Transcription factors as key molecular target to strengthen the drought stress tolerance in plants

OsBBP1, a newly identified protein containing DUF630 and DUF632 domains confers drought tolerance in rice

Domain of unknown function (DUF) protein families, which are uncharacterized and numerous within the Pfam database. Recently, studies have demonstrated that DUFs played crucial roles in plant development, but whether, or how, they function in drought resistance remain unclear. In this study, we identified the Os03g0321500 gene, encoding OsbZIP72 binding protein 1 (OsBBP1), as a target of OsbZIP72 using chromatin immunoprecipitation sequencing in rice. OsBBP1 is a novel member of DUFs, which localize both in the nuclei and cytoplasm of rice protoplasts. Furthermore, yeast one-hybrid and electrophoretic mobility shift assays confirmed the specific binding between OsbZIP72 and OsBBP1. Additionally, a luciferase reporter analysis illustrated that OsbZIP72 activated the expression of OsBBP1. Drought tolerance experiments demonstrate that the OsBBP1 CRISPER-CAS9 transgenic mutants were sensitive to drought stress, but the transgenic OsBBP1 over-expressing rice plants showed enhanced drought resistance. Moreover, drought tolerance experiments in a paddy field suggested that OsBBP1 contributed to less yield or yield-related losses under drought conditions. Mechanistically, OsBBP1 might confer drought resistance by inducing more efficient reactive oxygen species (ROS) scavenging. Several ROS scavenging-related genes showed increased expression levels in OsBBP1 overexpression lines and decreased expression levels in OsBBP1 CRISPER-CAS9 mutants under drought conditions. Thus, OsBBP1, acting downstream of OsbZIP72, contributes to drought resistance and causes less yield or yield-related losses under drought conditions.

A simplified and improved protocol of rice transformation to cater wide range of rice cultivars

The latest CRISPR-Cas9-mediated genome editing technology is expected to bring about revolution in rice yield and quality improvement, and thus validation of rice transformation protocols using CRISPR-Cas9-gRNA constructs is the need of the hour. Moreover, regeneration of more number of transgenic rice plants is prerequisite for developing genome-edited rice lines, as recalcitrant rice varieties were shown to have lower editing efficiencies which necessities screening of large number of transgenic plants to find the suitable edits. In the present study, we have simplified the Agrobacterium-mediated rice transformation protocol for both Indica and Japonica rice cultivars using CRISPR/Cas9 empty vector construct, and the protocols have been suitably optimized for getting large numbers of the regenerated plantlets within the shortest possible time. The Japonica transgenic lines were obtained within 65 days and for the Indica cultivars, it took about 76-78 days. We also obtained about 90% regeneration efficiency for both Japonica and Indica cultivars. The transformation efficiency was about 97% in the case of Japonica and 69-83% in the case of Indica rice cultivars. Furthermore, we screened the OsWRKY24 gene editing efficiency by transforming rice cultivars with CRISPR/Cas9 construct harbouring sgRNA against OsWRKY24 gene and found about 90% editing efficiency in Japonica rice cultivars, while 30% of the transformed Indica cultivars were found to be edited. This implicated the presence of a robust repair mechanism in the Indica rice cultivars.

Seed priming with potassium nitrate alleviates the high temperature stress by modulating growth and antioxidant potential in carrot seeds and seedlings

Early season carrot (Daucus carota) production is being practiced in Punjab, Pakistan to meet the market demand but high temperature hampers the seed germination and seedling establishment which cause marked yield reduction. Seed priming with potassium nitrate breaks the seed dormancy and improves the seed germination and seedling growth potential but effects vary among the species and ecological conditions. The mechanism of KNO3 priming in high temperature stress tolerance is poorly understood yet. Thus, present study aimed to evaluate high temperature stress tolerance potential of carrot seeds primed with potassium nitrate and impacts on growth, physiological, and antioxidant defense systems. Carrot seeds of a local cultivar (T-29) were primed with various concentration of KNO3 (T0: unprimed (negative control), T1: hydroprimed (positive control), T2: 50 mM, T3:100mM, T4: 150 mM, T5: 200 mM, T6: 250 mM and T7: 300 mM) for 12 h each in darkness at 20 ± 2℃. Seed priming with 50 mM of KNO3 significantly enhanced the seed germination (36%), seedling growth (28%) with maximum seedling vigor (55%) and also exhibited 16.75% more carrot root biomass under high temperature stress as compared to respective control. Moreover, enzymatic activities including peroxidase, catalase, superoxidase dismutase, total phenolic contents, total antioxidants contents and physiological responses of plants were also improved in response to seed priming under high temperature stress. By increasing the level of KNO3, seed germination, growth and root biomass were reduced. These findings suggest that seed priming with 50 mM of KNO3 can be an effective strategy to improve germination, growth and yield of carrot cultivar (T-29) under high temperature stress in early cropping. This study also proposes that KNO3 may induces the stress memory by heritable modulations in chromosomal structure and methylation and acetylation of histones that may upregulate the hormonal and antioxidant activities to enhance the stress tolerance in plants.

Apple MdZAT5 mediates root development under drought stress

Root plays an important role in plant drought tolerance, especially in horticultural crops like apples. However, the crucial regulator and molecular mechanism in root development of apple trees under drought are not well unknown. Cys2/His2-type Zinc-finger proteins are essential for plant response to drought, while the members of C2H2 Zinc-finger proteins in apple are largely unknown. In this study, we identified the members of the C1-2i subclass family of C2H2 Zinc-finger proteins in apple (Malus × domestica). Among them, MdZAT5 is significantly induced in apple roots under drought conditions and positively regulates apple root development under drought. Further investigation revealed that MdZAT5 positively regulates root development and root hydraulic conductivity by mediating the transcription level of MdMYB88 under drought stress. Taken together, our results demonstrate the importance of MdZAT5 in root development under drought in apple trees. This finding provides a new candidate direction for apple breeding for drought resistance.

Unraveling the genetic and molecular basis of heat stress in cotton

Human activities and climate change have resulted in frequent and intense weather fluctuations, leading to diverse abiotic stresses on crops which hampers greatly their metabolic activities. Heat stress, a prevalent abiotic factor, significantly influences cotton plant biological activities resulting in reducing yield and production. We must deepen our understanding of how plants respond to heat stress across various dimensions, encompassing genes, RNAs, proteins, metabolites for effective cotton breeding. Multi-omics methods, primarily genomics, transcriptomics, proteomics, metabolomics, and phenomics, proves instrumental in studying cotton's responses to abiotic stresses. Integrating genomics, transcriptomics, proteomics, and metabolomic is imperative for our better understanding regarding genetics and molecular basis of heat tolerance in cotton. The current review explores fundamental omics techniques, covering genomics, transcriptomics, proteomics, and metabolomics, to highlight the progress made in cotton omics research.

Unlocking nature's secrets: The pivotal role of WRKY transcription factors in plant flowering and fruit development

The WRKY transcription factor family is a key player in the regulatory mechanisms of flowering plants, significantly influencing both their biotic and abiotic response systems as well as being vital to numerous physiological and biological functions. Over the past two decades, the functionality of WRKY proteins has been the subject of extensive research in over 50 plant species, with a strong focus on their roles in responding to various stresses. Despite this extensive research, there remains a notable gap in comprehensive studies aimed at understanding how specific WRKY genes directly influence the timing of flowering and fruit development. This review offers an up-to-date look at WRKY family genes and provides insights into the key genes of WRKY to control flowering, enhance fruit ripening and secondary metabolism synthesis, and maintain fruit quality of various plants, including annuals, perennials, medicinal, and crop plants. The WRKY transcription factors serve as critical regulators within the transcriptional regulatory network, playing a crucial role in the precise enhancement of flowering processes. It is also involved in the up-regulation of fruit ripening was strongly demonstrated by combined transcriptomics and metabolomic investigation. Therefore, we speculated that the WRKY family is known to be a key regulator of flowering and fruiting in plants. This detailed insight will enable the identification of the series of molecular occurrences featuring WRKY proteins throughout the stages of flowering and fruiting.

Regulatory mechanisms used by ZmMYB39 to enhance drought tolerance in maize (Zea mays) seedlings

Drought is a significant abiotic stressor that limits maize (Zea mays L.) growth and development. Thus, enhancing drought tolerance is critical for promoting maize production. Our findings demonstrated that ZmMYB39 is an MYB transcription factor with transcriptional activation activity. Drought stress experiments involving ZmMYB39 overexpression and knockout lines indicated that ZmMYB39 positively regulated drought stress tolerance in maize. DAP-Seq, EMSA, dual-LUC, and RT-qPCR provided initial insights into the molecular regulatory mechanisms by which ZmMYB39 enhances drought tolerance in maize. ZmMYB39 directly promoted the expression of ZmP5CS1, ZmPOX1, ZmSOD2, ZmRD22, ZmNAC49, and ZmDREB2A, which are involved in stress resistance. ZmMYB39 enhanced drought tolerance by interacting with and promoting the expression of ZmFNR1, ZmHSP20, and ZmDOF6. Our study offers a theoretical basis for understanding the molecular regulatory networks involved in maize drought stress response. Furthermore, ZmMYB39 serves as a valuable genetic resource for breeding drought-resistant maize.

