Root system architecture, physiological and transcriptional traits of soybean (Glycine max L.) in response to water deficit: A review

Comparative effects of biocontrol agent and pathogen on Nicotiana tabacum: insights into fungal-plant interactions

Tobacco (Nicotiana tabacum) black shank disease, caused by Phytophthora nicotianae, is a significant threat to tobacco crops, leading to severe economic losses. Prolonged use of agrochemicals to control this disease has prompted the exploration of eco-friendly biological control strategies. This study investigated the effects of Trichoderma harzianum, a biocontrol agent, on N. tabacum in comparison to P. nicotianae, focusing on growth, biomass, root morphology and anatomy, hormonal changes, and osmotic regulation. T. harzianum significantly enhanced plant growth, biomass accumulation, root system development, and physiological attributes such as photosynthetic pigment levels and antioxidant enzyme activity. In contrast, P. nicotianae negatively impacted these parameters, inhibiting growth and physiological function. Notably, T. harzianum increased proline content and enhanced induced resistance mechanisms, mitigating stress and promoting overall plant health. These findings highlight the potential of T. harzianum as a sustainable solution for managing black shank disease while improving tobacco crop productivity.

Physiological and transcriptomic analysis of Spartina alterniflora in response to imazapyr acid stress

As a key aspect of managing of invasive alien species in China, the prevention and control of Spartina alterniflora have become an important part of the work in coastal provinces, and imazapyr acid has been gradually applied in the control work due to its advantages of high efficiency and low toxicity. In this study, we applied 6.0 L/acre of 25% imazapyr acid aqueous stress treatment, and determined and analyzed the physiological activities and transcriptome profiles of S. alterniflora under sustained stress. Chlorophyll fluorescence was used as a technical tool to analyze the mechanism of photosynthesis and the photosynthetic physiological status of S. alterniflora. We analyzed the root system structure of S. alterniflora using a root system imaging system, and characterized the transcriptome of S. alterniflora by high-throughput sequencing technology. Specifically, after imazapyr acid exposure, the fluorescence imaging area of leaves were all decreased, and the fluorescence indexes such as Fv/Fm, Y(II) and PIabs were significantly decreased, while Y(NO) was significantly increased, and Y(NPQ) showed an increase followed by a decrease. Meanwhile, total root length, root surface area and biomass of S. alterniflora were suppressed after imazapyr acid exposure. In transcriptomic analysis, imazapyr acid inhibited the expression of genes involved in phenylpropanoid biosynthesis, nucleotide sugar-related metabolism, valine, leucine and isoleucine biosynthesis, and DNA replication in S. alterniflora. These results indicate that the effects of imazapyr acid stress on the leaves of S. alterniflora are heterogeneous, with the leaves initiating photoprotective mechanisms to ensure the normal functioning of the photosystem in the early stage of stress, and the PSII reaction centers being damaged in the late stage of stress, ultimately destroying the photosynthetic system. Meanwhile, imazapyr acid stress alters basic physiological processes such as metabolism and growth and development of S. alterniflora, thus affecting the growth and development of the plant root system, and ultimately leading to the death of S. alterniflora.

Metabonomics reveals the mechanism of stress resistance in Vetiveria zizanioides inoculated with AMF under copper stress

Vetiveria zizanioides, renowned for its robust stability and exceptional capacity to sequester heavy metals, has garnered widespread application in tailings ecological restoration efforts. Arbuscular mycorrhizal fungi (AMF), which are capable of forming symbiotic relationships with more than 80% of terrestrial plant roots, play a pivotal role in enhancing plant nutrient uptake and bolstering resilience. In this study, we conducted a comprehensive investigation into the physiological and biochemical responses of Vetiveria zizanioides subjected to varying levels of copper stress (with copper concentrations ranging from 0 mg/kg to 400 mg/kg), with or without AMF inoculation. Additionally, we performed nontargeted metabonomic analyses to gain deeper insights into the metabolic changes that occur in vetiver grass under AMF inoculation and copper stress. Our findings revealed that Vetiveria zizanioides inoculated with AMF consistently demonstrated superior growth performance across all copper stress levels compared with noninoculated counterparts. Using nontargeted metabonomic analyses, inoculation with AMF affects the metabolism of phenylalanine and related pathways in vetiver as well as contributing to the promotion of the formation of phytochelatins (PCs) from glutamate, thereby alleviating copper stress. The results highlight the potential of AMF-inoculated Vetiveria zizanioides as a promising bioremediation tool capable of effectively mitigating the adverse effects of heavy metal pollution.

Integration of Genetic and Imaging Data to Detect QTL for Root Traits in Interspecific Soybean Populations

Wild soybean, which has many desirable traits, such as adaptability to climate change-related stresses, is a valuable resource for expanding the narrow genetic diversity of cultivated soybeans. Plants require roots to adapt to different environments and optimize water and nutrient uptake to support growth and facilitate the storage of metabolites; however, it is challenging and costly to evaluate root traits under field conditions. Previous studies of quantitative trait loci (QTL) have been mainly based on cultivated soybean populations. In this study, an interspecific mapping population from a cross between wild soybean 'PI483463' and cultivar 'Hutcheson' was used to investigate QTLs associated with root traits using image data. Our results showed that 39 putative QTLs were distributed across 10 chromosomes (chr.). Seventeen of these were clustered in regions on chr. 8, 14, 15, 16, and 17, accounting for 19.92% of the phenotypic variation. We identified five significant QTL clusters influencing root-related traits, such as total root length, surface area, lateral total length, and number of tips, across five chr., with favorable alleles from both wild and cultivated soybeans. Furthermore, we identified eight candidate genes controlling these traits based on functional annotation. These genes were highly expressed in root tissues and directly or indirectly affected soybean root growth, development, and stress responses. Our results provide valuable insights for breeders aiming to optimize soybean root traits and leveraging genetic diversity from wild soybean species to develop varieties with improved root morphological traits, ultimately enhancing overall plant growth, productivity, and resilience.

