Two homologous LHY pairs negatively control soybean drought tolerance by repressing the abscisic acid responses

Advances in Soybean Genetic Improvement

The soybean (Glycine max) is a globally important crop due to its high protein and oil content, which serves as a key resource for human and animal nutrition, as well as bioenergy production. This review assesses recent advancements in soybean genetic improvement by conducting an extensive literature analysis focusing on enhancing resistance to biotic and abiotic stresses, improving nutritional profiles, and optimizing yield. We also describe the progress in breeding techniques, including traditional approaches, marker-assisted selection, and biotechnological innovations such as genetic engineering and genome editing. The development of transgenic soybean cultivars through Agrobacterium-mediated transformation and biolistic methods aims to introduce traits such as herbicide resistance, pest tolerance, and improved oil composition. However, challenges remain, particularly with respect to genotype recalcitrance to transformation, plant regeneration, and regulatory hurdles. In addition, we examined how wild soybean germplasm and polyploidy contribute to expanding genetic diversity as well as the influence of epigenetic processes and microbiome on stress tolerance. These genetic innovations are crucial for addressing the increasing global demand for soybeans, while mitigating the effects of climate change and environmental stressors. The integration of molecular breeding strategies with sustainable agricultural practices offers a pathway for developing more resilient and productive soybean varieties, thereby contributing to global food security and agricultural sustainability.

The overexpression of the switchgrass (Panicum virgatum L.) genes PvTOC1-N or PvLHY-K affects circadian rhythm and hormone metabolism in transgenic Arabidopsis seedlings

Switchgrass (Panicum virgatum L.) is a perennial C4 warm-season grass known for its high-biomass yield and wide environmental adaptability, making it an ideal bioenergy crop. Despite its potential, switchgrass seedlings grow slowly, often losing out to weeds in field conditions and producing limited biomass in the first year of planting. Furthermore, during the reproductive growth stage, the above-ground biomass rapidly increases in lignin content, creating a significant saccharification barrier. Previous studies have identified rhythm-related genes TOC1 and LHY as crucial to the slow seedling development in switchgrass, yet the precise regulatory functions of these genes remain largely unexplored. In this study, the genes TOC1 and LHY were characterized within the tetraploid genome of switchgrass. Gene expression analysis revealed that PvTOC1 and PvLHY exhibit circadian patterns under normal growth conditions, with opposing expression levels over time. PvTOC1 genes were predominantly expressed in florets, vascular bundles, and seeds, while PvLHY genes showed higher expression in stems, leaf sheaths, and nodes. Overexpression of PvTOC1 from the N chromosome group (PvTOC1-N) or PvLHY from the K chromosome group (PvLHY-K) in Arabidopsis thaliana led to alterations in circadian rhythm and hormone metabolism, resulting in shorter roots, delayed flowering, and decreased resistance to oxidative stress. These transgenic lines exhibited reduced sensitivity to hormones and hormone inhibitors, and displayed altered gene expression in the biosynthesis and signal transduction pathways of abscisic acid (ABA), gibberellin (GA), 3-indoleacetic acid (IAA), and strigolactone (SL). These findings highlight roles of PvTOC1-N and PvLHY-K in plant development and offer a theoretical foundation for genetic improvements in switchgrass and other crops.

Clock protein LHY targets SNAT1 and negatively regulates the biosynthesis of melatonin in Hypericum perforatum

Hypericum perforatum, also known as "natural fluoxetine," is a commonly used herbal remedy for treating depression. It is unclear whether melatonin in plants regulated by the endogenous circadian clock system is like in vertebrates. In this work, we found that the melatonin signal and melatonin biosynthesis gene, serotonin N-acetyltransferase HpSNAT1, oscillates in a 24-hour cycle in H. perforatum. First, we constructed a yeast complementary DNA library of H. perforatum and found a clock protein HpLHY that can directly bind to the HpSNAT1 promoter. Second, it was confirmed that HpLHY inhibits the expression of HpSNAT1 by targeting the Evening Element. Last, it indicated that HpLHY-overexpressing plants had reduced levels of melatonin in 12-hour light/12-hour dark cycle photoperiod, while loss-of-function mutants exhibited high levels, but this rhythm seems to disappear as well. The results revealed the regulatory role of LHY in melatonin biosynthesis, which may make an important contribution to the field of melatonin synthesis regulation.

Transcriptome Analysis Revealed the Paternal Importance to Vegetative Growth Heterosis in Populus

Parental selection is important for heterosis formation during crossbreeding of Populus. However, in poplar hybrids, the effect of parents on vegetative growth heterosis is not well understood. In this study, one female parent (P. simonii XY4) and two male parents (P. nigra OH and P. deltoides × P. nigra BJLY3#) were used to produce two progenies (Hyb1 and Hyb2). Vegetative growth investigation showed that both Hyb1 and Hyb2 performed heterosis in plant growth and ground diameter. The vegetative growth of hybrids was strongly correlated with the male parents but not with the female parents. The gene expression levels in the hybrids were more biased toward the male parents. In Hyb1 and Hyb2, 51.93% and 45.03% of the expressed genes showed the non-additive effect, respectively, and over 65% of the non-additively expressed genes showed the dominant effect. It is noteworthy that genes of paternal expression dominant effect (ELD_♂) account for the majority of dominantly expressed genes, suggesting the paternal contribution to heterosis. KEGG enrichment analysis indicated that a large number of non-additively expressed genes were enriched in the plant hormone signal transduction pathway. WGCNA analysis showed that MEcyan was significantly correlated with the traits of hybrids, and 12 plant hormone signal transduction pathway genes were enriched in this module. Transcription factors (TFs) MYB88, LHY, and TCP4 may be involved in the regulation of these pathway genes. This finding supported that the male parents play an important role in the formation of vegetative growth heterosis of Populus. In addition, the non-additively expressed genes of the signal transduction pathway and the regulation of TFs related to these pathway genes may be one of the reasons for the generation of heterosis.

The MADS-box transcription factor GmFULc promotes GmZTL4 gene transcription to modulate maturity in soybean

Flowering time and maturity are crucial agronomic traits that affect the regional adaptability of soybean plants. The development of soybean cultivars with early maturity adapted to longer days and colder climates of high latitudes is very important for ensuring normal ripening before frost begins. FUL belongs to the MADS-box transcription factor family and has several duplicated members in soybeans. In this study, we observed that overexpression of GmFULc in the Dongnong 50 cultivar promoted soybean maturity, while GmFULc knockout mutants exhibited late maturity. Chromatin immunoprecipitation sequencing (ChIP-seq) and RNA sequencing (RNA-seq) revealed that GmFULc could bind to the CArG, bHLH and homeobox motifs. Further investigation revealed that GmFULc could directly bind to the CArG motif in the promoters of the GmZTL3 and GmZTL4 genes. Overexpression of GmZTL4 promoted soybean maturity, whereas the ztl4 mutants exhibited delayed maturity. Moreover, we found that the cis element box 4 motif of the GmZTL4 promoter, a motif of light response elements, played an important role in controlling the growth period. Deletion of this motif shortened the growth period by increasing the expression levels of GmZTL4. Functional investigations revealed that short-day treatment promoted the binding of GmFULc to the promoter of GmZTL4 and inhibited the expression of E1 and E1Lb, ultimately resulting in the promotion of flowering and early maturation. Taken together, these findings suggest a novel photoperiod regulatory pathway in which GmFULc directly activates GmZTL4 to promote earlier maturity in soybean.

