GmLCLs negatively regulate ABA perception and signalling genes in soybean leaf dehydration response

Appropriate induction of TOC1 ensures optimal MYB44 expression in ABA signaling and stress response in Arabidopsis

Plants possess the remarkable ability to integrate the circadian clock with various signalling pathways, enabling them to quickly detect and react to both external and internal stress signals. However, the interplay between the circadian clock and biological processes in orchestrating responses to environmental stresses remains poorly understood. TOC1, a core component of the plant circadian clock, plays a vital role in maintaining circadian rhythmicity and participating in plant defences. Here, our study reveals a direct interaction between TOC1 and the promoter region of MYB44, a key gene involved in plant defence. TOC1 rhythmically represses MYB44 expression, thereby ensuring elevated MYB44 expression at dawn to help the plant in coping with lowest temperatures during diurnal cycles. Additionally, both TOC1 and MYB44 can be induced by cold stress in an Abscisic acid (ABA)-dependent and independent manner. TOC1 demonstrates a rapid induction in response to lower temperatures compared to ABA treatment, suggesting timely flexible regulation of TOC1-MYB44 regulatory module by the circadian clock in ensuring a proper response to diverse stresses and maintaining a balance between normal physiological processes and energy-consuming stress responses. Our study elucidates the role of TOC1 in effectively modulating expression of MYB44, providing insights into the regulatory network connecting the circadian clock, ABA signalling, and stress-responsive genes.

The rice LATE ELONGATED HYPOCOTYL enhances salt tolerance by regulating Na+/K+ homeostasis and ABA signalling

The circadian clock plays multiple functions in the regulation of plant growth, development and response to various abiotic stress. Here, we showed that the core oscillator component late elongated hypocotyl (LHY) was involved in rice response to salt stress. The mutations of OsLHY gene led to reduced salt tolerance in rice. Transcriptomic analyses revealed that the OsLHY gene regulates the expression of genes related to ion homeostasis and the abscisic acid (ABA) signalling pathway, including genes encoded High-affinity K+ transporters (OsHKTs) and the stress-activated protein kinases (OsSAPKs). We demonstrated that OsLHY directly binds the promoters of OsHKT1;1, OsHKT1;4 and OsSAPK9 to regulate their expression. Moreover, the ossapk9 mutants exhibited salt tolerance under salt stress. Taken together, our findings revealed that OsLHY integrates ion homeostasis and the ABA pathway to regulate salt tolerance in rice, providing insights into our understanding of how the circadian clock controls rice response to salt stress.

The interplay between the circadian clock and abiotic stress responses mediated by ABF3 and CCA1/LHY

Climate change is a global concern for all life on our planet, including humans and plants. Plants' growth and development are significantly affected by abiotic stresses, including adverse temperature, inadequate or excess water availability, nutrient deficiency, and salinity. The circadian clock is a master regulator of numerous developmental and metabolic processes in plants. In an effort to identify new clock-related genes and outputs through bioinformatic analysis, we have revealed that CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY) play a crucial role in regulating a wide range of abiotic stress responses and target ABSCISIC ACID RESPONSIVE ELEMENTS-BINDING FACTOR3 (ABF3), a key transcription factor in the plant hormone Abscisic acid (ABA)-signaling pathway. Specifically, we found that CCA1 and LHY regulate the expression of ABF3 under diel conditions, as well as seed germination under salinity. Conversely, ABF3 controls the expression of core clock genes and orchestrates the circadian period in a stress-responsive manner. ABF3 delivers the stress signal to the central oscillator by binding to the promoter of CCA1 and LHY. Overall, our study uncovers the reciprocal regulation between ABF3 and CCA1/LHY and molecular mechanisms underlying the interaction between the circadian clock and abiotic stress. This finding may aid in developing molecular and genetic solutions for plants to survive and thrive in the face of climate change.