Characteristics of NAC transcription factors in Solanaceae crops and their roles in responding to abiotic and biotic stresses

As one of the largest transcription factor (TF) families in plants, the NAC (NAM, ATAF1/2, and CUC2) family plays important roles in response pathways to various abiotic and biotic stresses, such as drought, high salinity, low temperature, and pathogen infection. Although, there are a number of reviews on the involvement of NAC TF in plant responses to biotic and abiotic stresses, most of them are focused on the model plants Arabidopsis thaliana and Oryza sativa, and there is a lack of systematic evaluation of specific species. Solanaceae, the world's third most significant cash crop, has been seriously affected by environmental disturbances in recent years in terms of yield and quality, posing a severe threat to global food security. This review focuses on the functional roles of NAC transcription factors in response to external stresses involved in five important Solanaceae crops: tomato, potato, pepper, eggplant and tobacco, and analyzes the affinities between them. It will provide resources for stress-resistant breeding of Solanaceae crops using transgenic technology.

Comprehensive identification of maize ZmE2F transcription factors and the positive role of ZmE2F6 in response to drought stress

BACKGROUND

The early 2 factor (E2F) family is characterized as a kind of transcription factor that plays an important role in cell division, DNA damage repair, and cell size regulation. However, its stress response has not been well revealed.

RESULTS

In this study, ZmE2F members were comprehensively identified in the maize genome, and 21 ZmE2F genes were identified, including eight E2F subclade members, seven DEL subfamily genes, and six DP genes. All ZmE2F proteins possessed the DNA-binding domain (DBD) characterized by conserved motif 1 with the RRIYD sequence. The ZmE2F genes were unevenly distributed on eight maize chromosomes, showed diversity in gene structure, expanded by gene duplication, and contained abundant stress-responsive elements in their promoter regions. Subsequently, the ZmE2F6 gene was cloned and functionally verified in drought response. The results showed that the ZmE2F6 protein interacted with ZmPP2C26, localized in the nucleus, and responded to drought treatment. The overexpression of ZmE2F6 enhanced drought tolerance in transgenic Arabidopsis with longer root length, higher survival rate, and biomass by upregulating stress-related gene transcription.

CONCLUSIONS

This study provides novel insights into a greater understanding and functional study of the E2F family in the stress response.

Transcriptional repression of GTL1 under water-deficit stress promotes anthocyanin biosynthesis to enhance drought tolerance

The transcription factor GT2-LIKE 1 (GTL1) has been implicated in orchestrating a transcriptional network of diverse physiological, biochemical, and developmental processes. In response to water-limiting conditions, GTL1 is a negative regulator of stomatal development, but its potential rolein other water-deficit responses is unknown. We hypothesized that GTL1 regulates transcriptome changes associated with drought tolerance over leaf developmental stages. To test the hypothesis, gene expression was profiled by RNA-seq analysis in emerging and expanding leaves of wild-type and a drought-tolerant gtl1-4 knockout mutant under well-watered and water-deficit conditions. Our comparative analysis of genotype-treatment combinations within leaf developmental age identified 459 and 1073 differentially expressed genes in emerging and expanding leaves, respectively, as water-deficit responsive GTL1-regulated genes. Transcriptional profiling identified a potential role of GTL1 in two important pathways previously linked to drought tolerance: flavonoid and polyamine biosynthesis. In expanding leaves, negative regulation of GTL1 under water-deficit conditions promotes biosynthesis of flavonoids and anthocyanins that may contribute to drought tolerance. Quantification of polyamines did not support a role for GTL1 in these drought-responsive pathways, but this is likely due to the complex nature of polyamine synthesis and turnover. Our global transcriptome analysis suggests that transcriptional repression of GTL1 by water deficit allows plants to activate diverse pathways that collectively contribute to drought tolerance.

Plant secondary metabolism in a fluctuating world: climate change perspectives

Climate changes have unpredictable effects on ecosystems and agriculture. Plants adapt metabolically to overcome these challenges, with plant secondary metabolites (PSMs) being crucial for plant-environment interactions. Thus, understanding how PSMs respond to climate change is vital for future cultivation and breeding strategies. Here, we review PSM responses to climate changes such as elevated carbon dioxide, ozone, nitrogen deposition, heat and drought, as well as a combinations of different factors. These responses are complex, depending on stress dosage and duration, and metabolite classes. We finally identify mechanisms by which climate change affects PSM production ecologically and molecularly. While these observations provide insights into PSM responses to climate changes and the underlying regulatory mechanisms, considerable further research is required for a comprehensive understanding.

The miR166 targets CsHDZ3 genes to negatively regulate drought tolerance in tea plant (Camellia sinensis)

Drought is the stressor with a significant adverse impact on the yield stability of tea plants. HD-ZIP III transcription factors (TFs) play important regulatory roles in plant growth, development, and stress responses. However, whether and how HD-ZIP III TFs are involved in drought response and tolerance in tea plants remains unclear. Here, we identified seven HD-ZIP III genes (CsHDZ3-1 to CsHDZ3-7) in tea plant genome. The evolutionary analysis demonstrated that CsHDZ3 members were subjected to purify selection. Subcellular localization analysis revealed that all seven CsHDZ3s located in the nucleus. Yeast self-activation and dual-luciferase reporter assays demonstrated that CsHDZ3-1 to CsHDZ3-4 have trans-activation ability whereas CsHDZ3-5 to CsHDZ3-7 served as transcriptional inhibitors. The qRT-PCR assay showed that all seven CsHDZ3 genes could respond to simulated natural drought stress and polyethylene glycol treatment. Further assays verified that all CsHDZ3 genes can be cleaved by csn-miR166. Overexpression of csn-miR166 inhibited the expression of seven CsHDZ3 genes and weakened drought tolerance of tea leaves. In contrast, suppression of csn-miR166 promoted the expression of seven CsHDZ3 genes and enhanced drought tolerance of tea leaves. These findings established the foundation for further understanding the mechanism of CsHDZ3-miR166 modules' participation in drought responses and tolerance.

Integrative physiological, metabolomic, and transcriptomic analysis reveals the drought responses of two apple rootstock cultivars

BACKGROUND

Drought is considered the main environmental factor restricting apple production and thus the development of the apple industry. Rootstocks play an important role in enhancing the drought tolerance of apple plants. Studies of the physiology have demonstrated that 'ZC9-3' is a strong drought-resistant rootstock, whereas 'Jizhen-2' is a weak drought-resistant rootstock. However, the metabolites in these two apple rootstock varieties that respond to drought stress have not yet been characterized, and the molecular mechanisms underlying their responses to drought stress remain unclear.

RESULTS

In this study, the physiological and molecular mechanisms underlying differences in the drought resistance of 'Jizhen-2' (drought-sensitive) and 'ZC9-3' (drought-resistant) apple rootstocks were explored. Under drought stress, the relative water content of the leaves was maintained at higher levels in 'ZC9-3' than in 'Jizhen-2', and the photosynthetic, antioxidant, and osmoregulatory capacities of 'ZC9-3' were stronger than those of 'Jizhen-2'. Metabolome analysis revealed a total of 95 and 156 differentially accumulated metabolites in 'Jizhen-2' and 'ZC9-3' under drought stress, respectively. The up-regulated metabolites in the two cultivars were mainly amino acids and derivatives. Transcriptome analysis revealed that there were more differentially expressed genes and transcription factors in 'ZC9-3' than in 'Jizhen-2' throughout the drought treatment. Metabolomic and transcriptomic analysis revealed that amino acid biosynthesis pathways play key roles in mediating drought resistance in apple rootstocks. A total of 13 metabolites, including L-α-aminoadipate, L-homoserine, L-threonine, L-isoleucine, L-valine, L-leucine, (2S)-2-isopropylmalate, anthranilate, L-tryptophan, L-phenylalanine, L-tyrosine, L-glutamate, and L-proline, play an important role in the difference in drought resistance between 'ZC9-3' and 'Jizhen-2'. In addition, 13 genes encoding O-acetylserine-(thiol)-lyase, S-adenosylmethionine synthetase, ketol-acid isomeroreductase, dihydroxyacid dehydratase, isopropylmalate isomerase, branched-chain aminotransferase, pyruvate kinase, 3-dehydroquinate dehydratase/shikimate 5-dehydrogenase, N-acetylglutamate-5-P-reductase, and pyrroline-5-carboxylate synthetase positively regulate the response of 'ZC9-3' to drought stress.

CONCLUSIONS

This study enhances our understanding of the response of apple rootstocks to drought stress at the physiological, metabolic, and transcriptional levels and provides key insights that will aid the cultivation of drought-resistant apple rootstock cultivars. Especially, it identifies key metabolites and genes underlying the drought resistance of apple rootstocks.