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.

GmANKTM21 Positively Regulates Drought Tolerance and Enhanced Stomatal Response through the MAPK Signaling Pathway in Soybean

Drought stress is one of the significant abiotic stresses that limit soybean (Glycine max [L.] Merr.) growth and production. Ankyrin repeat (ANK) proteins, being highly conserved, occupy a pivotal role in diverse biological processes. ANK genes were classified into nine subfamilies according to conserved domains in the soybean genome. However, the function of ANK-TM subfamily proteins (Ankyrin repeat proteins with a transmembrane domain) in the abiotic-stress response to soybean remains poorly understood. In this study, we first demonstrated the subcellular localization of GmANKTM21 in the cell membrane and nucleus. Drought stress-induced mRNA levels of GmANKTM21, which encodes proteins belonging to the ANK-TM subfamily, Transgenic 35S:GmANKTM21 soybean improved drought tolerance at the germination and seedling stages, with higher stomatal closure in soybean, lower water loss, lower malondialdehyde (MDA) content, and less reactive oxygen species (ROS) production compared with the wild-type soybean (Dongnong50). RNA-sequencing (RNA-seq) and RT-qPCR analysis of differentially expressed transcripts in overexpression of GmANKTM21 further identified potential downstream genes, including GmSPK2, GmSPK4, and GmCYP707A1, which showed higher expression in transgenic soybean, than those in wild-type soybean and KEGG enrichment analysis showed that MAPK signaling pathways were mostly enriched in GmANKTM21 overexpressing soybean plants under drought stress conditions. Therefore, we demonstrate that GmANKTM21 plays an important role in tolerance to drought stress in soybeans.

Genome-Wide Identification and Characterization of the CCT Gene Family in Rapeseed (Brassica napus L.)

The CCT gene family is present in plants and is involved in biological processes such as flowering, circadian rhythm regulation, plant growth and development, and stress resistance. We identified 87, 62, 46, and 40 CCTs at the whole-genome level in B. napus, B. rapa, B. oleracea, and A. thaliana, respectively. The CCTs can be classified into five groups based on evolutionary relationships, and each of these groups can be further subdivided into three subfamilies (COL, CMF, and PRR) based on function. Our analysis of chromosome localization, gene structure, collinearity, cis-acting elements, and expression patterns in B. napus revealed that the distribution of the 87 BnaCCTs on the chromosomes of B. napus was uneven. Analysis of gene structure and conserved motifs revealed that, with the exception of a few genes that may have lost structural domains, the majority of genes within the same group exhibited similar structures and conserved domains. The gene collinearity analysis identified 72 orthologous genes, indicating gene duplication and expansion during the evolution of BnaCCTs. Analysis of cis-acting elements identified several elements related to abiotic and biotic stress, plant hormone response, and plant growth and development in the promoter regions of BnaCCTs. Expression pattern and protein interaction network analysis showed that BnaCCTs are differentially expressed in various tissues and under stress conditions. The PRR subfamily genes have the highest number of interacting proteins, indicating their significant role in the growth, development, and response to abiotic stress of B. napus.

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.

Soybean RVE8a confers salt and drought tolerance in Arabidopsis

Soybean is an economically important crop, which often suffers various abiotic stresses. REVEILLE (RVE) genes have been generally considered as circadian oscillators to mediate diverse developmental processes and plant response to environmental stresses. Addressing their roles is of significance for utilizing them to enhance agronomic traits in crops. However, our understanding of soybean RVEs is extremely limited. In the study, we investigated the expression patterns of soybean CCA1-like genes under salt stress using our RNA-Seq data. Subsequently, a salt stress-inducible gene, GmRVE8a, was chosen for further study. Phylogenetic analysis indicated that GmRVE8a is most closely related to Arabidopsis RVE4 and RVE8. Also, GmRVE8a showed circadian expression pattern with 24 h rhythmic period, suggesting that it might be a clock-regulated gene. Moreover, transgenic Arabidopsis lines over-expressing GmRVE8a were generated. It was observed that ectopic over-expression of GmRVE8a caused a significant delay in flowering. Further observation indicated that under salt and drought stress, transgenic seedlings were stronger than wild type. Consistently, three-week-old transgenic plants grew better than wild type under salt and drought conditions, and the MDA content in transgenic lines was significantly lower than wild type, suggesting that GmRVE8a might be a positive regulator in response to salt and drought stress. Intriguingly, Y2H assay indicated that GmRVE8a physically interacted with a drought-tolerant protein, GmNAC17. Overall, our findings provided preliminary information regarding the functional roles of GmRVE8a in response to salt and drought stress.

Development of KASP markers assisted with soybean drought tolerance in the germination stage based on GWAS

Soybean [Glycine max(L.)Merr.] is a leading oil-bearing crop and cultivated globally over a vast scale. The agricultural landscape in China faces a formidable challenge with drought significantly impacting soybean production. In this study, we treated a natural population of 264 Chinese soybean accessions using 15% PEG-6000 and used GR, GE, GI, RGR, RGE, RGI and ASFV as evaluation index. Using the ASFV, we screened 17 strong drought-tolerant soybean germplasm in the germination stage. Leveraging 2,597,425 high-density SNP markers, we conducted Genome-Wide Association Studies (GWAS) and identified 92 SNPs and 9 candidate genes significantly associated with drought tolerance. Furthermore, we developed two KASP markers for S14_5147797 and S18_53902767, which closely linked to drought tolerance. This research not only enriches the pool of soybean germplasm resources but also establishes a robust foundation for the molecular breeding of drought tolerance soybean varieties.

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.

CsLHY positively regulates cold tolerance by activating CsSWEET17 in tea plants

Low temperature is one of the most important environmental factors limiting tea plants' geographic distribution and severely affects spring tea's yield and quality. Circadian components contribute to plant responses to low temperatures; however, comparatively little is known about these components in tea plants. In this study, we identified a core clock component the LATE ELONGATED HYPOCOTYL, CsLHY, which is mainly expressed in tea plants' mature leaves, flowers, and roots. Notably, CsLHY maintained its circadian rhythmicity of expression in summer, but was disrupted in winter and held a high expression level. Meanwhile, we found that CsLHY expression rhythm was not affected by different photoperiods but was quickly broken by cold, and the low temperature induced and kept CsLHY expression at a relatively high level. Yeast one-hybrid and dual-luciferase assays confirmed that CsLHY can bind to the promoter of Sugars Will Eventually be Exported Transporters 17 (CsSWEET17) and function as a transcriptional activator. Furthermore, suppression of CsLHY expression in tea leaves not only reduced CsSWEET17 expression but also impaired the freezing tolerance of leaves compared to the control. Our results demonstrate that CsLHY plays a positive role in the low-temperature response of tea plants by regulating CsSWEET17 when considered together.

