growth and Yield

The roles of cell wall polysaccharides in response to waterlogging stress in Brassica napus L. root

BACKGROUND

Brassica napus L. (B. napus) is susceptible to waterlogging stress during different cultivation periods. Therefore, it is crucial to enhance the resistance to waterlogging stress to achieve a high and stable yield of B. napus.

RESULTS

Here we observed significant differences in the responses of two B. napus varieties in root under waterlogging stress. The sensitive variety (23651) exhibited a more pronounced and rapid reduction in cell wall thickness and root integrity compared with the tolerant variety (Santana) under waterlogging stress. By module clustering analysis based on transcriptome data, we identified that cell wall polysaccharide metabolism responded to waterlogging stress in root. It was found that pectin content was significantly reduced in the sensitive variety compared with the tolerant variety. Furthermore, transcriptome analysis revealed that the expression of two homologous genes encoding polygalacturonase-inhibiting protein 2 (PGIP2), involved in polysaccharide metabolic pathways, was highly upregulated in root of the tolerant variety under waterlogging stress. BnaPGIP2s probably confer waterlogging resistance by inhibiting the activity of polygalacturonases (PGs), which in turn reduces the degradation of the pectin backbone polygalacturonic acid.

CONCLUSIONS

Our findings demonstrate that cell wall polysaccharides in root plays a vital role in response to the waterlogging stress and provide a theoretical foundation for breeding waterlogging resistance in B. napus varieties.

Oat-an alternative crop under waterlogging stress?

Introduction

Waterlogging is one vast environmental constraint that limits crop growth and yield worldwide. Most major crop species are very sensitive to waterlogging, leading to enormous yield losses every year. Much is already known about wheat, barley or maize; however, hardly any data exist on oat and its tolerance against waterlogging. Thus, this study aimed to investigate if oats can be an adequate alternative in crop rotation under conditions of temporal submergence and if cultivar differences exist. Furthermore, this study was to test (1) whether yield was differently affected when stress is applied at different developmental stages (BBCH 31 and 51), and (2) nutrient imbalances are the reason for growth restrictions.

Methods

In a large-scale container experiment, three different oat varieties were cultivated and exposed to 14 consecutive days of waterlogging stress at two developmental stages.

Results

Even though vegetative growth was impaired after early waterlogging and which persists till maturity, mainly due to transient nutrient deficiencies, growth performance after late waterlogging and grain yield of all three oat varieties at maturity was not affected. A high tolerance was also confirmed after late waterlogging in the beginning generative stage: grain yield was even increased.

Discussion

Overall, all oat varieties performed well under both stress treatments, even though transient nutrient imbalances occurred, but which were ineffective on grain yield. Based on these results, we conclude that oats, independently of the cultivar, should be considered a good alternative in crop production, especially when waterlogging is to be expected during the cultivation phase.

Does humic acid foliar application affect growth and nutrient status of water-stressed maize?

Maize (Zea mays L.) is one of the world's most important crops, but its productivity is at high risk as climate change increases the risk of water stress. Therefore, the development of mitigation strategies to combat water stress in agriculture is fundamental to ensure food security. Humic acids are known to have a positive effect on drought tolerance, but data on their efficacy under waterlogging are lacking. This study aimed to elucidate the effect of a new humic acid product, a by-product of Ukrainian bentonite mining, on maize growth and nutrient status under waterlogging. Maize was grown for 9 weeks and three water stress treatments, which were applied for 14 days: waterlogging, alternating waterlogging and drought, and drought. On the day of stress application, the humic acid product (1% v/v) was applied to the leaves. Soil Plant Analysis Development (SPAD) values were recorded during the stress treatments. Plants were harvested after stressing ceased and fresh weight and P and Zn status were analyzed. Drought reduced shoot fresh weight, while it was unaffected under waterlogging. This is in contrast to SPAD readings, which showed a significant decrease over time under submergence, but not under drought. Under alternating stress, although SPAD values declined under waterlogging but stabilized when switched to drought, no growth reduction was apparent. Application of the humic acid product was ineffective in all cases. Although anthocyanin discoloration occurred under waterlogging stress, P deficiency, which is usually the main factor driving anthocyanin formation, was not the reason. Interestingly, Zn concentration decreased under waterlogging but not under the other stresses, which was alleviated by humic acid application. However, no effect of foliar-applied humic acids was observed under alternating and drought stress. It can be concluded that the tested humic acid product has the potential to improve the Zn status of maize under waterlogging.

Root system architecture change in response to waterlogging stress in a 448 global collection of rapeseeds (Brassica napus L.)

MAIN CONCLUSIONS

A novel image-based screening method for precisely identifying genotypic variations in rapeseed RSA under waterlogging stress was developed. Five key root traits were confirmed as good indicators of waterlogging and might be employed in breeding, particularly when using the MFVW approach. Waterlogging is a vital environmental factor that has detrimental effects on the growth and development of rapeseed (Brassica napus L.). Plant roots suffer from hypoxia under waterlogging, which ultimately confers yield penalty. Therefore, it is crucially important to understand the genetic variation of root system architecture (RSA) in response to waterlogging stress to guide the selection of new tolerant cultivars with favorable roots. This research was conducted to investigate RSA traits using image-based screening techniques to better understand how RSA changes over time during waterlogging at the seedling stage. First, we performed a t-test by comparing the relative root trait value between four tolerant and four sensitive accessions. The most important root characteristics associated with waterlogging tolerance at 12 h are total root length (TRL), total root surface area (TRSA), total root volume (TRV), total number of tips (TNT), and total number of forks (TNF). The root structures of 448 rapeseed accessions with or without waterlogging showed notable genetic diversity, and all traits were generally restrained under waterlogging conditions, except for the total root average diameter. Additionally, according to the evaluation and integration analysis of 448 accessions, we identified that five traits, TRL, TRSA, TRV, TNT, and TNF, were the most reliable traits for screening waterlogging-tolerant accessions. Using analysis of the membership function value (MFVW) and D-value of the five selected traits, 25 extremely waterlogging-tolerant materials were screened out. Waterlogging significantly reduced RSA, inhibiting root growth compared to the control. Additionally, waterlogging increased lipid peroxidation, accompanied by a decrease in the activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT). This study effectively improves our understanding of the response of RSA to waterlogging. The image-based screening method developed in this study provides a new scientific guidance for quickly examining the basic RSA changes and precisely predicting waterlogging-tolerant rapeseed germplasms, thus expanding the genetic diversity of waterlogging-tolerant rapeseed germplasm available for breeding.

