GmHsp90A2 is involved in soybean heat stress as a positive regulator

CRISPR/Cas9 opens new horizon of crop improvement under stress condition

Plants are exposed to a myriad of stresses, stemming from abiotic and biotic sources, significantly threatening agricultural productivity. The low crop yield, coupled with the global burden of population has resulted in the scarcity of quality food, exacerbating socio-economic issues like poverty, hunger, and malnutrition. Conventional breeding methods for the generation of stress-tolerant plants are time-consuming, limit genetic diversity, and are not sustainable for the consistent production of high-yielding crops. In recent years, the use of high-throughput, genome editing (GE) technique has revolutionized the crop-improvement paradigm, ushering greater prospects for agricultural progress. Among these tools, the Clustered regularly interspaced short palindromic repeat (CRISPR), and its associated nuclease protein Cas9, have appeared as a ground-breaking technology, allowing precise knockout (KO), upregulation, and downregulation of target gene expression. Apart from its high efficacy and speed, this programmable nuclease offers exceptional specificity with minimal off-target effects. Here in, we aim to review the latest findings on the application of the CRISPR/Cas9 genome editing tool for generating resilience in plants against environmental stresses.

Revolutionizing soybean genomics: How CRISPR and advanced sequencing are unlocking new potential

Soybean Glycine max L., paleopolyploid genome, poses challenges to its genetic improvement. However, the development of reference genome assemblies and genome sequencing has completely changed the field of soybean genomics, allowing for more accurate and successful breeding techniques as well as research. During the single-cell revolution, one of the most advanced sequencing tools for examining the transcriptome landscape is single-cell RNA sequencing (scRNA-seq). Comprehensive resources for genetic improvement of soybeans may be found in the SoyBase and other genomics databases. CRISPR-Cas9 genome editing technology provides promising prospects for precise genetic modifications in soybean. This method has enhanced several soybean traits, including as yield, nutritional value, and resistance to both biotic and abiotic stresses. With base editing techniques that allow for precise DNA modifications, the use of CRISPR-Cas9 is further increased. With the availability of the reference genome for soybeans and the following assembly of wild and cultivated soybeans, significant chromosomal rearrangements and gene duplication events have been identified, offering new perspectives on the complex genomic structure of soybeans. Furthermore, major single nucleotide polymorphisms (SNPs) linked to stachyose and sucrose content have been found through genome-wide association studies (GWAS), providing important tools for enhancing soybean carbohydrate profiles. In order to open up new avenues for soybean genetic improvement, future research approaches include investigating transcriptional divergence processes, enhancing genetic resources, and incorporating CRISPR-Cas9 technologies.

CRISPR/Cas genome editing in soybean: challenges and new insights to overcome existing bottlenecks

BACKGROUND

Soybean is a worldwide-cultivated crop due to its applications in the food, feed, and biodiesel industries. Genome editing in soybean began with ZFN and TALEN technologies; however, CRISPR/Cas has emerged and shortly became the preferable approach for soybean genome manipulation since it is more precise, easy to handle, and cost-effective. Recent reports have focused on the conventional Cas9 nuclease, Cas9 nickase (nCas9) derived base editors, and Cas12a (formally Cpf1) as the most commonly used genome editors in soybean. Nonetheless, several challenges in the complex plant genetic engineering pipeline need to be overcome to effectively edit the genome of an elite soybean cultivar. These challenges include (1) optimizing CRISPR cassette design (i.e., gRNA and Cas promoters, gRNA design and testing, number of gRNAs, and binary vector), (2) improving transformation frequency, (3) increasing the editing efficiency ratio of targeted plant cells, and (4) improving soybean crop production.

AIM OF REVIEW

This review provides an overview of soybean genome editing using CRISPR/Cas technology, discusses current challenges, and highlights theoretical (insights) and practical suggestions to overcome the existing bottlenecks.

KEY SCIENTIFIC CONCEPTS OF REVIEW

The CRISPR/Cas system was discovered as part of the bacterial innate immune system. It has been used as a biotechnological tool for genome editing and efficiently applied in soybean to unveil gene function, improve agronomic traits such as yield and nutritional grain quality, and enhance biotic and abiotic stress tolerance. To date, the efficiency of gRNAs has been validated using protoplasts and hairy root assays, while stable plant transformation relies on Agrobacterium-mediated and particle bombardment methods. Nevertheless, most steps of the CRISPR/Cas workflow require optimizations to achieve a more effective genome editing in soybean plants.

Function Analysis of a Maize Endo-1,4-β-xylanase Gene ZmHSL in Response to High-Temperature Stress

Rising temperature is a major threat to the normal growth and development of maize, resulting in low yield production and quality. The mechanism of maize in response to heat stress remains uncertain. In this study, a maize mutant Zmhsl-1 (heat sensitive leaves) with wilting and curling leaves under high temperatures was identified from maize Zheng 58 (Z58) mutant lines generated by ethyl methanesulfonate (EMS) mutagenesis. The Zmhsl-1 plants were more sensitive to increased temperature than Z58 in the field during growth season. The Zmhsl-1 plants had lower plant height, lower yield, and lower content of photosynthetic pigments. A bulked segregant analysis coupled with whole-genome sequencing (BSA-seq) enabled the identification of the corresponding gene, named ZmHSL, which encodes an endo-β-1,4-xylanase from the GH10 family. The loss-of-function of ZmHSL resulted in reduced lignin content in Zmhsl-1 plants, leading to defects in water transport and more severe leaf wilting with the increase in temperature. RNA-seq analysis revealed that the differentially expressed genes identified between Z58 and Zmhsl-1 plants are mainly related to heat stress-responsive genes and unfolded protein response genes. All these data indicated that ZmHSL plays a key role in lignin synthesis, and its defective mutation causes changes in the cell wall structure and gene expression patterns, which impedes water transport and confers higher sensitivity to high-temperature stress.