Multiple Tissues Transcriptome of Zig-Zag Eel (Mastacembelus armatus) with Different Growth Rates

In order to explore the main regulatory genes and related pathways of growth traits, transcriptome sequencing was first performed on the brain, liver, and muscle tissues of 3-month-old M. armatus with different growth rates. By comparative transcriptome analysis of fast-growing and slow-growing groups of M. armatus, a total of 2887 DEGs were screened, of which 59 up-regulated genes and 105 down-regulated genes were detected in the brain, 146 up-regulated genes and 202 down-regulated genes were detected in the liver, and 529 up-regulated genes and 1846 down-regulated genes were detected in muscle, including insulin-like growth factor binding protein 1a (IGFBP1A), insulin-like growth factor binding protein 1b (IGFBP1B), myosin, light chain 1 (MYL1), and myoglobin (MB). Through Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, we identified a total of 288 significantly enriched GO entries and 68 significantly enriched KEGG pathways related to growth, such as skeletal muscle tissue development, insulin-like growth factor binding, and the mitotic cell cycle. These key genes and signaling pathways may play a key role in regulating the growth of M. armatus. Digging into the regulatory mechanisms of these key genes will provide a theoretical basis for further exploration of the molecular mechanisms related to the growth and development of M. armatus, and help to breed new varieties of M. armatus with rapid growth.

Function identification of miR159a, a positive regulator during poplar resistance to drought stress

Drought seriously affects the growth and development of plants. MiR159 is a highly conserved and abundant microRNA family that plays a crucial role in plant growth and stress responses. However, studies of its function in woody plants are still lacking. Here, the expression of miR159a was significantly upregulated after drought treatment in poplar, and the overexpression of miR159a (OX159a) significantly reduced the open area of the stomata and improved water-use efficiency in poplar. After drought treatment, OX159a lines had better scavenging ability of reactive oxygen species and damage of the membrane system was less than that in wild-type lines. MYB was the target gene of miR159a, as verified by psRNATarget prediction, RT-qPCR, degradome sequencing, and 5' rapid amplification of cDNA ends (5' RACE). Additionally, miR159a-short tandem target mimic suppression (STTM) poplar lines showed increased sensitivity to drought stress. Transcriptomic analysis comparing OX159a lines with wild-type lines revealed upregulation of a series of genes related to response to water deprivation and metabolite synthesis. Moreover, drought-responsive miR172d and miR398 were significantly upregulated and downregulated respectively in OX159a lines. This investigation demonstrated that miR159a played a key role in the tolerance of poplar to drought by reducing stomata open area, increasing the number and total area of xylem vessels, and enhancing water-use efficiency, and provided new insights into the role of plant miR159a and crucial candidate genes for the molecular breeding of trees with tolerance to drought stress.

The Soybean Expression Atlas v2: A comprehensive database of over 5000 RNA-seq samples

Soybean is a crucial crop worldwide, used as a source of food, feed, and industrial products due to its high protein and oil content. Previously, the rapid accumulation of soybean RNA-seq data in public databases and the computational challenges of processing raw RNA-seq data motivated us to develop the Soybean Expression Atlas, a gene expression database of over a thousand RNA-seq samples. Over the past few years, our database has allowed researchers to explore the expression profiles of important gene families, discover genes associated with agronomic traits, and understand the transcriptional dynamics of cellular processes. Here, we present the Soybean Expression Atlas v2, an updated version of our database with a fourfold increase in the number of samples, featuring transcript- and gene-level transcript abundance matrices for 5481 publicly available RNA-seq samples. New features in our database include the availability of transcript-level abundance estimates and equivalence classes to explore differential transcript usage, abundance estimates in bias-corrected counts to increase the accuracy of differential gene expression analyses, a new web interface with improved data visualization and user experience, and a reproducible and scalable pipeline available as an R package. The Soybean Expression Atlas v2 is available at https://soyatlas.venanciogroup.uenf.br/, and it will accelerate soybean research, empowering researchers with high-quality and easily accessible gene expression data.

Physiological responses and transcriptome analysis of soybean under gradual water deficit

Soybean is an important food and oil crop widely cultivated globally. However, water deficit can seriously affect the yield and quality of soybeans. In order to ensure the stability and increase of soybean yield and improve agricultural water use efficiency (WUE), research on improving drought tolerance and the efficiency of water utilization of soybeans under drought stress has become particularly important. This study utilized the drought-tolerant variety Heinong 44 (HN44) and the drought-sensitive variety Suinong 14 (SN14) to analyze physiological responses and transcriptome changes during the gradual water deficit at the early seed-filling stage. The results indicated that under drought conditions, HN44 had smaller stomata, higher stomatal density, and lower stomatal conductance (Gs) and transpiration rate as compared to SN14. Additionally, HN44 had a higher abscisic acid (ABA) content and faster changes in stomatal morphology and Gs to maintain a dynamic balance between net photosynthetic rate (Pn) and Gs. Additionally, drought-tolerant variety HN44 had high instantaneous WUE under water deficit. Further, HN44 retained a high level of superoxide dismutase (SOD) activity and proline content, mitigating malondialdehyde (MDA) accumulation and drought-induced damage. Comprehensive analysis of transcriptome data revealed that HN44 had fewer differentially expressed genes (DEGs) under light drought stress, reacting insensitivity to water deficit. At the initial stage of drought stress, both varieties had a large number of upregulated DEGs to cope with the drought stress. Under severe drought stress, HN44 had fewer downregulated genes enriched in the photosynthesis pathway than SN14, while it had more upregulated genes enriched in the ABA-mediated signaling and glutathione metabolism pathways than SN14. During gradual water deficit, HN44 demonstrated better drought-tolerant physiological characteristics and water use efficiency than SN14 through key DEGs such as GmbZIP4, LOC100810474, and LOC100819313 in the major pathways. Key transcription factors were screened and identified, providing further clarity on the molecular regulatory pathways responsible for the physiological differences in drought tolerance among these varieties. This study deepened the understanding of the drought resistance mechanisms in soybeans, providing valuable references for drought-resistant soybean breeding.

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.

Allelic variation in transcription factor PtoWRKY68 contributes to drought tolerance in Populus

Drought stress limits woody species productivity and influences tree distribution. However, dissecting the molecular mechanisms that underpin drought responses in forest trees can be challenging due to trait complexity. Here, using a panel of 300 Chinese white poplar (Populus tomentosa) accessions collected from different geographical climatic regions in China, we performed a genome-wide association study (GWAS) on seven drought-related traits and identified PtoWRKY68 as a candidate gene involved in the response to drought stress. A 12-bp insertion and/or deletion and three nonsynonymous variants in the PtoWRKY68 coding sequence categorized natural populations of P. tomentosa into two haplotype groups, PtoWRKY68hap1 and PtoWRKY68hap2. The allelic variation in these two PtoWRKY68 haplotypes conferred differential transcriptional regulatory activities and binding to the promoters of downstream abscisic acid (ABA) efflux and signaling genes. Overexpression of PtoWRKY68hap1 and PtoWRKY68hap2 in Arabidopsis (Arabidopsis thaliana) ameliorated the drought tolerance of two transgenic lines and increased ABA content by 42.7% and 14.3% compared to wild-type plants, respectively. Notably, PtoWRKY68hap1 (associated with drought tolerance) is ubiquitous in accessions in water-deficient environments, whereas the drought-sensitive allele PtoWRKY68hap2 is widely distributed in well-watered regions, consistent with the trends in local precipitation, suggesting that these alleles correspond to geographical adaptation in Populus. Moreover, quantitative trait loci analysis and an electrophoretic mobility shift assay showed that SHORT VEGETATIVE PHASE (PtoSVP.3) positively regulates the expression of PtoWRKY68 under drought stress. We propose a drought tolerance regulatory module in which PtoWRKY68 modulates ABA signaling and accumulation, providing insight into the genetic basis of drought tolerance in trees. Our findings will facilitate molecular breeding to improve the drought tolerance of forest trees.