Advanced Biotechnological Interventions in Mitigating Drought Stress in Plants

This comprehensive article critically analyzes the advanced biotechnological strategies to mitigate plant drought stress. It encompasses an in-depth exploration of the latest developments in plant genomics, proteomics, and metabolomics, shedding light on the complex molecular mechanisms that plants employ to combat drought stress. The study also emphasizes the significant advancements in genetic engineering techniques, particularly CRISPR-Cas9 genome editing, which have revolutionized the creation of drought-resistant crop varieties. Furthermore, the article explores microbial biotechnology's pivotal role, such as plant growth-promoting rhizobacteria (PGPR) and mycorrhizae, in enhancing plant resilience against drought conditions. The integration of these cutting-edge biotechnological interventions with traditional breeding methods is presented as a holistic approach for fortifying crops against drought stress. This integration addresses immediate agricultural needs and contributes significantly to sustainable agriculture, ensuring food security in the face of escalating climate change challenges.

GhWRKY4 binds to the histone deacetylase GhHDA8 promoter to regulate drought and salt tolerance in Gossypium hirsutum

Soil drought and salinization, caused by water deficiency, have become the greatest concerns limiting crop production. Up to now, the WRKY transcription factor and histone deacetylase have been shown to be involved in drought and salt responses. However, the molecular mechanism underlying their interaction remains unclear in cotton. Herein, we identified GhWRKY4, a member of WRKY gene family, which is induced by drought and salt stress and is located in the nucleus. The ectopic expression of GhWRKY4 in Arabidopsis enhanced drought and salt tolerance, and suppressing GhWRKY4 in cotton increased susceptibility to drought and salinity. Subsequently, DAP-seq analysis revealed that the W box element in the promoter of stress-induced genes could potentially be the binding target for GhWRKY4 protein. GhWRKY4 binds to the promoters of GhHDA8 and GhNHX7 via W box element, and the expression level of GhHDA8 was increased in GhWRKY4-silenced plants. In addition, GhHDA8-overexpressed Arabidopsis were found to be hypersensitive to drought and salt stress, while silencing of GhHDA8 enhanced drought and salt tolerance in cotton. The stress-related genes, such as GhDREB2A, GhRD22, GhP5CS, and GhNHX7, were induced in GhHDA8-silenced plants. Our findings indicate that the GhWRKY4-GhHDA8 module regulates drought and salt tolerance in cotton. Collectively, the results provide new insights into the coordination of transcription factors and histone deacetylases in regulating drought and salt stress responses in plants.

Enhancing stress resilience in rice (Oryza sativa L.) through profiling early-stage morpho-physiological and molecular responses to multiple abiotic stress tolerance

Under changing climatic conditions, crop plants are more adversely affected by a combination of various abiotic stresses than by a single abiotic stress. Therefore, it is essential to identify potential donors to multiple abiotic stresses for developing climate-resilient crop varieties. Hence, the present study was undertaken with 41 germplasm accessions comprising native landraces of Tamil Nadu, Prerelease lines and cultivars were screened independently for drought, salinity, and submergence at the seedling stage during Kharif and Rabi 2022-2023. Stress was imposed separately for these three abiotic stresses on 21-day-old seedlings and was maintained for 10 days. The studied genotypes showed a significant reduction in plant biomass (PB), Relative Growth Index (RGI), relative water content (RWC), leaf photosynthesis, chlorophyll fluorescence, and Chlorophyll Concentration Index (CCI) under drought followed by salinity and submergence. Stress-tolerant indices for drought, salinity, and submergence revealed significant variation for plant biomass. Furthermore, a set of 30 SSR markers linked to drought, salinity, and submergence QTLs has been used to characterize 41 rice germplasm accessions. Our analysis suggests a significantly high polymorphism, with 28 polymorphic markers having a 93.40% in 76 loci. The mean values of polymorphic information content (PIC), heterozygosity index (HI), marker index (MI), and resolving power (RP) were 0.369, 0.433, 1.140, and 2.877, respectively. Jaccard clustering grouped all the genotypes into two major and six subclusters. According to STRUCTURE analysis, all genotypes were grouped into two major clusters, which are concurrent with a very broad genetic base (K = 2). Statistically significant marker-trait associations for biomass were observed for five polymorphic markers, viz., RM211, RM212 (drought), RM10694 (salinity), RM219, and RM21 (submergence). Similarly, significant markers for relative shoot length were observed for RM551 (drought), RM10694 (salinity), and ART5 (submergence). Notably, the genotypes Mattaikar, Varigarudan samba, Arupatham samba, and APD19002 were identified as potential donors for multiple abiotic stress tolerance. Thus, identifying the genetic potential of germplasm could be useful for enhancing stress resilience in rice.

Characterization of NAC Gene Family in Ammopiptanthus mongolicus and Functional Analysis of AmNAC24, an Osmotic and Cold-Stress-Induced NAC Gene

The NAC family of transcription factors (TFs) is recognized as a significant group within the plant kingdom, contributing crucially to managing growth and development processes in plants, as well as to their response and adaptation to various environmental stressors. Ammopiptanthus mongolicus, a temperate evergreen shrub renowned for its remarkable resilience to low temperatures and drought stress, presents an ideal subject for investigating the potential involvement of NAC TFs in stress response mechanisms. Here, the structure, evolution, and expression profiles of NAC family TFs were analyzed systematically, and a cold and osmotic stress-induced member, AmNAC24, was selected and functionally characterized. A total of 86 NAC genes were identified in A. mongolicus, and these were divided into 15 groups. Up to 48 and 8 NAC genes were generated by segmental duplication and tandem duplication, respectively, indicating that segmental duplication is a predominant mechanism in the expansion of the NAC gene family in A. mongolicus. A considerable amount of NAC genes, including AmNAC24, exhibited upregulation in response to cold and osmotic stress. This observation is in line with the detection of numerous cis-acting elements linked to abiotic stress response in the promoters of A. mongolicus NAC genes. Subcellular localization revealed the nuclear residence of the AmNAC24 protein, coupled with demonstrable transcriptional activation activity. AmNAC24 overexpression enhanced the tolerance of cold and osmotic stresses in Arabidopsis thaliana, possibly by maintaining ROS homeostasis. The present study provided essential data for understanding the biological functions of NAC TFs in plants.

TgLUT1 regulated by TgWRKY10 enhances the tolerance of Torreya grandis to drought stress

Drought stress is a major abiotic stress which severely reduces the plant growth and limits agricultural productivity. Previous studies have demonstrated that lutein directly synthesized by the carotenoid epsilon-ring hydroxylase gene (LUT1) played crucial roles in regulating drought response. Notwithstanding the myriad studies on LUT1's response to drought stress in certain plant species such as Arabidopsis, the precise function mechanisms within tree species remain ambiguously understood. Our study reveals that under drought stress, TgLUT1, a novel LUT gene instrumental in β-lutein biosynthesis, was markedly up-regulated in Torreya grandis. Subcellular localization assay indicated that TgLUT1 protein was localized to chloroplasts. Phenotypic analysis showed that overexpression of TgLUT1 enhanced the tolerance of tomato to drought stress. Overexpressing of TgLUT1 increased the values of maximal photochemical efficiency of photosystem II (Fv/Fm), net photosynthetic rate (Pn) and non-photochemical quenching (NPQ), and reduced the accumulation of hydrogen peroxide (H2O2), malondialdehyde (MDA) content and electrolyte leakage percentage in response to drought stress. Furthermore, overexpression of TgLUT1 decreased the stomatal conductance to reduce the water loss rate exposed to drought stress. In addition, yeast one-hybrid assay, dual luciferase assay system and qRT-PCR results showed that TgWRKY10 down-regulated by drought stress inhibited the expression of TgLUT1 by directly binding to the TgLUT1 promoter. Collectively, our results show that TgWRKY10, down-regulated by drought stress, negatively regulates the expression of TgLUT1 to modulate the drought stress response. This study contributes to a more comprehensive understanding of LUT1's function in the stress responses of economically significant forest plants.

Maize GOLDEN2-LIKE proteins enhance drought tolerance in rice by promoting stomatal closure

Drought has become one of the most severe abiotic stresses experienced in agricultural production across the world. Plants respond to water deficit via stomatal movements in the leaves, which are mainly regulated by abscisic acid (ABA). A previous study from our lab showed that constitutive expression of maize (Zea mays L.) GOLDEN2-LIKE (GLK) transcription factors in rice (Oryza sativa L.) can improve stomatal conductance and plant photosynthetic capacity under field conditions. In the present study, we uncovered a function of ZmGLK regulation of stomatal movement in rice during drought stress. We found that elevated drought tolerance in rice plants overexpressing ZmGLK1 or GOLDEN2 (ZmG2) was conferred by rapid ABA-mediated stomatal closure. Comparative analysis of RNA-sequencing (RNA-seq) data from the rice leaves and DNA affinity purification sequencing (DAP-seq) results obtained in vitro revealed that ZmGLKs played roles in regulating ABA-related and stress-responsive pathways. Four upregulated genes closely functioning in abiotic stress tolerance with strong binding peaks in the DAP-seq data were identified as putative target genes of ZmGLK1 and ZmG2 in rice. These results demonstrated that maize GLKs play an important role in regulating stomatal movements to coordinate photosynthesis and stress tolerance. This trait is a valuable target for breeding drought-tolerant crop plants without compromising photosynthetic capacity.