CRISPR-Cas9 mediated understanding of plants' abiotic stress-responsive genes to combat changing climatic patterns

Multiple abiotic stresses like extreme temperatures, water shortage, flooding, salinity, and exposure to heavy metals are confronted by crop plants with changing climatic patterns. Prolonged exposure to these adverse environmental conditions leads to stunted plant growth and development with significant yield loss in crops. CRISPR-Cas9 genome editing tool is being frequently employed to understand abiotic stress-responsive genes. Noteworthy improvements in CRISPR-Cas technology have been made over the years, including upgradation of Cas proteins fidelity and efficiency, optimization of transformation protocols for different crop species, base and prime editing, multiplex gene-targeting, transgene-free editing, and graft-based heritable CRISPR-Cas9 approaches. These developments helped to improve the knowledge of abiotic stress tolerance in crops that could potentially be utilized to develop knock-out varieties and over-expressed lines to tackle the adverse effects of altered climatic patterns. This review summarizes the mechanistic understanding of heat, drought, salinity, and metal stress-responsive genes characterized so far using CRISPR-Cas9 and provides data on potential candidate genes that can be exploited by modern-day biotechnological tools to develop transgene-free genome-edited crops with better climate adaptability. Furthermore, the importance of early-maturing crop varieties to withstand abiotic stresses is also discussed in this review.

Optimization of soybean physiochemical, agronomic, and genetic responses under varying regimes of day and night temperatures

Soybean is an important oilseed crop worldwide; however, it has a high sensitivity to temperature variation, particularly at the vegetative stage to the pod-filling stage. Temperature change affects physiochemical and genetic traits regulating the soybean agronomic yield. In this regard, the current study aimed to comparatively evaluate the effects of varying regimes of day and night temperatures (T1 = 20°C/12°C, T2 = 25°C/17°C, T3 = 30°C/22°C, T4 = 35°C/27°C, and T5 = 40°C/32°C) on physiological (chlorophyll, photosynthesis, stomatal conductance, transpiration, and membrane damage) biochemical (proline and antioxidant enzymes), genetic (GmDNJ1, GmDREB1G;1, GmHSF-34, GmPYL21, GmPIF4b, GmPIP1;6, GmGBP1, GmHsp90A2, GmTIP2;6, and GmEF8), and agronomic traits (pods per plant, seeds per plant, pod weight per plant, and seed yield per plant) of soybean cultivars (Swat-84 and NARC-1). The experiment was performed in soil plant atmosphere research (SPAR) units using two factorial arrangements with cultivars as one factor and temperature treatments as another factor. A significant increase in physiological, biochemical, and agronomic traits with increased gene expression was observed in both soybean cultivars at T4 (35°C/27°C) as compared to below and above regimes of temperatures. Additionally, it was established by correlation, principal component analysis (PCA), and heatmap analysis that the nature of soybean cultivars and the type of temperature treatments have a significant impact on the paired association of agronomic and biochemical traits, which in turn affects agronomic productivity. Furthermore, at corresponding temperature regimes, the expression of the genes matched the expression of physiochemical traits. The current study has demonstrated through extensive physiochemical, genetic, and biochemical analyses that the ideal day and night temperature for soybeans is T4 (35°C/27°C), with a small variation having a significant impact on productivity from the vegetative stage to the grain-filling stage.

Unveiling HSP40/60/70/90/100 gene families and abiotic stress response in Jerusalem artichoke

Heat shock proteins (HSPs) are essential for plant growth, development, and stress adaptation. However, their roles in Jerusalem artichoke are largely unexplored. Using bioinformatics, we classified 143 HSP genes into distinct families: HSP40 (82 genes), HSP60 (22 genes), HSP70 (29 genes), HSP90 (6 genes), and HSP100 (4 genes). Our analysis covered their traits, evolution, and structures. Using RNA-seq data, we uncovered unique expression patterns of these HSP genes across growth stages and tissues. Notably, HSP40, HSP60, HSP70, HSP90, and HSP100 families each had specific roles. We also studied how these gene families responded to various stresses, from extreme temperatures to drought and salinity, revealing intricate expression dynamics. Remarkably, HSP40 showed remarkable flexibility, while HSP60, HSP70, HSP90, and HSP100 responded specifically to stress types. Moreover, our analysis unveiled significant correlations between gene pairs under stress, implying cooperative interactions. qRT-PCR validation underscored the significance of particular genes such as HtHSP60-7, HtHSP90-5, HtHSP100-2, and HtHSP100-3 in responding to stress. In summary, our study advances the understanding of how HSP gene families collectively manage stresses in Jerusalem artichoke. This provides insights into specific gene functions and broader plant stress responses.