Fertigation with alpha-tocopherol enhances morphological, physiological, and antioxidant responses in radish (Raphanus sativus L.) under drought stress

Water scarcity is a foremost environmental concern and is expected to hasten in the forthcoming years due to severe fluctuations in weather patterns worldwide. The present work was designed to explore the potential role of alpha-tocopherol (α-Toc), a form of vitamin E, on the morphological, physio-biochemical, and cellular antioxidant responses of two radish genotypes grown under drought conditions (38 ± 3% of field capacity). The individual and combined applications of α-Toc (100 ppm) were used as T0- Control, T1- Control + TF (TF-alpha-tocopherol), T2- Drought (D), and T3- D + TF with three replications. In general, drought conditions cause a marked reduction in, growth traits such as root length (RL), shoot dry weight (SDW), and shoot fresh weight (SFW). However, the sole and combined applications of α-Toc significantly enhanced the SDW, SFW, and RL in both radish genotypes. Drought stress causes a significant upsurge in hydrogen peroxide (H2O2) and lipid peroxidation (LPX) in leaves. At the same time, exogenous fertigation of α-Toc protects the membranes by reducing the level of LPX, enhancing antioxidants such as catalase (CAT) and peroxidase (POX) to scavenge the reactive oxygen species (ROS), and enhancing the osmolyte as total soluble proteins to maintain cell internal osmotic potential. Also, the α-Toc enhanced the photosynthetic pigments and significantly increased photosynthetic activity in the Early Milo (G2) as compared to Laal Pari (G1) genotype under drought, enhancing water use efficiency by maintaining transpiration rate and stomatal conductance. The α-Toc also regulates the beneficial inorganic ions (K+, Ca2+, and PO₄³⁻) in the shoots of both genotypes. Our present findings demonstrate the potential role of α-Toc in mitigating drought stress and infer that it can enhance plant growth under drought conditions.

Enhancing soybean germination and vigor under water stress: the efficacy of bio-priming with sodium carboxymethyl cellulose and gum arabic

Seed priming can significantly enhance the tolerance of soybean against different environmental stresses by improving seed water uptake and modulating stress-response mechanisms. In particular, seed priming with sodium carboxymethylcellulose (SCMC) and gum Arabic (GA) can support seeds to withstand extreme conditions better, promoting more consistent germination and robust seedling establishment, which is crucial for achieving stable agricultural yields. The present study investigated the effects of seed priming using a combination of SCMC and GA (10% CG) on the germination, growth, and biochemical responses of six soybean varieties under drought and flooding stress conditions. The results revealed significant differences among varieties and applied treatments on germination, vigor, and physiological traits. Under drought stress, seed priming with 10% CG significantly improved germination percentage, germination rate, shoot length, root length, and biomass compared to unprimed seeds. Notable reductions in malondialdehyde (MDA) content and enhanced antioxidant enzyme activities, including superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD), suggest that 10% CG priming mitigates oxidative damage through enhanced antioxidant defense mechanisms. Moreover, 10% CG seed priming improved germination and growth parameters under flooding stress, but the advantages were less significant. In addition, the priming treatment significantly reduced electrolyte conductivity (EC) across all varieties compared to unprimed seeds, indicating improved membrane stability. Overall, 10% CG seed priming was more effective under drought and flooding conditions, demonstrating a potential strategy for enhancing stress tolerance in soybean varieties.

ZmDnaJ-ZmNCED6 module positively regulates drought tolerance via modulating stomatal closure in maize

Heat Shock Protein plays a vital role in maintaining protein homeostasis and protecting cells from stress stimulation. As one of the HSP40 proteins, DnaJ is a stress response protein widely existing in plant cells. The function and regulatory mechanism of ZmDnaJ, a novel chloroplast-localized type-III HSP40, in maize drought tolerance were characterized. Tissue-specific expression analysis showed that ZmDnaJ is highly expressed in the leaves, and is strongly drought-induced in maize seedlings. Overexpression of ZmDnaJ improved maize drought tolerance by enhancing stomatal closure and increasing ABA content to mediate photosynthesis. In contrast, the CRISPR-Cas9 knockout zmdnaj mutant showed lower relative water content and high sensitivity to drought stress. Moreover, Y2H, BiFC and Co-IP analyses revealed that ZmDnaJ interacts with an ABA synthesis-related protein ZmNCED6 to regulate drought tolerance. Similarly, ZmNCED6 overexpressed lines showed stronger oxidation resistance, enhanced photosynthetic rate, stomatal closure and ABA content, whilst the CRISPR-Cas9 knockout mutant showed sensitive to drought stress. More importantly, ZmDnaJ could regulate key drought tolerance genes (ZmPYL10, ZmPP2C44, ZmEREB65, ZmNCED4, ZmNCED6 and ZmABI5), involved in ABA signal transduction pathways. Taken together, our findings suggest that ZmDnaJ-ZmNCED6 module improves drought tolerance in maize.

Genome-wide association study and genomic selection of brace root traits related to lodging resistance in maize

Brace roots are the primary organs for water and nutrient absorption, and play an important role in lodging resistance. Dissecting the genetic basis of brace root traits will facilitate breeding new varieties with lodging resistance and high yield. In present study, genome-wide association study (GWAS) and genomic selection (GS) for brace root penetrometer resistance (PR), root number (RN), and tier number (TN) were conducted in a multi-parent doubled haploid (DH) population. Although the three brace root traits were significantly influenced by genotype-by-environment interactions, relatively high heritabilities were observed for RN (79.25%), TN (81.00%), and PR (74.28%). At the threshold of P-value < 7.42 × 10- 6, 22 SNPs distributed on all 10 chromosomes, except for chromosome 7, and 50 candidate genes were identified using the FarmCPU model. Zm00001d028733, Zm00001d002350, Zm00001d002349, and Zm00001d043694 may be involved in brace root growth. The prediction accuracies of RN, TN, and PR estimated by five-fold cross-validation method with genome-wide SNPs were 0.39, 0.36, and 0.51, respectively, which can be greatly improved by using 100-300 significant SNPs. This study provides new insights into the genetic architecture of brace root traits and genomic selection for breeding lodging resistance maize varieties.