Flooding stress and responses to hypoxia in plants

In recent years, research on flooding stress and hypoxic responses in plants has gathered increasing attention due to climate change and the important role of O2 in metabolism and signalling. This Collection of Functional Plant Biology on 'Flooding stress and responses to hypoxia in plants' presents key contributions aimed at progressing our current understanding on how plants respond to low-O2 conditions, flooding stress and a combination of stresses commonly found in flooded areas. The Collection emphasises the characterisation of diverse plant responses across different developmental stages, from seed germination to fully developed plants, and under different water stress conditions ranging from waterlogging to complete submergence, or simply low-O2 conditions resulting from limited O2 diffusivity in bulky tissues. Additionally, this Collection highlights diverse approaches, including eco-physiological characterisation of plant responses, detailed descriptions of root anatomical characteristics and their surrounding microenvironments, evaluation of the seed microbiota under flooding stress, the modification of gene expression, and evaluations of diverse germplasm collections.

The mechanisms behind the contrasting responses to waterlogging in black-grass (Alopecurus myosuroides) and wheat (Triticum aestivum)

Black-grass (Alopecurus myosuroides ) is one of the most problematic agricultural weeds of Western Europe, causing significant yield losses in winter wheat (Triticum aestivum ) and other crops through competition for space and resources. Previous studies link black-grass patches to water-retaining soils, yet its specific adaptations to these conditions remain unclear. We designed pot-based waterlogging experiments to compare 13 biotypes of black-grass and six cultivars of wheat. These showed that wheat roots induced aerenchyma when waterlogged whereas aerenchyma-like structures were constitutively present in black-grass. Aerial biomass of waterlogged wheat was smaller, whereas waterlogged black-grass was similar or larger. Variability in waterlogging responses within and between these species was correlated with transcriptomic and metabolomic changes in leaves of control or waterlogged plants. In wheat, transcripts associated with regulation and utilisation of phosphate compounds were upregulated and sugars and amino acids concentrations were increased. Black-grass biotypes showed limited molecular responses to waterlogging. Some black-grass amino acids were decreased and one transcript commonly upregulated was previously identified in screens for genes underpinning metabolism-based resistance to herbicides. Our findings provide insights into the different waterlogging tolerances of these species and may help to explain the previously observed patchiness of this weed's distribution in wheat fields.

Ethylene-induced improvement in photosynthetic performance of Zanthoxylum armatum under reoxygenation conditions

In this study, we evaluated the photosynthetic performance of Zanthoxylum armatum seedlings to test the tolerance to reoxygenation after waterlogging. The experiment included a control group without waterlogging (NW) and three reoxygenation groups with reoxygenation after 1day (WR1), 2days (WR2) and 3days (WR3). Seedlings were pretreated with concentrations of 0, 200 and 400μmolL-1 of ethylene. The results showed that reoxygenation after waterlogging for 1-3days decreased photosynthetic pigments content, enzymes activity, stomatal conductance (G s ), net photosynthetic rate (P n ), transpiration rate (T r ) and water-use efficiency (WUE). However, pretreatment with ethylene increased photosynthetic pigments content, enzymes activity and gas exchange parameters under both NW and WR3 treatments. The chlorophyll fluorescence results showed that the maximum quantum yield of PSII (F v /F m ) and actual photochemical efficiency of PSII (Φ PSII ) remained no significant changes under the NW and WR1 treatments, while they were significantly reduced with an increase in waterlogging days followed by reoxygenation under WR2 and WR3 treatments. Exogenous ethylene inhibited F v /F m and the non-photochemical quenching coefficient (NPQ), while enhanced Φ PSII and electron transfer efficiency (ETR) under WR2 treatments. Moreover, the accumulation of exogenous ethylene reduced photosynthetic ability. These findings provide insights into the role of ethylene in enhancing the tolerance of Z. armatum to reoxygenation stress, which could help mitigate the impact of continued climate change.

Study on the causes of growth differences in three conifers after the rainy season in the Xiong'an New Area

Background

The implementation of the Millennium Forestry Plan was accompanied by growth discomfort exhibiting varying degrees of symptoms in some coniferous forests after the rainy season.

Hypothesis

High soil water content affects the underground root growth and distribution characteristics of conifers, and the above-ground parts show corresponding variability. To determine the factors contributing to the significant growth disparities among the three conifers in Xiong'an New Area after the rainy season, we conducted a study investigating the growth characteristics of conifers. This study involved analyzing the external morphology of the plants, assessing leaf pigment content, measuring the root morphological index and root vigor, as well as respiratory characteristics, to evaluate the growth attributes of their root systems in a high soil moisture environment.

Methods

In the "Millennium Forest" area of Xiong'an New Area, we selected three coniferous trees, Pinus tabuliformis, Pinus bungeana and Pinus armandii, and set up three standard sample plots for each conifer. The conifers were classified into 3 levels according to their growth performance (vigorous or suppressed), leaf condition (color change, wilting or not) and relevant grading criteria.

Results

(1) The growth of the three conifers displayed discernible differences in external morphology. Moreover, a decrease in growth condition corresponded to a reduction in crown size, ground diameter, diameter at breast height, leaf length, and new growths. (2) The root biomass, length, surface area, and root volume of conifers growing N class were significantly reduced than those of L class conifers. Conifers with a higher proportion of root systems in the 40-60 cm soil layer experienced more severe stress. (3) The significant decline in root respiration and vigor among all three conifer growth classes (M and N) suggested that the root system was undergoing anoxic stress, particularly at a soil depth of 40-60 cm where root respiration and vigor were notably reduced. (4) The persistent anoxic stress created by long-term exposure to high soil moisture content primarily impacted P. armandii to a greater extent than P. tabuliformis and P. bungeana. Additionally, the transporting and absorbing root ratios varied among conifers with differing growth conditions. The long-term high moisture environment also caused partial death of absorbing roots, which played a key role in the observed differences in growth. (5) As the soil depth increases, the soil water content increases accordingly. Plants with more root distribution in the deeper soil layers grow worse than those distributed in the top soil layers. Soil water content is related to aeration, root distribution, growth and growth of above-ground parts. The variability of root distribution and growth led to the differentiation of the growth of the above-ground part of the plant in terms of external morphology, which inhibited the overall plant growth. The results of the study provide a theoretical basis for the cultivation and management of three conifers in high soil moisture environments.

Tissue-Specific Transcriptome and Metabolome Analysis Reveals the Response Mechanism of Brassica napus to Waterlogging Stress

During the growth period of rapeseed, if there is continuous rainfall, it will easily lead to waterlogging stress, which will seriously affect the growth of rapeseed. Currently, the mechanisms of rapeseed resistance to waterlogging stress are largely unknown. In this study, the rapeseed (Brassica napus) inbred lines G230 and G218 were identified as waterlogging-tolerant rapeseed and waterlogging-sensitive rapeseed, respectively, through a potted waterlogging stress simulation and field waterlogging stress experiments. After six days of waterlogging stress at the seedling stage, the degree of leaf aging and root damage of the waterlogging-tolerant rapeseed G230 were lower than those of the waterlogging-sensitive rapeseed G218. A physiological analysis showed that waterlogging stress significantly increased the contents of malondialdehyde, soluble sugar, and hydrogen peroxide in rape leaves and roots. The transcriptomic and metabolomic analysis showed that the differential genes and the differential metabolites of waterlogging-tolerant rapeseed G230 were mainly enriched in the metabolic pathways, biosynthesis of secondary metabolites, flavonoid biosynthesis, and vitamin B6 metabolism. Compared to G218, the expression levels of some genes associated with flavonoid biosynthesis and vitamin B metabolism were higher in G230, such as CHI, DRF, LDOX, PDX1.1, and PDX2. Furthermore, some metabolites involved in flavonoid biosynthesis and vitamin B6 metabolism, such as naringenin and epiafzelechin, were significantly up-regulated in leaves of G230, while pyridoxine phosphate was only significantly down-regulated in roots and leaves of G218. Furthermore, foliar spraying of vitamin B6 can effectively improve the tolerance to waterlogging of G218 in the short term. These results indicate that flavonoid biosynthesis and vitamin B6 metabolism pathways play a key role in the waterlogging tolerance and hypoxia stress resistance of Brassica napus and provide new insights for improving the waterlogging tolerance and cultivating waterlogging-tolerant rapeseed varieties.

