Analyses of flooding tolerance of soybean varieties at emergence and varietal differences in their proteomes

Silicon: A valuable soil element for improving plant growth and CO2 sequestration

BACKGROUND

Silicon (Si), the second most abundant and quasi-essential soil element, is locked as a recalcitrant silicate mineral in the Earth's crust. The physical abundance of silicates can play an essential role in increasing plant productivity. Plants store Si as biogenic silica (phytoliths), which is mobilized through a chemical weathering process in the soil.

AIM OF REVIEW

Although Si is a critical element for plant growth, there is still a considerable need to understand its dissolution, uptake, and translocation in agroecosystems. Here, we show recent progress in understanding the interactome of Si, CO2, the microbiome, and soil chemistry, which can sustainably govern silicate dissolution and cycling in agriculture.

KEY SCIENTIFIC CONCEPTS OF THIS REVIEW

Si cycling is directly related to carbon cycling, and the resulting climate stability can be enhanced by negative feedback between atmospheric CO2 and the silicate uptake process. Improved Si mobilization in the rhizosphere by the presence of reactive elements (for example, Ca, Na, Al, Zn, and Fe) and Si uptake through genetic transporters in plants are crucial to achieving the dual objectives of (i) enhancing crop productivity and (ii) abiotic stress tolerance. Furthermore, the microbiome is a symbiotic partner of plants. Bacterial and fungal microbiomes can solubilize silicate minerals through intriguingly complex bioweathering mechanisms by producing beneficial metabolites and enzymes. However, the interaction of Si with CO2 and the microbiome's function in mobilization have been understudied. This review shows that enhancing our understanding of Si, CO2, the microbiome, and soil chemistry can help in sustainable crop production during climatic stress events.

Microbiome structure variation and soybean's defense responses during flooding stress and elevated CO2

Introduction

With current trends in global climate change, both flooding episodes and higher levels of CO2 have been key factors to impact plant growth and stress tolerance. Very little is known about how both factors can influence the microbiome diversity and function, especially in tolerant soybean cultivars. This work aims to (i) elucidate the impact of flooding stress and increased levels of CO2 on the plant defenses and (ii) understand the microbiome diversity during flooding stress and elevated CO2 (eCO2).

Methods

We used next-generation sequencing and bioinformatic methods to show the impact of natural flooding and eCO2 on the microbiome architecture of soybean plants' below- (soil) and above-ground organs (root and shoot). We used high throughput rhizospheric extra-cellular enzymes and molecular analysis of plant defense-related genes to understand microbial diversity in plant responses during eCO2 and flooding.

Results

Results revealed that bacterial and fungal diversity was substantially higher in combined flooding and eCO2 treatments than in non-flooding control. Microbial diversity was soil>root>shoot in response to flooding and eCO2. We found that sole treatment of eCO2 and flooding had significant abundances of Chitinophaga, Clostridium, and Bacillus. Whereas the combination of flooding and eCO2 conditions showed a significant abundance of Trichoderma and Gibberella. Rhizospheric extra-cellular enzyme activities were significantly higher in eCO2 than flooding or its combination with eCO2. Plant defense responses were significantly regulated by the oxidative stress enzyme activities and gene expression of Elongation factor 1 and Alcohol dehydrogenase 2 in floodings and eCO2 treatments in soybean plant root or shoot parts.

Conclusion

This work suggests that climatic-induced changes in eCO2 and submergence can reshape microbiome structure and host defenses, essential in plant breeding and developing stress-tolerant crops. This work can help in identifying core-microbiome species that are unique to flooding stress environments and increasing eCO2.

The intervention of classical and molecular breeding approaches to enhance flooding stress tolerance in soybean - An review

Abiotic stresses and climate changes cause severe loss of yield and quality of crops and reduce the production area worldwide. Flooding stress curtails soybean growth, yield, and quality and ultimately threatens the global food supply chain. Flooding tolerance is a multigenic trait. Tremendous research in molecular breeding explored the potential genomic regions governing flood tolerance in soybean. The most robust way to develop flooding tolerance in soybean is by using molecular methods, including quantitative trait loci (QTL) mapping, identification of transcriptomes, transcription factor analysis, CRISPR/Cas9, and to some extent, genome-wide association studies (GWAS), and multi-omics techniques. These powerful molecular tools have deepened our knowledge about the molecular mechanism of flooding stress tolerance. Besides all this, using conventional breeding methods (hybridization, introduction, and backcrossing) and other agronomic practices is also helpful in combating the rising flooding threats to the soybean crop. The current review aims to summarize recent advancements in breeding flood-tolerant soybean, mainly by using molecular and conventional tools and their prospects. This updated picture will be a treasure trove for future researchers to comprehend the foundation of flooding tolerance in soybean and cover the given research gaps to develop tolerant soybean cultivars able to sustain growth under extreme climatic changes.