Decoding the Double Stress Puzzle: Investigating Nutrient Uptake Efficiency and Root Architecture in Soybean Under Heat- and Water-Stresses

In the context of climate change, associated with increasingly frequent water deficits and heat waves, there is an urgent need to maintain the performance of soybean, a leading legume crop worldwide, before its yield declines. The objective of this study was to explore which plant traits improve soybean tolerance to heat and/or water stress, with a focus on traits involved in plant architecture and nutrient uptake. For this purpose, two soybean genotypes were grown under controlled conditions in a high-throughput phenotyping platform where either optimal conditions, heat waves, water stress or both heat waves and water stresses were applied during the vegetative stage. By correlating architectural to functional traits, related to water, carbon allocation and nutrient absorption, we were able to explain the stress susceptibility level of the two genotypes. We have shown that water flow in the plant is central to the uptake and allocation of mineral elements in the plant, despite its modulation by stress and in a genotype-dependent manner. This cross-analysis of plant ecophysiology and plant nutrition under different stresses provides new information, especially on the importance of mineral elements in the different plant organs, and can inform future crop design, particularly under changing climatic conditions.

Soybean Yield Simulation and Sustainability Assessment Based on the DSSAT-CROPGRO-Soybean Model

In order to ensure national grain and oil security, it is imperative to expand the soybean planting area in the Xinjiang region. However, the scarcity of water resources in southern Xinjiang, the relatively backward soybean planting technology, and the lack of a supporting irrigation system have negatively impacted soybean planting and yield. In 2022 and 2023, we conducted an experiment which included three irrigation amounts of 27 mm, 36 mm, and 45 mm and analyzed the changes in dry mass and yield. Additionally, we simulated the potential yield using the corrected DSSAT-CROPGRO-Soybean model and biomass based on the meteorological data from 1994 to 2023. The results demonstrated that the model was capable of accurately predicting soybean emergence (the relative root mean square error (nRMSE) = 0, the absolute relative error (ARE) = 0), flowering (nRMSE = 0, ARE = 2.78%), maturity (nRMSE = 0, ARE = 3.21%). The model demonstrated high levels of accuracy in predicting soybean biomass (R2 = 0.98, nRMSE = 20.50%, ARE = 20.63%), 0-80 cm soil water storage (R2 = 0.64, nRMSE = 7.78%, ARE = 3.24%), and yield (R2 = 0.81, nRMSE = 10.83%, ARE = 8.79%). The biomass of soybean plants increases with the increase in irrigation amount. The highest biomass of 63 mm is 9379.19 kg·hm-2. When the irrigation yield is 36-45 mm (p < 0.05), the maximum yield can reach 4984.73 kg·hm-2; the maximum efficiency of soybean irrigation water was 33-36 mm. In light of the impact of soybean yield and irrigation water use efficiency, the optimal irrigation amount for soybean cultivation in southern Xinjiang is estimated to be between 36 and 42 mm. The simulation results provide a theoretical foundation for soybean cultivation in southern Xinjiang.

Poly-γ-glutamic acid enhanced the yield and photosynthesis of soybeans by adjusting soil aggregates and water distribution

BACKGROUND

Poly-γ-glutamic acid (γ-PGA) is employed extensively in agriculture to enhance soil water retention; however, the underlying mechanism by which γ-PGA improves soil structure and soybean productivity in arid regions remains poorly understood. A micro-scale field experiment was conducted in the arid region of northwest China, employing five concentrations of γ-PGA to investigate its impacts on soybean yield, photosynthesis, and water-use efficiency, as well as soil aggregates and water distribution. The five levels of γ-PGA were 0 (CK), 10 (P1), 20 (P2), 40 (P3), and 80 kg ha-1 (P4).

RESULTS

The results demonstrated that the application of γ-PGA significantly improved soybean yield, photosynthesis, and chlorophyll content. It resulted in a decrease in soil aggregate content with a maximum diameter of less than 0.053 mm and an increase in the stability of soil aggregates in the uppermost layer of the soil (0-30 cm). The application of γ-PGA significantly increased soil water content, particularly in the uppermost layer of the soil, and effectively reduced water consumption and improving water use efficiency in soybeans. Overall, the P3 treatment exhibited the most pronounced improvement of soybean yield, photosynthesis, water-use efficiency, as well as distribution of soil aggregates and water. The correlation matrix heatmap also revealed a strong correlation between improvement of soybean yield or photosynthesis at various γ-PGA application levels and the enhancement of soil stability or soil water content.

CONCLUSION

The multivariate regression analysis revealed that an optimal application level of 46 kg ha-1 γ-PGA could enhance effectively both yield and water use efficiency of soybean in the arid region of northwest China. © 2024 Society of Chemical Industry.

From phenotyping to genetic mapping: identifying water-stress adaptations in legume root traits

BACKGROUND

Climate change induces perturbation in the global water cycle, profoundly impacting water availability for agriculture and therefore global food security. Water stress encompasses both drought (i.e. water scarcity) that causes the drying of soil and subsequent plant desiccation, and flooding, which results in excess soil water and hypoxia for plant roots. Terrestrial plants have evolved diverse mechanisms to cope with soil water stress, with the root system serving as the first line of defense. The responses of roots to water stress can involve both structural and physiological changes, and their plasticity is a vital feature of these adaptations. Genetic methodologies have been extensively employed to identify numerous genetic loci linked to water stress-responsive root traits. This knowledge is immensely important for developing crops with optimal root systems that enhance yield and guarantee food security under water stress conditions.

RESULTS

This review focused on the latest insights into modifications in the root system architecture and anatomical features of legume roots in response to drought and flooding stresses. Special attention was given to recent breakthroughs in understanding the genetic underpinnings of legume root development under water stress. The review also described various root phenotyping techniques and examples of their applications in different legume species. Finally, the prevailing challenges and prospective research avenues in this dynamic field as well as the potential for using root system architecture as a breeding target are discussed.