Wheat Crop under Waterlogging: Potential Soil and Plant Effects

Inundation, excessive precipitation, or inadequate field drainage can cause waterlogging of cultivated land. It is anticipated that climate change will increase the frequency, intensity, and unpredictability of flooding events. This stress affects 10-15 million hectares of wheat every year, resulting in 20-50% yield losses. Since this crop greatly sustains a population's food demands, providing ca. 20% of the world's energy and protein diets requirements, it is crucial to understand changes in soil and plant physiology under excess water conditions. Variations in redox potential, pH, nutrient availability, and electrical conductivity of waterlogged soil will be addressed, as well as their impacts in major plant responses, such as root system and plant development. Waterlogging effects at the leaf level will also be addressed, with a particular focus on gas exchanges, photosynthetic pigments, soluble sugars, membrane integrity, lipids, and oxidative stress.

Waterlogging during the reproductive growth stage causes physiological and biochemical modifications in the leaves of cowpea (Vigna unguiculata L.) genotypes with contrasting tolerance

Waterlogging causes various metabolic, physiological, and morphological changes in crops, resulting in yield loss of most legumes in rainfed and irrigated agriculture. However, research on cowpea genotypes using physiological and biochemical traits as a measure of tolerance to waterlogging stress is limited. We evaluated the impacts of 7 days of waterlogging (DOW) and 7 days of recovery (DOR) on the physiology and biochemistry of two cowpea (Vigna unguiculata (L.) Walp) genotypes (UCR 369 and EpicSelect.4) with contrasting waterlogging tolerance. Cowpea genotypes were grown in a controlled environment until the R2 stage and then subjected to 7 DOW. Later, the waterlogged plants were reoxygenated for an additional 7 DOR. Overall, cowpea genotypes had a contrasting response to waterlogging using different mechanisms. Compared to the control, the photosynthetic parameters of both cowpea genotypes were impaired under 7 DOW and could not recover at 7 DOR, with a larger decline in EpicSelect.4.7 DOW caused significant loss in the chlorophyll and carotenoid content of both genotypes. However, only waterlogged UCR 369 was not photo-inhibited and able to restore the levels of chlorophyll and carotenoids at 7 DOR. In addition, 7 DOW induced intense stress in UCR 369 with increased zeaxanthin, sucrose, and flavonoid content, while these metabolites were decreased in EpicSelect.4. On the other hand, glucose, fructose, and phenolic content were increased in EpicSelect.4 but decreased in UCR 369 at 7 DOR. In summary, compared to EpicSelect.4, UCR 369 restored their photosynthetic pigments and metabolites to the control levels at 7 DOR, indicating a likely tolerance to waterlogging stress.

Effects of hydrogen peroxide priming on yield, photosynthetic capacity and chlorophyll fluorescence of waterlogged summer maize

Extreme rainfall events during the summer maize growth and development periods, which have induced losses in summer maize production. There was a completely randomized block experiment being designed with four treatments: waterlogging for 6 days at the V3 stage (C-W), H₂O₂-priming + non-waterlogging (H-CK), H₂O₂-priming + waterlogging for 6 days at the V3 stage (H-W) and control (C-CK). This study investigated the effects of H₂O₂ priming on yield and photosynthetic parameters of (Zea mays. L) summer maize hybrid DengHai605 (DH605) by measuring the leaf area index (LAI), soil and plant analyzer development (SPAD) value, stomatal morphology, gas exchange parameters, and chlorophyll fluorescence parameters. The results showed that the net photosynthetic rate (Pn) was decreased after waterlogging through the stomatal limitation of CO₂ supply and reduction of PSII photochemical efficiency, which led to the decrease in dry matter accumulation and grain yield. H₂O₂ priming increased the number of opening stomas, the stomatal length, and width, thus increasing Ci by 12.1%, which enhanced the Pn by 37.5%. Additionally, H₂O₂ priming could improve the energy of dark reaction carbohydrates by increasing the light energy absorption and utilization, alleviating the function of PSII reaction centers, protecting the PSII receptor and donor side, and the electron transport chain. The φEo, φPo, φRo, and Ψo of H-W were increased by 89.9%, 16.2%, 55.4%, and 63.9% respectively, and the φDo was decreased by 23.5%, compared with C-W. Therefore, H₂O₂ priming significantly enhanced the PSII photochemical efficiency, and increased the CO₂ supply in dark reactions to promote carbon assimilation, alleviating the waterlogging-induced damage to maize plant growth and grain yield.

Growth and Photosynthetic Responses of Cowpea Genotypes under Waterlogging at the Reproductive Stage

Waterlogging is an important environmental stress limiting the productivity of crops worldwide. Cowpea (Vigna unguiculata L.) is particularly sensitive to waterlogging stress during the reproductive stage, with a consequent decline in pod formation and yield. However, little is known about the critical processes underlying cowpea’s responses to waterlogging during the reproductive stage. Thus, we investigated the key parameters influencing carbon fixation, including stomatal conductance (g_s), intercellular CO₂ concentration, chlorophyll content, and chlorophyll fluorescence, of two cowpea genotypes with contrasting waterlogging tolerance. These closely related genotypes have starkly contrasting responses to waterlogging during and after 7 days of waterlogging stress (DOW). In the intolerant genotype (‘EpicSelect.4’), waterlogging resulted in a gradual loss of pigment and decreased photosynthetic capacity as a consequent decline in shoot biomass. On the other hand, the waterlogging-tolerant genotype (‘UCR 369’) maintained CO₂ assimilation rate (A), stomatal conductance (g_s), biomass, and chlorophyll content until 5 DOW. Moreover, there was a highly specific downregulation of the mesophyll conductance (g_m), maximum rate of Rubisco (V_cmax), and photosynthetic electron transport rate (J_max) as non-stomatal limiting factors decreasing A in EpicSelect.4. Exposure of EpicSelect.4 to 2 DOW resulted in the loss of PSII photochemistry by downregulating the PSII quantum yield (F_v/F_m), photochemical efficiency (Φ_PSII), and photochemical quenching (qP). In contrast, we found no substantial change in the photosynthesis and chlorophyll fluorescence of UCR 369 in the first 5 DOW. Instead, UCR 369 maintained biomass accumulation, chlorophyll content, and Rubisco activity, enabling the genotype to maintain nutrient absorption and photosynthesis during the early period of waterlogging. However, compared to the control, both cowpea genotypes could not fully recover their photosynthetic capacity after 7 DOW, with a more significant decline in EpicSelect.4. Overall, our findings suggest that the tolerant UCR 369 genotype maintains higher photosynthesis under waterlogging stress attributable to higher photochemical efficiency, Rubisco activity, and less stomatal restriction. After recovery, the incomplete recovery of A can be attributed to the reduced g_s caused by severe waterlogging damage in both genotypes. Thus, promoting the rapid recovery of stomata from waterlogging stress may be crucial for the complete restoration of carbon fixation in cowpeas during the reproductive stage.