When drought meets heat - a plant omics perspective

Changes in weather patterns with emerging drought risks and rising global temperature are widespread and negatively affect crop growth and productivity. In nature, plants are simultaneously exposed to multiple biotic and abiotic stresses, but most studies focus on individual stress conditions. However, the simultaneous occurrence of different stresses impacts plant growth and development differently than a single stress. Plants sense the different stress combinations in the same or in different tissues, which could induce specific systemic signalling and acclimation responses; impacting different stress-responsive transcripts, protein abundance and modifications, and metabolites. This mini-review focuses on the combination of drought and heat, two abiotic stress conditions that often occur together. Recent omics studies indicate common or independent regulators involved in heat or drought stress responses. Here, we summarize the current research results, highlight gaps in our knowledge, and flag potential future focus areas.

Late Elongated Hypocotyl Positively Regulates Salt Stress Tolerance in Medicago truncatula

Abiotic stress, such as drought, osmotic, and salinity stresses, seriously affects plant growth and crop production. Studying stress-resistant genes that enhance plant stress tolerance is an efficient way to facilitate the breeding of crop species with high stress tolerance. In this study, we reported that the core circadian clock component, the LATE ELONGATED HYPOCOTYL (LHY) orthologue MtLHY, plays a positive role in salt stress response in Medicago truncatula. The expression of MtLHY was induced by salt stress, and loss-of-function mutants of MtLHY were shown to be hypersensitive to salt treatment. However, overexpression of MtLHY improved salt stress tolerance through a higher accumulation of flavonoids. Consistently, exogenous flavonol application improved the salt stress tolerance in M. truncatula. Additionally, MtLHY was identified as a transcriptional activator of the flavonol synthase gene, MtFLS. Our findings revealed that MtLHY confers plant salt stress tolerance, at least by modulating the flavonoid biosynthesis pathway, which provides insight into salt stress tolerance that links the circadian clock with flavonoid biosynthesis.

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.

Genome-wide identification of genes encoding SWI/SNF components in soybean and the functional characterization of GmLFR1 in drought-stressed plants

ATP-dependent SWI/SNF chromatin remodeling complexes (CRCs) are evolutionarily conserved multi-component machines that regulate transcription, replication, and genome stability in eukaryotes. SWI/SNF components play pivotal roles in development and various stress responses in plants. However, the compositions and biological functions of SWI/SNF complex subunits remain poorly understood in soybean. In this study, we used bioinformatics to identify 39 genes encoding SWI/SNF subunit distributed on the 19 chromosomes of soybean. The promoter regions of the genes were enriched with several cis-regulatory elements that are responsive to various hormones and stresses. Digital expression profiling and qRT-PCR revealed that most of the SWI/SNF subunit genes were expressed in multiple tissues of soybean and were sensitive to drought stress. Phenotypical, physiological, and molecular genetic analyses revealed that GmLFR1 (Leaf and Flower-Related1) plays a negative role in drought tolerance in soybean and Arabidopsis thaliana. Together, our findings characterize putative components of soybean SWI/SNF complex and indicate possible roles for GmLFR1 in plants under drought stress. This study offers a foundation for comprehensive analyses of soybean SWI/SNF subunit and provides mechanistic insight into the epigenetic regulation of drought tolerance in soybean.

Plant growth promoting potential of urea doped calcium phosphate nanoparticles in finger millet (Eleusine coracana (L.) Gaertn.) under drought stress

Drought is a leading threat that impinges on plant growth and productivity. Nanotechnology is considered an adequate tool for resolving various environmental issues by offering avant-garde and pragmatic solutions. Using nutrients in the nano-scale including CaP-U NPs is a novel fertilization strategy for crops. The present study was conducted to develop and utilize environment-friendly urea nanoparticles (NPs) based nano-fertilizers as a crop nutrient. The high solubility of urea molecules was controlled by integrating them with a matrix of calcium phosphate nanoparticles (CaP NPs). CaP NPs contain high phosphorous and outstanding biocompatibility. Scanning electron microscopy (FE-SEM), transmission electron microscopy (TEM) and X-ray diffraction analysis (XRD) were used to characterize the fabricated NPs. FE-SEM determined no areas of phase separation in urea and calcium phosphate, indicating the successful formation of an encapsulated nanocomposite between the two nano matrices. TEM examination confirmed a fiber-like structure of CaP-U NPs with 15 to 50 nm diameter and 100 to 200 nm length. The synthesized CaP-U NPs and bulk urea (0.0, 0.1% and 0.5%) were applied by foliar sprays at an interval of 15 days on pre-sowed VL-379 variety of finger millet (Eleusine coracana (L.) Gaertn.), under irrigated and drought conditions. The application of the CaP-U NPs significantly enhanced different plant growth attributes such as shoot length (29.4 & 41%), root length (46.4 & 51%), shoot fresh (33.6 & 55.8%) and dry weight (63 & 59.1%), and root fresh (57 & 61%) and dry weight (78 & 80.7%), improved pigment system (chlorophyll) and activated plant defense enzymes such as proline (35.4%), superoxide dismutase (47.7%), guaiacol peroxidase (30.2%), ascorbate peroxidase (70%) under both irrigated and drought conditions. Superimposition of five treatment combinations on drought suggested that CaP-U NPs at 0.5 followed by 0.1% provided the highest growth indices and defense-related enzymes, which were significantly different. Overall, our findings suggested that synthesized CaP-U NPs treatment of finger millet seeds improved plant growth and enzymatic regulation, particularly more in drought conditions providing insight into the strategy for not only finger millet but probably for other commercial cereals crops which suffer from fluctuating environmental 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 Potential of CRISPR/Cas Technology to Enhance Crop Performance on Adverse Soil Conditions

Worldwide food security is under threat in the actual scenery of global climate change because the major staple food crops are not adapted to hostile climatic and soil conditions. Significant efforts have been performed to maintain the actual yield of crops, using traditional breeding and innovative molecular techniques to assist them. However, additional strategies are necessary to achieve the future food demand. Clustered regularly interspaced short palindromic repeat/CRISPR-associated protein (CRISPR/Cas) technology, as well as its variants, have emerged as alternatives to transgenic plant breeding. This novelty has helped to accelerate the necessary modifications in major crops to confront the impact of abiotic stress on agriculture systems. This review summarizes the current advances in CRISPR/Cas applications in crops to deal with the main hostile soil conditions, such as drought, flooding and waterlogging, salinity, heavy metals, and nutrient deficiencies. In addition, the potential of extremophytes as a reservoir of new molecular mechanisms for abiotic stress tolerance, as well as their orthologue identification and edition in crops, is shown. Moreover, the future challenges and prospects related to CRISPR/Cas technology issues, legal regulations, and customer acceptance will be discussed.