Plant-Based Titanium Dioxide Nanoparticles Trigger Biochemical and Proteome Modifications in Triticum aestivum L. under Biotic Stress of Puccinia striiformis

In this study, we evaluated bioinspired titanium dioxide nanoparticles (TiO2 NPs) that elicited biochemical and proteome modifications in wheat plants under the biotic stress caused by Puccinia striiformis f. sp. tritici (Pst). Biosynthesis of TiO2 NPs was confirmed using UV–Vis spectrophotometry, energy dispersive X-ray spectroscopy (EDX), scanning electron microscopy (SEM), and Fourier transform infrared (FTIR) spectroscopy. We found that the nanoparticles with crystalline nature were smaller than 100 nm. The results of FTIR analysis showed the presence of potential functional groups exhibiting O-H, N-H, C-C, and Ti-O stretching. The TiO2 NPs of different concentrations (20, 40, 60, and 80 mg L−1) were exogenously applied to wheat plants under the biotic stress caused by Pst, which is responsible for yellow stripe rust disease. The results of the assessment of disease incidence and percent disease index displayed time- and dose-dependent responses. The 40 mg L−1 TiO2 NPs were the most effective in decreasing disease severity. The bioinspired TiO2 NPs were also evaluated for enzymatic (superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT)), and nonenzymatic metabolites (total proline, phenolic, and flavonoid contents) in wheat plants under stripe rust stress. The 40 mg L−1 TiO2 NPs were effective in eliciting biochemical modifications to reduce biotic stress. We further evaluated the effects of TiO2 NPs through gel- and label-free liquid chromatography-mass spectrometry (LC-MS) proteome analysis. We performed proteome analysis of infected wheat leaves and leaves treated with 40 mg L−1 TiO2 NPs under stripe rust stress. The functional classification of the proteins showed downregulation of proteins related to protein and carbohydrate metabolism, as well as of photosynthesis in plants under biotic stress. An upregulation of stress-related proteins was observed, including the defense mechanisms and primary metabolic pathways in plants treated with 40 mg L−1 TiO2 NPs under stress. The experimental results showed the potential of applying biogenic TiO2 NPs to combat fungal diseases of wheat plants and provided insight into the protein expression of plants in response to biotic stress.

Proteomic and Biochemical Analyses of the Mechanism of Tolerance in Mutant Soybean Responding to Flooding Stress

To investigate the mechanism of flooding tolerance of soybean, flooding-tolerant mutants derived from gamma-ray irradiated soybean were crossed with parent cultivar Enrei for removal of other factors besides the genes related to flooding tolerance in primary generated mutant soybean. Although the growth of the wild type was significantly suppressed by flooding compared with the non-flooding condition, that of the mutant lines was better than that of the wild type even if it was treated with flooding. A two-day-old mutant line was subjected to flooding for 2 days and proteins were analyzed using a gel-free/label-free proteomic technique. Oppositely changed proteins in abundance between the wild type and mutant line under flooding stress were associated in endoplasmic reticulum according to gene-ontology categorization. Immunoblot analysis confirmed that calnexin accumulation increased in both the wild type and mutant line; however, calreticulin accumulated in only the mutant line under flooding stress. Furthermore, although glycoproteins in the wild type decreased by flooding compared with the non-flooding condition, those in the mutant line increased even if it was under flooding stress. Alcohol dehydrogenase accumulated in the wild type and mutant line; however, this enzyme activity significantly increased and mildly increased in the wild type and mutant line, respectively, under flooding stress compared with the non-flooding condition. Cell death increased and decreased in the wild type and mutant line, respectively, by flooding stress. These results suggest that the regulation of cell death through the fermentation system and glycoprotein folding might be an important factor for the acquisition of flooding tolerance in mutant soybean.