Phenotyping for waterlogging tolerance in crops: current trends and future prospects

Yield losses to waterlogging are expected to become an increasingly costly and frequent issue in some regions of the world. Despite the extensive work that has been carried out examining the molecular and physiological responses to waterlogging, phenotyping for waterlogging tolerance has proven difficult. This difficulty is largely due to the high variability of waterlogging conditions such as duration, temperature, soil type, and growth stage of the crop. In this review, we highlight use of phenotyping to assess and improve waterlogging tolerance in temperate crop species. We start by outlining the experimental methods that have been utilized to impose waterlogging stress, ranging from highly controlled conditions of hydroponic systems to large-scale screenings in the field. We also describe the phenotyping traits used to assess tolerance ranging from survival rates and visual scoring to precise photosynthetic measurements. Finally, we present an overview of the challenges faced in attempting to improve waterlogging tolerance, the trade-offs associated with phenotyping in controlled conditions, limitations of classic phenotyping methods, and future trends using plant-imaging methods. If effectively utilized to increase crop resilience to changing climates, crop phenotyping has a major role to play in global food security.

High-throughput unmanned aerial vehicle-based phenotyping provides insights into the dynamic process and genetic basis of rapeseed waterlogging response in the field

Waterlogging severely affects the growth, development, and yield of crops. Accurate high-throughput phenotyping is important for exploring the dynamic crop waterlogging response in the field, and the genetic basis of waterlogging tolerance. In this study, a multi-model remote sensing phenotyping platform based on an unmanned aerial vehicle (UAV) was used to assess the genetic response of rapeseed (Brassica napus) to waterlogging, by measuring morphological traits and spectral indices over 2 years. The dynamic responses of the morphological and spectral traits indicated that the rapeseed waterlogging response was severe before the middle stage within 18 d after recovery, but it subsequently decreased partly. Genome-wide association studies identified 289 and 333 loci associated with waterlogging tolerance in 2 years. Next, 25 loci with at least nine associations with waterlogging-related traits were defined as highly reliable loci, and 13 loci were simultaneously identified by waterlogging tolerance coefficients of morphological traits, spectral indices, and common factors. Forty candidate genes were predicted in the regions of 13 overlapping loci. Our study provides insights into the understanding of the dynamic process and genetic basis of rapeseed waterlogging response in the field by a high-throughput UAV phenotyping platform. The highly reliable loci identified in this study are valuable for breeding waterlogging-tolerant rapeseed cultivars.

Effects of Kiwifruit Rootstocks with Opposite Tolerance on Physiological Responses of Grafting Combinations under Waterlogging Stress

Kiwifruit is commonly sensitive to waterlogging stress, and grafting onto a waterlogging-tolerant rootstock is an efficient strategy for enhancing the waterlogging tolerance of kiwifruit plants. KR5 (Actinidia valvata) is more tolerant to waterlogging than ‘Hayward’ (A. deliciosa) and is a potential resistant rootstock for kiwifruit production. Here, we focused on evaluating the performance of the waterlogging-sensitive kiwifruit scion cultivar ‘Zhongmi 2′ when grafted onto KR5 (referred to as ZM2/KR5) and Hayward (referred to as ZM2/HWD) rootstocks, respectively, under waterlogging stress. The results showed ‘Zhongmi 2′ performed much better when grafted onto KR5 than when grafted onto ‘Hayward’, exhibiting higher photosynthetic efficiency and reduced reactive oxygen species (ROS) damage. Furthermore, the roots of ZM2/KR5 plants showed greater root activity and energy supply, lower ROS damage, and more stable osmotic adjustment ability than the roots of ZM2/HWD plants under waterlogging stress. In addition, we detected the expression of six key genes involved in the kiwifruit waterlogging response mechanism, and these genes were remarkably induced in the ZM2/KR5 roots but not in the ZM2/HWD roots under waterlogging stress. Moreover, principal component analysis (PCA) further demonstrated the differences in the physiological responses of the ZM2/KR5 and ZM2/HWD plants under waterlogging stress. These results demonstrated that the KR5 rootstock can improve the waterlogging tolerance of grafted kiwi plants by regulating physiological and biochemical metabolism and molecular responses.

Waterlogging Stress Induces Antioxidant Defense Responses, Aerenchyma Formation and Alters Metabolisms of Banana Plants

Flooding caused or exacerbated by climate change has threatened plant growth and food production worldwide. The lack of knowledge on how crops respond and adapt to flooding stress imposes a major barrier to enhancing their productivity. Hence, understanding the flooding-responsive mechanisms of crops is indispensable for developing new flooding-tolerant varieties. Here, we examined the banana (Musa acuminata cv. Berangan) responses to soil waterlogging for 1, 3, 5, 7, 14, and 24 days. After waterlogging stress, banana root samples were analyzed for their molecular and biochemical changes. We found that waterlogging treatment induced the formation of adventitious roots and aerenchyma with conspicuous gas spaces. In addition, the antioxidant activities, hydrogen peroxide, and malondialdehyde contents of the waterlogged bananas increased in response to waterlogging stress. To assess the initial response of bananas toward waterlogging stress, we analyzed the transcriptome changes of banana roots. A total of 3508 unigenes were differentially expressed under 1-day waterlogging conditions. These unigenes comprise abiotic stress-related transcription factors, such as ethylene response factors, basic helix-loop-helix, myeloblastosis, plant signal transduction, and carbohydrate metabolisms. The findings of the study provide insight into the complex molecular events of bananas in response to waterlogging stress, which could later help develop waterlogging resilient crops for the future climate.