CONCLUSIONS

This review integrated the latest knowledge of the genetic components governing the adaptability of legume roots to water stress, providing a reference for using root traits as the new crop breeding targets.

Root suberization in the response mechanism of melon to autotoxicity

Continuous cropping obstacles poses significant challenges for melon cultivation, with autotoxicity being a primary inducer. Suberization of cells or tissues is a vital mechanism for plant stress response. Our study aimed to elucidate the potential mechanism of root suberization in melon's response to autotoxicity. Cinnamic acid was used to simulate autotoxicity. Results showed that autotoxicity worsened the root morphology and activity of seedlings. Significant reductions were observed in root length, diameter, surface area, volume and fork number compared to the control in the later stage of treatment, with a decrease ranging from 20% to 50%. The decrease in root activity ranged from 16.74% to 29.31%. Root suberization intensified, and peripheral suberin deposition became more prominent. Autotoxicity inhibited phenylalanineammonia-lyase activity, the decrease was 50% at 16 h. The effect of autotoxicity on cinnamylalcohol dehydrogenase and cinnamate 4-hydroxylase activity showed an initial increase followed by inhibition, resulting in reductions of 34.23% and 44.84% at 24 h, respectively. The peroxidase activity only significantly increased at 24 h, with an increase of 372%. Sixty-three differentially expressed genes (DEGs) associated with root suberization were identified, with KCS, HCT, and CYP family showing the highest gene abundance. GO annotated DEGs into nine categories, mainly related to binding and catalytic activity. DEGs were enriched in 27 KEGG pathways, particularly those involved in keratin, corkene, and wax biosynthesis. Seven proteins, including C4H, were centrally positioned within the protein interaction network. These findings provide insights for improving stress resistance in melons and breeding stress-tolerant varieties.

Water regimes in selected fodder radish (Raphanus sativus) genotypes: Effects on nutritional value and in vitro ruminal dry matter degradability

Fodder radish is widely used as a livestock supplement, however, the nutritional value of fodder radish under different water conditions remains insufficiently understood. This study aimed to assess the chemical components and in vitro, ruminal dry matter degradability of two fodder radish genotypes (Endurance and Line 2) subjected to three irrigation regimes: well-watered (W1), moderate water stress (W2), and severe water stress (W3). The analysis revealed statistically significant effects of the main factors on the chemical composition and estimates of fodder radish leaves and tubers, particularly in terms of Crude Protein (CP) and Ether Extract (EE) across genotypes. Both Endurance and Line 2 leaves exhibited interaction effects on N, P, Ca, Mg, K, Na, Fe, Zn, Cu, Mn and Al. Meanwhile only Na, K, Zn, and Cu were affected in tubers. Endurance tubers, specifically, displayed significantly higher (p < 0.05) CP content, with Line 2 tubers showing the highest CP content under W1. Furthermore, Endurance leaves had higher levels of Neutral Detergent Fibre, EE, and Non-Structural Carbohydrate (NSC) compared to Line 2 leaves under W1. Notable differences in tuber fibres were found, specifically in Acid Detergent Fibre for Endurance, with W3 exhibiting a higher concentration level. Both genotypes displayed higher NSC under W3. Significant variations in macro and mmicro minerals were observed between water levels in both genotypes. In terms of in vitro degradability during the 24 h and 48 h incubation periods, all treatments met the acceptable level of 60-80 %. Regardless of water regimes, both Endurance and Line 2 showed nutrient concentrations meeting the minimum requirements for optimal animal production. Though, Line 2 exhibits significantly higher nutritional value and in vitro ruminal dry matter degradability than Endurance, evident in both leaves and tubers. Notably, moderate water stress conditions yielded better nutritional quality and in vitro ruminal dry matter degradability compared to both well-watered and severe water stress treatments. This suggests that applying 180-220 mm of water per season can also yield better nutritive value of these genotypes.

Cultivating potential: Harnessing plant stem cells for agricultural crop improvement

Meristems are stem cell-containing structures that produce all plant organs and are therefore important targets for crop improvement. Developmental regulators control the balance and rate of cell divisions within the meristem. Altering these regulators impacts meristem architecture and, as a consequence, plant form. In this review, we discuss genes involved in regulating the shoot apical meristem, inflorescence meristem, axillary meristem, root apical meristem, and vascular cambium in plants. We highlight several examples showing how crop breeders have manipulated developmental regulators to modify meristem growth and alter crop traits such as inflorescence size and branching patterns. Plant transformation techniques are another innovation related to plant meristem research because they make crop genome engineering possible. We discuss recent advances on plant transformation made possible by studying genes controlling meristem development. Finally, we conclude with discussions about how meristem research can contribute to crop improvement in the coming decades.

The Gma-miR394a/GmFBX176 module is involved in regulating the soybean (Glycine max L.) response to drought stress

Drought seriously affects the yield and quality of soybean. Previous studies have shown that the gma-miR394a/GmFBX176 module regulates the response of Arabidopsis to drought stress. However, whether the gma-miR394a/GmFBX176 module is involved in the regulation of the soybean drought stress response remains unclear. Here, the function of the gma-miR394a/GmFBX176 module in the soybean drought stress response was evaluated. In soybean hairy roots, drought stress induced the transcription of gma-miR394a and inhibited the transcription of GmFBX176. GUS histochemical staining showed that transgenic GmFBX176p:GUS soybean hairy root staining was weak and that GUS transcript levels decreased under drought stress. A transient expression experiment in tobacco showed that gma-miR394a inhibited GmFBX176 transcription. Under drought stress, composite soybean plants overexpressing gma-miR394a showed increased drought resistance compared with control K599 composite soybean plants (K599); their survival rate and peroxidase activity were higher than those of K599, and their malondialdehyde content was lower. In contrast, composite soybean plants overexpressing GmFBX176m3 (gma-miR394a complement site mutation) presented lower drought resistance than K599 plants. Transcriptomic sequencing showed that the gma-miR394a/GmFBX176 module affected the transcript levels of stress response genes and transcription factors. These results indicate that the gma-miR394a/GmFBX176 module can be used to improve the drought resistance of soybean.