Proteomic analysis reveals the effects of melatonin on soybean root tips under flooding stress

Flooding constrains soybean growth, while melatonin enhances the ability of plants to tolerate abiotic stresses. To interpret the melatonin-mediated flooding response in soybeans, proteomic analysis was performed in root tips. Retarded growth and severe cell death were observed in flooded soybeans, but these phenotypes were ameliorated by melatonin treatment. A total of 634, 1401, and 1205 proteins were identified under control, flood, and flood plus melatonin conditions, respectively; and these proteins were predominantly associated with metabolism of protein, RNA, and the cell wall. Among these melatonin-induced proteins, eukaryotic aspartyl protease family protein was increased after flood compared with melatonin treatment group, in accordance with its upregulated transcript levels during stress. Eukaryotic translation initiation factor 5A was decreased after flood compared with melatonin. When stress was prolonged, its transcript levels were upregulated by flood, while they were not changed by melatonin. Furthermore, 13-hydroxylupanine O-tigloyltransferase was decreased by flood compared with melatonin; however, its transcription was upregulated by melatonin. In addition, reduced lignification in root tips of flooded soybeans was restored by melatonin. These results suggest that factors related to protein degradation and functional states of RNA play critical roles in promoting the effects of melatonin on soybean plants under flooding. SIGNIFICANCE: Flooding stress threatens soybean growth, while melatonin treatment enhances plant tolerance to stress stimuli. To examine the effects of melatonin on flooded soybeans, morphological analysis was performed. Melatonin promoted soybean growth as judged from greater fresh weight of plant, longer seedling length, and less evident cell death in flooding-stressed soybeans treated with melatonin than those plants exposed to flood alone. Proteomic analysis was conducted to explore the promoting effects of melatonin on soybeans under flooding stress. As a result, metabolism of protein metabolism, RNA regulation, and cell wall was enriched by proteins identified under control, flood, and flood plus melatonin conditions. Among these melatonin-induced proteins, abundance of eukaryotic aspartyl protease family protein, eukaryotic translation initiation factor 5A, and 13-hydroxylupanine O-tigloyltransferase displayed similar change patterns between the control and melatonin compared with flood; and transcript levels of genes encoding these proteins responded to flooding stress and melatonin treatment. In addition, activated cell degradation, expanded intercellular spaces, and reduced lignification in root tips of flooded soybeans were ameliorated by melatonin treatment.

Prioritization and Evaluation of Flooding Tolerance Genes in Soybean [Glycine max (L.) Merr.]

Soybean [Glycine max (L.) Merr.] is one of the most important legume crops abundant in edible protein and oil in the world. In recent years there has been increasingly more drastic weather caused by climate change, with flooding, drought, and unevenly distributed rainfall gradually increasing in terms of the frequency and intensity worldwide. Severe flooding has caused extensive losses to soybean production and there is an urgent need to breed strong soybean seeds with high flooding tolerance. The present study demonstrates bioinformatics big data mining and integration, meta-analysis, gene mapping, gene prioritization, and systems biology for identifying prioritized genes of flooding tolerance in soybean. A total of 83 flooding tolerance genes (FTgenes), according to the appropriate cut-off point, were prioritized from 36,705 test genes collected from multidimensional genomic features linking to soybean flooding tolerance. Several validation results using independent samples from SoyNet, genome-wide association study, SoyBase, GO database, and transcriptome databases all exhibited excellent agreement, suggesting these 83 FTgenes were significantly superior to others. These results provide valuable information and contribution to research on the varieties selection of soybean.

Review: Proteomic Techniques for the Development of Flood-Tolerant Soybean

Soybean, which is rich in protein and oil as well as phytochemicals, is cultivated in several climatic zones. However, its growth is markedly decreased by flooding stress, which is caused by climate change. Proteomic techniques were used for understanding the flood-response and -tolerant mechanisms in soybean. Subcellular proteomics has potential to elucidate localized cellular responses and investigate communications among subcellular components during plant growth and under stress stimuli. Furthermore, post-translational modifications play important roles in stress response and tolerance to flooding stress. Although many flood-response mechanisms have been reported, flood-tolerant mechanisms have not been fully clarified for soybean because of limitations in germplasm with flooding tolerance. This review provides an update on current biochemical and molecular networks involved in soybean tolerance against flooding stress, as well as recent developments in the area of functional genomics in terms of developing flood-tolerant soybeans. This work will expedite marker-assisted genetic enhancement studies in crops for developing high-yielding stress-tolerant lines or varieties under abiotic stress.

