Identification and expression analysis of the Glycine max CYP707A gene family in response to drought and salt stresses

MsCYP71 is a positive regulator for drought resistance in alfalfa

Cytochrome P450 (CYP450) family proteins play key roles in plant growth, development, stress responses, and other physiological processes. Here, we cloned the cytochrome P450 gene MsCYP71 in alfalfa and found that the expression of MsCYP71 was induced by drought stress. Silencing the MsCYP71 gene using virus-induced gene silencing technology significantly decreased the drought resistance of alfalfa, as indicated by their lower relative water content, net photosynthetic rate, and chlorophyll fluorescence maximum (Fm); further, the heterologous overexpression of MsCYP71 in tobacco significantly enhanced the drought resistance and Fm of transgenic tobacco. Furthermore, the expression of MsCYP71 across 45 alfalfa accessions under drought stress was investigated. A significant positive correlation between drought resistance and MsCYP71 expression was observed. The 45 alfalfa accessions were clustered into four groups, and drought resistance, Fm, and MsCYP71 were higher in group I than in the other groups, indicating that group I accessions can be used as candidate germplasm resources for the breeding of drought-resistant alfalfa varieties. Overall, our findings indicated that MsCYP71 is a positive regulator of drought resistance in alfalfa, and its expression can be used to evaluate the drought resistance of alfalfa.

A Transcription Factor SlNAC4 Gene of Suaeda liaotungensis Enhances Salt and Drought Tolerance through Regulating ABA Synthesis

The NAC (NAM, ATAF1/2 and CUC2) transcription factors are ubiquitously distributed in plants and play critical roles in the construction of plant organs and abiotic stress response. In this study, we described the cloning of a Suaeda liaotungensis K. NAC transcription factor gene SlNAC4, which contained 1450 bp, coding a 331 amino acid. We found that SlNAC4 was highly expressed in stems of S. liaotungensis, and the expression of SlNAC4 was considerably up-regulated after salt, drought, and ABA treatments. Transcription analysis and subcellular localization demonstrated that the SlNAC4 protein was located both in the nucleus and cytoplasm, and contained a C-terminal transcriptional activator. The SlNAC4 overexpression Arabidopsis lines significantly enhanced the tolerance to salt and drought treatment and displayed obviously increased activity of antioxidant enzymes under salt and drought stress. Additionally, transgenic plants overexpressing SlNAC4 had a significantly higher level of physiological indices. Interestingly, SlNAC4 promoted the expression of ABA metabolism-related genes including AtABA1, AtABA3, AtNCED3, AtAAO3, but inhibited the expression of AtCYP707A3 in overexpression lines. Using a yeast one-hybrid (Y1H) assay, we identified that the SlNAC4 transcription factor could bind to the promoters of those ABA metabolism-related genes. These results indicate that overexpression of SlNAC4 in plants enhances the tolerance to salt and drought stress by regulating ABA metabolism.

Cytochrome P450 Gene Families: Role in Plant Secondary Metabolites Production and Plant Defense

Cytochrome P450s (CYPs) are the most prominent family of enzymes involved in NADPH- and O2-dependent hydroxylation processes throughout all spheres of life. CYPs are crucial for the detoxification of xenobiotics in plants, insects, and other organisms. In addition to performing this function, CYPs serve as flexible catalysts and are essential for producing secondary metabolites, antioxidants, and phytohormones in higher plants. Numerous biotic and abiotic stresses frequently affect the growth and development of plants. They cause a dramatic decrease in crop yield and a deterioration in crop quality. Plants protect themselves against these stresses through different mechanisms, which are accomplished by the active participation of CYPs in several biosynthetic and detoxifying pathways. There are immense potentialities for using CYPs as a candidate for developing agricultural crop species resistant to biotic and abiotic stressors. This review provides an overview of the plant CYP families and their functions to plant secondary metabolite production and defense against different biotic and abiotic stresses.

Changes in endogenous abscisic acid and stomata of the resurrection fern, Pleopeltis polypodioides, in response to de- and rehydration

PREMISE

While angiosperms respond uniformly to abscisic acid (ABA) by stomatal closure, the response of ferns to ABA is ambiguous. We evaluated the effect of endogenous ABA, hydrogen peroxide (H₂ O₂ ), nitric oxide (NO), and Ca²⁺ , low and high light intensities, and blue light (BL) on stomatal opening of Pleopeltis polypodioides.

METHODS

Endogenous ABA was quantified using gas chromatography-mass spectrometry; microscopy results and stomatal responses to light and chemical treatments were analyzed with Image J.

RESULTS

The ABA content increases during initial dehydration, peaks at 15 h and then decreases to one fourth of the ABA content of hydrated fronds. Following rehydration, ABA content increases within 24 h to the level of hydrated tissue. The stomatal aperture opens under BL and remains open even in the presence of ABA. Closure was strongly affected by BL, NO, and Ca²⁺ , regardless of ABA, H₂ O₂ effect was weak.

CONCLUSIONS

The decrease in the ABA content during extended dehydration and insensitivity of the stomata to ABA suggests that the drought tolerance mechanism of Pleopeltis polypodioides is independent of ABA.