Transcriptomic insights into shared responses to Fusarium crown rot infection and drought stresses in bread wheat (Triticum aestivum L.)

KEY MESSAGE

Shared changes in transcriptomes caused by Fusarium crown rot infection and drought stress were investigated based on a single pair of near-isogenic lines developed for a major locus conferring tolerance to both stresses. Fusarium crown rot (FCR) is a devastating disease in many areas of cereal production worldwide. It is well-known that drought stress enhances FCR severity but possible molecular relationship between these two stresses remains unclear. To investigate their relationships, we generated several pairs of near isogenic lines (NILs) targeting a locus conferring FCR resistance on chromosome 2D in bread wheat. One pair of these NILs showing significant differences between the two isolines for both FCR resistance and drought tolerance was used to investigate transcriptomic changes in responsive to these two stresses. Our results showed that the two isolines likely deployed different strategies in dealing with the stresses, and significant differences in expressed gene networks exist between the two time points of drought stresses evaluated in this study. Nevertheless, results from analysing Gene Ontology terms and transcription factors revealed that similar regulatory frameworks were activated in coping with these two stresses. Based on the position of the targeted locus, changes in expression following FCR infection and drought stresses, and the presence of non-synonymous variants between the two isolines, several candidate genes conferring resistance or tolerance to these two types of stresses were identified. The NILs generated, the large number of DEGs with single-nucleotide polymorphisms detected between the two isolines, and the candidate genes identified would be invaluable in fine mapping and cloning the gene(s) underlying the targeted locus.

Screening and Structural Characterization of Heat Shock Response Elements (HSEs) in Entamoeba histolytica Promoters

Entamoeba histolytica (E. histolytica) exhibits a remarkable capacity to respond to thermal shock stress through a sophisticated genetic regulation mechanism. This process is carried out via Heat Shock Response Elements (HSEs), which are recognized by Heat Shock Transcription Factors (EhHSTFs), enabling fine and precise control of gene expression. Our study focused on screening for HSEs in the promoters of the E. histolytica genome, specifically analyzing six HSEs, including Ehpgp5, EhrabB1, EhrabB4, EhrabB5, Ehmlbp, and Ehhsp100. We discovered 2578 HSEs, with 1412 in promoters of hypothetical genes and 1166 in coding genes. We observed that a single promoter could contain anywhere from one to five HSEs. Gene ontology analysis revealed the presence of HSEs in essential genes for the amoeba, including cysteine proteinases, ribosomal genes, Myb family DNA-binding proteins, and Rab GTPases, among others. Complementarily, our molecular docking analyses indicate that these HSEs are potentially recognized by EhHSTF5, EhHSTF6, and EhHSTF7 factors in their trimeric conformation. These findings suggest that E. histolytica has the capability to regulate a wide range of critical genes via HSE-EhHSTFs, not only for thermal stress response but also for vital functions of the parasite. This is the first comprehensive study of HSEs in the genome of E. histolytica, significantly contributing to the understanding of its genetic regulation and highlighting the complexity and precision of this mechanism in the parasite's survival.

Biotechnology and urban agriculture: A partnership for the future sustainability

The global population is growing rapidly, and with it, the demand for food. In the coming decades, more and more people will be living in urban areas, where land for traditional agriculture is scarce. Urban agriculture can help to meet this growing demand for food in a sustainable way. Urban agriculture is the practice of growing food in urban areas. It can be done on rooftops, balconies, vacant lots, and even in alleyways. Urban agriculture can produce a variety of crops, including fruits, vegetables, and herbs. It can also help to improve air quality, reduce stormwater runoff, and create jobs. Biotechnology can be used to improve the efficiency and sustainability of urban agriculture. Biotechnological tools can be used to develop crops that are resistant to pests and diseases, that are more tolerant of drought and heat, and that have higher yields. Biotechnology can also be used to improve the nutritional value of crops. This review article discusses the need for and importance of urban agriculture, biotechnology, and genome editing in meeting the growing demand for food in urban areas. It also discusses the potential of biotechnology to improve the sustainability of urban agriculture.

Genetic and Epigenetic Responses of Autochthonous Grapevine Cultivars from the 'Epirus' Region of Greece upon Consecutive Drought Stress

Within the framework of preserving and valorizing the rich grapevine germplasm of the Epirus region of Greece, indigenous grapevine (Vitis vinifera L.) cultivars were characterized and assessed for their resilience to abiotic stresses in the context of climate change. The cultivars 'Debina' and 'Dichali' displayed significant differences in their response to drought stress as judged by morpho-physiological analysis, indicating higher drought tolerance for Dichali. Hence, they were selected for further study aiming to identify genetic and epigenetic mechanisms possibly regulating drought adaptability. Specifically, self-rooted and heterografted on 'Richter 110' rootstock plants were subjected to two phases of drought with a recovery period in between. Gene expression analysis was performed for two stress-related miRNAs and their target genes: (a) miRNA159 and putative targets, VvMYB101, VvGATA-26-like, VvTOPLESS-4-like and (b) miRNA156 and putative target gene VvCONSTANS-5. Overall, grafted plants exhibited a higher drought tolerance than self-rooted plants, suggesting beneficial rootstock-scion interactions. Comparative analysis revealed differential gene expression under repetitive drought stresses between the two cultivars as well as between the self-rooted and grafted plants. 'Dichali' exhibited an up-regulation of most of the genes examined, which may be associated with increased tolerance. Nevertheless, the profound down-regulation of VvTOPLESS-4-like (a transcriptional co-repressor of transcription factors) upon drought and the concomitant up-regulation of miRNA159 highlights the importance of this 'miRNA-target' module in drought responsiveness. DNA methylation profiling using MSAP analysis revealed differential methylation patterns between the two genotypes in response to drought. Further investigations of gene expression and DNA methylation will contribute to our understanding of the epigenetic mechanisms underlying grapevine tolerance to drought stress.

SmWRKY11 acts as a positive regulator in eggplant response to salt stress

Salt stress is one of the most threatening abiotic stresses to plants, which can seriously affect plant growth, development, reproduction, and yield. However, the mechanisms of plant against salt stress largely remain unclear. Herein, SmWRKY11, an assumed WRKY transcription factor, was functionally characterized in eggplant against salt stress. SmWRKY11 was significantly up-regulated by salt, dehydration stress, and ABA treatment. SmWRKY11 located in the nucleus, and the Plant_zn_clust conserved domain exhibited transcriptional activation activity. Silencing of SmWRKY11 enhanced the susceptibility of eggplant to salt stress, accompanied by significantly down-regulation of transcript expression levels of salt stress defense-related genes SmNCED1, SmGSTU10, and positive regulator of salt stress response SmERF1 as well as increase of hydrogen peroxide (H2O2) content and decrease of the enzyme activities of catalase (CAT), peroxidase (POD), and ascorbate peroxidase (APX). In addition, silencing of SmERF1 also could significantly down-regulate SmWRKY11 expression in eggplant response to salt stress. By luciferase reporter assay and chromatin immunoprecipitation PCR assay, SmERF1 expression was found to be indirectly activated by SmWRKY11. These data indicate that SmWRKY11 acts as a positive regulator by forming positive feedback loop with SmERF1 via an indirect regulatory manner in eggplant response to salt stress.

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.

Brevundimonas vesicularis (S1T13) Mitigates Drought-Stress-Associated Damage in Arabidopsis thaliana

Drought stress is a significant threat to agricultural productivity and poses challenges to plant survival and growth. Research into microbial plant biostimulants faces difficulties in understanding complicated ecological dynamics, molecular mechanisms, and specificity; to address these knowledge gaps, collaborative efforts and innovative strategies are needed. In the present study, we investigated the potential role of Brevundimonas vesicularis (S1T13) as a microbial plant biostimulant to enhance drought tolerance in Arabidopsis thaliana. We assessed the impact of S1T13 on Col-0 wild-type (WT) and atnced3 mutant plants under drought conditions. Our results revealed that the inoculation of S1T13 significantly contributed to plant vigor, with notable improvements observed in both genotypes. To elucidate the underlying mechanisms, we studied the role of ROS and their regulation by antioxidant genes and enzymes in plants inoculated with S1T13. Interestingly, the inoculation of S1T13 enhanced the activities of GSH, SOD, POD, and PPO by 33, 35, 41, and 44% in WT and 24, 22, 26, and 33% in atnced3, respectively. In addition, S1T13 upregulated the expression of antioxidant genes. This enhanced antioxidant machinery played a crucial role in neutralizing ROS and protecting plant cells from oxidative damage during drought stress. Furthermore, we investigated the impact of S1T13 on ABA and drought-stress-responsive genes. Similarly, S1T13 modulated the production of ABA and expression of AO3, ABA3, DREB1A, and DREB2A by 31, 42, 37, 41, and 42% in WT and 20, 29, 27, 38, and 29% in atnced3. The improvement in plant vigor, coupled with the induction of the antioxidant system and modulation of ABA, indicates the pivotal role of S1T13 in enhancing the drought stress tolerance of the plants. Conclusively, the current study provides valuable insights for the application of multitrait S1T13 as a novel strain to improve drought stress tolerance in plants and could be added to the consortium of biofertilizers.