Identification of loci associated with water use efficiency and symbiotic nitrogen fixation in soybean

Soybean (Glycine max) production is greatly affected by persistent and/or intermittent droughts in rainfed soybean-growing regions worldwide. Symbiotic N2 fixation (SNF) in soybean can also be significantly hampered even under moderate drought stress. The objective of this study was to identify genomic regions associated with shoot carbon isotope ratio (δ13C) as a surrogate measure for water use efficiency (WUE), nitrogen isotope ratio (δ15N) to assess relative SNF, N concentration ([N]), and carbon/nitrogen ratio (C/N). Genome-wide association mapping was performed with 105 genotypes and approximately 4 million single-nucleotide polymorphism markers derived from whole-genome resequencing information. A total of 11, 21, 22, and 22 genomic loci associated with δ13C, δ15N, [N], and C/N, respectively, were identified in two environments. Nine of these 76 loci were stable across environments, as they were detected in both environments. In addition to the 62 novel loci identified, 14 loci aligned with previously reported quantitative trait loci for different C and N traits related to drought, WUE, and N2 fixation in soybean. A total of 58 Glyma gene models encoding for different genes related to the four traits were identified in the vicinity of the genomic loci.

Evaluation of efficacy of non-coding RNA in abiotic stress management of field crops: Current status and future prospective

Abiotic stresses are responsible for the major losses in crop yield all over the world. Stresses generate harmful ROS which can impair cellular processes in plants. Therefore, plants have evolved antioxidant systems in defence against the stress-induced damages. The frequency of occurrence of abiotic stressors has increased several-fold due to the climate change experienced in recent times and projected for the future. This had particularly aggravated the risk of yield losses and threatened global food security. Non-coding RNAs are the part of eukaryotic genome that does not code for any proteins. However, they have been recently found to have a crucial role in the responses of plants to both abiotic and biotic stresses. There are different types of ncRNAs, for example, miRNAs and lncRNAs, which have the potential to regulate the expression of stress-related genes at the levels of transcription, post-transcription, and translation of proteins. The lncRNAs are also able to impart their epigenetic effects on the target genes through the alteration of the status of histone modification and organization of the chromatins. The current review attempts to deliver a comprehensive account of the role of ncRNAs in the regulation of plants' abiotic stress responses through ROS homeostasis. The potential applications ncRNAs in amelioration of abiotic stresses in field crops also have been evaluated.

Haplotype-Resolution Transcriptome Analysis Reveals Important Responsive Gene Modules and Allele-Specific Expression Contributions under Continuous Salt and Drought in Camellia sinensis

The tea plant, Camellia sinensis (L.) O. Kuntze, is one of the most important beverage crops with significant economic and cultural value. Global climate change and population growth have led to increased salt and drought stress, negatively affecting tea yield and quality. The response mechanism of tea plants to these stresses remains poorly understood due to the lack of reference genome-based transcriptional descriptions. This study presents a high-quality genome-based transcriptome dynamic analysis of C. sinensis' response to salt and drought stress. A total of 2244 upregulated and 2164 downregulated genes were identified under salt and drought stress compared to the control sample. Most of the differentially expression genes (DEGs) were found to involve divergent regulation processes at different time points under stress. Some shared up- and downregulated DEGs related to secondary metabolic and photosynthetic processes, respectively. Weighted gene co-expression network analysis (WGCNA) revealed six co-expression modules significantly positively correlated with C. sinensis' response to salt or drought stress. The MEpurple module indicated crosstalk between the two stresses related to ubiquitination and the phenylpropanoid metabolic regulation process. We identified 1969 salt-responsive and 1887 drought-responsive allele-specific expression (ASE) genes in C. sinensis. Further comparison between these ASE genes and tea plant heterosis-related genes suggests that heterosis likely contributes to the adversity and stress resistance of C. sinensis. This work offers new insight into the underlying mechanisms of C. sinensis' response to salt and drought stress and supports the improved breeding of tea plants with enhanced salt and drought tolerance.

Cultivation model and deficit irrigation strategy for reducing leakage of bundle sheath cells to CO2, improve 13C carbon isotope, photosynthesis and soybean yield in semi-arid areas

A better understanding of the photosynthesis and soil water storage regulation of soybean production will be helpful to develop a water conservation strategy under a rain-fed farming system. Reducing the leakage of CO2 bundle sheath cells and improving the photosynthesis capacity and gas exchange characteristics of soybean leaves will contribute to increase yield under the dryland agricultural system and provide a scientific basis. Therefore, during 2019 and 2020, soybean exposed to different cultivation modes to analyze the response curves of photosynthesis and CO2 under different deficit irrigation strategies. In this study, we used two cultivation models: RB: ridge covered with biodegradable film and furrow area not covered; CF: conventional flat land planting under four deficit irrigation modes (R: rainwater irrigation; IB: branch stage irrigation (220 mm); IP: Irrigation during podding (220 mm); IBP: branch stage irrigation (110 mm), podding stage irrigation (110 mm). Compared with CF-IBP treatment, RB-IBP had significant effects on rainwater collection, SWS, and soybean yield. Photo-response curve analysis showed that RB-IBP treatment a significant increase in Pn, Gs, Ci, Tr, leaf WUE, and chlorophyll ab content. Under different irrigation strategies, maximum net photosynthetic rate (Pnmax), light saturation point (LSP), and apparent quantum efficiency under RB-IBP treatment (α), Pn under respiration rate and CO2 response curve were significantly higher than that under CF cultivation mode. Compared with RB culture mode under different irrigation strategies, CF cultivation mode significantly increases Δ13C and CO2 sheath cell leakage (Փ); it also led to a significant decline in the ratio of Ci/Ca concentration. This study shows that RB-IBP treatment is the best water-saving strategy because it means reducing the leakage of CO2 from the bundle sheath, thus significantly increasing soil water storage, photosynthetic capacity, and soybean yield.

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.