Origin, variation, and selection of natural alleles controlling flowering and adaptation in wild and cultivated soybean

Soybean (Glycine max) is an economically important crop worldwide, serving as a major source of oil and protein for human consumption and animal feed. Cultivated soybean was domesticated from wild soybean (Glycine soja) which both species are highly sensitive to photoperiod and can grow over a wide geographical range. The extensive ecological adaptation of wild and cultivated soybean has been facilitated by a series of genes represented as quantitative trait loci (QTLs) that control photoperiodic flowering and maturation. Here, we review the molecular and genetic basis underlying the regulation of photoperiodic flowering in soybean. Soybean has experienced both natural and artificial selection during adaptation to different latitudes, resulting in differential molecular and evolutionary mechanisms between wild and cultivated soybean. The in-depth study of natural and artificial selection for the photoperiodic adaptability of wild and cultivated soybean provides an important theoretical and practical basis for enhancing soybean adaptability and yield via molecular breeding. In addition, we discuss the possible origin of wild soybean, current challenges, and future research directions in this important topic.

Warming and microplastic pollution shape the carbon and nitrogen cycles of algae

Oceans absorb most excess heat from anthropogenic activities, leading to ocean warming. Moreover, microplastic pollution from anthropogenic activities is serious in marine environments and is accessible to various organisms. However, the combined effects of environmentally realistic ocean warming and microplastic pollution (OW+MP) on dominant marine species phytoplankton and related biochemical cycles are unclear. We investigated the combined effects on the dominant genera of diatoms (Chaetoceros gracilis, C. gracilis) over 100 generations. As a biological adjustment strategy, the growth rates of C. gracilis were nonsignificantly changed by OW+MP, body size decreased, and the chlorophyll a (Chl a) content and photosynthetic efficiency significantly decreased by 32.5% and 10.86%, respectively. The OW+MP condition inhibited carbon and nitrogen assimilation and sequestration capacity and allocated carbon into flexible forms of carbohydrates instead of proteins. Furthermore, the decrease in Si:C and Si:N ratios affected carbon transport to both the mesopelagic layer and deep ocean. Integrated transcriptomics and metabolomics showed that OW+MP disturbed ribosome and nitrogen metabolism. Given the rising concurrence of warming and MP pollution, the changes in metabolism suggest that the covariation in carbon, nitrogen and silicon biochemical cycles and the hidden influence on biodiversity and food web changes in the ocean should be reconsidered.

Developing drought-smart, ready-to-grow future crops

Breeding crop plants with increased yield potential and improved tolerance to stressful environments is critical for global food security. Drought stress (DS) adversely affects agricultural productivity worldwide and is expected to rise in the coming years. Therefore, it is vital to understand the physiological, biochemical, molecular, and ecological mechanisms associated with DS. This review examines recent advances in plant responses to DS to expand our understanding of DS-associated mechanisms. Suboptimal water sources adversely affect crop growth and yields through physical impairments, physiological disturbances, biochemical modifications, and molecular adjustments. To control the devastating effect of DS in crop plants, it is important to understand its consequences, mechanisms, and the agronomic and genetic basis of DS for sustainable production. In addition to plant responses, we highlight several mitigation options such as omics approaches, transgenics breeding, genome editing, and biochemical to mechanical methods (foliar treatments, seed priming, and conventional agronomic practices). Further, we have also presented the scope of conventional and speed breeding platforms in helping to develop the drought-smart future crops. In short, we recommend incorporating several approaches, such as multi-omics, genome editing, speed breeding, and traditional mechanical strategies, to develop drought-smart cultivars to achieve the 'zero hunger' goal.

Constitutive expression of AtSINA2 from Arabidopsis improves grain yield, seed oil and drought tolerance in transgenic soybean

The SEVEN IN Absentia (SINA), a typical member of the RING E3 ligase family, plays a crucial role in plant growth, development and response to abiotic stress. However, its biological functions in oil crops are still unknown. Previously, we reported that overexpression of AtSINA2 in Arabidopsis positively regulated the drought tolerance of transgenic plants. In this work, we demonstrate that ectopic expression of AtSINA2 in soybean improved the shoot growth, grain yield, drought tolerance and seed oil content in transgenic plants. Compared to wild type, transgenic soybean produced greater shoot biomass and grain yield, and showed improved seed oil and drought tolerance. Physiological analyses exhibited that the increased drought tolerance of transgenic plants was accompanied with a higher chlorophyll content, and a lower malondialdehyde accumulation and water loss during drought stress. Further transcriptomic analyses revealed that the expressions of genes related to plant growth, flowering and stress response were up- or down-regulated in transgenic soybean under both normal and drought stress conditions. Our findings imply that AtSINA2 improved both agricultural production and drought tolerance, and it can be used as a candidate gene for the genetic engineering of new soybean cultivars with improved grain yield and drought resistance.

Understanding water conservation vs. profligation traits in vegetable legumes through a physio-transcriptomic-functional approach

Vegetable soybean and cowpea are related warm-season legumes showing contrasting leaf water use behaviors under similar root drought stresses, whose mechanisms are not well understood. Here we conducted an integrative phenomic-transcriptomic study on the two crops grown in a feedback irrigation system that enabled precise control of soil water contents. Continuous transpiration rate monitoring demonstrated that cowpea used water more conservatively under earlier soil drought stages, but tended to maintain higher transpiration under prolonged drought. Interestingly, we observed a soybean-specific transpiration rate increase accompanied by phase shift under moderate soil drought. Time-series transcriptomic analysis suggested a dehydration avoidance mechanism of cowpea at early soil drought stage, in which the VuHAI3 and VuTIP2;3 genes were suggested to be involved. Multifactorial gene clustering analysis revealed different responsiveness of genes to drought, time of day and their interactions between the two crops, which involved species-dependent regulation of the circadian clock genes. Gene network analysis identified two co-expression modules each associated with transpiration rate in cowpea and soybean, including a pair of negatively correlated modules between species. Module hub genes, including the ABA-degrading gene GmCYP707A4 and the trehalose-phosphatase/synthase gene VuTPS9 were identified. Inter-modular network analysis revealed putative co-players of the hub genes. Transgenic analyses verified the role of VuTPS9 in regulating transpiration rate under osmotic stresses. These findings propose that species-specific transcriptomic reprograming in leaves of the two crops suffering similar soil drought was not only a result of the different drought resistance level, but a cause of it.

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.

Crucial Abiotic Stress Regulatory Network of NF-Y Transcription Factor in Plants

Nuclear Factor-Y (NF-Y), composed of three subunits NF-YA, NF-YB and NF-YC, exists in most of the eukaryotes and is relatively conservative in evolution. As compared to animals and fungi, the number of NF-Y subunits has significantly expanded in higher plants. The NF-Y complex regulates the expression of target genes by directly binding the promoter CCAAT box or by physical interaction and mediating the binding of a transcriptional activator or inhibitor. NF-Y plays an important role at various stages of plant growth and development, especially in response to stress, which attracted many researchers to explore. Herein, we have reviewed the structural characteristics and mechanism of function of NF-Y subunits, summarized the latest research on NF-Y involved in the response to abiotic stresses, including drought, salt, nutrient and temperature, and elaborated the critical role of NF-Y in these different abiotic stresses. Based on the summary above, we have prospected the potential research on NF-Y in response to plant abiotic stresses and discussed the difficulties that may be faced in order to provide a reference for the in-depth analysis of the function of NF-Y transcription factors and an in-depth study of plant responses to abiotic stress.