Cloning of the Soybean GmNHL1 Gene and Functional Analysis under Salt Stress

When encountered in the soybean seedling stage, salt stress has serious impacts on plant growth and development. This study explores the role of the soybean NDR1/HIN1-like family gene GmNHL1 under salt stress. First, the GmNHL1 gene was successfully cloned, and bioinformatic analysis revealed multiple cis-acting elements which are related to adversity stress and involved in the oxidative response in the promoter region. Sub-cellular localization analysis indicated that the protein expressed by GmNHL1 was localized on the cell membrane. An over-expression vector of the target gene and a CRISPR/Cas9 gene-editing vector were constructed, and the recipient soybean variety Jinong 74 was genetically transformed using the Agrobacterium tumefaciens-mediated method. By analyzing the performance of the different plants under salt stress, the results showed that GmNHL1 was over-expressed in the T2 generation. The germination potential, germination rate, germination index, and vitality index of the strain were significantly higher than those of the recipient control JN74. Under salt stress conditions, the root microanatomical structure of the GmNHL1 over-expressing material remained relatively intact, and its growth was better than that of the recipient control JN74. Measurement of physiological and biochemical indicators demonstrated that, compared with the receptor control JN74, the malondialdehyde and O2- contents of the GmNHL1 over-expressing material were significantly reduced, while the antioxidant enzyme activity, proline content, and chlorophyll content significantly increased; however, the results for GmNHL1 gene-edited materials were the opposite. In summary, over-expression of GmNHL1 can improve the salt tolerance of plants and maintain the integrity of the root anatomical structure, thereby more effectively and rapidly reducing the accumulation of malondialdehyde and O2- content and increasing antioxidant enzyme activity. This reduces cell membrane damage, thereby improving the salt tolerance of soybean plants. These results help to better understand the mechanism of salt tolerance in soybean plants, laying a theoretical foundation for breeding new stress-resistant varieties of soybean.

Comparative Transcriptomic and Proteomic Analyses Provide New Insights into the Tolerance to Cyclic Dehydration in a Lichen Phycobiont

Desiccation tolerance (DT) is relatively frequent in non-vascular plants and green algae. However, it is poorly understood how successive dehydration/rehydration (D/R) cycles shape their transcriptomes and proteomes. Here, we report a comprehensive analysis of adjustments on both transcript and protein profiles in response to successive D/R cycles in Coccomyxa simplex (Csol), isolated from the lichen Solorina saccata. A total of 1833 transcripts and 2332 proteins were differentially abundant as a consequence of D/R; however, only 315 of these transcripts/proteins showed similar trends. Variations in both transcriptomes and proteomes along D/R cycles together with functional analyses revealed an extensive decrease in transcript and protein levels during dehydration, most of them involved in gene expression, metabolism, substance transport, signalling and folding catalysis, among other cellular functions. At the same time, a series of protective transcripts/proteins, such as those related to antioxidant defence, polyol metabolism and autophagy, was upregulated during dehydration. Overall, our results show a transient decrease in most cellular functions as a result of drying and a gradual reactivation of specific cell processes to accommodate the hydration status along successive D/R cycles. This study provides new insights into key mechanisms involved in the DT of Csol and probably other dehydration-tolerant microalgae. In addition, functionally characterising the high number of genes/proteins of unknown functions found in this study may lead to the discovery of new DT mechanisms.

Interaction between phenylpropane metabolism and oil accumulation in the developing seed of Brassica napus revealed by high temporal-resolution transcriptomes

BACKGROUND

Brassica napus is an important oilseed crop providing high-quality vegetable oils for human consumption and non-food applications. However, the regulation between embryo and seed coat for the synthesis of oil and phenylpropanoid compounds remains largely unclear.

RESULTS

Here, we analyzed the transcriptomes in developing seeds at 2-day intervals from 14 days after flowering (DAF) to 64 DAF. The 26 high-resolution time-course transcriptomes are clearly clustered into five distinct groups from stage I to stage V. A total of 2217 genes including 136 transcription factors, are specifically expressed in the seed and show high temporal specificity by being expressed only at certain stages of seed development. Furthermore, we analyzed the co-expression networks during seed development, which mainly included master regulatory transcription factors, lipid, and phenylpropane metabolism genes. The results show that the phenylpropane pathway is prominent during seed development, and the key enzymes in the phenylpropane metabolic pathway, including TT5, BAN, and the transporter TT19, were directly or indirectly related to many key enzymes and transcription factors involved in oil accumulation. We identified candidate genes that may regulate seed oil content based on the co-expression network analysis combined with correlation analysis of the gene expression with seed oil content and seed coat content.

CONCLUSIONS

Overall, these results reveal the transcriptional regulation between lipid and phenylpropane accumulation during B. napus seed development. The established co-expression networks and predicted key factors provide important resources for future studies to reveal the genetic control of oil accumulation in B. napus seeds.

Integrated Analysis of Transcriptome and Metabolome Reveals Molecular Mechanisms of Rice with Different Salinity Tolerances

Rice is a crucial global food crop, but it lacks a natural tolerance to high salt levels, resulting in significant yield reductions. To gain a comprehensive understanding of the molecular mechanisms underlying rice's salt tolerance, further research is required. In this study, the transcriptomic and metabolomic differences between the salt-tolerant rice variety Lianjian5 (TLJIAN) and the salt-sensitive rice variety Huajing5 (HJING) were examined. Transcriptome analysis revealed 1518 differentially expressed genes (DEGs), including 46 previously reported salt-tolerance-related genes. Notably, most of the differentially expressed transcription factors, such as NAC, WRKY, MYB, and EREBP, were upregulated in the salt-tolerant rice. Metabolome analysis identified 42 differentially accumulated metabolites (DAMs) that were upregulated in TLJIAN, including flavonoids, pyrocatechol, lignans, lipids, and trehalose-6-phosphate, whereas the majority of organic acids were downregulated in TLJIAN. The interaction network of 29 differentially expressed transporter genes and 19 upregulated metabolites showed a positive correlation between the upregulated calcium/cation exchange protein genes (OsCCX2 and CCX5_Ath) and ABC transporter gene AB2E_Ath with multiple upregulated DAMs in the salt-tolerant rice variety. Similarly, in the interaction network of differentially expressed transcription factors and 19 upregulated metabolites in TLJIAN, 6 NACs, 13 AP2/ERFs, and the upregulated WRKY transcription factors were positively correlated with 3 flavonoids, 3 lignans, and the lipid oleamide. These results suggested that the combined effects of differentially expressed transcription factors, transporter genes, and DAMs contribute to the enhancement of salt tolerance in TLJIAN. Moreover, this study provides a valuable gene-metabolite network reference for understanding the salt tolerance mechanism in rice.

Metabolic pathways engineering for drought or/and heat tolerance in cereals

Drought (D) and heat (H) are the two major abiotic stresses hindering cereal crop growth and productivity, either singly or in combination (D/+H), by imposing various negative impacts on plant physiological and biochemical processes. Consequently, this decreases overall cereal crop production and impacts global food availability and human nutrition. To achieve global food and nutrition security vis-a-vis global climate change, deployment of new strategies for enhancing crop D/+H stress tolerance and higher nutritive value in cereals is imperative. This depends on first gaining a mechanistic understanding of the mechanisms underlying D/+H stress response. Meanwhile, functional genomics has revealed several stress-related genes that have been successfully used in target-gene approach to generate stress-tolerant cultivars and sustain crop productivity over the past decades. However, the fast-changing climate, coupled with the complexity and multigenic nature of D/+H tolerance suggest that single-gene/trait targeting may not suffice in improving such traits. Hence, in this review-cum-perspective, we advance that targeted multiple-gene or metabolic pathway manipulation could represent the most effective approach for improving D/+H stress tolerance. First, we highlight the impact of D/+H stress on cereal crops, and the elaborate plant physiological and molecular responses. We then discuss how key primary metabolism- and secondary metabolism-related metabolic pathways, including carbon metabolism, starch metabolism, phenylpropanoid biosynthesis, γ-aminobutyric acid (GABA) biosynthesis, and phytohormone biosynthesis and signaling can be modified using modern molecular biotechnology approaches such as CRISPR-Cas9 system and synthetic biology (Synbio) to enhance D/+H tolerance in cereal crops. Understandably, several bottlenecks hinder metabolic pathway modification, including those related to feedback regulation, gene functional annotation, complex crosstalk between pathways, and metabolomics data and spatiotemporal gene expressions analyses. Nonetheless, recent advances in molecular biotechnology, genome-editing, single-cell metabolomics, and data annotation and analysis approaches, when integrated, offer unprecedented opportunities for pathway engineering for enhancing crop D/+H stress tolerance and improved yield. Especially, Synbio-based strategies will accelerate the development of climate resilient and nutrient-dense cereals, critical for achieving global food security and combating malnutrition.

