Comparative Proteomic Analysis of Grapevine Rootstock in Response to Waterlogging Stress

Waterlogging severely affects global agricultural production. Clarifying the regulatory mechanism of grapevine in response to waterlogging stress will help to improve the waterlogging tolerance of grapevine. In the present study, the physiological and proteomic responses of SO4 grapevine rootstock to different waterlogging tolerances were comparatively assayed. The results showed that the activities of SOD and POD first increased and then decreased, while the change trend of CAT and APX activities was the opposite. In addition, the MDA and H2O2 contents increased after waterlogging treatment, but the chlorophyll a and chlorophyll b contents decreased. A total of 5,578 grapevine proteins were identified by the use of the tandem mass tag (TMT) labeling technique. Among them, 214 (103 and 111 whose expression was upregulated and downregulated, respectively), 314 (129 and 185 whose expression was upregulated and downregulated, respectively), and 529 (248 and 281 whose expression was upregulated and downregulated, respectively) differentially expressed proteins (DEPs) were identified in T0d vs. T10d, T10d vs. T20d, and T0d vs. T20d comparison groups, respectively. Enrichment analysis showed that these DEPs were mainly involved in glutathione metabolism, carbon fixation, amino sugar and nucleotide sugar metabolism, biosynthesis of amino acids, photosynthesis, carbon metabolism, starch, and sucrose metabolism, galactose metabolism, protein processing and ribosomes. To further verify the proteomic data, the expression of corresponding genes that encode eight DEPs was confirmed by quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR). The results of this study presented an important step toward understanding the resistance mechanisms of grapevine in response to waterlogging stress at the proteome level.

Responses of nitrogen efficiency and antioxidant system of summer maize to waterlogging stress under different tillage

Waterlogging was one of the main abiotic stresses affecting maize yield and growth in the North China Plain, while ridge tillage effectually improved soil environment, enhanced crop stress resistance to waterlogging, and increased grain yield of waterlogged maize. In order to explore the responses of nitrogen (N) efficiency and antioxidant system of summer maize to waterlogging stress under different tillage, a field experiment was conducted to explore N use efficiency, leaf activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), and malondialdehyde (MDA) content of waterlogged maize Denghai 605 (DH605) and Zhengdan 958 (ZD958) under different tillage system (ridge planting and flat planting). Our results showed that ridge tillage was beneficial to ameliorate waterlogging damages on antioxidant system by increasing SOD, POD, and CAT activities, and decreasing MDA content. Moreover, ridge tillage significantly increased N efficiency of waterlogged maize. N translocation amount (NTA), N translocation efficiency (NTE), N contribution proportion (NCP), N harvest index (NHI), and N use efficiency (NUE) of waterlogging treatment under ridge planting system (W-V3+R) for DH605 was increased by 108%, 69%, 60%, 8% and 16%, while ZD958 increased by 248%, 132%, 146%, 13% and 16%, respectively, compared to those of waterlogging treatment under flat planting system (W-V3). Ultimately, ridge tillage led to a significant yield improvement by 39% and 50% for DH605 and ZD958, respectively, compared to that of W-V3. In conclusion, ridge tillage was conducive to retard leaf aging, and enhance nitrogen efficiency, thereby resulting in a yield improvement of waterlogged summer maize.

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.

Long-Term Waterlogging as Factor Contributing to Hypoxia Stress Tolerance Enhancement in Cucumber: Comparative Transcriptome Analysis of Waterlogging Sensitive and Tolerant Accessions

Waterlogging (WL), excess water in the soil, is a phenomenon often occurring during plant cultivation causing low oxygen levels (hypoxia) in the soil. The aim of this study was to identify candidate genes involved in long-term waterlogging tolerance in cucumber using RNA sequencing. Here, we also determined how waterlogging pre-treatment (priming) influenced long-term memory in WL tolerant (WL-T) and WL sensitive (WL-S) i.e., DH2 and DH4 accessions, respectively. This work uncovered various differentially expressed genes (DEGs) activated in the long-term recovery in both accessions. De novo assembly generated 36,712 transcripts with an average length of 2236 bp. The results revealed that long-term waterlogging had divergent impacts on gene expression in WL-T DH2 and WL-S DH4 cucumber accessions: after 7 days of waterlogging, more DEGs in comparison to control conditions were identified in WL-S DH4 (8927) than in WL-T DH2 (5957). Additionally, 11,619 and 5007 DEGs were identified after a second waterlogging treatment in the WL-S and WL-T accessions, respectively. We identified genes associated with WL in cucumber that were especially related to enhanced glycolysis, adventitious roots development, and amino acid metabolism. qRT-PCR assay for hypoxia marker genes i.e., alcohol dehydrogenase (adh), 1-aminocyclopropane-1-carboxylate oxidase (aco) and long chain acyl-CoA synthetase 6 (lacs6) confirmed differences in response to waterlogging stress between sensitive and tolerant cucumbers and effectiveness of priming to enhance stress tolerance.