Understandings and future challenges in soybean functional genomics and molecular breeding

Soybean (Glycine max) is a major source of plant protein and oil. Soybean breeding has benefited from advances in functional genomics. In particular, the release of soybean reference genomes has advanced our understanding of soybean adaptation to soil nutrient deficiencies, the molecular mechanism of symbiotic nitrogen (N) fixation, biotic and abiotic stress tolerance, and the roles of flowering time in regional adaptation, plant architecture, and seed yield and quality. Nevertheless, many challenges remain for soybean functional genomics and molecular breeding, mainly related to improving grain yield through high-density planting, maize-soybean intercropping, taking advantage of wild resources, utilization of heterosis, genomic prediction and selection breeding, and precise breeding through genome editing. This review summarizes the current progress in soybean functional genomics and directs future challenges for molecular breeding of soybean.

Characterization of the REVEILLE family in Rosaceae and role of PbLHY in flowering time regulation

BACKGROUND

The circadian clock integrates endogenous and exogenous signals and regulates various physiological processes in plants. REVEILLE (RVE) proteins play critical roles in circadian clock system, especially CCA1 (CIRCADIAN CLOCK ASSOCIATED 1) and LHY (LATE ELONGATED HYPOCOTYL), which also participate in flowering regulation. However, little is known about the evolution and function of the RVE family in Rosaceae species, especially in Pyrus bretschneideri.

RESULTS

In this study, we performed a genome-wide analysis and identified 51 RVE genes in seven Rosaceae species. The RVE family members were classified into two groups based on phylogenetic analysis. Dispersed duplication events and purifying selection were the main drivers of evolution in the RVE family. Moreover, the expression patterns of ten PbRVE genes were diverse in P. bretschneideri tissues. All PbRVE genes showed diurnal rhythms under light/dark cycles in P. bretschneideri leaves. Four PbRVE genes also displayed robust rhythms under constant light conditions. PbLHY, the gene with the highest homology to AtCCA1 and AtLHY in P. bretschneideri, is localized in the nucleus. Ectopic overexpression of PbLHY in Arabidopsis delayed flowering time and repressed the expression of flowering time-related genes.

CONCLUSION

These results contribute to improving the understanding and functional research of RVE genes in P. bretschneideri.

An R2R3-MYB FtMYB11 from Tartary buckwheat has contrasting effects on abiotic tolerance in Arabidopsis

R2R3-MYB transcription factors play important roles in response to abiotic stresses in planta, such as salt, drought, and osmotic stress. However, the role of FtMYB11 in Tartary buckwheat (Fagopyrum tataricum) in drought and osmotic tolerance has not yet been elucidated. In this study, we found that FtMYB11 was markedly induced by exogenous abscisic acid (ABA), salinity, and mannitol. Further, FtMYB11-overexpressing Arabidopsis showed hypersensitivity to ABA-mediated seed germination and seedling establishment through regulating transcripts of AtCBF1, AtDREB2A, and AtRD20, compared with wild type, indicating that FtMYB11 plays a positive role in ABA signaling. In contrast, transgenic lines overexpressing FtMYB11 were sensitive to mannitol and NaCl treatments, suggesting that FtMYB11 plays a negative role in osmotic tolerance. Intriguingly, the transcripts of ABA biosynthetic enzyme genes were significantly elevated in plants overexpressing FtMYB11 after exposure to osmotic stresses, such as AtABA3 and AtNCED3. In addition, flavonoid biosynthesis genes were also upregulated in transgenic Arabidopsis under ABA, salt, and drought treatments, including AtC4H, AtF3H, AtANS, AtFLS, and At4CL. The drought tolerance assay showed that plants overexpressing FtMYB11 displayed greater tolerance to water deficit through regulating MDA and proline content. Taken together, FtMYB11 has opposite roles in response to abiotic stresses, but it may mediate flavonoid biosynthesis through regulation of related enzyme genes.

Identification of QTN-by-environment interactions and their candidate genes for soybean seed oil-related traits using 3VmrMLM

Introduction

Although seed oil content and its fatty acid compositions in soybean were affected by environment, QTN-by-environment (QEIs) and gene-by-environment interactions (GEIs) were rarely reported in genome-wide association studies.

Methods

The 3VmrMLM method was used to associate the trait phenotypes, measured in five to seven environments, of 286 soybean accessions with 106,013 SNPs for detecting QTNs and QEIs.

Results

Seven oil metabolism genes (GmSACPD-A, GmSACPD-B, GmbZIP123, GmSWEET39, GmFATB1A, GmDGAT2D, and GmDGAT1B) around 598 QTNs and one oil metabolism gene GmFATB2B around 54 QEIs were verified in previous studies; 76 candidate genes and 66 candidate GEIs were predicted to be associated with these traits, in which 5 genes around QEIs were verified in other species to participate in oil metabolism, and had differential expression across environments. These genes were found to be related to soybean seed oil content in haplotype analysis. In addition, most candidate GEIs were co-expressed with drought response genes in co-expression network, and three KEGG pathways which respond to drought were enriched under drought stress rather than control condition; six candidate genes were hub genes in the co-expression networks under drought stress.

Discussion

The above results indicated that GEIs, together with drought response genes in co-expression network, may respond to drought, and play important roles in regulating seed oil-related traits together with oil metabolism genes. These results provide important information for genetic basis, molecular mechanisms, and soybean breeding for seed oil-related traits.

Leaf transcriptome analysis of Medicago ruthenica revealed its response and adaptive strategy to drought and drought recovery

BACKGROUND

Drought is one of the main causes of losses in forage crop yield and animal production. Medicago ruthenica (L.) cv. Zhilixing is a high-yielding alfalfa cultivar also known for its high tolerance to drought. We analyzed the transcriptome profile of this cultivar throughout drought stress and recovery and we were able to describe its phased response through the expression profiles of overlapping gene networks and drought-specific genes.

RESULTS

The ABA and auxin signal transduction pathways are overlapping pathways in response to drought and drought recovery in forage crops. Medicago ruthenica (L.) cv. Zhilixing adopts different strategies at different degrees of drought stress. On the 9th day of drought, transcriptional regulations related to osmoregulation are enhanced mainly through increased activities of carbohydrate and amino acid metabolism, while photosynthetic activities were reduced to slow down growth. With drought prolonging, on the 12th day of drought, the synthesis of proline and other stored organic substances was suppressed in general. After recovery, Medicago ruthenica synthesizes flavonoids through the flavonoid biosynthesis pathway to remove accumulated ROS and repair the oxidative damage from water stress. In addition, the regulation of circadian rhythm seems to accelerate the drought recovery process.

CONCLUSIONS

Medicago ruthenica adapts to drought by regulating the osmoregulatory system and photosynthesis, which appears to involve the ABA and auxin signaling pathways as key regulators. Furthermore, the synthesis of flavonoids and the regulation of the circadian rhythm can accelerate the recovery process. These results enriched our knowledge of molecular responses to drought and drought recovery in Medicago ruthenica and provide useful information for the development of new legume forage grass varieties with improved adaptability to drought stress.