Environmental F actors coordinate circadian clock function and rhythm to regulate plant development

Changes in the external environment necessitate plant growth plasticity, with environmental signals such as light, temperature, and humidity regulating growth and development. The plant circadian clock is a biological time keeper that can be "reset" to adjust internal time to changes in the external environment. Exploring the regulatory mechanisms behind plant acclimation to environmental factors is important for understanding how plant growth and development are shaped and for boosting agricultural production. In this review, we summarize recent insights into the coordinated regulation of plant growth and development by environmental signals and the circadian clock, further discussing the potential of this knowledge.

The Circadian Clock Coordinates the Tradeoff between Adaptation to Abiotic Stresses and Yield in Crops

Plants have evolved a circadian clock to adapt to ever-changing diel and seasonal environmental conditions. The circadian clock is generally considered an internal system that has evolved to adapt to cyclic environmental cues, especially diel light and temperature changes, which is essential for higher plants as they are sessile organisms. This system receives environmental signals as input pathways which are integrated by circadian core oscillators to synchronize numerous output pathways, such as photosynthesis, the abiotic stress response, metabolism, and development. Extreme temperatures, salinity, and drought stresses cause huge crop losses worldwide, imposing severe pressure on areas of agricultural land. In crop production, the circadian system plays a significant role in determining flowering time and responding to external abiotic stresses. Extensive studies over the last two decades have revealed that the circadian clock can help balance the tradeoff between crop yield-related agronomic traits and adaptation to stress. Herein, we focus on summarizing how the circadian clock coordinates abiotic stress responses and crop yield. We also propose that there might be an urgent need to better utilize circadian biology in the future design of crop breeding to achieve high yields under stress conditions.

Overexpression of soybean GmNAC19 and GmGRAB1 enhances root growth and water-deficit stress tolerance in soybean

Soybean (Glycine max) is an important crop in agricultural production where water shortage limits yields in soybean. Root system plays important roles in water-limited environments, but the underlying mechanisms are largely unknown. In our previous study, we produced a RNA-seq dataset generated from roots of soybean at three different growth stages (20-, 30-, and 44-day-old plants). In the present study, we performed a transcriptome analysis of the RNA-seq data to select candidate genes with probable association with root growth and development. Candidate genes were functionally examined in soybean by overexpression of individual genes using intact soybean composite plants with transgenic hairy roots. Root growth and biomass in the transgenic composite plants were significantly increased by overexpression of the GmNAC19 and GmGRAB1 transcriptional factors, showing up to 1.8-fold increase in root length and/or 1.7-fold increase in root fresh/dry weight. Furthermore, greenhouse-grown transgenic composite plants had significantly higher seed yield by about 2-fold than control plants. Expression profiling in different developmental stages and tissues showed that GmNAC19 and GmGRAB1 were most highly expressed in roots, displaying a distinct root-preferential expression. Moreover, we found that under water-deficit conditions, overexpression of GmNAC19 enhanced water stress tolerance in transgenic composite plants. Taken together, these results provide further insights into the agricultural potential of these genes for development of soybean cultivars with improved root growth and enhanced tolerance to water-deficit conditions.

The Regulatory Networks of the Circadian Clock Involved in Plant Adaptation and Crop Yield

Global climatic change increasingly threatens plant adaptation and crop yields. By synchronizing internal biological processes, including photosynthesis, metabolism, and responses to biotic and abiotic stress, with external environmental cures, such as light and temperature, the circadian clock benefits plant adaptation and crop yield. In this review, we focus on the multiple levels of interaction between the plant circadian clock and environmental factors, and we summarize recent progresses on how the circadian clock affects yield. In addition, we propose potential strategies for better utilizing the current knowledge of circadian biology in crop production in the future.

The soybean ubiquitin-proteasome system: Current knowledge and future perspective

Increasing soybean [Glycine max (L.) Merr.] yield has become a worldwide scientific problem in the world. Many studies have shown that ubiquitination plays a key role in stress response and yield formation. In the UniProtKB database, 2,429 ubiquitin-related proteins were predicted in soybean, however, <20 were studied. One key way to address this lack of progress in increasing soybean yield will be a deeper understanding of the ubiquitin-proteasome system (UPS) in soybean. In this review, we summarized the current knowledge about soybean ubiquitin-related proteins and discussed the method of combining phenotype, mutant library, transgenic system, genomics, and proteomics approaches to facilitate the exploration of the soybean UPS. We also proposed the strategy of applying the UPS in soybean improvement based on related studies in model plants. Our review will be helpful for soybean scientists to learn current research progress of the soybean UPS and further lay a theoretical reference for the molecular improvement of soybean in future research by use of this knowledge.