Overexpression of GmPIF4b affects morpho-physiological traits to reduce heat-induced grain loss in soybean

Heat waves associated with climate change seriously threaten crop productivity. Crop seed yield depends on the success of reproduction. However, reproductive development is most vulnerable to heat stress conditions. Perception of heat and its conversion into cellular signals is a complex process. The basic helix loop helix (bHLH) transcription factor, Phytochrome Interacting Factor 4 (PIF4), plays a significant role in this process. However, studies on PIF4- mediated impacts on crop grain yield at a higher temperature are lacking. We investigated the overexpression of GmPIF4b in soybean to alleviate heat-induced damage and yield using a transgenic approach. Our results showed that under high-temperature conditions (38°C/28°C), overexpressing soybeans plants had higher chlorophyll a and b, and lower proline accumulation compared to WT. Further, overexpression of GmPIF4b improved pollen viability under heat stress and reduced heat-induced structural abnormalities in the male and female reproductive organs. Consequently, the transgenic plants produced higher pods and seeds per plant at high temperatures. Quantitative RT-PCR analysis showed that the overexpressing GmPIF4b soybeans had higher transcripts of heat shock factor, GmHSF-34, and heat-shock protein, GmHSP90A2. Collectively, our results suggest that GmPIF4b regulates multiple morpho-physiological traits for better yield under warmer climatic conditions.

Expeditious profiling of polycyclic aromatic hydrocarbons transport and obstruction mechanisms in crop xylem sap proteins via proteomics and molecular docking

Polycyclic aromatic hydrocarbons (PAHs) pose significant environmental risks due to their toxicity and carcinogenic properties. This research seeks to pinpoint protein targets in crop xylem sap related to PAH contamination and delve into their protein-ligand interactions using computational tools. Proteomic assessment revealed differentially expressed proteins (DEPs), which were subjected to virtual high-throughput screening. Notably, the phenanthrene's influence on xylem sap proteins in maize and wheat was more pronounced than in soybean, with DEPs expression peak at 24 h post-treatment. Maize DEPs were predominantly associated with lipid biosynthesis. Phenanthrene impacted cell membrane hydrophobicity, limiting PAH adsorption and decreasing its concentration in maize xylem sap. Wheat DEPs exhibited an increase in ABC transporters after 24 h of phenanthrene exposure. ABC transporters interacted with stress-responsive proteins like C6TIY1-Co-chaperone p23 and others that either facilitate or inhibit PAH transport, including Indeno[1,2,3-cd]Pyrene and C6TIY1-Co-chaperone protein p23. Both maize and wheat created high-affinity complexes between specific proteins and PAHs, influencing their transport. This study provides insights into the mechanisms of PAH regulation and movement within plant xylem.

CRISPR/Cas9-gene editing approaches in plant breeding

CRISPR/Cas9 gene editing system is recently developed robust genome editing technology for accelerating plant breeding. Various modifications of this editing system have been established for adaptability in plant varieties as well as for its improved efficiency and portability. This review provides an in-depth look at the various strategies for synthesizing gRNAs for efficient delivery in plant cells, including chemical synthesis and in vitro transcription. It also covers traditional analytical tools and emerging developments in detection methods to analyze CRISPR/Cas9 mediated mutation in plant breeding. Additionally, the review outlines the various analytical tools which are used to detect and analyze CRISPR/Cas9 mediated mutations, such as next-generation sequencing, restriction enzyme analysis, and southern blotting. Finally, the review discusses emerging detection methods, including digital PCR and qPCR. Hence, CRISPR/Cas9 has great potential for transforming agriculture and opening avenues for new advancements in the system for gene editing in plants.

A small heat shock protein GmHSP18.5a improves the male fertility restorability of cytoplasmic male sterility-based restorer line under high temperature stress in soybean

Small heat shock protein (sHSP) is involved in high temperature (HT) stress response. However, the function of sHSPs in regulating male fertility of soybean under HT stress remains largely unknown. Here, we identified a sHSP gene, GmHSP18.5a, which was responded to HT stress during flowering in cytoplasmic male sterility (CMS)-based restorer line of soybean. Moreover, GmHSFA6b turned out to directly activated the expression of GmHSP18.5a by binding to the heat shock cis-element in its promoter. Overexpression of GmHSP18.5a increased male fertility in transgenic Arabidopsis, soybean CMS-based restorer line and its hybrid F1 with CMS line under HT stress. Reactive oxygen species (ROS) content detection revealed that GmHSP18.5a promoted the ROS scavenging ability of Arabidopsis inflorescence and soybean flower bud under HT stress. Enzyme activity assay and gene expression analysis indicated that GmHS18.5a mainly increased the activity of antioxidant enzymes and the expression level of ROS metabolism-related genes under HT stress. Our results indicated that GmHSP18.5a improved the male fertility restorability of CMS-based restorer line in soybean by regulating ROS metabolic pathway and reducing ROS accumulation. Our findings not only revealed the molecular mechanism of sHSP regulating the male fertility of soybean under HT stress, but also provided a theoretical basis for creating strong restorer line with thermotolerance.

BcWRKY22 Activates BcCAT2 to Enhance Catalase (CAT) Activity and Reduce Hydrogen Peroxide (H2O2) Accumulation, Promoting Thermotolerance in Non-Heading Chinese Cabbage (Brassica campestris ssp. chinensis)

WRKY transcription factors (TFs) participate in plant defense mechanisms against biological and abiotic stresses. However, their regulatory role in heat resistance is still unclear in non-heading Chinese cabbage. Here, we identified the WRKY-IIe gene BcWRKY22(BraC09g001080.1), which is activated under high temperatures and plays an active role in regulating thermal stability, through transcriptome analysis. We further discovered that the BcWRKY22 protein is located in the nucleus and demonstrates transactivation activity in both the yeast and plant. Additionally, our studies showed that the transient overexpression of BcWRKY22 in non-heading Chinese cabbage activates the expression of catalase 2 (BcCAT2), enhances CAT enzyme activity, and reduces Hydrogen Peroxide (H2O2) accumulation under heat stress conditions. In addition, compared to its wild-type (WT) counterparts, Arabidopsis thaliana heterologously overexpresses BcWRKY22, improving thermotolerance. When the BcWRKY22 transgenic root was obtained, under heat stress, the accumulation of H2O2 was reduced, while the expression of catalase 2 (BcCAT2) was upregulated, thereby enhancing CAT enzyme activity. Further analysis revealed that BcWRKY22 directly activates the expression of BcCAT2 (BraC08g016240.1) by binding to the W-box element distributed within the promoter region of BcCAT2. Collectively, our findings suggest that BcWRKY22 may serve as a novel regulator of the heat stress response in non-heading Chinese cabbage, actively contributing to the establishment of thermal tolerance by upregulating catalase (CAT) activity and downregulating H2O2 accumulation via BcCAT2 expression.