Improving Flooding Tolerance of Crop Plants

A major problem of climate change is the increasing duration and frequency of heavy rainfall events. This leads to soil flooding that negatively affects plant growth, eventually leading to death of plants if the flooding persists for several days. Most crop plants are very sensitive to flooding, and dramatic yield losses occur due to flooding each year. This review summarizes recent progress and approaches to enhance crop resistance to flooding. Most experiments have been done on maize, barley, and soybean. Work on other crops such as wheat and rape has only started. The most promising traits that might enhance crop flooding tolerance are anatomical adaptations such as aerenchyma formation, the formation of a barrier against radial oxygen loss, and the growth of adventitious roots. Metabolic adaptations might be able to improve waterlogging tolerance as well, but more studies are needed in this direction. Reasonable approaches for future studies are quantitative trait locus (QTL) analyses or genome-wide association (GWA) studies in combination with specific tolerance traits that can be easily assessed. The usage of flooding-tolerant relatives or ancestral cultivars of the crop of interest in these experiments might enhance the chances of finding useful tolerance traits to be used in breeding.

Improvement of Soybean Products Through the Response Mechanism Analysis Using Proteomic Technique

Soybean is rich in protein/vegetable oil and contains several phytochemicals such as isoflavones and phenolic compounds. Because of the predominated nutritional values, soybean is considered as traditional health benefit food. Soybean is a widely cultivated crop; however, its growth and yield are markedly affected by adverse environmental conditions. Proteomic techniques make it feasible to map protein profiles both during soybean growth and under unfavorable conditions. The stress-responsive mechanisms during soybean growth have been uncovered with the help of proteomic studies. In this review, the history of soybean as food and the morphology/physiology of soybean are described. The utilization of proteomics during soybean germination and development is summarized. In addition, the stress-responsive mechanisms explored using proteomic techniques are reviewed in soybean.

Jasmonic acid induced protein response to biophoton emissions and flooding stress in soybean

Biophoton emissions were elevated by the exogenous plant hormone application such as jasmonic (JA) and salicylic acid (SA). To reveal the molecular mechanisms underlying flooding stress responses in soybean treated with JA and SA, biophoton emissions from plants were quantified in combination with proteomic analyses. Furthermore, treatment with exogenous JA inhibited lateral root growth and markedly reduced root weight. Out of 649 proteins identified in the JA- and JA/SA-treated plants, 44 were unique to JA-treated plants, 403 were unique to JA/SA-treated plants, and 202 were shared between the groups. These proteins were involved in stress, signaling, degradation, glycolysis, fermentation, and hormone metabolism. The abundances of glutathione-S-transferase, alanine aminotransferase, and malate dehydrogenase were decreased; however, the activities of these enzymes were increased. In contrast, the abundance and activity of monodehydroascorbate reductase increased in the roots of plants treated with JA and SA under flooding stress. This suggests that the quantity of lateral roots, total root mass, and free radicals generated during oxidation and reduction reactions and reactive oxygen species scavenging largely contribute to biophoton emission. Furthermore, monodehydroascorbate reductase, which is involved in detoxification and controlling hydrogen peroxide levels, may protect plant cells against oxidative damage during flooding.

BIOLOGICAL SIGNIFICANCE

To understand the source of biophoton emission and molecular mechanism by the application of jasmonic and salicylic acid under flooding conditions in soybean plants, the label-free quantitative techniques were performed in roots. Root lengths and weights were significantly reduced by the effect of jasmonic and salicylic acid while it inhibited growth of the lateral roots in normal conditions using the jasmonic acid. Finally, identified proteins were functionally annotated by MAPMAN software application; that were assigned to different functional categories, such as stress, signaling, protein, glycolysis, metabolism, cell wall, and cell organization. Consequently, this study offers to learn the photon emission in plants and to know the molecular mechanism under flooding stress in soybean.

