Abiotic Stress Tolerance In Plants Research Articles

Physiological and transcriptome analyses for assessing the effects of exogenous uniconazole on drought tolerance in hemp (Cannabis sativa L.)

Uniconazole (S-(+)-uniconazole), a plant growth retardant, exerts key roles in modulating growth and development and increasing abiotic stress tolerance in plants. However, the underlying mechanisms by which uniconazole regulates drought response remain largely unknown. Here, the effects of exogenous uniconazole on drought tolerance in hemp were studied via physiological and transcriptome analyses of the drought-sensitive industrial hemp cultivar Hanma No. 2 grown under drought stress. Exogenous uniconazole treatment increased hemp tolerance to drought-induced damage by enhancing chlorophyll content and photosynthesis capacity, regulating activities of enzymes involved in carbon and nitrogen metabolism, and altering endogenous hormone levels. Expression of genes associated with porphyrin and chlorophyll metabolism, photosynthesis-antenna proteins, photosynthesis, starch and sucrose metabolism, nitrogen metabolism, and plant hormone signal transduction were significantly regulated by uniconazole compared with that by control (distilled water) under drought stress. Numerous genes were differentially expressed to increase chlorophyll content, enhance photosynthesis, regulate carbon–nitrogen metabolism-related enzyme activities, and alter endogenous hormone levels. Thus, uniconazole regulated physiological and molecular characteristics of photosynthesis, carbon–nitrogen metabolism, and plant hormone signal transduction to enhance drought resistance in industrial hemp.

Transcriptome analysis revealed cellular pathways associated with abiotic stress tolerance and disease resistance induced by Pseudomonas aeruginosa in banana plants

Plants have evolved diverse cellular mechanisms to maintain their fitness under stressful environments. Banana (Musa spp.) plants inoculated with a new rhizobacterial isolate, Pseudomonas aeruginosa strain Y1 (PaY1), showed improved vegetative growth, and increased levels of H2O2, glucosinolates, phenolic compounds, and lignin contents. Plants treated with PaY1 had reduced membrane peroxidation and electrolyte leakages, and exhibited higher PSII efficiencies after drought and submergence treatments. Furthermore, PaY1 treatment reduced disease infection rates in the Foc TR4 (Fusarium wilt pathogen)-inoculated plants. RNA seq results identified signaling molecules activated by PaY1, including ROS/antioxidant molecules and signaling of G protein and sphingolipids. Besides, PaY1 exerted positive effects on hormonal signaling, including auxin, ABA, and jasmonic acid (JA) in banana seedlings. Genes associated with cellular pathways of cell division and flowering control were significantly affected; up-regulated genes were also implicated in cellular pathways regulating nutrient availability. The up-regulated genes functioning in abiotic stress tolerance comprised genes encoding DETOXIFICATION-like proteins, aquaporins, autophagy-like, and MAPKK2-like. Furthermore, genes encoding proteins participating in the regulatory network of disease resistance were discovered, which included members of pathogenesis-related proteins (PRs), cell death associated proteins, proteins implicated in the MAMP-trigger immunity (MTI), and genes such as RGA2-like and ETHYLENE-RESPONSIVE TRANSCRIPTION FACTOR 1B (ERF1B) with predicted functions regulating disease resistance against Fusarium oxysporum in different plant species. The transcriptome data presented here indicated that PaY1 is a potent activator of banana genes related to hormonal signaling and cellular pathways including antioxidant defense, detoxification, and MTI, which worked collaboratively to control plant growth, abiotic and biotic stress tolerance in banana plants.

Citric Acid-Mediated Abiotic Stress Tolerance in Plants.

Several recent studies have shown that citric acid/citrate (CA) can confer abiotic stress tolerance to plants. Exogenous CA application leads to improved growth and yield in crop plants under various abiotic stress conditions. Improved physiological outcomes are associated with higher photosynthetic rates, reduced reactive oxygen species, and better osmoregulation. Application of CA also induces antioxidant defense systems, promotes increased chlorophyll content, and affects secondary metabolism to limit plant growth restrictions under stress. In particular, CA has a major impact on relieving heavy metal stress by promoting precipitation, chelation, and sequestration of metal ions. This review summarizes the mechanisms that mediate CA-regulated changes in plants, primarily CA’s involvement in the control of physiological and molecular processes in plants under abiotic stress conditions. We also review genetic engineering strategies for CA-mediated abiotic stress tolerance. Finally, we propose a model to explain how CA’s position in complex metabolic networks involving the biosynthesis of phytohormones, amino acids, signaling molecules, and other secondary metabolites could explain some of its abiotic stress-ameliorating properties. This review summarizes our current understanding of CA-mediated abiotic stress tolerance and highlights areas where additional research is needed.

MiRNAs play critical roles in response to abiotic stress by modulating cross-talk of phytohormone signaling.