Subcellular Proteomics to Elucidate Soybean Response to Abiotic Stress

Climate change jeopardizes soybean production by declining seed yield and quality. In this review, the morphophysiological alterations of soybean in response to abiotic stress are summarized, followed by illustrations of cellular metabolisms and regulatory mechanisms to organellar stress based on subcellular proteomics. This highlights the communications associated with reactive oxygen species scavenging, molecular chaperones, and phytohormone signals among subcellular compartments. Given the complexity of climate change and the limitations of plants in coping with multiple abiotic stresses, a generic response to environmental constraints is proposed between calcium and abscisic acid signals in subcellular organelles. This review summarizes the findings of subcellular proteomics in stressed soybean and discusses the future prospects of subcellular proteomics for promoting the improvement of climate-tolerant crops.

Recent Developments in CRISPR/Cas9 Genome-Editing Technology Related to Plant Disease Resistance and Abiotic Stress Tolerance

The revolutionary CRISPR/Cas9 genome-editing technology has emerged as a powerful tool for plant improvement, offering unprecedented precision and efficiency in making targeted gene modifications. This powerful and practical approach to genome editing offers tremendous opportunities for crop improvement, surpassing the capabilities of conventional breeding techniques. This article provides an overview of recent advancements and challenges associated with the application of CRISPR/Cas9 in plant improvement. The potential of CRISPR/Cas9 in terms of developing crops with enhanced resistance to biotic and abiotic stresses is highlighted, with examples of genes edited to confer disease resistance, drought tolerance, salt tolerance, and cold tolerance. Here, we also discuss the importance of off-target effects and the efforts made to mitigate them, including the use of shorter single-guide RNAs and dual Cas9 nickases. Furthermore, alternative delivery methods, such as protein- and RNA-based approaches, are explored, and they could potentially avoid the integration of foreign DNA into the plant genome, thus alleviating concerns related to genetically modified organisms (GMOs). We emphasize the significance of CRISPR/Cas9 in accelerating crop breeding processes, reducing editing time and costs, and enabling the introduction of desired traits at the nucleotide level. As the field of genome editing continues to evolve, it is anticipated that CRISPR/Cas9 will remain a prominent tool for crop improvement, disease resistance, and adaptation to challenging environmental conditions.

Genome-wide characterization of DcHsp90 gene family in carnation (Dianthus caryophyllus L.) and functional analysis of DcHsp90-6 in heat tolerance

Plant heat shock protein 90 (Hsp90) participates in various physiological processes including protein folding, degradation, and signal transduction. However, the DcHsp90 gene family in carnation (Dianthus caryophyllus L.) has not been systematically analyzed. We thoroughly examined and comprehensively analyzed the carnation DcHsp90 gene family in this study and discovered 9 DcHsp90 genes. Based on the phylogenetic examination, DcHsp90 proteins may be divided into two groups. DcHsp90 structural features were similar but varied between groups. Promoter analysis revealed the presence of many cis-acting elements, most of which were connected to growth and development, hormones, and stress. DcHsp90 genes may play distinct functions in heat stress response, according to gene expression analyses. The DcHsp90-6 was isolated, and its role in the reaction to heat stress was studied. Thermotolerance and superoxide dismutase activity in transgenic seedlings were enhanced by Arabidopsis overexpression of DcHsp90-6. After heat stress, transgenic plants' electrolyte leakage and malondialdehyde levels were much lower than wild-type plants. Furthermore, overexpression of DcHsp90-6 altered the expressions of stress-responsive genes such as AtHsp101, AtHsp90, AtGolS1, AtRS4/5, and AtHsfB1. This study provides comprehensive information on the DcHsp90 gene family and suggests that overexpressed DcHsp90-6 positively regulates thermotolerance highlighting the adaptation mechanism of carnation under heat stress.

Gene Editing for Plant Resistance to Abiotic Factors: A Systematic Review

Agricultural crops are exposed to various abiotic stresses, such as salinity, water deficits, temperature extremes, floods, radiation, and metal toxicity. To overcome these challenges, breeding programs seek to improve methods and techniques. Gene editing by Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR/Cas-is a versatile tool for editing in all layers of the central dogma with focus on the development of cultivars of plants resistant or tolerant to multiple biotic or abiotic stresses. This systematic review (SR) brings new contributions to the study of the use of CRISPR/Cas in gene editing for tolerance to abiotic stress in plants. Articles deposited in different electronic databases, using a search string and predefined inclusion and exclusion criteria, were evaluated. This SR demonstrates that the CRISPR/Cas system has been applied to several plant species to promote tolerance to the main abiotic stresses. Among the most studied crops are rice and Arabidopsis thaliana, an important staple food for the population, and a model plant in genetics/biotechnology, respectively, and more recently tomato, whose number of studies has increased since 2021. Most studies were conducted in Asia, specifically in China. The Cas9 enzyme is used in most articles, and only Cas12a is used as an additional gene editing tool in plants. Ribonucleoproteins (RNPs) have emerged as a DNA-free strategy for genome editing without exogenous DNA. This SR also identifies several genes edited by CRISPR/Cas, and it also shows that plant responses to stress factors are mediated by many complex-signaling pathways. In addition, the quality of the articles included in this SR was validated by a risk of bias analysis. The information gathered in this SR helps to understand the current state of CRISPR/Cas in the editing of genes and noncoding sequences, which plays a key role in the regulation of various biological processes and the tolerance to multiple abiotic stresses, with potential for use in plant genetic improvement programs.