The pear genomics database (PGDB): a comprehensive multi-omics research platform for Pyrus spp

BACKGROUND

Pears are among the most important temperate fruit trees in the world, with significant research efforts increasing over the last years. However, available omics data for pear cannot be easily and quickly retrieved to enable further studies using these biological data.

DESCRIPTION

Here, we present a publicly accessible multi-omics pear resource platform, the Pear Genomics Database (PGDB). We collected and collated data on genomic sequences, genome structure, functional annotation, transcription factor predictions, comparative genomics, and transcriptomics. We provide user-friendly functional modules to facilitate querying, browsing and usage of these data. The platform also includes basic and useful tools, including JBrowse, BLAST, phylogenetic tree building, and additional resources providing the possibility for bulk data download and quick usage guide services.

CONCLUSIONS

The Pear Genomics Database (PGDB, http://pyrusgdb.sdau.edu.cn ) is an online data analysis and query resource that integrates comprehensive multi-omics data for pear. This database is equipped with user-friendly interactive functional modules and data visualization tools, and constitutes a convenient platform for integrated research on pear.

Investigating the dynamic responses of Aegilops tauschii Coss. to salinity, drought, and nitrogen stress: a comprehensive study of competitive growth and biochemical and molecular pathways

Aegilops tauschii (Coss.) is a highly deleterious, rapidly proliferating weed within the wheat, and its DD genome composition exhibits adaptability toward diverse abiotic stresses and demonstrates heightened efficacy in nutrient utilization. Current study investigated different variegated impacts of distinct nitrogen concentrations with varied plant densities, scrutinizing the behavior of Ae. tauschii under various salinity and drought stress levels through multiple physiological, biochemical, and molecular pathways. Different physiological parameters attaining high growth with different plant density and different nitrogen availability levels increased Ae. tauschii dominancy. Conversely, under the duress of salinity and drought, Ae. tauschii showcased an enhanced performance through a comprehensive array of physiological and biochemical parameters, including catalase, peroxidase, malondialdehyde, and proline content. Notably, salinity-associated traits such as sodium, potassium, and the sodium-potassium ratio exhibited significant variations and demonstrated remarkable tolerance capabilities. In the domain of molecular pathways, the HKT and DREB genes have displayed a remarkable upregulation, showcasing a comparatively elevated expression profile in reaction to different levels of salinity and drought-induced stress. Without a doubt, this information will make a substantial contribution to the understanding of the fundamental behavioral tendencies and the efficiency of nutrient utilization in Ae. tauschii. Moreover, it will offer innovative viewpoints for integrated management, thereby enabling the enhancement of strategies for adept control and alleviation.

Unraveling the regulatory role of MYC2 on ASMT gene expression in wheat: Implications for melatonin biosynthesis and drought tolerance

Recognized for its multifaceted functions, melatonin is a hormone found in both animals and plants. In the plant kingdom, it plays diverse roles, regulating growth, development, and stress responses. Notably, melatonin demonstrates its significance by mitigating the effects of abiotic stresses like drought. However, understanding the precise regulatory mechanisms controlling melatonin biosynthesis genes, especially during monocots' response to stresses, requires further exploration. Seeking to understand the molecular basis of drought stress tolerance in wheat, we analyzed RNA-Seq libraries of wheat exposed to drought stress using bioinformatics methods. In light of our findings, we identified that the Myelocytomatosis oncogenes 2 (MYC2) transcription factor is a hub gene upstream of a main melatonin biosynthesis gene, N-acetylserotonin methyltransferase (ASMT), in the wheat drought response-gene network. Promoter analysis of the ASMT gene suggested that it might be a target gene of MYC2. We conducted a set of molecular and physiochemical assays along with robust machine learning approaches to elevate those findings further. MYC2 and ASMT were co-regulated under Jasmonate, drought, and a combination of them in the leaf tissues of wheat was detected. A meaningful correlation was observed among gene expression profiles, melatonin contents, photosynthetic activities, antioxidant enzyme activities, H2 O2 levels, and plasma membrane damage. The results indicated an evident relationship between jasmonic acid and the melatonin biosynthesis pathway. Moreover, it seems that the MYC2-ASMT module might contribute to wheat drought tolerance by regulating melatonin contents.

The Over-Expression of Two R2R3-MYB Genes, PdMYB2R089 and PdMYB2R151, Increases the Drought-Resistant Capacity of Transgenic Arabidopsis

The R2R3-MYB genes in plants play an essential role in the drought-responsive signaling pathway. Plenty of R2R3-MYB S21 and S22 subgroup genes in Arabidopsis have been implicated in dehydration conditions, yet few have been covered in terms of the role of the S21 and S22 subgroup genes in poplar under drought. PdMYB2R089 and PdMYB2R151 genes, respectively belonging to the S21 and S22 subgroups of NL895 (Populus deltoides × P. euramericana cv. 'Nanlin895'), were selected based on the previous expression analysis of poplar R2R3-MYB genes that are responsive to dehydration. The regulatory functions of two target genes in plant responses to drought stress were studied and speculated through the genetic transformation of Arabidopsis thaliana. PdMYB2R089 and PdMYB2R151 could promote the closure of stomata in leaves, lessen the production of malondialdehyde (MDA), enhance the activity of the peroxidase (POD) enzyme, and shorten the life cycle of transgenic plants, in part owing to their similar conserved domains. Moreover, PdMYB2R089 could strengthen root length and lateral root growth. These results suggest that PdMYB2R089 and PdMYB2R151 genes might have the potential to improve drought adaptability in plants. In addition, PdMYB2R151 could significantly improve the seed germination rate of transgenic Arabidopsis, but PdMYB2R089 could not. This finding provides a clue for the subsequent functional dissection of S21 and S22 subgroup genes in poplar that is responsive to drought.

Genome-Wide Identification and Expression Analysis of the RADIALIS-like Gene Family in Camellia sinensis

The RADIALIS-like (RL) proteins are v-myb avian myeloblastosis viral oncogene homolog (MYB)-related transcription factors (TFs), and are involved in many biological processes, including metabolism, development, and response to biotic and abiotic stresses. However, the studies on the RL genes of Camellia sinensis are not comprehensive enough. Therefore, we undertook this study and identified eight CsaRLs based on the typical conserved domain SANT Associated domain (SANT) of RL. These genes have low molecular weights and theoretical pI values ranging from 5.67 to 9.76. Gene structure analysis revealed that six CsaRL genes comprise two exons and one intron, while the other two contain a single exon encompassing motifs 1 and 2, and part of motif 3. The phylogenetic analysis divided one hundred and fifty-eight RL proteins into five primary classes, in which CsaRLs clustered in Group V and were homologous with CssRLs of the Shuchazao variety. In addition, we selected different tissue parts to analyze the expression profile of CsaRLs, and the results show that almost all genes displayed variable expression levels across tissues, with CsaRL1a relatively abundant in all tissues. qRT-PCR (real-time fluorescence quantitative PCR) was used to detect the relative expression levels of the CsaRL genes under various abiotic stimuli, and it was found that CsaRL1a expression levels were substantially higher than other genes, with abscisic acid (ABA) causing the highest expression. The self-activation assay with yeast two-hybrid system showed that CsaRL1a has no transcriptional activity. According to protein functional interaction networks, CsaRL1a was well connected with WIN1-like, lysine histidine transporter-1-like, β-amylase 3 chloroplastic-like, carbonic anhydrase-2-like (CA2), and carbonic anhydrase dnaJC76 (DJC76). This study adds to our understanding of the RL family and lays the groundwork for further research into the function and regulatory mechanisms of the CsaRLs gene family in Camellia sinensis.

Co-Expression of JcNAC1- and JcZFP8-Improved Agronomic Traits of Tobacco and Enhanced Drought Resistance through NbbHLH1 and NbbHLH2

Previous studies have identified numerous transcription factors involved in drought response, each of which play different roles in plants. The objective of the present study was to evaluate the effectiveness of two transcription factors on drought response in Jatropha curcas L., JcNAC1 and JcZFP8. The overexpression of these transcription factors in tobacco (Nicotiana benthamiana L.) improved drought resistance, but JcZFP8 delayed germination and JcNAC1 reduced biomass and yield. By constitutively co-expressing these two genes in tobacco, drought resistance was improved, and the negative effects of each of them were overcome. The transgenic plants with double-gene co-expression showed stronger drought tolerance with 1.76-fold greater accumulation of proline and lower H2O2 and malondialdehyde (MDA) content to 43 and 65% of wildtype (WT) levels, respectively. The expression levels of NbbHLH1 and NbbHLH2 genes upregulated linearly with the increased drought tolerance of double genes co-expression plants. In drought conditions, the leaf water contents of bhlh1, bhlh2, and bhlh1bhlh2 deletion mutants obtained by CRISPR-CAS9 knockout technique were maintained at 99%, 97%, and 97% of WT. The bhlh1bhlh2 was found with lower germination rate but with higher reactive oxygen levels (1.64-fold H2O2 and 1.41-fold MDA levels). Thus, the co-expression of two transcription factors with different functions overcame the adverse traits brought by a single gene and enhanced the shared drought-tolerant traits, which can provide guidance on theory and selection of gene combinations for the application of multi-gene co-expression in agriculture in the future.