Waterlogging Priming Enhances Hypoxia Stress Tolerance of Wheat Offspring Plants by Regulating Root Phenotypic and Physiological Adaption

With global climate change, waterlogging stress is becoming more frequent. Waterlogging stress inhibits root growth and physiological metabolism, which ultimately leads to yield loss in wheat. Waterlogging priming has been proven to effectively enhance waterlogging tolerance in wheat. However, it is not known whether waterlogging priming can improve the offspring’s waterlogging resistance. Here, wheat seeds that applied waterlogging priming for one generation, two generations and three generations are separately used to test the hypoxia stress tolerance in wheat, and the physiological mechanisms are evaluated. Results found that progeny of primed plants showed higher plant biomass by enhancing the net photosynthetic rate and antioxidant enzyme activity. Consequently, more sugars are transported to roots, providing a metabolic substrate for anaerobic respiration and producing more ATP to maintain the root growth in the progeny of primed plants compared with non-primed plants. Furthermore, primed plants’ offspring promote ethylene biosynthesis and further induce the formation of a higher rate of aerenchyma in roots. This study provides a theoretical basis for improving the waterlogging tolerance of wheat.

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

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

Physiological and phenotypic characterization of diverse Camelina sativa lines in response to waterlogging

Waterlogging is a serious threat to agriculture that is expected to become more common due to climate change. It is well established that many plants are susceptible to waterlogging, including crops such as rapeseed. To investigate the responses and tolerance to waterlogging of the re-emerging oilseed crop camelina (Camelina sativa), camelina lines of different geographical origins were subjected to waterlogging. Camelina was very sensitive to waterlogging at vegetative growth stages, with a relatively short treatment of 4 days proving lethal for the plants. A treatment duration of 2 days resulted in growth inhibition and lower yields and was used to study the response of 8 different camelina lines to waterlogging at two different vegetative growth stages before bolting. Generally, younger plants (7-9 leaves) were more sensitive than older plants (15-16 leaves). In addition to morphological and agronomic traits, plants were phenotyped for physiological parameters such as chlorophyll content index and total antioxidant capacity of the leaves, which showed significant age-dependent changes due to waterlogging. These results underpin that waterlogging during the vegetative phase is a serious threat to camelina, which needs to be addressed by identifying and establishing tolerance to excess water to harness camelina's potential as a climate-smart crop.

Exploring the effects of land management change on productivity, carbon and nutrient balance: Application of an Ensemble Modelling Approach to the upper River Taw observatory, UK

Agriculture is challenged to produce healthy food and to contribute to cleaner energy whilst mitigating climate change and protecting ecosystems. To achieve this, policy-driven scenarios need to be evaluated with available data and models to explore trade-offs with robust accounting for the uncertainty in predictions. We developed a novel model ensemble using four complementary state-of-the-art agroecosystems models to explore the impacts of land management change. The ensemble was used to simulate key agricultural and environmental outputs under various scenarios for the upper River Taw observatory, UK. Scenarios assumed (i) reducing livestock production whilst simultaneously increasing the area of arable where it is feasible to cultivate (PG2A), (ii) reducing livestock production whilst simultaneously increasing bioenergy production in areas of the catchment that are amenable to growing bioenergy crops (PG2BE) and (iii) increasing both arable and bioenergy production (PG2A + BE). Our ensemble approach combined model uncertainty using the tower property of expectation and the law of total variance. Results show considerable uncertainty for predicted nutrient losses with different models partitioning the uncertainty into different pathways. Bioenergy crops were predicted to produce greatest yields from Miscanthus in lowland and from SRC-willow (cv. Endurance) in uplands. Each choice of management is associated with trade-offs; e.g. PG2A results in a significant increase of edible calories (6736 Mcal ha^-1) but reduced soil C (-4.32 t C ha^-1). Model ensembles in the agroecosystem context are difficult to implement due to challenges of model availability and input and output alignment. Despite these challenges, we show that ensemble modelling is a powerful approach for applications such as ours, offering benefits such as capturing structural as well as data uncertainty and allowing greater combinations of variables to be explored. Furthermore, the ensemble provides a robust means for combining uncertainty at different scales and enables us to identify weaknesses in system understanding.

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.

Transcriptional Response of Two Brassica napus Cultivars to Short-Term Hypoxia in the Root Zone

Waterlogging is one major stress for crops and causes multiple problems for plants, for example low gas diffusion, changes in redox potential and accumulation of toxic metabolites. Brassica napus is an important oil crop with high waterlogging sensitivity, which may cause severe yield losses. Its reactions to the stress are not fully understood. In this work the transcriptional response of rapeseed to one aspect of waterlogging, hypoxia in the root zone, was analyzed by RNAseq, including two rapeseed cultivars from different origin, Avatar from Europe and Zhongshuang 9 from Asia. Both cultivars showed a high number of differentially expressed genes in roots after 4 and 24 h of hypoxia. The response included many well-known hypoxia-induced genes such as genes coding for glycolytic and fermentative enzymes, and strongly resembled the hypoxia response of the model organism Arabidopsis thaliana. The carbohydrate status of roots, however, was minimally affected by root hypoxia, with a tendency of carbohydrate accumulation rather than a carbon starvation. Leaves did not respond to the root stress after a 24-h treatment. In agreement with the gene expression data, subsequent experiments with soil waterlogging for up to 14 days revealed no differences in response or tolerance to waterlogging between the two genotypes used in this study. Interestingly, using a 0.1% starch solution for waterlogging, which caused a lowered soil redox potential, resulted in much stronger effects of the stress treatment than using pure water suggesting a new screening method for rapeseed cultivars in future experiments.

Physiology of Plant Responses to Water Stress and Related Genes: A Review

Drought and waterlogging seriously affect the growth of plants and are considered severe constraints on agricultural and forestry productivity; their frequency and degree have increased over time due to global climate change. The morphology, photosynthetic activity, antioxidant enzyme system and hormone levels of plants could change in response to water stress. The mechanisms of these changes are introduced in this review, along with research on key transcription factors and genes. Both drought and waterlogging stress similarly impact leaf morphology (such as wilting and crimping) and inhibit photosynthesis. The former affects the absorption and transportation mechanisms of plants, and the lack of water and nutrients inhibits the formation of chlorophyll, which leads to reduced photosynthetic capacity. Constitutive overexpression of 9-cis-epoxydioxygenase (NCED) and acetaldehyde dehydrogenase (ALDH), key enzymes in abscisic acid (ABA) biosynthesis, increases drought resistance. The latter forces leaf stomata to close in response to chemical signals, which are produced by the roots and transferred aboveground, affecting the absorption capacity of CO2, and reducing photosynthetic substrates. The root system produces adventitious roots and forms aerenchymal to adapt the stresses. Ethylene (ETH) is the main response hormone of plants to waterlogging stress, and is a member of the ERFVII subfamily, which includes response factors involved in hypoxia-induced gene expression, and responds to energy expenditure through anaerobic respiration. There are two potential adaptation mechanisms of plants (“static” or “escape”) through ETH-mediated gibberellin (GA) dynamic equilibrium to waterlogging stress in the present studies. Plant signal transduction pathways, after receiving stress stimulus signals as well as the regulatory mechanism of the subsequent synthesis of pyruvate decarboxylase (PDC) and alcohol dehydrogenase (ADH) enzymes to produce ethanol under a hypoxic environment caused by waterlogging, should be considered. This review provides a theoretical basis for plants to improve water stress tolerance and water-resistant breeding.