Transcriptomic Analysis Provides Novel Insights into the Heat Stress-Induced Response in Codonopsis tangshen

Codonopsis tangshen Oliv (C. tangshen) is a valuable traditional Chinese medicinal herb with tremendous health benefits. However, the growth and development of C. tangshen are seriously affected by high temperatures. Therefore, understanding the molecular responses of C. tangshen to high-temperature stress is imperative to improve its thermotolerance. Here, RNA-Seq analysis was performed to investigate the genome-wide transcriptional changes in C. tangshen in response to short-term heat stress. Heat stress significantly damages membrane stability and chlorophyll biosynthesis in C. tangshen, as evidenced by pronounced malonaldehyde (MDA), electrolyte leakage (EL), and reduced chlorophyll content. Transcriptome analysis showed that 2691 differentially expressed genes (DEGs) were identified, including 1809 upregulated and 882 downregulated. Functional annotations revealed that the DEGs were mainly related to heat shock proteins (HSPs), ROS-scavenging enzymes, calcium-dependent protein kinases (CDPK), HSP-HSP network, hormone signaling transduction pathway, and transcription factors such as bHLHs, bZIPs, MYBs, WRKYs, and NACs. These heat-responsive candidate genes and TFs could significantly regulate heat stress tolerance in C. tangshen. Overall, this study could provide new insights for understanding the underlying molecular mechanisms of thermotolerance in C. tangshen.

NAC Transcription Factor GmNAC12 Improved Drought Stress Tolerance in Soybean

NAC transcription factors (TFs) could regulate drought stresses in plants; however, the function of NAC TFs in soybeans remains unclear. To unravel NAC TF function, we established that GmNAC12, a NAC TF from soybean (Glycine max), was involved in the manipulation of stress tolerance. The expression of GmNAC12 was significantly upregulated more than 10-fold under drought stress and more than threefold under abscisic acid (ABA) and ethylene (ETH) treatment. In order to determine the function of GmNAC12 under drought stress conditions, we generated GmNAC12 overexpression and knockout lines. The present findings showed that under drought stress, the survival rate of GmNAC12 overexpression lines increased by more than 57% compared with wild-type plants, while the survival rate of GmNAC12 knockout lines decreased by at least 46%. Furthermore, a subcellular localisation analysis showed that the GmNAC12 protein is concentrated in the nucleus of the tobacco cell. In addition, we used a yeast two-hybrid assay to identify 185 proteins that interact with GmNAC12. Gene ontology (GO) and KEGG analysis showed that GmNAC12 interaction proteins are related to chitin, chlorophyll, ubiquitin–protein transferase, and peroxidase activity. Hence, we have inferred that GmNAC12, as a key gene, could positively regulate soybean tolerance to drought stress.

Improvement of heat stress tolerance in soybean (Glycine max L), by using conventional and molecular tools

The soybean is a significant legume crop, providing several vital dietary components. Extreme heat stress negatively affects soybean yield and quality, especially at the germination stage. Continuous change in climatic conditions is threatening the global food supply and food security. Therefore, it is a critical need of time to develop heat-tolerant soybean genotypes. Different molecular techniques have been developed to improve heat stress tolerance in soybean, but until now complete genetic mechanism of soybean is not fully understood. Various molecular methods, like quantitative trait loci (QTL) mapping, genetic engineering, transcription factors (TFs), transcriptome, and clustered regularly interspaced short palindromic repeats (CRISPR), are employed to incorporate heat tolerance in soybean under the extreme conditions of heat stress. These molecular techniques have significantly improved heat stress tolerance in soybean. Besides this, we can also use specific classical breeding approaches and different hormones to reduce the harmful consequences of heat waves on soybean. In future, integrated use of these molecular tools would bring significant results in developing heat tolerance in soybean. In the current review, we have presented a detailed overview of the improvement of heat tolerance in soybean and highlighted future prospective. Further studies are required to investigate different genetic factors governing the heat stress response in soybean. This information would be helpful for future studies focusing on improving heat tolerance in soybean.

Molecular Bases of Heat Stress Responses in Vegetable Crops With Focusing on Heat Shock Factors and Heat Shock Proteins

The effects of the climate change including an increase in the average global temperatures, and abnormal weather events such as frequent and severe heatwaves are emerging as a worldwide ecological concern due to their impacts on plant vegetation and crop productivity. In this review, the molecular processes of plants in response to heat stress-from the sensing of heat stress, the subsequent molecular cascades associated with the activation of heat shock factors and their primary targets (heat shock proteins), to the cellular responses-have been summarized with an emphasis on the classification and functions of heat shock proteins. Vegetables contain many essential vitamins, minerals, antioxidants, and fibers that provide many critical health benefits to humans. The adverse effects of heat stress on vegetable growth can be alleviated by developing vegetable crops with enhanced thermotolerance with the aid of various genetic tools. To achieve this goal, a solid understanding of the molecular and/or cellular mechanisms underlying various responses of vegetables to high temperature is imperative. Therefore, efforts to identify heat stress-responsive genes including those that code for heat shock factors and heat shock proteins, their functional roles in vegetable crops, and also their application to developing vegetables tolerant to heat stress are discussed.