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

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

Proteomic analysis of flooded soybean root exposed to aluminum oxide nanoparticles

Aluminum oxide (Al2O3) nanoparticles are used in agricultural products and cause various adverse growth effects on different plant species. To study the effects of Al2O3 nanoparticles on soybean under flooding stress, a gel-free proteomic technique was used. Morphological analysis revealed that treatment with 50 ppm Al2O3 nanoparticles under flooding stress enhanced soybean growth compared to ZnO and Ag nanoparticles. A total of 172 common proteins that significantly changed in abundance among control, flooding-stressed, and flooding-stressed soybean treated with Al2O3 nanoparticles were mainly related to energy metabolism. Under Al2O3 nanoparticles the energy metabolism was decreased compared to flooding stress. Hierarchical clustering divided identified proteins into four clusters, with proteins related to glycolysis exhibiting the greatest changes in abundance. Al2O3 nanoparticle-responsive proteins were predominantly related to protein synthesis/degradation, glycolysis, and lipid metabolism. mRNA expression analysis of Al2O3 nanoparticle-responsive proteins that displayed a 5-fold change in abundance revealed that NmrA-like negative transcriptional regulator was up-regulated, and flavodoxin-like quinone reductase was down-regulated. Moreover, cell death in root including hypocotyl was less evident in flooding-stressed with Al2O3 nanoparticles compared to flooding-treated soybean. These results suggest that Al2O3 nanoparticles might promote the growth of soybean under flooding stress by regulating energy metabolism and cell death.

Proteomic Techniques and Management of Flooding Tolerance in Soybean

Climate change is considered a major threat to world agriculture and food security. To improve the agricultural productivity and sustainability, the development of high-yielding stress-tolerant, and climate-resilient crops is essential. Of the abiotic stresses, flooding stress is a very serious hazard because it markedly reduces plant growth and grain yield. Proteomic analyses indicate that the effects of flooding stress are not limited to oxygen deprivation but include many other factors. Although many flooding response mechanisms have been reported, flooding tolerance mechanisms have not been fully clarified for soybean. There were limitations in soybean materials, such as mutants and varieties, while they were abundant in rice and Arabidopsis. In this review, plant proteomic technologies are introduced and flooding tolerance mechanisms of soybeans are summarized to assist in the improvement of flooding tolerance in soybeans. This work will expedite transgenic or marker-assisted genetic enhancement studies in crops for developing high-yielding stress-tolerant lines or varieties under abiotic stress.

Proteomic analysis of soybean hypocotyl during recovery after flooding stress

Soybean is a nutritionally important crop, but exhibits reduced growth and yields under flooding stress. To investigate soybean responses during post-flooding recovery, a gel-free proteomic technique was used to examine the protein profile in the hypocotyl. Two-day-old soybeans were flooded for 2 days and hypocotyl was collected under flooding and during the post-flooding recovery period. A total of 498 and 70 proteins were significantly changed in control and post-flooding recovering soybeans, respectively. Based on proteomic and clustering analyses, three proteins were selected for mRNA expression and enzyme activity assays. Pyruvate kinase was increased under flooding, but gradually decreased during post-flooding recovery period at protein abundance, mRNA, and enzyme activity levels. Nucleotidylyl transferase was decreased under flooding and increased during post-flooding recovery at both mRNA expression and enzyme activity levels. Beta-ketoacyl reductase 1 was increased under flooding and decreased during recovery at protein abundance and mRNA expression levels, but its enzyme activity gradually increased during the post-flooding recovery period. These results suggest that pyruvate kinase, nucleotidylyl transferase, and beta-ketoacyl reductase play key roles in post-flooding recovery in soybean hypocotyl by promoting glycolysis for the generation of ATP and regulation of secondary metabolic pathways.

BIOLOGICAL SIGNIFICANCE

This study analyzed post-flooding recovery response mechanisms in soybean hypocotyl, which is a model organ for studying secondary growth, using a gel-free proteomic technique. Mass spectrometry analysis of proteins extracted from soybean hypocotyls identified 20 common proteins between control and flooding-stressed soybeans that changed significantly in abundance over time. The hypocotyl proteins that changed during post-flooding recovery were assigned to protein, development, secondary metabolism, and glycolysis categories. The analysis revealed that three proteins, pyruvate kinase, nucleotidylyl transferase, and beta-ketoacyl reductase, were increased in hypocotyl under flooding conditions and during post-flooding recovery. The proteins are involved in glycolysis, nucleotide synthesis and amino acid activation, and complex fatty acid biosynthesis.