GmTOC1b inhibits nodulation by repressing GmNIN2a and GmENOD40-1 in soybean

Symbiotic nitrogen fixation is an important factor affecting the yield and quality of leguminous crops. Nodulation is regulated by a complex network comprising several transcription factors. Here, we functionally characterized the role of a TOC1 family member, GmTOC1b, in soybean (Glycine max) nodulation. RT-qPCR assays showed that GmTOC1b is constitutively expressed in soybean. However, GmTOC1b was also highly expressed in nodules, and GmTOC1 localized to the cell nucleus, based on transient transformation in Nicotiana benthamiana leaves. Homozygous Gmtoc1b mutant plants exhibited increased root hair curling and produced more infection threads, resulting in more nodules and greater nodule fresh weight. By contrast, GmTOC1b overexpression inhibited nodulation. Furthermore, we also showed that GmTOC1b represses the expression of nodulation-related genes including GmNIN2a and GmENOD40-1 by binding to their promoters. We conclude that GmTOC1b functions as a transcriptional repressor to inhibit nodulation by repressing the expression of key nodulation-related genes including GmNIN2a, GmNIN2b, and GmENOD40-1 in soybean.

A crosstalk of circadian clock and alternative splicing under abiotic stresses in the plants

The circadian clock is an internal time-keeping mechanism that synchronizes the physiological adaptation of an organism to its surroundings based on day and night transition in a period of 24 h, suggesting the circadian clock provides fitness by adjusting environmental constrains. The circadian clock is driven by positive and negative elements that regulate transcriptionally and post-transcriptionally. Alternative splicing (AS) is a crucial transcriptional regulator capable of generating large numbers of mRNA transcripts from limited numbers of genes, leading to proteome diversity, which is involved in circadian to deal with abiotic stresses. Over the past decade, AS and circadian control have been suggested to coordinately regulate plant performance under fluctuating environmental conditions. However, only a few reports have reported the regulatory mechanism of this complex crosstalk. Based on the emerging evidence, this review elaborates on the existing links between circadian and AS in response to abiotic stresses, suggesting an uncovered regulatory network among circadian, AS, and abiotic stresses. Therefore, the rhythmically expressed splicing factors and core clock oscillators fill the role of temporal regulators participating in improving plant growth, development, and increasing plant tolerance against abiotic stresses.

Rice CIRCADIAN CLOCK ASSOCIATED 1 transcriptionally regulates ABA signaling to confer multiple abiotic stress tolerance

The circadian clock facilitates the survival and reproduction of crop plants under harsh environmental conditions such as drought and osmotic and salinity stresses, mainly by reprogramming the endogenous transcriptional landscape. Nevertheless, the genome-wide roles of core clock components in rice (Oryza sativa L.) abiotic stress tolerance are largely uncharacterized. Here, we report that CIRCADIAN CLOCK ASSOCIATED1 (OsCCA1), a vital clock component in rice, is required for tolerance to salinity, osmotic, and drought stresses. DNA affinity purification sequencing coupled with transcriptome analysis identified 692 direct transcriptional target genes of OsCCA1. Among them, the genes involved in abscisic acid (ABA) signaling, including group A protein phosphatase 2C genes and basic region and leucine zipper 46 (OsbZIP46), were substantially enriched. Moreover, OsCCA1 could directly bind the promoters of OsPP108 and OsbZIP46 to activate their expression. Consistently, oscca1 null mutants generated via genome editing displayed enhanced sensitivities to ABA signaling. Together, our findings illustrate that OsCCA1 confers multiple abiotic stress tolerance likely by orchestrating ABA signaling, which links the circadian clock with ABA signaling in rice.

Identification of MADS-Box Transcription Factors in Iris laevigata and Functional Assessment of IlSEP3 and IlSVP during Flowering

Iris laevigata is ideal for gardening and landscaping in northeast China because of its beautiful flowers and strong cold resistance. However, the short length of flowering time (2 days for individual flowers) greatly limits its applications. Molecular breeding and engineering hold high potential for producing I. laevigata of desirable flowering properties. A prerequisite is to identify and characterize key flowering control genes, the identity of which remains largely unknown in I. laevigata due to the lack of genome information. To fill this knowledge gap, we used sequencing data of the I. laevigata transcriptome to identify MADS-box gene-encoding transcription factors that have been shown to play key roles in developmental processes, including flowering. Our data revealed 41 putative MADS-box genes, which consisted of 8 type I (5 Mα and 3 Mβ, respectively) and 33 type II members (2 MIKC* and 31 MIKCC, respectively). We then selected IlSEP3 and IlSVP for functional studies and found that both are localized to the nucleus and that they interact physically in vitro. Ectopic expression of IlSEP3 in Arabidopsis resulted in early flowering (32 days) compared to that of control plants (36 days), which could be mediated by modulating the expression of FT, SOC1, AP1, SVP, SPL3, VRN1, and GA20OX. By contrast, plants overexpressing IlSVP were phenotypically similar to that of wild type. Our functional validation of IlSEP3 was consistent with the notion that SEP3 promotes flowering in multiple plant species and indicated that IlSEP3 regulates flowering in I. laevigata. Taken together, this work provided a systematic identification of MADS-box genes in I. laevigata and demonstrated that the flowering time of I. laevigata can be genetically controlled by altering the expression of key MADS-box genes.

SlSnRK2.3 interacts with SlSUI1 to modulate high temperature tolerance via Abscisic acid (ABA) controlling stomatal movement in tomato

Tomato is often exposed to high temperature stress during summer cultivation. Stomatal movement plays important roles in photosynthesis and transpiration which restricts the quality and yield of tomato under environmental stress. To elucidate the mechanism of stomatal movement in high temperature tolerance, SlSnRK2s (sucrose non-fermenting 1-related protein kinases) silenced plants were generated in tomato with CRISPR-Cas 9 gene editing techniques. Through the observation of stomatal parameters, SlSnRK2.3 regulated stomatal closure which was responded to ABA (abscisic acid) and activated signaling pathway of ROS (reactive oxygen species) in high temperature stress. Based on the positive functions of SlSnRK2.3, the cDNA library was generated to investigate interaction proteins of SlSnRK2s. The interaction between SlSnRK2.3 and SlSUI1 (protein translation factor SUI1 homolog) was employed by Yeast two hybrid assay (Y2H), Luciferase (LUC), and Bimolecular fluorescence complementation (BiFC). Finally, the specific interactive sites between SlSnRK2.3 and SlSUI1 were verified by site-directed mutagenesis. The consistent mechanism of SlSnRK2.3 and SlSUI1 in stomatal movement, indicating that SlSUI1 interacted with SlSnRK2.3 through ABA-dependent signaling pathway in high temperature stress. Our results provided evidence for improving the photosynthetic capacity of tomato under high temperature stress, and support the breeding and genetic engineering of tomato over summer facility cultivation.