Genome-Wide Identification of the AP2/ERF Gene Family and Functional Analysis of GmAP2/ERF144 for Drought Tolerance in Soybean

Drought is a major environmental constraint that causes substantial reductions in plant growth and yield. Expression of stress-related genes is largely regulated by transcription factors (TFs), including in soybean [Glycine max (L.) Merr.]. In this study, 301 GmAP2/ERF genes that encode TFs were identified in the soybean genome. The TFs were divided into five categories according to their homology. Results of previous studies were then used to select the target gene GmAP2/ERF144 from among those up-regulated by drought and salt stress in the transcriptome. According to respective tissue expression analysis and subcellular determination, the gene was highly expressed in leaves and encoded a nuclear-localized protein. To validate the function of GmAP2/ERF144, the gene was overexpressed in soybean using Agrobacterium-mediated transformation. Compared with wild-type soybean, drought resistance of overexpression lines increased significantly. Under drought treatment, leaf relative water content was significantly higher in overexpressed lines than in the wild-type genotype, whereas malondialdehyde content and electrical conductivity were significantly lower than those in the wild type. Thus, drought resistance of transgenic soybean increased with overexpression of GmAP2/ERF144. To understand overall function of the gene, network analysis was used to predict the genes that interacted with GmAP2/ERF144. Reverse-transcription quantitative PCR showed that expression of those interacting genes in two transgenic lines was 3 to 30 times higher than that in the wild type. Therefore, GmAP2/ERF144 likely interacted with those genes; however, that conclusion needs to be verified in further specific experiments.

Functional Characterization of Tomato Phytochrome A and B1B2 Mutants in Response to Heat Stress

Heat stress (HS) is a prevalent negative factor affecting plant growth and development, as it is predominant worldwide and threatens agriculture on a large scale. PHYTOCHROMES (PHYs) are photoreceptors that control plant growth and development, and the stress signaling response partially interferes with their activity. PHYA, B1, and B2 are the most well-known PHY types in tomatoes. Our study aimed to identify the role of tomato 'Money Maker' phyA and phyB1B2 mutants in stable and fluctuating high temperatures at different growth stages. In the seed germination and vegetative growth stages, the phy mutants were HS tolerant, while during the flowering stage the phy mutants revealed two opposing roles depending on the HS exposure period. The response of the phy mutants to HS during the fruiting stage showed similarity to WT. The most obvious stage that demonstrated phy mutants' tolerance was the vegetative growth stage, in which a high degree of membrane stability and enhanced water preservation were achieved by the regulation of stomatal closure. In addition, both mutants upregulated the expression of heat-responsive genes related to heat tolerance. In addition to lower malondialdehyde accumulation, the phyA mutant enhanced proline levels. These results clarified the response of tomato phyA and phyB1B2 mutants to HS.

Progress in Soybean Genetic Transformation Over the Last Decade

Soybean is one of the important food, feed, and biofuel crops in the world. Soybean genome modification by genetic transformation has been carried out for trait improvement for more than 4 decades. However, compared to other major crops such as rice, soybean is still recalcitrant to genetic transformation, and transgenic soybean production has been hampered by limitations such as low transformation efficiency and genotype specificity, and prolonged and tedious protocols. The primary goal in soybean transformation over the last decade is to achieve high efficiency and genotype flexibility. Soybean transformation has been improved by modifying tissue culture conditions such as selection of explant types, adjustment of culture medium components and choice of selection reagents, as well as better understanding the transformation mechanisms of specific approaches such as Agrobacterium infection. Transgenesis-based breeding of soybean varieties with new traits is now possible by development of improved protocols. In this review, we summarize the developments in soybean genetic transformation to date, especially focusing on the progress made using Agrobacterium-mediated methods and biolistic methods over the past decade. We also discuss current challenges and future directions.

Genome-wide characterization and functional analysis of class III peroxidase gene family in soybean reveal regulatory roles of GsPOD40 in drought tolerance

Class III peroxidases (PODs) are plant-specific glycoproteins, that play essential roles in various plant physiological processes and defence responses. To date, scarce information is available about the POD gene family in soybean. Hence, the present study is the first comprehensive report about the genome-wide characterization of GmPOD gene family in soybean (Glycine max L.). Here, we identified a total of 124 GmPOD genes in soybean, that are unevenly distributed across the genome. Phylogenetic analysis classified them into six distinct sub-groups (A-F), with one soybean specific subgroup. Exon-intron and motif analysis suggested the existence of structural and functional diversity among the sub-groups. Duplication analysis identified 58 paralogous gene pairs; segmental duplication and positive/Darwinian selection were observed as the major factors involved in the evolution of GmPODs. Furthermore, RNA-seq analysis revealed that 23 out of a total 124 GmPODs showed differential expression between drought-tolerant and drought-sensitive genotypes under stress conditions; however, two of them (GmPOD40 and GmPOD42) revealed the maximum deregulation in all contrasting genotypes. Overexpression (OE) lines of GsPOD40 showed considerably higher drought tolerance compared to wild type (WT) plants under stress treatment. Moreover, the OE lines showed enhanced photosynthesis and enzymatic antioxidant activities under drought stress, resulting in alleviation of ROS induced oxidative damage. Hence, the GsPOD40 enhanced drought tolerance in soybean by regulating the key physiological and biochemical pathways involved in the defence response. Lastly, the results of our study will greatly assist in further functional characterization of GsPODs in plant growth and stress tolerance in soybean.