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.

NtRAV4 negatively regulates drought tolerance in Nicotiana tabacum by enhancing antioxidant capacity and defence system

KEY MESSAGE

NtRAV4 is a nucleus-localised protein and no self-activation effect. ntrav4 mutants maintain the steady state of the ROS system under drought stress by enhancing antioxidant capacity and defence system. The APETALA2/ethylene response factor (AP2/ERF) transcription factor (TF) family plays an important role in plant responses to environmental stresses. In this study, we identified a novel NtRAV4 TF, a member of RAV subfamily among AP2/ERF gene family, which have AP2 and B3 domain in its N- and C-terminus, respectively. Subcellular localisation and self-activation activity analysis revealed that NtRAV4 localised in the nucleus and had no self-activation effect. The overexpression and gene editing vectors of NtRAV4 were constructed by homologous recombination and CRISPR/Cas9 gene editing methods, and transformed into tobacco by agrobacterium-mediated method. ntrav4 led to the appearance of termination codon in advance and lacked the unique B3 domain of RAV subfamily protein. Further analysis displayed that knockout of the NtRAV4 in tobacco increased drought tolerance with high relative water content, accompanied by reduced stomatal aperture, density, and stomatal opening ratio compared to overexpression lines and WT. Moreover, ntrav4 knockout plants also exhibited increased osmotic tolerance with low malondialdehyde (MDA) and ion leakage (EL), less accumulation of O2•- and H2O2, and high enzymatic antioxidant (SOD, POD, CAT) activities, non-enzymatic antioxidant (AsA-GSH cycle) contents and hormone (IAA, ABA, GA3, and ZR) levels under drought stress. Furthermore, ntrav4 mutants in tobacco improved the expression levels of ROS-related proline synthesis and stress-responsive genes under osmotic stress. Our results indicate that NtRAV4 negatively regulates plant tolerance to drought stress by reducing water loss and activating the antioxidant system and stress-related gene expression to maintain the steady state of the ROS system.

Time-series transcriptomics reveals a drought-responsive temporal network and crosstalk between drought stress and the circadian clock in foxtail millet

Drought stress is a serious factor affecting crop growth and production worldwide. The circadian clock has been identified as key to improving regional adaptability of plants. However, our understanding of the contribution of the circadian clock to drought response and the impacts of drought stress on the circadian clock in plants is still limited. To explore the interactions between the circadian clock and drought stress, foxtail millet seedlings were treated with simulated drought (20% polyethylene glycol-6000) treatment starting at the day (DD) onset zeitgeber time 0 (ZT0, lights on) and at the night (DN) onset zeitgeber time 16 (ZT16, lights off). A high temporal-resolution transcriptomic investigation was performed using DD and DN samples collected at intervals of 2 or 4 h within a 24-h drought-treatment period. Overall, we identified 13 294 drought-responsive genes (DRGs). Among these DRGs, 7931 were common between DD and DN samples, 2638 were specific to DD, and 2725 were specific to DN. Additionally, we identified 1257 circadian genes, of which 67% were DRGs. Interestingly, with drought treatment starting at the day for 8, 12 or 16 h, the circadian phase shifted to 12 h. We also found that the circadian clock led to different day and night drought-responsive pathways. The identification of DRG_Clock (DRG and circadian clock) and DRG_NonClock (DRG and not circadian clock) genes provides a reference for selecting candidate drought resistance genes. Our work reveals the temporal drought-response process and crosstalk between drought stress and the circadian clock in foxtail millet.