A Novel Role of Medicago truncatula KNAT3/4/5-like Class 2 KNOX Transcription Factors in Drought Stress Tolerance

Class 2 KNOX homeobox transcription factors (KNOX2) play a role in promoting cell differentiation in several plant developmental processes. In Arabidopsis, they antagonize the meristematic KNOX1 function during leaf development through the modulation of phytohormones. In Medicago truncatula, three KNOX2 genes belonging to the KNAT3/4/5-like subclass (Mt KNAT3/4/5-like or MtKNOX3-like) redundantly works upstream of a cytokinin-signaling module to control the symbiotic root nodule formation. Their possible role in the response to abiotic stress is as-of-yet unknown. We produced transgenic M. truncatula lines, in which the expression of four MtKNOX3-like genes was knocked down by RNA interference. When tested for response to water withdrawal in the soil, RNAi lines displayed a lower tolerance to drought conditions compared to the control lines, measured as increased leaf water loss, accelerated leaf wilting time, and faster chlorophyll loss. Reanalysis of a transcriptomic M. truncatula drought stress experiment via cluster analysis and gene co-expression networks pointed to a possible role of MtKNOX3-like transcription factors in repressing a proline dehydrogenase gene (MtPDH), specifically at 4 days after water withdrawal. Proline measurement and gene expression analysis of transgenic RNAi plants compared to the controls confirmed the role of KNOX3-like genes in inhibiting proline degradation through the regulation of the MtPDH gene.

Genome-wide characterization of the PLATZ gene family in watermelon (Citrullus lanatus L.) with putative functions in biotic and abiotic stress response

Plant AT-rich sequence and zinc-binding (PLATZ) proteins are plant-specific transcription factors involved in growth, development, and stress responses. Here, we conducted a genome-wide characterization of the watermelon ClPLATZ family and examined its expression responsiveness to defense hormones and pathogen infection along with putative functions in biotic and abiotic stress responses. The watermelon genome contains 12 putative ClPLATZ genes, encoding proteins with a characteristic PLATZ domain, and their promoters contain various cis-elements related to plant growth, development, phytohormones and stress response. The ClPLATZ genes, except ClPLATZ6, are differentially expressed in response to defense hormones (e.g., salicylic acid and methyl jasmonate) and fungal infections caused by Fusarium oxysporum f. sp. niveum and Stagonosporopsis cucurbitacearum. Most ClPLATZ proteins interact with other proteins (viz., ClDP, ClRPT2a, and ClRPC53). Among ClPLATZ proteins, ClPLATZ8, 9, 10, and 11 are predominately localized in the nucleus. ClPLATZ3 and 8 positively, but ClPLATZ11 negatively regulate resistance against Pseudomonas syringe pv. tomato DC3000 in transgenic Arabidopsis lines. ClPLATZ8 and 11 positively regulate stress tolerance to NaCl and mannitol during seed germination in transgenic Arabidopsis. In conclusion, the characterization of the ClPLATZ family provides insights into the biological functions of ClPLATZ genes in growth, development, and stress response in watermelon. Further, the involvement of certain ClPLATZ genes in biotic and abiotic stress response in transgenic Arabidopsis suggests their potential application in engineering stress-tolerant crops.

Analysis of the HD-Zip I transcription factor family in Salvia miltiorrhiza and functional research of SmHD-Zip12 in tanshinone synthesis

Background

The homeodomain-leucine zipper I (HD-Zip I) transcription factor is a plant-specific protein that plays an essential role in the abiotic stress response of plants. Research on the HD-Zip I family in Salvia miltiorrhiza is still lacking.

Methods and Results

In this study, a total of 25 SmHD-Zip I proteins were identified. Their characterizations, phylogenetic relationships, conserved motifs, gene structures, and cis-elements were analyzed comprehensively using bioinformatics methods. Expression profiling revealed that SmHD-Zip I genes exhibited distinctive tissue-specific patterns and divergent responses to ABA, PEG, and NaCl stresses. SmHD-Zip12 responded the most strongly to ABA, PEG, and NaCl, so it was used for transgenic experiments. The overexpression of SmHD-Zip12 significantly increased the content of cryptotanshinone, dihydrotanshinone I, tanshinone I, and tanshinone IIA by 2.89-fold, 1.85-fold, 2.14-fold, and 8.91-fold compared to the wild type, respectively. Moreover, in the tanshinone biosynthetic pathways, the overexpression of SmHD-Zip12 up-regulated the expression levels of SmAACT, SmDXS, SmIDS, SmGGPPS, SmCPS1, SmCPS2, SmCYP76AH1, SmCYP76AH3, and SmCYP76AK1 compared with the wild type.

Conclusions

This study provides information the possible functions of the HD-Zip I family and lays a theoretical foundation for clarifying the functional mechanism of the SmHD-Zip12 gene in regulating the synthesis of tanshinone in S. miltiorrhiza.

Physiological response and transcriptome analyses of leguminous Indigofera bungeana Walp. to drought stress

Objective

Indigofera bungeana is a shrub with high quality protein that has been widely utilized for forage grass in the semi-arid regions of China. This study aimed to enrich the currently available knowledge and clarify the detailed drought stress regulatory mechanisms in I. bungeana, and provide a theoretical foundation for the cultivation and resistance breeding of forage crops.

Methods

This study evaluates the response mechanism to drought stress by exploiting multiple parameters and transcriptomic analyses of a 1-year-old seedlings of I. bungeana in a pot experiment.

Results

Drought stress significantly caused physiological changes in I. bungeana. The antioxidant enzyme activities and osmoregulation substance content of I. bungeana showed an increase under drought. Moreover, 3,978 and 6,923 differentially expressed genes were approved by transcriptome in leaves and roots. The transcription factors, hormone signal transduction, carbohydrate metabolism of regulatory network were observed to have increased. In both tissues, genes related to plant hormone signaling transduction pathway might play a more pivotal role in drought tolerance. Transcription factors families like basic helix-loop-helix (bHLH), vian myeloblastosis viral oncogene homolog (MYB), basic leucine zipper (bZIP) and the metabolic pathway related-genes like serine/threonine-phosphatase 2C (PP2C), SNF1-related protein kinase 2 (SnRK2), indole-3-acetic acid (IAA), auxin (AUX28), small auxin up-regulated rna (SAUR), sucrose synthase (SUS), sucrosecarriers (SUC) were highlighted for future research about drought stress resistance in Indigofera bungeana.

Conclusion

Our study posited I. bungeana mainly participate in various physiological and metabolic activities to response severe drought stress, by regulating the expression of the related genes in hormone signal transduction. These findings, which may be valuable for drought resistance breeding, and to clarify the drought stress regulatory mechanisms of I. bungeana and other plants.

Dioscorea composita WRKY5 positively regulates AtSOD1 and AtABF2 to enhance drought and salt tolerances

KEY MESSAGE

DcWRKY5 increases the antioxidant enzyme activity and proline accumulation, oppositely, reduces the accumulation of ROS and MDA, through directly activating the genes expression, finally enhances the salt and drought tolerance. Drought and salinity are two main environmental factors that limit the large-scale cultivation of the medicinal plant Dioscorea composita (D. composita). WRKY transcription factors (TFs) play vital roles in regulating drought and salt tolerance in plants. Nevertheless, the molecular mechanism of WRKY TF mediates drought and salt resistance of D. composita remains largely unknown. Here, we isolated and characterized a WRKY TF from D. composita, namely DcWRKY5, which was localized to the nucleus and bound to the W-box cis-acting elements. Expression pattern analysis showed that it was highly expressed in root and significantly up-regulated in the presence of salt, polyethylene glycol-6000 (PEG-6000) and abscisic acid (ABA). Heterologous expression of DcWRKY5 increased salt and drought tolerance in Arabidopsis, but was insensitive to ABA. In addition, compared with the wild type, the DcWRKY5 overexpressing transgenic lines had more proline, higher antioxidant enzyme (POD, SOD, and CAT) activities, less reactive oxygen species (ROS) and malondialdehyde (MDA). Correspondingly, the overexpression of DcWRKY5 modulated the expression of genes related to salt and drought stresses, such as AtSS1, AtP5CS1, AtCAT, AtSOD1, AtRD22, and AtABF2. Dual luciferase assay and Y1H were further confirmed that DcWRKY5 activate the promoter of AtSOD1 and AtABF2 through directly binding to the enrichment region of the W-box cis-acting elements. These results suggest that DcWRKY5 is a positive regulator of the drought and salt tolerance in D. composita and has potential applications in transgenic breeding.