Distinct hormonal and morphological control of dormancy and germination in Chenopodium album dimorphic seeds

Dormancy and heteromorphism are innate seed properties that control germination timing through adaptation to the prevailing environment. The degree of variation in dormancy depth within a seed population differs considerably depending on the genotype and maternal environment. Dormancy is therefore a key trait of annual weeds to time seedling emergence across seasons. Seed heteromorphism, the production of distinct seed morphs (in color, mass or other morphological characteristics) on the same individual plant, is considered to be a bet-hedging strategy in unpredictable environments. Heteromorphic species evolved independently in several plant families and the distinct seed morphs provide an additional degree of variation. Here we conducted a comparative morphological and molecular analysis of the dimorphic seeds (black and brown) of the Amaranthaceae weed Chenopodium album. Freshly harvested black and brown seeds differed in their dormancy and germination responses to ambient temperature. The black seed morph of seedlot #1 was dormant and 2/3^rd of the seed population had non-deep physiological dormancy which was released by after-ripening (AR) or gibberellin (GA) treatment. The deeper dormancy of the remaining 1/3^rd non-germinating seeds required in addition ethylene and nitrate for its release. The black seeds of seedlot #2 and the brown seed morphs of both seedlots were non-dormant with 2/3^rd of the seeds germinating in the fresh mature state. The dimorphic seeds and seedlots differed in testa (outer seed coat) thickness in that thick testas of black seeds of seedlot #1 conferred coat-imposed dormancy. The dimorphic seeds and seedlots differed in their abscisic acid (ABA) and GA contents in the dry state and during imbibition in that GA biosynthesis was highest in brown seeds and ABA degradation was faster in seedlot #2. Chenopodium genes for GA and ABA metabolism were identified and their distinct transcript expression patterns were quantified in dry and imbibed C. album seeds. Phylogenetic analyses of the Amaranthaceae sequences revealed a high proportion of expanded gene families within the Chenopodium genus. The identified hormonal, molecular and morphological mechanisms and dormancy variation of the dimorphic seeds of C. album and other Amaranthaceae are compared and discussed as adaptations to variable and stressful environments.

Understanding of the various aspects of gene regulatory networks related to crop improvement

The hierarchical relationship between transcription factors, associated proteins, and their target genes is defined by a gene regulatory network (GRN). GRNs allow us to understand how the genotype and environment of a plant are incorporated to control the downstream physiological responses. During plant growth or environmental acclimatization, GRNs are diverse and can be differently regulated across tissue types and organs. An overview of recent advances in the development of GRN that speed up basic and applied plant research is given here. Furthermore, the overview of genome and transcriptome involving GRN research along with the exciting advancement and application are discussed. In addition, different approaches to GRN predictions were elucidated. In this review, we also describe the role of GRN in crop improvement, crop plant manipulation, stress responses, speed breeding and identifying genetic variations/locus. Finally, the challenges and prospects of GRN in plant biology are discussed.

Leafamine®, a Free Amino Acid-Rich Biostimulant, Promotes Growth Performance of Deficit-Irrigated Lettuce

Water deficit causes substantial yield losses that climate change is going to make even more problematic. Sustainable agricultural practices are increasingly developed to improve plant tolerance to abiotic stresses. One innovative solution amongst others is the integration of plant biostimulants in agriculture. In this work, we investigate for the first time the effects of the biostimulant -Leafamine®-a protein hydrolysate on greenhouse lettuce (Lactuca sativa L.) grown under well-watered and water-deficit conditions. We examined the physiological and metabolomic water deficit responses of lettuce treated with Leafamine® (0.585 g/pot) or not. Root application of Leafamine® increased the shoot fresh biomass of both well-watered (+40%) and deficit-irrigated (+20%) lettuce plants because the projected leaf area increased. Our results also indicate that Leafamine® application could adjust the nitrogen metabolism by enhancing the total nitrogen content, amino acid (proline) contents and the total protein level in lettuce leaves, irrespective of the water condition. Osmolytes such as soluble sugars and polyols, also increased in Leafamine®-treated lettuce. Our findings suggest that the protective effect of Leafamine is a widespread change in plant metabolism and could involve ABA, putrescine and raffinose.

Physiology and Gene Expression Analysis of Potato (Solanum tuberosum L.) in Salt Stress

The production of potato (Solanum tuberosum L.) faces a severe challenge due to the salinization of arable land worldwide. The cultivation of salt-tolerant potatoes is of great significance to ensure food security. In this study, two cultivars of 'Longshu 5' and 'Qingshu 9' were compared for physiological responses to salt stress, and then the salt tolerance of the two cultivars were assessed via principal component analysis. Furthermore, the Na⁺, K⁺, and Ca²⁺ flux of the cultivars under salt stress was recorded. Finally, the expression levels of ion transport-related genes and transcription factors in salt-tolerant cultivars were explored under NaCl stress. The results showed that the seven physiological indicators of salt tolerance were differed between the cultivars. Interestingly, soluble protein and sugar were early responsive to salt stress than proline in the salt-tolerance cultivar. Peroxidase and superoxide dismutase activity were significantly different in 'Longshu 5' under NaCl stress and without being significantly different in 'Qingshu9'. In addition, the salt tolerance of 'Longshu 5' was more tolerant than 'Qingshu 9' based on principal component evaluation. Meanwhile, the strong efflux of Na⁺, the stability of K⁺, and the high absorption of Ca²⁺ in 'Longshu 5' indicated salt adaption mechanisms in the salt-tolerant potato. In addition, we found that ion transport-related genes and transcription factors, such as StSOS1, StNHX4, StAKT1, StNAC24, and StCYP707A, played a role in the salt tolerance of 'Longshu 5'. In conclusion, the salt-tolerant potato can regulate physiological substances to adapt to salt stress, and ion transport related genes and transcription factors play a role in improving salt tolerance.