Screening of cowpea (Vigna unguiculata (L.) Walp.) genotypes for waterlogging tolerance using morpho-physiological traits at early growth stage

The majority of cowpea (Vigna unguiculata (L.) Walp.) produced in the U.S. is planted shortly after the summer rains and subsequently depends on rain or artificial irrigation. Therefore, excessive precipitation and poor soil drainage will cause cowpea plants to suffer temporary waterlogging, reducing the submerged tissue's oxygen level. Although cowpea is sensitive to waterlogging, excessive moisture can induce several morpho-physiological changes with adverse impacts on yield in its early stages of development. The current study subjected 30 cowpea genotypes to 10-days of waterlogging at the seedling stage under a controlled environment. The dynamic changes of 24 morpho-physiological parameters under waterlogging and optimal water conditions were analyzed to understand cowpea's response to waterlogging. Significant waterlogging treatment, cowpea genotypes, and their interactions (P < 0.001) were observed for most of the measured parameters. The results indicated that plant height (PH), leaf area (LA), fresh (FW) and dry weight (DW) of cowpea genotypes were significantly decreased under waterlogging compared to the control treatments. Similar results were obtained for net photosynthesis (P_n), stomatal conductance (g_s), intercellular CO₂ concentration (C_i), and transpiration rate (E). However, the water use efficiency (WUE) and adventitious roots (ARs) increased linearly under waterlogging conditions. Waterlogging also declined chlorophyll fluorescence parameters except non-photochemical quenching (qN), which increased with excess soil moisture. In addition, waterlogging tolerance coefficient (WTC) and multivariate analysis (MCA) methods were used to characterize cowpea genotypes for waterlogging tolerance. Accordingly, the cowpea genotype Dagupan Pangasinan, UCR 369, and Negro were classified as waterlogging tolerant, while EpicSelect.4 and ICARDA 140071, as the most waterlogging sensitive. The cowpea genotypes and morpho-physiological traits determined from this study may be useful for genetic engineering and breeding programs that integrate cowpea waterlogging tolerance.

Salicylic Acid Enhances Adventitious Root and Aerenchyma Formation in Wheat under Waterlogged Conditions

The present study investigated the role of salicylic acid (SA) in regulating morpho-anatomical adaptive responses of a wheat plant to waterlogging. Our pharmacological study showed that treatment of waterlogged wheat plants with exogenous SA promotes the formation axile roots and surface adventitious roots that originate from basal stem nodes, but inhibits their elongation, leading to the formation of a shallow root system. The treatment also enhanced axile root formation in non-waterlogged plants but with only slight reductions in their length and branch root formation. Exogenous SA enhanced the formation of root aerenchyma, a key anatomical adaptive response of plants to waterlogging. Consistent with these results, waterlogging enhanced SA content in the root via expression of specific isochorismate synthase (ICS; ICS1 and ICS2) and phenylalanine ammonia lyase (PAL; PAL4, PAL5 and PAL6) genes and in the stem nodes via expression of specific PAL (PAL5 and PAL6) genes. Although not to the same level observed in waterlogged plants, exogenous SA also induced aerenchyma formation in non-waterlogged plants. The findings of this study furthermore indicated that inhibition of ethylene synthesis in SA treated non-waterlogged and waterlogged plants does not have any effect on SA-induced emergence of axile and/or surface adventitious roots but represses SA-mediated induction of aerenchyma formation. These results highlight that the role of SA in promoting the development of axile and surface adventitious roots in waterlogged wheat plants is ethylene independent while the induction of aerenchyma formation by SA requires the presence of ethylene.

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.

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.

The Adaptation and Tolerance of Major Cereals and Legumes to Important Abiotic Stresses

Abiotic stresses, including drought, extreme temperatures, salinity, and waterlogging, are the major constraints in crop production. These abiotic stresses are likely to be amplified by climate change with varying temporal and spatial dimensions across the globe. The knowledge about the effects of abiotic stressors on major cereal and legume crops is essential for effective management in unfavorable agro-ecologies. These crops are critical components of cropping systems and the daily diets of millions across the globe. Major cereals like rice, wheat, and maize are highly vulnerable to abiotic stresses, while many grain legumes are grown in abiotic stress-prone areas. Despite extensive investigations, abiotic stress tolerance in crop plants is not fully understood. Current insights into the abiotic stress responses of plants have shown the potential to improve crop tolerance to abiotic stresses. Studies aimed at stress tolerance mechanisms have resulted in the elucidation of traits associated with tolerance in plants, in addition to the molecular control of stress-responsive genes. Some of these studies have paved the way for new opportunities to address the molecular basis of stress responses in plants and identify novel traits and associated genes for the genetic improvement of crop plants. The present review examines the responses of crops under abiotic stresses in terms of changes in morphology, physiology, and biochemistry, focusing on major cereals and legume crops. It also explores emerging opportunities to accelerate our efforts to identify desired traits and genes associated with stress tolerance.

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

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

Short-Term Waterlogging Depresses Early Growth of Sunflower (Helianthus annuus L.) on Saline Soils with a Shallow Water Table in the Coastal Zone of Bangladesh

Sunflower (Helianthus annuus L.), which is widely grown globally for its high-quality edible oil, is reasonably salt and drought tolerant but it is susceptible to waterlogging. In the saline coastal zone of the Ganges delta, sunflower is often exposed to sudden heavy rainfall during early growth but plant tolerance to such events is not known. Hence, we evaluated the effect of short-term soil inundation (referred to as waterlogging) for 0, 24, 48 and 72 h on sunflower at emergence, 2-leaf, and 4-leaf stages in early- and late-sown crops under field conditions (saline, clay-textured soil, and shallow groundwater). Waterlogging for 24 h did not affect sunflower at any stage but waterlogging for 48 and 72 h suppressed emergence and growth at the 2 and 4-leaf stages. Waterlogging for 72 h completely prevented the emergence for early sowing, whereas emergence was less affected for later sowing. Shoot and root dry weight were most affected at the emergence and 2-leaf stage, not at the 4-leaf stage. In conclusion, waterlogging caused by more than 24 h soil inundation at up to the 4-leaf stage severely depressed emergence and growth, indicating the need for effective drainage at sowing of sunflower in the low-lying coastal saline zone of Bangladesh.