Circadian clock in plants: Linking timing to fitness

Endogenous circadian clock integrates cyclic signals of environment and daily and seasonal behaviors of organisms to achieve spatiotemporal synchronization, which greatly improves genetic diversity and fitness of species. This review addresses recent studies on the plant circadian system in the field of chronobiology, covering topics on molecular mechanisms, internal and external Zeitgebers, and hierarchical regulation of physiological outputs. The architecture of the circadian clock involves the autoregulatory transcriptional feedback loops, post-translational modifications of core oscillators, and epigenetic modifications of DNA and histones. Here, light, temperature, humidity, and internal elemental nutrients are summarized to illustrate the sensitivity of the circadian clock to timing cues. In addition, the circadian clock runs cell-autonomously, driving independent circadian rhythms in various tissues. The core oscillators responds to each other with biochemical factors including calcium ions, mineral nutrients, photosynthetic products, and hormones. We describe clock components sequentially expressed during a 24-h day that regulate rhythmic growth, aging, immune response, and resistance to biotic and abiotic stresses. Notably, more data have suggested the circadian clock links chrono-culture to key agronomic traits in crops.

The circadian clock ticks in plant stress responses

The circadian clock, a time-keeping mechanism, drives nearly 24-h self-sustaining rhythms at the physiological, cellular, and molecular levels, keeping them synchronized with the cyclic changes of environmental signals. The plant clock is sensitive to external and internal stress signals that act as timing cues to influence the circadian rhythms through input pathways of the circadian clock system. In order to cope with environmental stresses, many core oscillators are involved in defense while maintaining daily growth in various ways. Recent studies have shown that a hierarchical multi-oscillator network orchestrates the defense through rhythmic accumulation of gene transcripts, alternative splicing of mRNA precursors, modification and turnover of proteins, subcellular localization, stimuli-induced phase separation, and long-distance transport of proteins. This review summarizes the essential role of circadian core oscillators in response to stresses in Arabidopsis thaliana and crops, including daily and seasonal abiotic stresses (low or high temperature, drought, high salinity, and nutrition deficiency) and biotic stresses (pathogens and herbivorous insects). By integrating time-keeping mechanisms, circadian rhythms and stress resistance, we provide a temporal perspective for scientists to better understand plant environmental adaptation and breed high-quality crop germplasm for agricultural production.

Progress in soybean functional genomics over the past decade

Soybean is one of the most important oilseed and fodder crops. Benefiting from the efforts of soybean breeders and the development of breeding technology, large number of germplasm has been generated over the last 100 years. Nevertheless, soybean breeding needs to be accelerated to meet the needs of a growing world population, to promote sustainable agriculture and to address future environmental changes. The acceleration is highly reliant on the discoveries in gene functional studies. The release of the reference soybean genome in 2010 has significantly facilitated the advance in soybean functional genomics. Here, we review the research progress in soybean omics (genomics, transcriptomics, epigenomics and proteomics), germplasm development (germplasm resources and databases), gene discovery (genes that are responsible for important soybean traits including yield, flowering and maturity, seed quality, stress resistance, nodulation and domestication) and transformation technology during the past decade. At the end, we also briefly discuss current challenges and future directions.

Abscisic Acid Machinery Is under Circadian Clock Regulation at Multiple Levels

Abscisic acid (ABA) is recognized as the key hormonal regulator of plant stress physiology. This phytohormone is also involved in plant growth and development under normal conditions. Over the last 50 years the components of ABA machinery have been well characterized, from synthesis to molecular perception and signaling; knowledge about the fine regulation of these ABA machinery components is starting to increase. In this article, we review a particular regulation of the ABA machinery that comes from the plant circadian system and extends to multiple levels. The circadian clock is a self-sustained molecular oscillator that perceives external changes and prepares plants to respond to them in advance. The circadian system constitutes the most important predictive homeostasis mechanism in living beings. Moreover, the circadian clock has several output pathways that control molecular, cellular and physiological downstream processes, such as hormonal response and transcriptional activity. One of these outputs involves the ABA machinery. The circadian oscillator components regulate expression and post-translational modification of ABA machinery elements, from synthesis to perception and signaling response. The circadian clock establishes a gating in the ABA response during the day, which fine tunes stomatal closure and plant growth response.