Functional study and elite haplotype identification of soybean phosphate starvation response transcription factors GmPHR14 and GmPHR32

Phosphorus (P) is one of the important mineral elements required for plant growth and development. However, because of the low mobility in soil, P deficiency has been an important factor limiting soybean production. Here, we identified 14 PHR (phosphate starvation response) genes in soybean genome and verified that two previously unreported GmPHR members, GmPHR14 and GmPHR32, were involved in low-P stress tolerance in soybean. GmPHR14 and GmPHR32 were present in two diverged branches of the phylogenic tree. Both genes were highly expressed in roots and root nodules and were induced by P deficiency. GmPHR14 and GmPHR32 both were expressed in the nucleus. The 211 amino acids in the N terminus of GmPHR32 were found to be required for the transcriptional activity. Overexpressing GmPHR14 or GmPHR32 in soybean hairy roots significantly increased roots and shoots dry weight under low-P condition, and overexpressing GmPHR14 additionally significantly increased roots P concentration under low-P condition. GmPHR14 and GmPHR32 were polymorphic in soybean population and the elite haplotype2 (Hap2) for both genes was preferentially present in improved cultivars and showed significantly higher shoots dry weight under low-P condition than the other two haplotypes. These results suggested GmPHR14 and GmPHR32 both positively regulated low-P responses in soybean, and would shed light on the molecular mechanism of low-P stress tolerance. Furthermore, the identified elite haplotypes would be useful in P-efficient soybean breeding.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-022-01301-z.

TaNBR1, a Novel Wheat NBR1-like Domain Gene Negatively Regulates Drought Stress Tolerance in Transgenic Arabidopsis

Drought stress is an important factor that severely affects crop yield and quality. Autophagy has a crucial role in the responses to abiotic stresses. In this study, we explore TaNBR1 in response to drought stress. Expression of the TaNBR1 gene was strongly induced by NaCl, PEG, and abscisic acid treatments. The TaNBR1 protein is localized in the Golgi apparatus and autophagosome. Transgenic Arabidopsis plants overexpressing TaNBR1 exhibited reduced drought tolerance. When subjected to drought stress, compared to the wild-type (WT) lines, the transgenic overexpressing TaNBR1 plants had a lower seed germination rate, relative water content, proline content, and reduced accumulation of antioxidant enzymes, i.e., superoxide dismutase, peroxidase, and catalase, as well as higher chlorophyll losses, malondialdehyde contents, and water loss. The transgenic plants overexpressing TaNBR1 produced much shorter roots in response to mannitol stress, in comparison to the WT plants, and they exhibited greater sensitivity to abscisic acid treatment. The expression levels of the genes related to stress in the transgenic plants were affected in response to drought stress. Our results indicate that TaNBR1 negatively regulates drought stress responses by affecting the expression of stress-related genes in Arabidopsis.

Physiological and Transcriptome Indicators of Salt Tolerance in Wild and Cultivated Barley

Barley is used as a model cereal to decipher salt tolerance mechanisms due to its simpler genome than wheat and enhanced salt tolerance compared to rice and wheat. In the present study, RNA-Seq based transcriptomic profiles were compared between salt-tolerant wild (Hordeum spontaneum, genotype no. 395) genotype and salt-sensitive cultivated (H. vulgare, 'Mona' cultivar) subjected to salt stress (300 mM NaCl) and control (0 mM NaCl) conditions. Plant growth and physiological attributes were also evaluated in a separate experiment as a comparison. Wild barley was significantly less impacted by salt stress than cultivated barley in growth and physiology and hence was more stress-responsive functionally. A total of 6,048 differentially expressed genes (DEGs) including 3,025 up-regulated and 3,023 down-regulated DEGs were detected in the wild genotype in salt stress conditions. The transcripts of salt-stress-related genes were profoundly lower in the salt-sensitive than the tolerant barley having a total of 2,610 DEGs (580 up- and 2,030 down-regulated). GO enrichment analysis showed that the DEGs were mainly enriched in biological processes associated with stress defenses (e.g., cellular component, signaling network, ion transporter, regulatory proteins, reactive oxygen species (ROS) scavenging, hormone biosynthesis, osmotic homeostasis). Comparison of the candidate genes in the two genotypes showed that the tolerant genotype contains higher functional and effective salt-tolerance related genes with a higher level of transcripts than the sensitive one. In conclusion, the tolerant genotype consistently exhibited better tolerance to salt stress in physiological and functional attributes than did the sensitive one. These differences provide a comprehensive understanding of the evolved salt-tolerance mechanism in wild barley. The shared mechanisms between these two sub-species revealed at each functional level will provide more reliable insights into the basic mechanisms of salt tolerance in barley species.

The soybean Phytoglobin1 (GmPgb1) is involved in water deficit responses through changes in ABA metabolism

Soybean (Glycine max), a major grain crop worldwide, is susceptible to severe yield loss due to drought. Soybean plants over-expressing and downregulating the soybean Phytoblobin1 (GmPgb1) were evaluated for their ability to cope with polyethylene glycol (PEG)-induced water deficit. Sense transformation of GmPgb1, which was more expressed in shoot tissue relative to roots, increased overall plant performance and tolerance to water stress by attenuating the PEG depression of photosynthetic gas exchange parameters and chlorophyll content, as well as reducing leaf injury and promoting root growth. The higher plant relative water content, as a result of GmPgb1 over-expression, was associated with higher transcript levels of three aquaporins: GmTIP1;5 and GmTIP2;5 GmPIP2;9, known to confer water stress tolerance. Opposite results were observed in plants suppressing GmPgb1, which were highly susceptible to PEG-induced stress. Transcriptional and metabolic analyses revealed higher ABA synthesis in dehydrating leaves of plants over-expressing GmPgb1 relative to those suppressing the same gene. The latter plants exhibited a transcriptional induction of ABA catabolic enzymes and higher accumulation of the ABA catabolite dehydrophaseic acid (DPA). Administration of 8'-acetylene ABA, an ABA agonist resistant to the ABA catabolic activity, was sufficient to restore tolerance in the GmPgb1 down-regulating plants suggesting that regulation of ABA catabolism is as important as ABA synthesis in conferring PEG-induced water stress tolerance. Screening of natural soybean germplasm also revealed a rapid and transient increase in foliar GmPgb1 in tolerant plants relative to their susceptible counterparts, thus confirming the key role exercised by this gene during water stress.