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

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

Genome-Wide Association Study of Waterlogging Tolerance in Barley (Hordeum vulgare L.) Under Controlled Field Conditions

Waterlogging is one of the main abiotic stresses severely reducing barley grain yield. Barley breeding programs focusing on waterlogging tolerance require an understanding of genetic loci and alleles in the current germplasm. In this study, 247 worldwide spring barley genotypes grown under controlled field conditions were genotyped with 35,926 SNPs with minor allele frequency (MAF) > 0.05. Significant phenotypic variation in each trait, including biomass, spikes per plant, grains per plant, kernel weight per plant, plant height and chlorophyll content, was observed. A genome-wide association study (GWAS) based on linkage disequilibrium (LD) for waterlogging tolerance was conducted. Population structure analysis divided the population into three subgroups. A mixed linkage model using both population structure and kinship matrix (Q+K) was performed. We identified 17 genomic regions containing 51 significant waterlogging-tolerance-associated markers for waterlogging tolerance response, accounting for 5.8-11.5% of the phenotypic variation, with a majority of them localized on chromosomes 1H, 2H, 4H, and 5H. Six novel QTL were identified and eight potential candidate genes mediating responses to abiotic stresses were located at QTL associated with waterlogging tolerance. To our awareness, this is the first GWAS for waterlogging tolerance in a worldwide barley collection under controlled field conditions. The marker-trait associations could be used in the marker-assisted selection of waterlogging tolerance and will facilitate barley breeding.

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

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

Physiological and Expressional Regulation on Photosynthesis, Starch and Sucrose Metabolism Response to Waterlogging Stress in Peanut

Waterlogging has negative effects on crop yield. Physiological and transcriptome data of two peanut cultivars [Zhongkaihua 1 (ZKH 1) and Huayu 39 (HY 39)] were studied under normal water supply and waterlogging stress for 5 or 10 days at the flowering stage. The results showed that the main stem height, the number of lateral branches, lateral branch length, and the stem diameter increased under waterlogging stress, followed by an increase in dry matter accumulation, which was correlated with the increase in the soil and plant analysis development (SPAD) and net photosynthetic rate (Pn) and the upregulation of genes related to porphyrin and chlorophyll metabolism and photosynthesis. However, the imbalance of the source-sink relationship under waterlogging was the main cause of yield loss, and waterlogging caused an increase in the sucrose and soluble sugar contents and a decrease in the starch content; it also decreased the activities of sucrose synthetase (SS) and sucrose phosphate synthetase (SPS), which may be due to the changes in the expression of genes related to starch and sucrose metabolism. However, the imbalance of the source-sink relationship led to the accumulation of photosynthate in the stems and leaves, which resulted in the decrease of the ratio of pod dry weight to total dry weight (PDW/TDW) and yield. Compared with ZKH 1, the PDW of HY 39 decreased more probably because more photosynthate accumulated in the stem and leaves of HY 39 and could not be effectively transported to the pod.

Short-term waterlogging-induced autophagy in root cells of wheat can inhibit programmed cell death

Autophagy is a pathway for the degradation of cytoplasmic components in eukaryotes. In wheat, the mechanism by which autophagy regulates programmed cell death (PCD) is unknown. Here, we demonstrated that short-term waterlogging-induced autophagy inhibited PCD in root cells of wheat. The waterlogging-tolerant wheat cultivar Huamai 8 and the waterlogging-sensitive wheat cultivar Huamai 9 were used as experimental materials, and their roots were waterlogged for 0-48 h. Waterlogging stress increased the number of autophagic structures, the expression levels of autophagy-related genes (TaATG), and the occurrence of PCD in root cells. PCD manifested as morphological changes in the cell nucleus, significant enhancement of DNA laddering bands, and increases in caspase-like protease activity and the expression levels of metacaspase genes. The autophagy promoter rapamycin (RAPA) reduced PCD levels, whereas the autophagy inhibitor 3-methyladenine (3-MA) enhanced them. The expression levels of TaATG genes and the number of autophagic structures were lower in cortex cells than in stele cells, but the levels of PCD were higher in cortex cells. The number of autophagic structures was greater in Huamai 8 than in Huamai 9, but the levels of PCD were lower. In summary, our results showed that short-term waterlogging induced autophagy which could inhibit PCD. Mechanisms of response to waterlogging stress differed between cortex and stele cells and between two wheat cultivars of contrasting waterlogging tolerance.

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.

Leaf nutrient content and transcriptomic analyses of endive (Cichorium endivia) stressed by downpour-induced waterlog reveal a gene network regulating kestose and inulin contents

Endive (Cichorium endivia L.), a vegetable consumed as fresh or packaged salads, is mostly cultivated outdoors and known to be sensitive to waterlogging in terms of yield and quality. Phenotypic, metabolic and transcriptomic analyses were used to study variations in curly- ('Domari', 'Myrna') and smooth-leafed ('Flester', 'Confiance') cultivars grown in short-term waterlog due to rainfall excess before harvest. After recording loss of head weights in all cultivars (6-35%), which was minimal in 'Flester', NMR untargeted profiling revealed variations as influenced by genotype, environment and interactions, and included drop of total carbohydrates (6-50%) and polyols (3-37%), gain of organic acids (2-30%) and phenylpropanoids (98-560%), and cultivar-specific fluctuations of amino acids (-37 to +15%). The analysis of differentially expressed genes showed GO term enrichment consistent with waterlog stress and included the carbohydrate metabolic process. The loss of sucrose, kestose and inulin recurred in all cultivars and the sucrose-inulin route was investigated by covering over 50 genes of sucrose branch and key inulin synthesis (fructosyltransferases) and catabolism (fructan exohydrolases) genes. The lowered expression of a sucrose gene subset together with that of SUCROSE:SUCROSE-1-FRUCTOSYLTRANSFERASE (1-SST) may have accounted for sucrose and kestose contents drop in the leaves of waterlogged plants. Two anti-correlated modules harbouring candidate hub-genes, including 1-SST, were identified by weighted gene correlation network analysis, and proposed to control positively and negatively kestose levels. In silico analysis further pointed at transcription factors of GATA, DOF, WRKY types as putative regulators of 1-SST.

Experimental comparison of two methods to study barley responses to partial submergence

BACKGROUND

Crop yield is dependent on climate conditions, which are becoming both more variable and extreme in some areas of the world as a consequence of global climate change. Increased precipitation and flooding events are the cause of important yield losses due to waterlogging or (partial) submergence of crops in the field. Our ability to screen efficiently and quickly for varieties that have increased tolerance to waterlogging or (partial) submergence is important. Barley, a staple crop worldwide, is particularly sensitive to waterlogging. Screening for waterlogging tolerant barley varieties has been ongoing for many years, but methods used to screen vary greatly, from the type of soil used to the time at which the treatment is applied. This variation makes it difficult to cross-compare results.

RESULTS

Here, we have devised a scoring system to assess barley tolerance to waterlogging and compare two different methods when partial submergence is applied with either water or a starch solution at an early developmental stage, which is particularly sensitive to waterlogging or partial submergence. The use of a starch solution has been previously shown to result in more reducing soil conditions and has been used to screen for waterlogging tolerance.

CONCLUSIONS

Our results show that the two methods provide similar results to qualitatively rank varieties as tolerant or sensitive, while also affecting plants differently, in that application of a starch solution results in stronger and earlier symptoms than applying partial submergence with water.