Adaptation Strategies to Improve the Resistance of Oilseed Crops to Heat Stress Under a Changing Climate: An Overview

Temperature is one of the decisive environmental factors that is projected to increase by 1. 5°C over the next two decades due to climate change that may affect various agronomic characteristics, such as biomass production, phenology and physiology, and yield-contributing traits in oilseed crops. Oilseed crops such as soybean, sunflower, canola, peanut, cottonseed, coconut, palm oil, sesame, safflower, olive etc., are widely grown. Specific importance is the vulnerability of oil synthesis in these crops against the rise in climatic temperature, threatening the stability of yield and quality. The natural defense system in these crops cannot withstand the harmful impacts of heat stress, thus causing a considerable loss in seed and oil yield. Therefore, a proper understanding of underlying mechanisms of genotype-environment interactions that could affect oil synthesis pathways is a prime requirement in developing stable cultivars. Heat stress tolerance is a complex quantitative trait controlled by many genes and is challenging to study and characterize. However, heat tolerance studies to date have pointed to several sophisticated mechanisms to deal with the stress of high temperatures, including hormonal signaling pathways for sensing heat stimuli and acquiring tolerance to heat stress, maintaining membrane integrity, production of heat shock proteins (HSPs), removal of reactive oxygen species (ROS), assembly of antioxidants, accumulation of compatible solutes, modified gene expression to enable changes, intelligent agricultural technologies, and several other agronomic techniques for thriving and surviving. Manipulation of multiple genes responsible for thermo-tolerance and exploring their high expressions greatly impacts their potential application using CRISPR/Cas genome editing and OMICS technology. This review highlights the latest outcomes on the response and tolerance to heat stress at the cellular, organelle, and whole plant levels describing numerous approaches applied to enhance thermos-tolerance in oilseed crops. We are attempting to critically analyze the scattered existing approaches to temperature tolerance used in oilseeds as a whole, work toward extending studies into the field, and provide researchers and related parties with useful information to streamline their breeding programs so that they can seek new avenues and develop guidelines that will greatly enhance ongoing efforts to establish heat stress tolerance in oilseeds.

Comparative Transcriptome Analysis Identifies Key Regulatory Genes Involved in Anthocyanin Metabolism During Flower Development in Lycoris radiata

Lycoris is used as a garden flower due to the colorful and its special flowers. Floral coloration of Lycoris is a vital trait that is mainly regulated via the anthocyanin biosynthetic pathway. In this study, we performed a comparative transcriptome analysis of Lycoris radiata petals at four different flower development stages. A total of 38,798 differentially expressed genes (DEGs) were identified by RNA sequencing, and the correlation between the expression level of the DEGs and the anthocyanin content was explored. The identified DEGs are significantly categorized into 'flavonoid biosynthesis,' 'phenylpropanoid biosynthesis,' 'Tropane, piperidine and pyridine alkaloid biosynthesis,' 'terpenoid backbone biosynthesis' and 'plant hormone signal transduction' by Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. The candidate genes involved in anthocyanin accumulation in L. radiata petals during flower development stages were also identified, which included 56 structural genes (especially LrDFR1 and LrFLS) as well as 27 key transcription factor DEGs (such as C3H, GATA, MYB, and NAC). In addition, a key structural gene namely LrDFR1 of anthocyanin biosynthesis pathway was identified as a hub gene in anthocyanin metabolism network. During flower development stages, the expression level of LrDFR1 was positively correlated with the anthocyanin content. Subcellular localization revealed that LrDFR1 is majorly localized in the nucleus, cytoplasm and cell membrane. Overexpression of LrDFR1 increased the anthocyanin accumulation in tobacco leaves and Lycoris petals, suggesting that LrDFR1 acts as a positively regulator of anthocyanin biosynthesis. Our results provide new insights for elucidating the function of anthocyanins in L. radiata petal coloring during flower development.

The barley SHN1-type transcription factor HvSHN1 imparts heat, drought and salt tolerances in transgenic tobacco

The APETAL2/Ethylene Responsive Factor (AP2/ERF) family was the subject of intensive research which led to the identification of several members involved in different stress responses such as salinity, drought and high temperature. The SHN/WIN clade of AP2/ERF participates in many important processes such as cutin and wax biosynthesis, ethylene signaling and gene expression. Here, we report the functional analysis of SHN1-type transcription factor, HvSHN1, from barely. The overexpression of HvSHN1 under the control of the duplicated 35S promoter in transgenic tobacco plants improved tolerance to salt, water stress and heat stress. Transgenic lines exhibited altered permeability of the cuticle and decreased stomatal density. Under heat stress, HvSHN1 transgenic lines exhibited higher superoxide dismutase (SOD) and catalase (CAT) activity and lower MDA and H2O2 contents than did WT. The overexpression of HvSHN1 upregulated different genes involved in osmotic stress, oxidative stress, sugar metabolism, and wax biosynthesis. To understand the involvement of HvSHN1 in heat stress tolerance, promoter regions of two tobacco genes homologous to Arabidopsis genes HSP90.1 and RAP2.6 were analyzed and DRE cis-elements; binding sites of HvSHN1, were found. Interaction network of HvSHN1, predicted using STRING software, contained proteins with predicted functions related to lipids metabolism and a gene encoding Cyclin-Dependent Kinase. These results suggest that HvSHN1 is an interesting candidate for the improvement of abiotic stress tolerance especially in the context of climate change.