OsCYP714D1 improves plant growth and salt tolerance through regulating gibberellin and ion homeostasis in transgenic poplar

Cytochrome P450 monooxygenases (CYP450s) play crucial roles in the regulation of plant growth and response to abiotic stress. However, their functions in woody trees are still largely unknown. Previously, we reported that expression of the rice cytochrome P450 monooxygenase gene OsCYP714D1 increased gibberellic acid (GA) accumulation and shoot growth in transgenic poplar. In this work, we demonstrate that expression of OsCYP714D1 improved the salt tolerance of transgenic poplar plants. Compared to wild type, plant height and K⁺ content were significantly higher, whereas plant growth inhibition and Na⁺ content were significantly lower, in transgenic plants grown under high salt stress condition. Transcriptomic analyses revealed that OsCYP714D1 expression up-regulated the expressions of GA biosynthesis, signaling and stress responsive genes in transgenic plants under both normal and high salt stress conditions. Further gene ontology (GO) analyses indicated that genes involved in plant hormone and ion metabolic activities were significantly enriched in transgenic plants. Our findings imply that OsCYP714D1 participated in the regulation of both shoot growth and salt resistance through regulating gibberellin and ion homeostasis in transgenic poplar, and it can be used as a candidate gene for the engineering of new tree varieties with improved biomass production and salt stress resistance.

Characterization of Dynamic Regulatory Gene and Protein Networks in Wheat Roots Upon Perceiving Water Deficit Through Comparative Transcriptomics Survey

A well-developed root system benefits host plants by optimizing water absorption and nutrient uptake and thereby increases plant productivity. In this study we have characterized the root transcriptome using RNA-seq and subsequential functional analysis in a set of drought tolerant and susceptible genotypes. The goal of the study was to elucidate and characterize water deficit-responsive genes in wheat landraces that had been through long-term field and biochemical screening for drought tolerance. The results confirm genotype differences in water-deficit tolerance in line with earlier results from field trials. The transcriptomics survey highlighted a total of 14,187 differentially expressed genes (DEGs) that responded to water deficit. The characterization of these genes shows that all chromosomes contribute to water-deficit tolerance, but to different degrees, and the B genome showed higher involvement than the A and D genomes. The DEGs were mainly mapped to flavonoid, phenylpropanoid, and diterpenoid biosynthesis pathways, as well as glutathione metabolism and hormone signaling. Furthermore, extracellular region, apoplast, cell periphery, and external encapsulating structure were the main water deficit-responsive cellular components in roots. A total of 1,377 DEGs were also predicted to function as transcription factors (TFs) from different families regulating downstream cascades. TFs from the AP2/ERF-ERF, MYB-related, B3, WRKY, Tify, and NAC families were the main genotype-specific regulatory factors. To further characterize the dynamic biosynthetic pathways, protein-protein interaction (PPI) networks were constructed using significant KEGG proteins and putative TFs. In PPIs, enzymes from the CYP450, TaABA8OH2, PAL, and GST families play important roles in water-deficit tolerance in connection with MYB13-1, MADS-box, and NAC transcription factors.

Plant cytochrome P450s: Role in stress tolerance and potential applications for human welfare

Cytochrome P450s (CYPs) are a versatile group of enzymes and one of the largest families of proteins, controlling various physiological processes via biosynthetic and detoxification pathways. CYPs perform multiple roles through a critical irreversible enzymatic reaction in which an oxygen atom is inserted within hydrophobic molecules, converting them into the reactive and hydro soluble components. During evolution, plants have acquired significantly more number of CYPs and represent about 1% of the encoded genes . CYPs are highly conserved proteins involved in growth, development and tolerance against biotic and abiotic stresses. Furthermore, CYPs reinforce plants' molecular and chemical defense mechanisms by regulating the biosynthesis of secondary metabolites, enhancing reactive oxygen species (ROS) scavenging and controlling biosynthesis and homeostasis of phytohormones, including abscisic acid (ABA) and jasmonates. Thus, they are the critical targets of metabolic engineering for enhancing plant defense against environmental stresses. Additionally, CYPs are also used as biocatalysts in the fields of pharmacology and phytoremediation. Herein, we highlight the role of CYPs in plant stress tolerance and their applications for human welfare.

Transcriptomics of Biostimulation of Plants Under Abiotic Stress

Plant biostimulants are compounds, living microorganisms, or their constituent parts that alter plant development programs. The impact of biostimulants is manifested in several ways: via morphological, physiological, biochemical, epigenomic, proteomic, and transcriptomic changes. For each of these, a response and alteration occur, and these alterations in turn improve metabolic and adaptive performance in the environment. Many studies have been conducted on the effects of different biotic and abiotic stimulants on plants, including many crop species. However, as far as we know, there are no reviews available that describe the impact of biostimulants for a specific field such as transcriptomics, which is the objective of this review. For the commercial registration process of products for agricultural use, it is necessary to distinguish the specific impact of biostimulants from that of other legal categories of products used in agriculture, such as fertilizers and plant hormones. For the chemical or biological classification of biostimulants, the classification is seen as a complex issue, given the great diversity of compounds and organisms that cause biostimulation. However, with an approach focused on the impact on a particular field such as transcriptomics, it is perhaps possible to obtain a criterion that allows biostimulants to be grouped considering their effects on living systems, as well as the overlap of the impact on metabolism, physiology, and morphology occurring between fertilizers, hormones, and biostimulants.