Soybean GmMYB133 Inhibits Hypocotyl Elongation and Confers Salt Tolerance in Arabidopsis

REVEILLE (RVE) genes generally act as core circadian oscillators to regulate multiple developmental events and stress responses in plants. It is of importance to document their roles in crops for utilizing them to improve agronomic traits. Soybean is one of the most important crops worldwide. However, the knowledge regarding the functional roles of RVEs is extremely limited in soybean. In this study, the soybean gene GmMYB133 was shown to be homologous to the RVE8 clade genes of Arabidopsis. GmMYB133 displayed a non-rhythmical but salt-inducible expression pattern. Like AtRVE8, overexpression of GmMYB133 in Arabidopsis led to developmental defects such as short hypocotyl and late flowering. Seven light-responsive or auxin-associated genes including AtPIF4 were transcriptionally depressed by GmMYB133, suggesting that GmMYB133 might negatively regulate plant growth. Noticeably, the overexpression of GmMYB133 in Arabidopsis promoted seed germination and plant growth under salt stress, and the contents of chlorophylls and malondialdehyde (MDA) were also enhanced and decreased, respectively. Consistently, the expressions of four positive regulators responsive to salt tolerance were remarkably elevated by GmMYB133 overexpression, indicating that GmMYB133 might confer salt stress tolerance. Further observation showed that GmMYB133 overexpression perturbed the clock rhythm of AtPRR5, and yeast one-hybrid assay indicated that GmMYB133 could bind to the AtPRR5 promoter. Moreover, the retrieved ChIP-Seq data showed that AtPRR5 could directly target five clients including AtPIF4. Thus, a regulatory module GmMYB133-PRR5-PIF4 was proposed to regulate plant growth and salt stress tolerance. These findings laid a foundation to further address the functional roles of GmMYB133 and its regulatory mechanisms in soybean.

Genome-wide association study revealed genetic variations of ABA sensitivity controlled by multiple stress-related genes in rice

Abscisic acid (ABA) is a critical phytohormone that regulates multiple physiological processes including plant growth and stress tolerance. The core ABA signaling pathway has been well established, but genetic variations mediating ABA responses remain largely unknown. In this study, we performed genome-wide association study (GWAS) to identify loci and genes associated with ABA sensitivity (reflected by seed germination inhibition by ABA) in a panel of 425 rice accessions. The seed germination assay revealed that Aus and indica rice had stronger ABA sensitivity than japonica rice. A total of 48 non-redundant association loci were detected in the indica subpopulation and whole population, and 386 genes in these loci were responsive to ABA or abiotic stresses. Eight association loci were overlapped with previously reported loci for yield under drought stress or for drought-indicative image traits. Haplotype analyses of important candidate genes such as OsSAPK6, a key component in the ABA signaling core, were performed to identify key SNPs/InDels that may affect gene functions through promoter activity regulation, amino acid variation, or gene splicing. These results provide insights into the genetic basis of ABA sensitivity related to stress responses.

Towards Developing Drought-smart Soybeans

Drought is one of the significant abiotic stresses threatening crop production worldwide. Soybean is a major legume crop with immense economic significance, but its production is highly dependent on optimum rainfall or abundant irrigation. Also, in dry periods, it may require supplemental irrigation for drought-susceptible soybean varieties. The effects of drought stress on soybean including osmotic adjustments, growth morphology and yield loss have been well studied. In addition, drought-resistant soybean cultivars have been investigated for revealing the mechanisms of tolerance and survival. Advanced high-throughput technologies have yielded remarkable phenotypic and genetic information for producing drought-tolerant soybean cultivars, either through molecular breeding or transgenic approaches. Further, transcriptomics and functional genomics have led to the characterisation of new genes or gene families controlling drought response. Interestingly, genetically modified drought-smart soybeans are just beginning to be released for field applications cultivation. In this review, we focus on breeding and genetic engineering approaches that have successfully led to the development of drought-tolerant soybeans for commercial use.