The calcium-dependent protein kinase ZmCDPK7 functions in heat-stress tolerance in maize

Global warming poses a serious threat to crops. Calcium-dependent protein kinases (CDPKs)/CPKs play vital roles in plant stress responses, but their exact roles in plant thermotolerance remains elusive. Here, we explored the roles of heat-induced ZmCDPK7 in thermotolerance in maize. ZmCDPK7-overexpressing maize plants displayed higher thermotolerance, photosynthetic rates, and antioxidant enzyme activity but lower H₂ O₂ and malondialdehyde (MDA) contents than wild-type plants under heat stress. ZmCDPK7-knockdown plants displayed the opposite patterns. ZmCDPK7 is attached to the plasma membrane but can translocate to the cytosol under heat stress. ZmCDPK7 interacts with the small heat shock protein sHSP17.4, phosphorylates sHSP17.4 at Ser-44 and the respiratory burst oxidase homolog RBOHB at Ser-99, and upregulates their expression. Site-directed mutagenesis of sHSP17.4 to generate a Ser-44-Ala substitution reduced ZmCDPK7's enhancement of catalase activity but enhanced ZmCDPK7's suppression of MDA accumulation in heat-stressed maize protoplasts. sHSP17.4, ZmCDPK7, and RBOHB were less strongly upregulated in response to heat stress in the abscisic acid-deficient mutant vp5 versus the wild type. Pretreatment with an RBOH inhibitor suppressed sHSP17.4 and ZmCDPK7 expression. Therefore, abscisic acid-induced ZmCDPK7 functions both upstream and downstream of RBOH and participates in thermotolerance in maize by mediating the phosphorylation of sHSP17.4, which might be essential for its chaperone function.

Functional analysis of tomato CHIP ubiquitin E3 ligase in heat tolerance

Plants have evolved genetic and physiological mechanisms to mitigate the adverse effects of high temperature. CARBOXYL TERMINUS OF THE HSC70-INTERACTING PROTEINS (CHIP) is a conserved chaperone-dependent ubiquitin E3 ligase that targets misfolded proteins. Here, we report functional analysis of the SlCHIP gene from tomato (Solanum lycopersicum) in heat tolerance. SlCHIP encodes a CHIP protein with three tandem tetracopeptide repeat (TPR) motifs and a C-terminal U box domain. Phylogenetic analysis of CHIP homologs from animals, spore-bearing and seed plants revealed a tree topology similar to the evolutionary tree of the organisms. Expression of SlCHIP was induced under high temperature and was also responsive to plant stress hormones. Silencing of SlCHIP in tomato reduced heat tolerance based on increased heat stress symptoms, reduced photosynthetic activity, elevated electrolyte leakage and accumulation of insoluble protein aggregates. The accumulated protein aggregates in SlCHIP-silenced plants were still highly ubiquitinated, suggesting involvement of other E3 ligases in ubiquitination. SlCHIP restored the heat tolerance of Arabidopsis chip mutant to the wild type levels. These results indicate that tomato SlCHIP plays a critical role in heat stress responses most likely by targeting degradation of misfolded proteins that are generated during heat stress.

Recent Advances in the Roles of HSFs and HSPs in Heat Stress Response in Woody Plants

A continuous increase in ambient temperature caused by global warming has been considered a worldwide threat. As sessile organisms, plants have evolved sophisticated heat shock response (HSR) to respond to elevated temperatures and other abiotic stresses, thereby minimizing damage and ensuring the protection of cellular homeostasis. In particular, for perennial trees, HSR is crucial for their long life cycle and development. HSR is a cell stress response that increases the number of chaperones including heat shock proteins (HSPs) to counter the negative effects on proteins caused by heat and other stresses. There are a large number of HSPs in plants, and their expression is directly regulated by a series of heat shock transcription factors (HSFs). Therefore, understanding the detailed molecular mechanisms of woody plants in response to extreme temperature is critical for exploring how woody species will be affected by climate changes. In this review article, we summarize the latest findings of the role of HSFs and HSPs in the HSR of woody species and discuss their regulatory networks and cross talk in HSR. In addition, strategies and programs for future research studies on the functions of HSFs and HSPs in the HSR of woody species are also proposed.

GmNAC8 acts as a positive regulator in soybean drought stress

NAC proteins represent one of the largest transcription factor (TF) families involved in the regulation of plant development and the response to abiotic stress. In the present study, we elucidated the detailed role of GmNAC8 in the regulation of drought stress tolerance in soybean. The GmNAC8 protein was localized in the nucleus, and expression of the GmNAC8 gene was significantly induced in response to drought, abscisic acid (ABA), ethylene (ETH) and salicylic acid (SA) treatments. Thus, we generated GmNAC8 overexpression (OE1 and OE2) and GmNAC8 knockout (KO1 and KO2) lines to determine the role of GmNAC8 in drought stress tolerance. Our results revealed that, compared with the wild type (WT) plant, GmNAC8 overexpression and GmNAC8 knockout lines exhibited significantly higher and lower drought tolerance, respectively. Furthermore, the SOD activity and proline content were significantly higher in the GmNAC8 overexpression lines and significantly lower in the GmNAC8 knockout lines than in the WT plants under drought stress. In addition, GmNAC8 protein was found to physically interact with the drought-induced protein GmDi19-3 in the nucleus. Moreover, the GmDi19-3 expression pattern showed the same trend as the GmNAC8 gene did under drought and hormone (ABA, ETH and SA) treatments, and GmDi19-3 overexpression lines (GmDi19-3-OE9, GmDi19-3-OE10 and GmDi19-3-OE31) showed enhanced drought tolerance compared to that of the WT plants. Hence, the above results indicated that GmNAC8 acts as a positive regulator of drought tolerance in soybean and inferred that GmNAC8 probably functions by interacting with another positive regulatory protein, GmDi19-3.