Acclimation of photosynthetic processes and metabolic responses to elevated temperatures in cereals

The aim of the present work was to better understand the molecular mechanisms of heat acclimation processes in cereals. A large number of winter and spring wheat, barley and oat varieties were grown under either control conditions (22/20°C) or under a mild heat stress (30°C) that induce the acclimation processes. The temperature dependence of chlorophyll a fluorescence induction and gas exchange parameters showed that heat acclimation increased the thermotolerance of the photosynthetic apparatus, but these changes did not differ sharply in the winter-spring type cereals. Similarly, to wheat, elevated temperature also led to increasing transpiration rate and reduced water use efficiency in barley and oat plants. A non-targeted metabolomic analysis focusing on polar metabolites in two selected barley (winter type Mv Initium and spring type Conchita) and in two oat varieties (winter type Mv Hópehely and spring type Mv Pehely) revealed substantial differences between both the two species and between the acclimated and non-acclimated plants. Several compounds, including sugars, organic acids, amino acids and alcohols could be separated and detected. The expression level of the CYP707, HSP90, galactinol synthase, raffinose synthase and α-galactosidase genes showed genotype-dependent changes after 1 day; however, the CYP707 was the only one, which was still upregulated in at least some of the genotypes. Results suggest that heat acclimation itself does not require general induction of primary metabolites. However, induction of specific routes, e.g. the induction of the raffinose family oligosaccharides, especially the synthesis of galactinol, may also contribute the improved heat tolerance in cereals.

Dissecting the molecular responses of lentil to individual and combined drought and heat stresses by comparative transcriptomic analysis

Lentil cultivation could be challenged by combined heat and drought stress in semi-arid regions. We used RNA-seq approach to profile transcriptome changes of Lens culinaris exposed to individual and combined heat and drought stresses. It was determined that most of the differentially expressed genes observed in response to combined stress, could not be identified by analysis of transcriptome exposed to corresponding individual stresses. Interestingly, this study results revealed that the expression of ribosome generation and protein biosynthesis and starch degradation pathways related genes were uniquely up-regulated under the combined stress. Although multiple genes related to antioxidant activity were up-regulated in response to all stresses, variation in types and expression levels of these genes under the combined stress were higher than that of individual stresses. Using this comparative approach, for the first time, we reported up-regulation of several TF, CDPK, CYP, and antioxidant genes in response to combined stress in plants.

Embryogenic Calli Induction and Salt Stress Response Revealed by RNA-Seq in Diploid Wild Species Gossypium sturtianum and Gossypium raimondii

Wild cotton species can contribute to a valuable gene pool for genetic improvement, such as genes related to salt tolerance. However, reproductive isolation of different species poses an obstacle to produce hybrids through conventional breeding. Protoplast fusion technology for somatic cell hybridization provides an opportunity for genetic manipulation and targeting of agronomic traits. Transcriptome sequencing analysis of callus under salt stress is conducive to study salt tolerance genes. In this study, calli were induced to provide materials for extracting protoplasts and also for screening salt tolerance genes. Calli were successfully induced from leaves of Gossypium sturtianum (C₁ genome) and hypocotyls of G. raimondii (D₅ genome), and embryogenic calli of G. sturtianum and G. raimondii were induced on a differentiation medium with different concentrations of 2, 4-D, KT, and IBA, respectively. In addition, embryogenic calli were also induced successfully from G. raimondii through suspension cultivation. Transcriptome sequencing analysis was performed on the calli of G. raimondii and G. sturtianum, which were treated with 200 mM NaCl at 0, 6, 12, 24, and 48 h, and a total of 12,524 genes were detected with different expression patterns under salt stress. Functional analysis showed that 3,482 genes, which were differentially expressed in calli of G. raimondii and G. sturtianum, were associated with biological processes of nucleic acid binding, plant hormone (such as ABA) biosynthesis, and signal transduction. We demonstrated that DEGs or TFs which related to ABA metabolism were involved in the response to salt stress, including xanthoxin dehydrogenase genes (ABA2), sucrose non-fermenting 1-related protein kinases (SnRK2), NAM, ATAT1/2, and CUC2 transcription factors (NAC), and WRKY class of zinc-finger proteins (WRKY). This research has successfully induced calli from two diploid cotton species and revealed new genes responding to salt stress in callus tissue, which will lay the foundation for protoplast fusion for further understanding of salt stress responses in cotton.

The Role of Stress-Responsive Transcription Factors in Modulating Abiotic Stress Tolerance in Plants

Abiotic stresses, such as drought, high temperature, and salinity, affect plant growth and productivity. Furthermore, global climate change may increase the frequency and severity of abiotic stresses, suggesting that development of varieties with improved stress tolerance is critical for future sustainable crop production. Improving stress tolerance requires a detailed understanding of the hormone signaling and transcriptional pathways involved in stress responses. Abscisic acid (ABA) and jasmonic acid (JA) are key stress-response hormones in plants, and some stress-responsive transcription factors such as ABFs and MYCs function as direct components of ABA and JA signaling, playing a pivotal role in plant tolerance to abiotic stress. In addition, extensive studies have identified other stress-responsive transcription factors belonging to the NAC, AP2/ERF, MYB, and WRKY families that mediate plant response and tolerance to abiotic stress. These suggest that transcriptional regulation of stress-responsive genes is an essential step to determine the mechanisms underlying plant stress responses and tolerance to abiotic stress, and that these transcription factors may be important targets for development of crops with enhanced abiotic stress tolerance. In this review, we briefly describe the mechanisms underlying plant abiotic stress responses, focusing on ABA and JA metabolism and signaling pathways. We then summarize the diverse array of transcription factors involved in plant responses to abiotic stress, while noting their potential applications for improvement of stress tolerance.