Comparative metabolomics of root-tips reveals distinct metabolic pathways conferring drought tolerance in contrasting genotypes of rice

Background

The mechanisms underlying rice root responses to drought during the early developmental stages are yet unknown.

Results

This study aimed to determine metabolic differences in IR64, a shallow-rooting, drought-susceptible genotype, and Azucena, a drought-tolerant and deep-rooting genotype under drought stress. The morphological evaluation revealed that Azucena might evade water stress by increasing the lateral root system growth, the root surface area, and length to access water. At the same time, IR64 may rely mainly on cell wall thickening to tolerate stress. Furthermore, significant differences were observed in 49 metabolites in IR64 and 80 metabolites in Azucena, for which most metabolites were implicated in secondary metabolism, amino acid metabolism, nucleotide acid metabolism and sugar and sugar alcohol metabolism. Among these metabolites, a significant positive correlation was found between allantoin, galactaric acid, gluconic acid, glucose, and drought tolerance. These metabolites may serve as markers of drought tolerance in genotype screening programs. Based on corresponding biological pathways analysis of the differentially abundant metabolites (DAMs), biosynthesis of alkaloid-derivatives of the shikimate pathway, fatty acid biosynthesis, purine metabolism, TCA cycle and amino acid biosynthesis were the most statistically enriched biological pathway in Azucena in drought response. However, in IR64, the differentially abundant metabolites of starch and sucrose metabolism were the most statistically enriched biological pathways.

Conclusion

Metabolic marker candidates for drought tolerance were identified in both genotypes. Thus, these markers that were experimentally determined in distinct metabolic pathways can be used for the development or selection of drought-tolerant rice genotypes.

Machine Learning in the Classification of Soybean Genotypes for Primary Macronutrients’ Content Using UAV–Multispectral Sensor

Using spectral data to quantify nitrogen (N), phosphorus (P), and potassium (K) contents in soybean plants can help breeding programs develop fertilizer-efficient genotypes. Employing machine learning (ML) techniques to classify these genotypes according to their nutritional content makes the analyses performed in the programs even faster and more reliable. Thus, the objective of this study was to find the best ML algorithm(s) and input configurations in the classification of soybean genotypes for higher N, P, and K leaf contents. A total of 103 F2 soybean populations were evaluated in a randomized block design with two repetitions. At 60 days after emergence (DAE), spectral images were collected using a Sensefly eBee RTK fixed-wing remotely piloted aircraft (RPA) with autonomous take-off, flight plan, and landing control. The eBee was equipped with the Parrot Sequoia multispectral sensor. Reflectance values were obtained in the following spectral bands (SBs): red (660 nm), green (550 nm), NIR (735 nm), and red-edge (790 nm), which were used to calculate the vegetation index (VIs): normalized difference vegetation index (NDVI), normalized difference red edge (NDRE), green normalized difference vegetation index (GNDVI), soil-adjusted vegetation index (SAVI), modified soil-adjusted vegetation index (MSAVI), modified chlorophyll absorption in reflectance index (MCARI), enhanced vegetation index (EVI), and simplified canopy chlorophyll content index (SCCCI). At the same time of the flight, leaves were collected in each experimental unit to obtain the leaf contents of N, P, and K. The data were submitted to a Pearson correlation analysis. Subsequently, a principal component analysis was performed together with the k-means algorithm to define two clusters: one whose genotypes have high leaf contents and another whose genotypes have low leaf contents. Boxplots were generated for each cluster according to the content of each nutrient within the groups formed, seeking to identify which set of genotypes has higher nutrient contents. Afterward, the data were submitted to machine learning analysis using the following algorithms: decision tree algorithms J48 and REPTree, random forest (RF), artificial neural network (ANN), support vector machine (SVM), and logistic regression (LR, used as control). The clusters were used as output variables of the classification models used. The spectral data were used as input variables for the models, and three different configurations were tested: using SB only, using VIs only, and using SBs+VIs. The J48 and SVM algorithms had the best performance in classifying soybean genotypes. The best input configuration for the algorithms was using the spectral bands as input.

Functional characterization of wild soybean (Glycine soja) GsSnRK1.1 protein kinase in plant resistance to abiotic stresses

Protein kinases play crucial roles in the regulation of plant resistance to various stresses. In this work, we determined that GsSnRK1.1 was actively responsive to saline-alkali, drought, and abscisic acid (ABA) stresses by histochemical staining and qRT-PCR analyses. The wild-type GsSnRK1.1 but not the kinase-dead mutant, GsSnRK1.1(K49M), demonstrated in vitro kinase activity by phosphorylating GsABF2. Intriguingly, we found that GsSnRK1.1 could complement the loss of SNF1 kinase in yeast Msy1193 (-snf1) mutant, rescue growth defects of yeast cells on medium with glycerol as a carbon resource, and promote yeast resistance to NaCl or NaHCO₃. To further elucidate GsSnRK1.1 function in planta, we knocked out SnRK1.1 gene from the Arabidopsis genome by the CRISPR/Cas9 approach, and then expressed GsSnRK1.1 and a series of mutants into snrk1.1-null lines. The transgenic Arabidopsis lines were subjected to various abiotic stress treatments. The results showed that GsSnRK1.1(T176E) mutant with enhanced protein kinase activity significantly promoted, but GsSnRK1.1(K49M) and GsSnRK1.1(T176A) mutants with disrupted protein kinase activity abrogated, plant stomatal closure and tolerance to abiotic stresses. In conclusion, this study provides the molecular clues to fully understand the physiological functions of plant SnRK1 protein kinases.