Plant Tolerance to Drought Stress with Emphasis on Wheat

Environmental stresses, such as drought, have negative effects on crop yield. Drought is a stress whose impact tends to increase in some critical regions. However, the worldwide population is continuously increasing and climate change may affect its food supply in the upcoming years. Therefore, there is an ongoing effort to understand the molecular processes that may contribute to improving drought tolerance of strategic crops. These investigations should contribute to delivering drought-tolerant cultivars by selective breeding. For this reason, it is worthwhile to review regularly the literature concerning the molecular mechanisms and technologies that could facilitate gene pyramiding for drought tolerance. This review summarizes achievements obtained using QTL mapping, genomics, synteny, epigenetics, and transgenics for the selective breeding of drought-tolerant wheat cultivars. Synthetic apomixis combined with the msh1 mutation opens the way to induce and stabilize epigenomes in crops, which offers the potential of accelerating selective breeding for drought tolerance in arid and semi-arid regions.

Revisiting the role of MAPK signalling pathway in plants and its manipulation for crop improvement

The mitogen-activated protein kinase (MAPK) pathway is an important signalling event associated with every aspect of plant growth, development, yield, abiotic and biotic stress adaptation. Being a central metabolic pathway, it is a vital target for manipulation for crop improvement. In this review, we have summarised recent advancements in understanding involvement of MAPK signalling in modulating abiotic and biotic stress tolerance, architecture and yield of plants. MAPK signalling cross talks with reactive oxygen species (ROS) and abscisic acid (ABA) signalling events in bringing about abiotic stress adaptation in plants. The intricate involvement of MAPK pathway with plant's pathogen defence ability has also been identified. Further, recent research findings point towards participation of MAPK signalling in shaping plant architecture and yield. These make MAPK pathway an important target for crop improvement and we discuss here various strategies to tweak MAPK signalling components for designing future crops with improved physiology and phenotypes.

Modulation of the Berry Skin Transcriptome of cv. Tempranillo Induced by Water Stress Levels

Climate change in the Mediterranean area is making summers warmer and dryer. Grapevine (Vitis vinifera L.) is mostly important for wine production in Mediterranean countries, and the variety Tempranillo is one of the most cultivated in Spain and Portugal. Drought decreases yield and quality and causes important economic losses. As full irrigation has negative effects on quality and water is scarce in this region, deficit irrigation is often applied. In this research, we studied the effects of two deficit irrigation treatments, Sustained Deficit Irrigation (SDI) and Regulated Deficit Irrigation (RDI), on the transcriptome of grape berries at full maturation, through RNAseq. The expression of differentially regulated genes (DEGs) was also monitored through RT-qPCR along berry development. Most transcripts were regulated by water stress, with a similar distribution of up- and down-regulated transcripts within functional categories (FC). Primary metabolism was the more severely affected FC under water stress, followed by signaling and transport. Almost all DEGs monitored were significantly up-regulated by severe water stress at veraison. The modulation of an auxin response repression factor, AUX22D, by water stress indicates a role of this gene in the response to drought. Further, the expression of WRKY40, a TF that regulates anthocyanin biosynthesis, may be responsible for changes in grape quality under severe water stress.

MeJA-mediated enhancement of salt-tolerance of Populus wutunensis by 5-aminolevulinic acid

BACKGROUND

5-Aminolevulinic acid (ALA) is a natural and environmentally benign multifunctional plant growth regulator involved in the regulation of plant tolerance to various environmental stresses. This research aimed to explore the molecular mechanisms of salt tolerance in Populus wutunensis induced by exogenous ALA using physiological and transcriptomic analyses.

RESULTS

Physiological results showed that 50 mg·L^- 1 ALA-treatment significantly reduced the malondialdehyde (MDA) content and the relative electrical conductivity (REC) and enhanced antioxidant activities of enzymes such as SOD, POD and CAT in salt-stressed P. wutunensis seedlings. Transcriptome analysis identified ALA-induced differentially expressed genes (DEGs) associating with increased salt-tolerance in P. wutunensis. GO and KEGG enrichment analyses showed that ALA activated the jasmonic acid signaling and significantly enhanced the protein processing in endoplasmic reticulum and the flavonoid biosynthesis pathways. Results of the hormone-quantification by LC-MS/MS-based assays showed that ALA could increase the accumulation of methyl jasmonate (MeJA) in salt-stressed P. wutunensis. Induced contents of soluble proteins and flavonoids by exogenous ALA in salt-treated seedlings were also correlated with the MeJA content.

CONCLUSION

5-aminolevulinic acid improved the protein-folding efficiency in the endoplasmic reticulum and the flavonoid-accumulation through the MeJA-activated jasmonic acid signaling, thereby increased salt-tolerance in P. wutunensis.

Genome-Wide Identification and Expression Analysis of the SHI-Related Sequence Family in Cassava

The SHORT INTERNODES (SHI)-related sequences (SRS) are plant-specific transcription factors that have been quantitatively characterized during plant growth, regeneration, and stress responses. However, the genome-wide discovery of SRS family genes and their involvement in abiotic stress-related activities in cassava have not been documented. A genome-wide search strategy was used to identify eight family members of the SRS gene family in cassava (Manihot esculenta Crantz). Based on their evolutionary linkages, all MeSRS genes featured homologous RING-like zinc finger and IXGH domains. Genetic architecture and conserved motif analysis validated the categorization of MeSRS genes into four groups. Eight pairs of segmental duplications were detected, resulting in an increase in the number of MeSRS genes. Orthologous studies of SRS genes among cassava and three different plant species (Arabidopsis thaliana, Oryza sativa, and Populus trichocarpa) provided important insights into the probable history of the MeSRS gene family. The functionality of MeSRS genes was elucidated through the prediction of protein–protein interaction networks and cis-acting domains. RNA-seq data demonstrated tissue/organ expression selectivity and preference of the MeSRS genes. Furthermore, qRT-PCR investigation of MeSRS gene expression after exposure to salicylic acid (SA) and methyl jasmonate (MeJA) hormone treatments, as well as salt (NaCl) and osmotic (polyethylene glycol, PEG) stresses, showed their stress-responsive patterns. This genome-wide characterization and identification of the evolutionary relationships and expression profiles of the cassava MeSRS family genes will be helpful for further research into this gene family and its function in stress response. It may also assist future agricultural efforts to increase the stress tolerance of cassava.

Multi-Omics Analysis Provides Crucial Insights into the Drought Adaptation of Glycyrrhiza uralensis Fisch

Drought adaptation of plants is closely related to resistance and tolerance to drought stress as well as the ability to recover after the elimination of the stress. Glycyrrhiza uralensis Fisch is a commonly applied herb whose growth and development are greatly affected by drought. Here, we provide the first comprehensive analysis of the transcriptomic, epigenetic, and metabolic responses of G. uralensis to drought stress and rewatering. The hyper-/hypomethylation of genes may lead to up-/downregulated gene expression, and epigenetic changes can be regarded as an important regulatory mechanism of G. uralensis under drought stress and rewatering. Moreover, integrated transcriptome and metabolome analysis revealed that genes and metabolites involved in pathways of antioxidation, osmoregulation, phenylpropanoid biosynthesis, and flavonoid biosynthesis may regulate the drought adaptation of G. uralensis. This work provides crucial insights into the drought adaptation of G. uralensis and offers epigenetic resources for cultivating G. uralensis with high drought adaptation.

AgMYB5, an MYB transcription factor from celery, enhanced β-carotene synthesis and promoted drought tolerance in transgenic Arabidopsis

BACKGROUND

Water shortage caused by global warming seriously affects the yield and quality of vegetable crops. β-carotene, the lipid-soluble natural product with important pharmacological value, is abundant in celery. Transcription factor MYB family extensively disperses in plants and plays regulatory roles in carotenoid metabolism and water scarcity response.

RESULTS

Here, the AgMYB5 gene encoding 196 amino acids was amplified from celery cv. 'Jinnanshiqin'. In celery, the expression of AgMYB5 exhibited transactivation activity, tissue specificity, and drought-condition responsiveness. Further analysis proved that ectopic expression of AgMYB5 increased β-carotene content and promoted drought tolerance in transgenic Arabidopsis thaliana. Moreover, AgMYB5 expression promoted β-carotene biosynthesis by triggering the expression of AtCRTISO and AtLCYB, which in turn increased antioxidant enzyme activities, and led to the decreased contents of H₂O₂ and MDA, and the inhibition of O₂^- generation. Meanwhile, β-carotene accumulation promoted endogenous ABA biosynthesis of transgenic Arabidopsis, which resulted in ABA-induced stomatal closing and delayed water loss. In addition, ectopic expression of AgMYB5 increased expression levels of AtERD1, AtP5CS1, AtRD22, and AtRD29.

CONCLUSIONS

The findings indicated that AgMYB5 up-regulated β-carotene biosynthesis and drought tolerance of Arabidopsis.