Role of Cytochrome P450 Enzymes in Plant Stress Response

Cytochrome P450s (CYPs) are the largest enzyme family involved in NADPH- and/or O₂-dependent hydroxylation reactions across all the domains of life. In plants and animals, CYPs play a central role in the detoxification of xenobiotics. In addition to this function, CYPs act as versatile catalysts and play a crucial role in the biosynthesis of secondary metabolites, antioxidants, and phytohormones in higher plants. The molecular and biochemical processes catalyzed by CYPs have been well characterized, however, the relationship between the biochemical process catalyzed by CYPs and its effect on several plant functions was not well established. The advent of next-generation sequencing opened new avenues to unravel the involvement of CYPs in several plant functions such as plant stress response. The expression of several CYP genes are regulated in response to environmental stresses, and they also play a prominent role in the crosstalk between abiotic and biotic stress responses. CYPs have an enormous potential to be used as a candidate for engineering crop species resilient to biotic and abiotic stresses. The objective of this review is to summarize the latest research on the role of CYPs in plant stress response.

Promoted ABA Hydroxylation by Capsicum annuum CYP707As Overexpression Suppresses Pollen Maturation in Nicotiana tabacum

Abscisic acid (ABA) is a key signaling molecule that mediates plant response to stress. Increasing evidence indicates that ABA also regulates many aspects of plant development, such as seed germination, leaf development, and ripening. ABA metabolism, including ABA biosynthesis and degradation, is an essential aspect of ABA response in plants. In this study, we identified four cytochrome P450 genes (CaCYP707A1, 2, 3, and 4) that mediate ABA hydroxylation, which is required for ABA degradation in Capsicum annuum. We observed that CaCYP707A-mediated ABA hydroxylation promotes ABA degradation, leading to low levels of ABA and a dehydration phenotype in 35S:CaCYP707A plants. Importantly, seed formation was strongly inhibited in 35S:CaCYP707A plants, and a cross-pollination test suggested that the defect in seed formation is caused by improper pollen development. Phenotypic analysis showed that pollen maturation is suppressed in 35S:CaCYP707A1 plants. Consequently, most 35S:CaCYP707A1 pollen grains degenerated, unlike non-transgenic (NT) pollen, which developed into mature pollen grains. Together our results indicate that CaCYP707A mediates ABA hydroxylation and thereby influences pollen development, helping to elucidate the mechanism underlying ABA-regulated pollen development.

CYP707As are effectors of karrikin and strigolactone signalling pathways in Arabidopsis thaliana and parasitic plants

Karrikins stimulate Arabidopsis thaliana germination, whereas parasitic weeds of the Orobanchaceae family have evolved to respond to host-exuded compounds such as strigolactones, dehydrocostus lactone, and 2-phenylethyl isothiocyanate. In Phelipanche ramosa, strigolactone-induced germination was shown to require one of the CYP707A proteins involved in abscisic acid catabolism. Here, germination and gene expression were analysed to investigate the role of CYP707As in germination of both parasitic plants and Arabidopsis upon perception of germination stimulants, after using pharmacological inhibitors and Arabidopsis mutants disrupting germination signals. CYP707A genes were up-regulated upon treatment with effective germination stimulants in both parasitic plants and Arabidopsis. Obligate parasitic plants exhibited both intensified up-regulation of CYP707A genes and increased sensitivity to the CYP707A inhibitor abscinazole-E2B, whereas Arabidopsis cyp707a mutants still positively responded to germination stimulation. In Arabidopsis, CYP707A regulation required the canonical karrikin signalling pathway KAI2/MAX2/SMAX1 and the transcription factor WRKY33. Finally, CYP707As and WRKY33 also modulated Arabidopsis root architecture in response to the synthetic strigolactone rac-GR24, and wrky33-1 exhibited a shoot hyperbranched phenotype. This study suggests that the lack of host-independent germination in obligate parasites is associated with an exacerbated CYP707A induction and that CYP707As and WRKY33 are new players involved in a variety of strigolactone/karrikin responses.

Integrated analysis of mRNA-seq and miRNA-seq in calyx abscission zone of Korla fragrant pear involved in calyx persistence

BACKGROUND

The objective of this study was to characterize molecular mechanism of calyx persistence in Korla fragrant pear by transcriptome and small RNA sequencing. Abscission zone tissues of flowers at three stages (the first, fifth and ninth days of the late bloom stage), with 50 mg/L GA₃ (calyx persistence treatment, C_1, C_5, C_9) or 500 mg/L PP₃₃₃ (calyx abscission treatment, T_1, T_5, T_9), were collected and simultaneously conducted transcriptome and small RNA sequencing.