Two Brassica napus cultivars differ in gene expression, but not in their response to submergence

Heavy rainfall causes flooding of natural ecosystems as well as farmland, negatively affecting plant performance. While the responses of the wild model organism Arabidopsis thaliana to such stress conditions is well understood, little is known about the responses of its relative, the important oil crop plant Brassica napus. For the first time, we analyzed the molecular response of Brassica napus seedlings to full submergence in a natural light-dark cycle. We used two cultivars in this study, a European hybrid cultivar and an Asian flood-tolerant cultivar. Despite their genomic differences, those genotypes showed no major differences in their responses to submergence. The molecular responses to submergence included the induction of defense- and hormone-related pathways and the repression of biosynthetic processes. Furthermore, RNAseq revealed a strong carbohydrate-starvation response under submergence in daylight, which corresponded with a fast depletion of sugars. Consequently, both B. napus cultivars exhibited a strong growth repression under water, but there was no indication of a low-oxygen response. The ability of the European hybrid cultivar to form a short-lived leaf gas film neither increased underwater net photosynthesis, underwater dark respiration nor growth during submergence. Due to the high sensitivity of both cultivars, the analysis of other cultivars or related species with higher submergence tolerance is required in order to improve flood tolerance of this crop species. One major target could be the improvement of underwater photosynthesis efficiency in order to enhance submergence survival.

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.

Genome-wide identification and analysis of high-affinity nitrate transporter 2 (NRT2) family genes in rapeseed (Brassica napus L.) and their responses to various stresses

BACKGROUND

High-affinity nitrate transporter 2 (NRT2) genes have been implicated in nitrate absorption and remobilization under nitrogen (N) starvation stress in many plant species, yet little is known about this gene family respond to various stresses often occurs in the production of rapeseed (Brassica napus L.).

RESULTS

This report details identification of 17 NRT2 gene family members in rapeseed, as well as, assessment of their expression profiles using RNA-seq analysis and qRT-PCR assays. In this study, all BnNRT2.1 members, BnNRT2.2a and BnNRT2.4a were specifically expressed in root tissues, while BnNRT2.7a and BnNRT2.7b were mainly expressed in aerial parts, including as the predominantly expressed NRT2 genes detected in seeds. This pattern of shoot NRT expression, along with homology to an Arabidopsis NRT expressed in seeds, strongly suggests that both BnNRT2.7 genes play roles in seed nitrate accumulation. Another rapeseed NRT, BnNRT2.5 s, exhibited intermediate expression, with transcripts detected in both shoot and root tissues. Functionality of BnNRT2s genes was further outlined by testing for adaptive responses in expression to exposure to a series of environmental stresses, including N, phosphorus (P) or potassium (K) deficiency, waterlogging and drought. In these tests, most NRT2 gene members were up-regulated by N starvation and restricted by the other stresses tested herein. In contrast to this overall trend, transcription of BnNRT2.1a was up-regulated under waterlogging and K deficiency stress, and BnNRT2.5 s was up-regulated in roots subjected to waterlogging. Furthermore, the mRNA levels of BnNRT2.7 s were enhanced under both waterlogging stress and P or K deficiency conditions. These results suggest that these three BnNRT2 genes might participate in crosstalk among different stress response pathways.

CONCLUSIONS

The results presented here outline a diverse set of NRT2 genes present in the rapeseed genome that collectively carry out specific functions throughout rapeseed development, while also responding not just to N deficiency, but also to several other stresses. Targeting of individual BnNRT2 members that coordinate rapeseed nitrate uptake and transport in response to cues from multiple stress response pathways could significantly expand the genetic resources available for improving rapeseed resistance to environmental stresses.

Effects of supplemental nitrogen application on physiological characteristics, dry matter and nitrogen accumulation of winter rapeseed (Brassica napus L.) under waterlogging stress

Waterlogging stress is a common limiting factor for winter rapeseed, which greatly affects the growth and potential production. The present study was conducted to investigate the effects of waterlogging with different durations (0day (D0), 6days (D6) and 9days (D9)) and supplemental nitrogen fertilization (N1, 0 kg ha^-1; N2, 30 kg ha^-1; N3, 60 kg ha^-1 and N4, 90 kg ha^-1) on the physiological characteristics, dry matter and nitrogen accumulation in winter rapeseed (Chuanyou36). The results showed that the supplementary application of nitrogen fertilizer could effectively improve the physiological indexes of winter rapeseed in both pot and field experiments. The supplemental nitrogen increased the chlorophyll content in leaves, enhanced the activities of SOD, CAT, and POD, and decreased the MDA content in leaves and roots of rapeseed. The chlorophyll contents, the antioxidant enzyme activity of leaves and roots significantly increased under D6N3 and D9N4 conditions in both (pot and field) experiments. However, MDA contents significantly decreased compared with waterlogging without nitrogen application. Moreover, the application of nitrogen fertilizer after waterlogging increased the accumulation of dry matter and nitrogen in rapeseed at different growth stages. Therefore, waterlogging stress significantly inhibited the growth and development of rapeseed, but the application of nitrogen fertilizer could effectively reduce the damage of waterlogging. The N-induced increase in waterlogging tolerance of rapeseed might be attributed to the strong antioxidant defense system, maintenance of photosynthetic pigments and the nutrient balance.

Reduced Growth and Nitrogen Uptake During Waterlogging at Tillering Permanently Affect Yield Components in Late Sown Oats

In Mediterranean Europe, winter cereals can experience soil waterlogging starting from crop establishment up to stem elongation and, in late sowings, this stress is combined with temperatures favorable to plant metabolism. Oats response to waterlogging has been rarely investigated, but these species seems to recover better than other cereals. In a 2-year experiment, Avena sativa and Avena byzantina were sown at the end of winter in pots placed outdoors. At the two-tiller stage, plants were exposed to waterlogging for periods ranging from 0 to 35 days. The dry weight and the N-concentration of shoots and roots were determined on waterlogged plants and drained controls at the start and the end of each waterlogging period, and at maturity. At maturity, the grain yield and its components were determined. To relate oat response to its specific morphological and developmental traits, results were compared to the published results in wheat and barley. Both oat species suffered severe damage during waterlogging: the uptake of nitrogen and the N-concentration of shoots were reduced after 7 days, tiller initiation and root growth after 14 days, and shoot growth after 21 days. All plants survived waterlogging, and the relative growth rates of roots and shoots and the net uptake rate of nitrogen were resumed during recovery. Nevertheless, at maturity, the straw and root biomass were markedly lower with all waterlogging durations, and grain yield decreased by 42% up to approximately 81% following an asymptotic equation. The most affected yield components were the number of panicles per plant and the number of kernels per panicle, but their relative sensitivity changed according to waterlogging duration. The slight increase in tiller fertility in response to short waterlogging and the small and irregular decrease in the number of kernels per spikelet suggest that the two oats could recover the initiation and size of inflorescences better than other winter cereals. Despite this, waterlogging in spring was highly detrimental to these oats because of severe damage under waterlogging and because of the inability to initiate new tillers and adequately resume root growth during recovery, once plants had achieved the phase of stem elongation.

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.