The AP2/ERF GmERF113 Positively Regulates the Drought Response by Activating GmPR10-1 in Soybean

Ethylene response factors (ERFs) are involved in biotic and abiotic stress; however, the drought resistance mechanisms of many ERFs in soybeans have not been resolved. Previously, we proved that GmERF113 enhances resistance to the pathogen Phytophthora sojae in soybean. Here, we determined that GmERF113 is induced by 20% PEG-6000. Compared to the wild-type plants, soybean plants overexpressing GmERF113 (GmERF113-OE) displayed increased drought tolerance which was characterized by milder leaf wilting, less water loss from detached leaves, smaller stomatal aperture, lower Malondialdehyde (MDA) content, increased proline accumulation, and higher Superoxide dismutase (SOD) and Peroxidase (POD) activities under drought stress, whereas plants with GmERF113 silenced through RNA interference were the opposite. Chromatin immunoprecipitation and dual effector-reporter assays showed that GmERF113 binds to the GCC-box in the GmPR10-1 promoter, activating GmPR10-1 expression directly. Overexpressing GmPR10-1 improved drought resistance in the composite soybean plants with transgenic hairy roots. RNA-seq analysis revealed that GmERF113 downregulates abscisic acid 8′-hydroxylase 3 (GmABA8’-OH 3) and upregulates various drought-related genes. Overexpressing GmERF113 and GmPR10-1 increased the abscisic acid (ABA) content and reduced the expression of GmABA8’-OH3 in transgenic soybean plants and hairy roots, respectively. These results reveal that the GmERF113-GmPR10-1 pathway improves drought resistance and affects the ABA content in soybean, providing a theoretical basis for the molecular breeding of drought-tolerant soybean.

The Central Circadian Clock Protein TaCCA1 Regulates Seedling Growth and Spike Development in Wheat (Triticum aestivum L.)

The biological functions of the circadian clock on growth and development have been well elucidated in model plants, while its regulatory roles in crop species, especially the roles on yield-related traits, are poorly understood. In this study, we characterized the core clock gene CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1) homoeologs in wheat and studied their biological functions in seedling growth and spike development. TaCCA1 homoeologs exhibit typical diurnal expression patterns, which are positively regulated by rhythmic histone modifications including histone H3 lysine 4 trimethylation (H3K4me3), histone H3 lysine 9 acetylation (H3K9Ac), and histone H3 lysine 36 trimethylation (H3K36me3). TaCCA1s are preferentially located in the nucleus and tend to form both homo- and heterodimers. TaCCA1 overexpression (TaCCA1-OE) transgenic wheat plants show disrupted circadian rhythmicity coupling with reduced chlorophyll and starch content, as well as biomass at seedling stage, also decreased spike length, grain number per spike, and grain size at the ripening stage. Further studies using DNA affinity purification followed by deep sequencing [DNA affinity purification and sequencing (DAP-seq)] indicated that TaCCA1 preferentially binds to sequences similarly to "evening elements" (EE) motif in the wheat genome, particularly genes associated with photosynthesis, carbon utilization, and auxin homeostasis, and decreased transcriptional levels of these target genes are observed in TaCCA1-OE transgenic wheat plants. Collectively, our study provides novel insights into a circadian-mediated mechanism of gene regulation to coordinate photosynthetic and metabolic activities in wheat, which is important for optimal plant growth and crop yield formation.

Citrus FRIGIDA cooperates with its interaction partner dehydrin to regulate drought tolerance

Drought is a major environmental stress that severely affects plant growth and crop productivity. FRIGIDA (FRI) is a key regulator of flowering time and drought tolerance in model plants. However, little is known regarding its functions in woody plants, including citrus. Thus, we explored the functional role of the citrus FRI ortholog (CiFRI) under drought. Drought treatment induced CiFRI expression. CiFRI overexpression enhanced drought tolerance in transgenic Arabidopsis and citrus, while CiFRI suppression increased drought susceptibility in citrus. Moreover, transcriptomic profiling under drought conditions suggested that CiFRI overexpression altered the expression of numerous genes involved in the stress response, hormone biosynthesis, and signal transduction. Mechanistic studies revealed that citrus dehydrin likely protects CiFRI from stress-induced degradation, thereby enhancing plant drought tolerance. In addition, a citrus brassinazole-resistant (BZR) transcription factor family member (CiBZR1) directly binds to the CiFRI promoter to activate its expression under drought conditions. CiBZR1 also enhanced drought tolerance in transgenic Arabidopsis and citrus. These findings further our understanding of the molecular mechanisms underlying the CiFRI-mediated drought stress response in citrus.

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.

Metabolic Pathways Involved in the Drought Stress Response of Nitraria tangutorum as Revealed by Transcriptome Analysis

Drought resistance in plants is controlled by multiple genes. To identify the genes that mediate drought stress responses and to assess the associated metabolic pathways in the desert shrub Nitraria tangutorum, we conducted a transcriptome analysis of plants under control (maximum field capacity) and drought (20% of the maximum field capacity) conditions. We analyzed differentially expressed genes (DEGs) of N. tangutorum and their enrichment in the KEGG metabolic pathways database, and explored the molecular biological mechanisms underlying the answer to its drought tolerance. Between the control and drought groups, 119 classified metabolic pathways annotated 3047 DEGs in the KEGG database. For drought tolerance, nitrate reductase (NR) gene expression was downregulated, indicating that NR activity was decreased to improve drought tolerance. In ammonium assimilation, drought stress inhibited glutamine formation. Protochlorophyllide reductase (1.3.1.33) expression was upregulated to promote chlorophyll a synthesis, whereas divinyl reductase (1.3.1.75) expression was downregulated to inhibit chlorophyll-ester a synthesis. The expression of the chlorophyll synthase (2.5.1.62) gene was downregulated, which affected the synthesis of chlorophyll a and b. Overall, drought stress appeared to improve the ability to convert chlorophyll b into chlorophyll a. Our data serve as a theoretical foundation for further elucidating the growth regulatory mechanism of desert xerophytes, thereby facilitating the development and cultivation of new, drought-resistant genotypes for the purpose of improving desert ecosystems.

Mycorrhizal fungi regulate daily rhythm of circadian clock in trifoliate orange under drought stress

The circadian rhythm of plants is associated with stress responses; however, it is not clear whether increased host plant drought tolerance by arbuscular mycorrhizal fungi (AMF) is associated with changes in the circadian clock. The present study aimed to analyze the effect of Funneliformis mosseae (Nicol. & Gerd.) Schüßler & Walker on the circadian clock gene expression patterns in trifoliate orange (Poncirus trifoliata L. Raf.) along with gas exchange, abscisic acid (ABA) levels and antioxidant enzyme gene expression under well-watered (WW) and drought stress (DS) conditions. Plant growth, net photosynthetic rate, stomatal conductance and ABA levels were significantly higher in AMF- than in non-AMF-inoculated plants regardless of soil water regimes. Six circadian clock genes, including PtPRR7, PtLHY, PtCCA1, PtGI, PtPIF3 and PtSRR1, were identified and showed rhythmic expression patterns over the course of the day. The AMF inoculation reduced the expression of most circadian clock genes in different time periods. However, AMF treatment significantly increased PtPRR7 and PtGI expression at 5:00 p.m. under WW and DS conditions, PtLHY expression at 1:00 a.m. and PtSRR1 expression at 9:00 p.m. At 1:00 a.m., AMF inoculation up-regulated the expression of the circadian clock genes PtPRR7, PtCCA1, PtLHY and PtPIF3 and the antioxidant enzyme genes PtFe-SOD, PtMn-SOD, PtCu/Zn-SOD, PtPOD and PtCAT1. Correlation analysis revealed that these changes in circadian clock gene expression were associated with antioxidant enzyme gene expression, root ABA and gas exchange. We concluded that mycorrhizal fungi have the ability to regulate the daily rhythm of the circadian clock in trifoliate orange plants in response to drought.

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.