Potassium Alleviates Post-anthesis Photosynthetic Reductions in Winter Wheat Caused by Waterlogging at the Stem Elongation Stage

Waterlogging occurs frequently at the stem elongation stage of wheat in southern China, decreasing post-anthesis photosynthetic rates and constraining grain filling. This phenomenon, and the mitigating effect of nutrient application, should be investigated as it could lead to improved agronomic guidelines. We exposed pot-cultured wheat plants at the stem elongation stage to waterlogging treatment in combination with two rates of potassium (K) application. Waterlogging treatment resulted in grain yield losses, which we attributed to a reduction in the 1,000-grain weight caused by an early decline in the net photosynthetic rate (Pn) post-anthesis. These decreases were offset by increasing K application. Stomatal conductance (Gs) and the intercellular CO2 concentration (Ci) decreased in the period 7–21 days after anthesis (DAA), and these reductions were exacerbated by waterlogging. However, in the period 21–28 DAA, Gs and Ci increased, while Pn decreased continuously, suggesting that non-stomatal factors constrained photosynthesis. On DAA 21, Pn was reduced by waterlogging, but photochemical efficiency (ΦPSII) remained unchanged, indicating a reduction in the dissipation of energy captured by photosystem II (PSII) through the CO2 assimilation pathway. This reduction in energy dissipation increased the risk of photodamage, as shown by early reductions in ΦPSII in waterlogged plants on DAA 28. However, increased K application promoted root growth and nutrient status under waterlogging, thereby improving photosynthesis post-anthesis. In conclusion, the decrease in Pn caused by waterlogging was attributable to stomatal closure during early senescence; during later senescence, a reduction in CO2 assimilation accounted for the reduced Pn and elevated the risk of photodamage. However, K application mitigated waterlogging-accelerated photosynthetic reductions and reduced yield losses.

Understanding physiological and molecular mechanisms of Populus deltoides ‘DanHongYang’ tolerance to waterlogging by comparative transcriptome analysis

Populus deltoides ‘DanHongYang’ (DHY) was identified as a waterlogging-resistant cultivar in our previous study. Here, the phenotype, physiological features and transcriptome profiling of P. deltoides ‘DHY’ between the treatments of waterlogging and control were compared. Waterlogging treatment led to distinctly formation of adventitious roots from P. deltoides ‘DHY’ stems. The activities of ascorbate peroxidase and glutathione reductase significantly increased in the leaves of P. deltoides ‘DHY’ by waterlogging treatment. Comparative transcriptomic analysis showed that 2,447 and 9,465 differentially expressed genes (DEGs) were screened between the leaves and roots of P. deltoides ‘DHY’ under waterlogging and control, respectively. The KEGG analysis showed the most significantly up-regulated DEGs in the leaves and roots were enriched to the pathways of glycolyis and proline synthesis. Some genes involved in stress response, endogenous hormones, antioxidant system and adventitious root development in the waterlogged were identified to contribute to the waterlogging tolerance of P. deltoides ‘DHY’. In addition, some candidate transcription factors such as RAP, NAC, WRKY, and bHLH were also found to be associated with the waterlogging tolerance of P. deltoides ‘DHY’. These findings provided the insights into the physiological and molecular mechanisms underlying the tolerance of P. deltoides ‘DHY’ to waterlogging stresses.