RESULTS

Through association analysis of transcriptome and small RNA sequencing, mRNA-miRNA network was conducted. Compared calyx persistence groups with calyx abscission groups during the same stage, 145, 56 and 150 mRNA-miRNA pairs were obtained in C_1 vs T_1, C_5 vs T_5 and C_9 vs T_9, respectively; When C_1 compared with C_5 and C_9, 90 and 506 mRNA-miRNA pairs were screened respectively, and 255 mRNA-miRNA pairs were obtained from the comparison between C_5 and C_9; When T_1 compared with the T_5 and T_9, respectively, 206 and 796 mRNA-miRNA pairs were obtained, and 383 mRNA-miRNA pairs were obtained from the comparison between T_5 and T_9. These mRNAs in miRNA-mRNA pairs were significantly enriched into the terpenoid backbone biosynthesis, photosynthesis - antenna proteins, porphyrin and chlorophyll metabolism, carotenoid biosynthesis, zeatin biosynthesis and plant hormone signal transduction. In addition, we obtained some key genes from miRNA-mRNA pairs that may be associated with calyx abscission, including protein phosphatase 2C (psi-miR394a-HAB1), receptor-like protein kinase (psi-miR396a-5p-HERK1), cellulose synthase-like protein D3 (psi-miR827-CSLD3), beta-galactosidase (psi-miR858b-β-galactosidase), SPL-psi-miR156j/157d, abscisic acid 8'-hydroxylase 1 (psi-miR396a-5p-CYP707A1) and auxin response factor (psi-miR160a-3p-ARF6, psi-miR167d-ARF18, psi-miR167a-5p-ARF25), etc. CONCLUSION: By integrated analysis mRNA and miRNA, our study gives a better understanding of the important genes and regulation pathway related to calyx abscission in Korla fragrant pear. We have also established the network of miRNA-mRNA pairs to learn about precise regulation of miRNA on calyx abscission.

Seaweed extract improve drought tolerance of soybean by regulating stress-response genes

There is an increasing global concern about the availability of water for agricultural use. Drought stress negatively impacts plant physiology and crop productivity. Soybean (Glycine max) is one of the important oilseed crops, and its productivity is often reduced by drought. In this study, a commercial extract of Ascophyllum nodosum (ANE) was evaluated for its potential to alleviate drought stress in soybean. The aim of this study was to determine the effects of ANE on the response of soybean plants to drought stress by monitoring stomatal conductance, relative leaf water content, antioxidant activity and expression of stress-responsive genes. Plants treated with ANE had higher relative water content and higher stomatal conductance under drought stress. During early recovery in the post-drought phase, ANE treated plants had significantly higher stomatal conductance. The antioxidant activity was also found higher in the plants treated with ANE. In addition, ANE-treatment led to changes in the expression of stress-responsive genes: GmCYP707A1a, GmCYP707A3b, GmRD22, GmRD20, GmDREB1B, GmERD1, GmNFYA3, FIB1a, GmPIP1b, GmGST, GmBIP and GmTp55. Taken together, these results suggest that applications of ANE improve the drought tolerance of soybean by changing physiology and gene expression.

Constitutive expression of Brassica juncea annexin, AnnBj2 confers salt tolerance and glucose and ABA insensitivity in mustard transgenic plants

Annexins belong to a plasma membrane binding (in a calcium dependent manner), multi-gene family of proteins, which play ameliorating roles in biotic and abiotic stresses. The expression of annexin AnnBj2 of Indian mustard is tissue specific with higher expression in roots and under treatments with sodium chloride and abscisic acid (ABA) at seedling stage. The effect of constitutive expression of AnnBj2 in mustard was analyzed in detail. AnnBj2 OE (over expression) plants exhibited insensitivity to ABA, glucose and sodium chloride. The insensitivity/tolerance of the transgenic plants was associated with enhanced total chlorophylls, relative water content, proline, calcium and potassium with reduced thiobarbituric acid reactive substances and sodium ion accumulation. The altered ABA insensitivity of AnnBj2 OE lines is linked to downregulation of ABI4 and ABI5 transcription factors and upregulation of ABA catabolic gene CYP707A2. Furthermore, we found that overexpression of AnnBj2 upregulated the expression of ABA-dependent RAB18 and ABA-independent DREB2B stress marker genes suggesting that the tolerance phenotype exhibited by AnnBj2 OE lines is probably controlled by both ABA-dependent and -independent mechanisms.

Insights into soybean transcriptome reconfiguration under hypoxic stress: Functional, regulatory, structural, and compositional characterization

Soybean (Glycine max) is one of the major crops worldwide and flooding stress affects the production and expansion of cultivated areas. Oxygen is essential for mitochondrial aerobic respiration to supply the energy demand of plant cells. Because oxygen diffusion in water is 10,000 times lower than in air, partial (hypoxic) or total (anoxic) oxygen deficiency is important component of flooding. Even when oxygen is externally available, oxygen deficiency frequently occurs in bulky, dense or metabolically active tissues such as phloem, meristems, seeds, and fruits. In this study, we analyzed conserved and divergent root transcriptional responses between flood-tolerant Embrapa 45 and flood-sensitive BR 4 soybean cultivars under hypoxic stress conditions with RNA-seq. To understand how soybean genes evolve and respond to hypoxia, stable and differentially expressed genes were characterized structurally and compositionally comparing its mechanistic relationship. Between cultivars, Embrapa 45 showed less up- and more down-regulated genes, and stronger induction of phosphoglucomutase (Glyma05g34790), unknown protein related to N-terminal protein myristoylation (Glyma06g03430), protein suppressor of phyA-105 (Glyma06g37080), and fibrillin (Glyma10g32620). RNA-seq and qRT-PCR analysis of non-symbiotic hemoglobin (Glyma11g12980) indicated divergence in gene structure between cultivars. Transcriptional changes for genes in amino acids and derivative metabolic process suggest involvement of amino acids metabolism in tRNA modifications, translation accuracy/efficiency, and endoplasmic reticulum stress in both cultivars under hypoxia. Gene groups differed in promoter TATA box, ABREs (ABA-responsive elements), and CRT/DREs (C-repeat/dehydration-responsive elements) frequency. Gene groups also differed in structure, composition, and codon usage, indicating biological significances. Additional data suggests that cis-acting ABRE elements can mediate gene expression independent of ABA in soybean roots under hypoxia.