Melatonin in Micro-Tom Tomato: Improved Drought Tolerance via the Regulation of the Photosynthetic Apparatus, Membrane Stability, Osmoprotectants, and Root System

Environmental variations caused by global climate change significantly affect plant yield and productivity. Because water scarcity is one of the most significant risks to agriculture's future, improving the performance of plants to cope with water stress is critical. Our research scrutinized the impact of melatonin application on the photosynthetic machinery, photosynthetic physiology, root system, osmoprotectant accumulation, and oxidative stress in tomato plants during drought. The results showed that melatonin-treated tomato plants had remarkably higher water levels, gas exchange activities, root system morphological parameters (average diameter, root activity, root forks, projected area, root crossings, root volume, root surface area, root length, root tips, and root numbers), osmoprotectant (proline, trehalose, fructose, sucrose, and GB) accumulation, and transcript levels of the photosynthetic genes SlPsb28, SlPetF, SlPsbP, SlPsbQ, SlPetE, and SlPsbW. In addition, melatonin effectively maintained the plants' photosynthetic physiology. Moreover, melatonin treatment maintained the soluble protein content and antioxidant capacity during drought. Melatonin application also resulted in membrane stability, evidenced by less electrolyte leakage and lower H₂O₂, MDA, and O₂^- levels in the drought-stress environment. Additionally, melatonin application enhanced the antioxidant defense enzymes and antioxidant-stress-resistance-related gene (SlCAT1, SlAPX, SlGR, SlDHAR, SlPOD, and SOD) transcript levels in plants. These outcomes imply that the impacts of melatonin treatment on improving drought resistance could be ascribed to the mitigation of photosynthetic function inhibition, the enhancement of the water status, and the alleviation of oxidative stress in tomato plants. Our study findings reveal new and incredible aspects of the response of melatonin-treated tomato plants to drought stress and provide a list of candidate targets for increasing plant tolerance to the drought-stress environment.

The Plastidial DIG5 Protein Affects Lateral Root Development by Regulating Flavonoid Biosynthesis and Auxin Transport in Arabidopsis

To reveal the mechanisms underlying root adaptation to drought stress, we isolated and characterized an Arabidopsis mutant, dig5 (drought inhibition of lateral root growth 5), which exhibited increased sensitivity to the phytohormone abscisic acid (ABA) for the inhibition of lateral root growth. The dig5 mutant also had fewer lateral roots under normal conditions and the aerial parts were yellowish with a lower level of chlorophylls. The mutant seedlings also displayed phenotypes indicative of impaired auxin transport, such as abnormal root curling, leaf venation defects, absence of apical hook formation, and reduced hypocotyl elongation in darkness. Auxin transport assays with [3H]-labeled indole acetic acid (IAA) confirmed that dig5 roots were impaired in polar auxin transport. Map-based cloning and complementation assays indicated that the DIG5 locus encodes a chloroplast-localized tRNA adenosine deaminase arginine (TADA) that is involved in chloroplast protein translation. The levels of flavonoids, which are naturally occurring auxin transport inhibitors in plants, were significantly higher in dig5 roots than in the wild type roots. Further investigation showed that flavonoid biosynthetic genes were upregulated in dig5. Introduction of the flavonoid biosynthetic mutation transparent testa 4 (tt4) into dig5 restored the lateral root growth of dig5. Our study uncovers an important role of DIG5/TADA in retrogradely controlling flavonoid biosynthesis and lateral root development. We suggest that the DIG5-related signaling pathways, triggered likely by drought-induced chlorophyll breakdown and leaf senescence, may potentially help the plants to adapt to drought stress through optimizing the root system architecture.

Root traits in Crambe abyssinica Hochst and Raphanus sativus L. plants are associated with differential tolerance to water deficit and post-stress recovery

Background

Previous studies have shown that Crambe abyssinica and Raphanus sativus are physiologically tolerant to water deficits; however, there is a lack of information on the mechanisms responsible for their tolerance regarding root morphological characteristics. This study aimed to characterize morphological changes in the root system of C. abyssinica and R. sativus subjected water deficit, as well as to identify the responses that improve tolerance and post-stress recovery capacity of these plants.

Methods

Independent experiments for each specieswere performed in a controlled greenhouse, where plants were randomly set in a randomized block design with five replicates. Plants of C. abyssinica and R. sativus were cultivated in pots and exposed to well-watered treatment (WW; 90% water holding capacity–WHC of the substrate) or water deficit (WD; 40% WHC) conditions, at 28 days after planting. The plants were kept under WD for 7, 14, or 21 days with rehydration soon after each episode of water deficit. Assessment of water relations, biomass allocation, leaf and root system morphological characteristics and gas exchange were performed after each period of water deficit and 48 h after rehydration.

Results

The water deficit reduced the water status of both species, and morphological and biomass allocation were not recovered after rehydration. Photosynthesis of C. abyssinica decreased with prolonged water deficit, which was also not recovered after rehydration. In R. sativus, photosynthesis was not altered by WD for 21 days, and a higher WUE was recorded. Root morphology of R. sativus was mainly affected at 14 days of WD, while the traits related to very fine roots increased at 21 days of WD, when compared to WW plants. Thus, R. sativus has shown greater tolerance to water deficits mainly due to the presence of very fine roots throughout the period of stress, when compared to C. abyssinica in which the fine roots predominated.

Combined Drought and Heat Stress Influences the Root Water Relation and Determine the Dry Root Rot Disease Development Under Field Conditions: A Study Using Contrasting Chickpea Genotypes

Abiotic stressors such as drought and heat predispose chickpea plants to pathogens of key importance leading to significant crop loss under field conditions. In this study, we have investigated the influence of drought and high temperature on the incidence and severity of dry root rot disease (caused by Macrophomina phaseolina) in chickpea, under extensive on- and off-season field trials and greenhouse conditions. We explored the association between drought tolerance and dry root rot resistance in two chickpea genotypes, ICC 4958 and JG 62, with contrasting resistance to dry root rot. In addition, we extensively analyzed various patho-morphological and root architecture traits altered by combined stresses under field and greenhouse conditions in these genotypes. We further observed the role of edaphic factors in dry root rot incidence under field conditions. Altogether, our results suggest a strong negative correlation between the plant water relations and dry root rot severity in chickpeas, indicating an association between drought tolerance and dry root rot resistance. Additionally, the significant role of heat stress in altering the dynamics of dry root rot and the importance of combinatorial screening of chickpea germplasm for dry root rot resistance, drought, and heat stress have been revealed.