SALICYLIC ACID INDUCES PHYSIOLOGICAL AND BIOCHEMICAL CHANGES IN PEONY UNDER WATERLOGGING STRESS

In this study, the effects of salicylic acid to antioxidative activity and photosynthetic characteristics in waterlogging stress of two peony cultivars (‘Fengdanbai’ and ‘Mingxing’) were investigated. 4-year-old peony grown in different levels of waterlogging stress and then different concentration prepared SA (0.0, 0.1, 0.5 and 1.0 mmol L–1) sprayed on fresh leaves of peony. The antioxidative enzymes activities include superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT), chlorophyll content, relative conductivity and MDA content were measured in leaves about different waterlogging treatment, the photosynthetic characteristics were also measured using photosynthetic measurement system. The results showed that waterlogging stress decreased the chlorophyll content in all peony cultivars leaves, but with SA treatment can inhibit the decrease of chlorophyll content. Relative conductivity increased as the extension of waterlogging time in two cultivars. SA treatment could effectively inhibit the increase of relative conductivity, and 0.5 mmol L–1 of SA was the most suitable concentration. SOD, POD, CAT activity increased first and then decreased in different waterlogging condition, SA significantly increased the activity of various enzymes. MDA content was increase as the expansion of waterlogging time in two cultivars. SA inhibits the increase of MDA content. Of all concentration of SA, 0.5 mmol L–1 was the best concentration to inhibit the waterlogging stress. For the photosynthetic characteristics, the net assimilation rate (Pn), stomatal conductance (Gs), transpiration rate (Tr) and intercellular CO2 (Ci) were decreased under different waterlogging condition. SA treatment can increase Pn, Gs, Tr and Ci of peony.

Effects of ABA on Physiological Characteristics of Tomato under Waterlogging

The effects of waterlogging on antioxidant enzyme activities responses in five different lines, i.e. ABA-deficient mutant (0673) and its control (0535), two ABA over-production transgenic rd29A:NCED1 lines (#2, #7) and Mill. L. cv. New Yorker (WT) were investigated. The waterlogging was mimicked by treating pot plants with flooding. The malondialdehyde (MDA) content, superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) activity in the leaves were evaluated in all treatments. The results showed that after 7 days waterlogging treatment, the malondialdehyde (MDA) was increased in all plants, especially in LA0673. Compared with the LA0673, #2 and #7 significantly increase the activities of SOD, POD and CAT under waterlogging stress. Therefore, ABA could improve the waterlogging tolerance of tomato by increasing the activities of antioxidant enzymes under waterlogging stress.

Transcriptomic profiling of sesame during waterlogging and recovery

Sesame is naturally adapted to arid environments but highly susceptible to waterlogging stress. A few hours of waterlogging (lasting over 36 h) are detrimental to the crop growth, yield and survival. To better understand the molecular mechanisms underlying sesame responses to waterlogging and recovery, it is essential to design a high-resolution time-series experiment. In this study, we reported the RNA-seq profiling of two contrasting genotypes under waterlogging and recovery. The plants were grown in pots and subjected to waterlogging treatment at the flowering stage for 36 h and subsequently, 12 h drainage. Root samples were collected in triplicate at 22 time points under waterlogging/drainage treatments and at 10 time points in the control condition. This represents a total of 195 biological samples and the RNA-seq yielded over eight billion reads. Basic data analyses demonstrated a clear separation of transcriptomes from control, waterlogging and drainage treatments. Overall, the generated high-quality and comprehensive RNA-seq resources will undoubtedly advance our understanding of waterlogging/drainage responses in a non-model sensitive crop.

Oxidative Damage and Antioxidant Defense in Sesamum indicum after Different Waterlogging Durations

The present study was designed to investigate the duration-dependent changes in the biochemical attributes of sesame in response to waterlogging stress. Sesame plants (Sesamum indicum L. cv. BARI Til-4) were subjected to waterlogging for 2, 4, 6, and 8 days during the vegetative stage and data were measured following waterlogging treatment. The present study proves that waterlogging causes severe damage to different attributes of the sesame plant. The plants showed an increasing trend in lipid peroxidation as well as hydrogen peroxide (H2O2) and methylglyoxal contents that corresponded to increased stress duration. A prolonged period of waterlogging decreased leaf relative water content and proline content. Photosynthetic pigments, like chlorophyll (chl) a, b, and chl (a+b) and carotenoid contents, also decreased over time in stressed plants. Glutathione (GSH) and oxidized glutathione (GSSG) contents increased under waterlogging, while the GSH/GSSG ratio and ascorbate content decreased, indicating the disruption of redox balance in the cell. Ascorbate peroxidase, monodehydroascorbate reductase, and glutathione peroxidase activity increased under waterlogging, while dehydroascorbate reductase, glutathione reductase, and catalase activity mostly decreased. Waterlogging modulated the glyoxalase system mostly by enhancing glyoxalase II activity, with a slight increase in glyoxalase I activity. The present study also demonstrates the induction of oxidative stress via waterlogging in sesame plants and that stress levels increase with increased waterlogging duration.