Global Gene-Expression Analysis to Identify Differentially Expressed Genes Critical for the Heat Stress Response in Brassica rapa

Genome-wide dissection of the heat stress response (HSR) is necessary to overcome problems in crop production caused by global warming. To identify HSR genes, we profiled gene expression in two Chinese cabbage inbred lines with different thermotolerances, Chiifu and Kenshin. Many genes exhibited >2-fold changes in expression upon exposure to 0.5– 4 h at 45°C (high temperature, HT): 5.2% (2,142 genes) in Chiifu and 3.7% (1,535 genes) in Kenshin. The most enriched GO (Gene Ontology) items included ‘response to heat’, ‘response to reactive oxygen species (ROS)’, ‘response to temperature stimulus’, ‘response to abiotic stimulus’, and ‘MAPKKK cascade’. In both lines, the genes most highly induced by HT encoded small heat shock proteins (Hsps) and heat shock factor (Hsf)-like proteins such as HsfB2A (Bra029292), whereas high-molecular weight Hsps were constitutively expressed. Other upstream HSR components were also up-regulated: ROS-scavenging genes like glutathione peroxidase 2 (BrGPX2, Bra022853), protein kinases, and phosphatases. Among heat stress (HS) marker genes in Arabidopsis, only exportin 1A (XPO1A) (Bra008580, Bra006382) can be applied to B. rapa for basal thermotolerance (BT) and short-term acquired thermotolerance (SAT) gene. CYP707A3 (Bra025083, Bra021965), which is involved in the dehydration response in Arabidopsis, was associated with membrane leakage in both lines following HS. Although many transcription factors (TF) genes, including DREB2A (Bra005852), were involved in HS tolerance in both lines, Bra024224 (MYB41) and Bra021735 (a bZIP/AIR1 [Anthocyanin-Impaired-Response-1]) were specific to Kenshin. Several candidate TFs involved in thermotolerance were confirmed as HSR genes by real-time PCR, and these assignments were further supported by promoter analysis. Although some of our findings are similar to those obtained using other plant species, clear differences in Brassica rapa reveal a distinct HSR in this species. Our data could also provide a springboard for developing molecular markers of HS and for engineering HS tolerant B. rapa.

Expression of ABA Metabolism-Related Genes Suggests Similarities and Differences Between Seed Dormancy and Bud Dormancy of Peach (Prunus persica)

Dormancy inhibits seed and bud growth of perennial plants until the environmental conditions are optimal for survival. Previous studies indicated that certain co-regulation pathways exist in seed and bud dormancy. In our study, we found that seed and bud dormancy are similar to some extent but show different reactions to chemical treatments that induce breaking of dormancy. Whether the abscisic acid (ABA) regulatory networks are similar in dormant peach seeds and buds is not well known; however, ABA is generally believed to play a critical role in seed and bud dormancy. In peach, some genes putatively involved in ABA synthesis and catabolism were identified and their expression patterns were studied to learn more about ABA homeostasis and the possible crosstalk between bud dormancy and seed dormancy mechanisms. The analysis demonstrated that two 9-cis-epoxycarotenoid dioxygenase-encoding genes seem to be key in regulating ABA biosynthesis to induce seed and bud dormancy. Three CYP707As play an overlapping role in controlling ABA inactivation, resulting in dormancy-release. In addition, Transcript analysis of ABA metabolism-related genes was much similar demonstrated that ABA pathways was similar in the regulation of vegetative and flower bud dormancy, whereas, expression patterns of ABA metabolism-related genes were different in seed dormancy showed that ABA pathway maybe different in regulating seed dormancy in peach.

Cloning and expression analysis of cDNAs encoding ABA 8'-hydroxylase in peanut plants in response to osmotic stress

Abscisic acid (ABA) catabolism is one of the determinants of endogenous ABA levels affecting numerous aspects of plant growth and abiotic-stress responses. The major ABA catabolic pathway is triggered by ABA 8'-hydroxylation catalysed by ABA 8'-hydroxylase, the cytochrome P450 CYP707A family. In this study, the full-length cDNAs of AhCYP707A1 and AhCYP707A2 were cloned and characterized from peanut. Expression analyses showed that AhCYP707A1 and AhCYP707A2 were expressed ubiquitously in peanut roots, stems, and leaves with different transcript accumulation levels, including the higher expression of AhCYP707A1 in roots. The expression of AhCYP707A2 was significantly up-regulated by 20% PEG6000 or 250 mmol/L NaCl in peanut roots, stems, and leaves, whereas the up-regulation of AhCYP707A1 transcript level by PEG6000 or NaCl was observed only in roots instead of leaves and stems. Due to the osmotic and ionic stresses of high concentration of NaCl to plants simultaneously, low concentration of LiCl (30 mmol/L, at which concentration osmotic status of cells is not seriously affected, the toxicity of Li⁺ being higher than that of Na⁺) was used to examine whether the effect of NaCl might be related to osmotic or ionic stress. The results revealed visually the susceptibility to osmotic stress and the resistance to salt ions in peanut seedlings. The significant up-regulation of AhCYP707A1, AhCYP707A2 and AhNCED1 transcripts and endogenous ABA levels by PEG6000 or NaCl instead of LiCl, showed that the osmotic stress instead of ionic stress affected the expression of those genes and the biosynthesis of ABA in peanut. The functional expression of AhCYP707A1 cDNA in yeast showed that the microsomal fractions prepared from yeast cell expressing recombinant AhCYP707A1 protein exhibited the catalytic activity of ABA 8'-hydroxylase. These results demonstrate that the expressions of AhCYP707A1 and AhCYP707A2 play an important role in ABA catabolism in peanut, particularly in response to osmotic stress.