Shaping the root system architecture in plants for adaptation to drought stress

Root system architecture plays an important role in plant adaptation to drought stress. The root system architecture (RSA) consists of several structural features, which includes number and length of main and lateral roots along with the density and length of root hairs. These features exhibit plasticity under water-limited environments and could be critical to developing crops with efficient root systems for adaptation under drought. Recent advances in the omics approaches have significantly improved our understanding of the regulatory mechanisms of RSA remodeling under drought and the identification of genes and other regulatory elements. Plant response to drought stress at physiological, morphological, biochemical, and molecular levels in root cells is regulated by various phytohormones and their crosstalk. Stress-induced reactive oxygen species play a significant role in regulating root growth and development under drought stress. Several transcription factors responsible for the regulation of RSA under drought have proven to be beneficial for developing drought tolerant crops. Molecular breeding programs for developing drought-tolerant crops have been greatly benefitted by the availability of quantitative trait loci (QTLs) associated with the RSA regulation. In the present review, we have discussed the role of various QTLs, signaling components, transcription factors, microRNAs and crosstalk among various phytohormones in shaping RSA and present future research directions to better understand various factors involved in RSA remodeling for adaptation to drought stress. We believe that the information provided herein may be helpful in devising strategies to develop crops with better RSA for efficient uptake and utilization of water and nutrients under drought conditions.

Unravelling the treasure trove of drought-responsive genes in wild-type peanut through transcriptomics and physiological analyses of root

Peanut is one of the most valuable legumes, grown mainly in arid and semi-arid regions, where its production may be hindered by the lack of water. Therefore, breeding drought tolerant varieties is of great importance for peanut breeding programs around the world. Unlike cultivated peanuts, wild peanuts have greater genetic diversity and are an important source of alleles conferring tolerance/resistance to abiotic and biotic stresses. To decipher the transcriptome changes under drought stress, transcriptomics of roots of highly tolerant Arachis duranensis (ADU) and moderately susceptible A. stenosperma (AST) genotypes were performed. Transcriptome analysis revealed an aggregate of 1465 differentially expressed genes (DEGs), and among the identified DEGs, there were 366 single nucleotide polymorphisms (SNPs). Gene ontology and Mapman analyses revealed that the ADU genotype had a higher number of transcripts related to DNA methylation or demethylation, phytohormone signal transduction and flavonoid production, transcription factors, and responses to ethylene. The transcriptome analysis was endorsed by qRT-PCR, which showed a strong correlation value (R² = 0.96). Physio-biochemical analysis showed that the drought-tolerant plants produced more osmolytes, ROS phagocytes, and sugars, but less MDA, thus attenuating the effects of drought stress. In addition, three SNPs of the gene encoding transcription factor NFAY (Aradu.YE2F8), expansin alpha (Aradu.78HGD), and cytokinin dehydrogenase 1-like (Aradu.U999X) exhibited polymorphism in selected different genotypes. Such SNPs could be useful for the selection of drought-tolerant genotypes.

Characterization of Root System Architecture Traits in Diverse Soybean Genotypes Using a Semi-Hydroponic System

Phenotypic variation and correlations among root traits form the basis for selecting and breeding soybean varieties with efficient access to water and nutrients and better adaptation to abiotic stresses. Therefore, it is important to develop a simple and consistent system to study root traits in soybean. In this study, we adopted the semi-hydroponic system to investigate the variability in root morphological traits of 171 soybean genotypes popularized in the Yangtze and Huaihe River regions, eastern China. Highly diverse phenotypes were observed: shoot height (18.7-86.7 cm per plant with a median of 52.3 cm); total root length (208-1663 cm per plant with a median of 885 cm); and root mass (dry weight) (19.4-251 mg per plant with a median of 124 mg). Both total root length and root mass exhibited significant positive correlation with shoot mass (p ≤ 0.05), indicating their relationship with plant growth and adaptation strategies. The nine selected traits contributed to one of the two principal components (eigenvalues > 1), accounting for 78.9% of the total genotypic variation. Agglomerative hierarchical clustering analysis separated the 171 genotypes into five major groups based on these root traits. Three selected genotypes with contrasting root systems were validated in soil-filled rhizoboxes (1.5 m deep) until maturity. Consistent ranking of the genotypes in some important root traits at various growth stages between the two experiments indicates the reliability of the semi-hydroponic system in phenotyping root trait variability at the early growth stage in soybean germplasms.

Integrated transcriptome and small RNA sequencing analyses reveal a drought stress response network in Sophora tonkinensis

BACKGROUND

Sophora tonkinensis Gagnep is a traditional Chinese medical plant that is mainly cultivated in southern China. Drought stress is one of the major abiotic stresses that negatively impacts S. tonkinensis growth. However, the molecular mechanisms governing the responses to drought stress in S. tonkinensis at the transcriptional and posttranscriptional levels are not well understood.

RESULTS

To identify genes and miRNAs involved in drought stress responses in S. tonkinensis, both mRNA and small RNA sequencing was performed in root samples under control, mild drought, and severe drought conditions. mRNA sequencing revealed 66,476 unigenes, and the differentially expressed unigenes (DEGs) were associated with several key pathways, including phenylpropanoid biosynthesis, sugar metabolism, and quinolizidine alkaloid biosynthesis pathways. A total of 10 and 30 transcription factors (TFs) were identified among the DEGs under mild and severe drought stress, respectively. Moreover, small RNA sequencing revealed a total of 368 miRNAs, including 255 known miRNAs and 113 novel miRNAs. The differentially expressed miRNAs and their target genes were involved in the regulation of plant hormone signal transduction, the spliceosome, and ribosomes. Analysis of the regulatory network involved in the response to drought stress revealed 37 differentially expressed miRNA-mRNA pairs.

CONCLUSION

This is the first study to simultaneously profile the expression patterns of mRNAs and miRNAs on a genome-wide scale to elucidate the molecular mechanisms of the drought stress responses of S. tonkinensis. Our results suggest that S. tonkinensis implements diverse mechanisms to modulate its responses to drought stress.