One of the most interesting signaling molecules that regulates a wide array of adaptive stress responses in plants are the micro RNAs (miRNAs) that are a unique class of non-coding RNAs constituting novel mechanisms of post-transcriptional gene regulation. Recent studies revealed the role of miRNAs in several biotic and abiotic stresses by regulating various phytohormone signaling pathways as well as by targeting a number of transcription factors (TFs) and defense related genes. Phytohormones are signal molecules modulating the plant growth and developmental processes by regulating gene expression. Studies concerning miRNAs in abiotic stress response also show their vital roles in abiotic stress signaling. Current research indicates that miRNAs may act as possible candidates to create abiotic stress tolerant crop plants by genetic engineering. Yet, the detailed mechanism governing the dynamic expression networks of miRNAs in response to stress tolerance remains unclear. In this review, we provide recent updates on miRNA-mediated regulation of phytohormones combating various stress and its role in adaptive stress response in crop plants.

In silico analysis of glycosyltransferase 2 family genes in duckweed (Spirodela polyrhiza) and its role in salt stress tolerance.

Plant glycosyltransferase 2 (GT2) family genes are involved in plant abiotic stress tolerance. However, the roles of GT2 genes in the abiotic resistance in freshwater plants are largely unknown. We identified seven GT2 genes in duckweed, remarkably more than those in the genomes of Arabidopsis thaliana, Oryza sativa, Amborella trichopoda, Nymphaea tetragona, Persea americana, Zostera marina, and Ginkgo biloba, suggesting a significant expansion of this family in the duckweed genome. Phylogeny resolved the GT2 family into two major clades. Six duckweed genes formed an independent subclade in Clade I, and the other was clustered in Clade II. Gene structure and protein domain analysis showed that the lengths of the seven duckweed GT2 genes were varied, and the majority of GT2 genes harbored two conserved domains, PF04722.12 and PF00535.25. The expression of all Clade I duckweed GT2 genes was elevated at 0 h after salt treatment, suggesting a common role of these genes in rapid response to salt stress. The gene Sp01g00794 was highly expressed at 12 and 24 h after salt treatment, indicating its association with salt stress resilience. Overall, these results are essential for studies on the molecular mechanisms in stress response and resistance in aquatic plants.

Meta-analysis of the effect of expression of MYB transcription factor genes on abiotic stress.

BackgroundMYB proteins are a large group of transcription factors. The overexpression of MYB genes has been reported to improve abiotic stress tolerance in plant. However, due to the variety of plant species studied and the types of gene donors/recipients, along with different experimental conditions, it is difficult to interpret the roles of MYB in abiotic stress tolerance from published data.MethodsUsing meta-analysis approach, we investigated the plant characteristics involved in cold, drought, and salt stress in MYB-overexpressing plants and analyzed the degrees of influence on plant performance by experimental variables.ResultsThe results show that two of the four measured plant parameters in cold-stressed plants, two of the six in drought-stressed, and four of the 13 in salt-stressed were significantly impacted by MYB overexpression by 22% or more, and the treatment medium, donor/recipient species, and donor type significantly influence the effects of MYB-overexpression on drought stress tolerance. Also, the donor/recipient species, donor type, and stress duration all significantly affected the extent of MYB-mediated salt stress tolerance. In summary, this study compiles and analyzes the data across studies to help us understand the complex interactions that dictate the efficacy of heterologous MYB expression designed for improved abiotic stress tolerance in plants.

Climate-specific biosynthetic gene clusters in populations of a lichen-forming fungus.

Natural products can contribute to abiotic stress tolerance in plants and fungi. We hypothesize that biosynthetic gene clusters (BGCs), the genomic elements that underlie natural product biosynthesis, display structured differences along elevation gradients. We analysed biosynthetic gene variation in natural populations of the lichen-forming fungus Umbilicaria pustulata. We collected a total of 600 individuals from the Mediterranean and cold-temperate climates. Population genomic analyses indicate that U. pustulata contains three clusters that are highly differentiated between the Mediterranean and cold-temperate populations. One entire cluster is exclusively present in cold-temperate populations, and a second cluster is putatively dysfunctional in all cold-temperate populations. In the third cluster variation is fixed in all cold-temperate populations due to hitchhiking. In these two clusters the presence of consistent allele frequency differences among replicate populations/gradients suggests that selection rather than drift is driving the pattern. We advocate that the landscape of fungal biosynthetic genes is shaped by both positive and hitchhiking selection. We demonstrate, for the first time, the presence of climate-associated BGCs and BGC variations in lichen-forming fungi. While the associated secondary metabolites of the candidate clusters are presently unknown, our study paves the way for targeted discovery of natural products with ecological significance.

Integration of Gas Exchange With Metabolomics: High-Throughput Phenotyping Methods for Screening Biostimulant-Elicited Beneficial Responses to Short-Term Water Deficit.

Biostimulants are emerging as a feasible tool for counteracting reduction in climate change-related yield and quality under water scarcity. As they are gaining attention, the necessity for accurately assessing phenotypic variables in their evaluation is emerging as a critical issue. In light of this, high-throughput phenotyping techniques have been more widely adopted. The main bottleneck of these techniques is represented by data management, which needs to be tailored to the complex, often multifactorial, data. This calls for the adoption of non-linear regression models capable of capturing dynamic data and also the interaction and effects between multiple factors. In this framework, a commercial glycinebetaine- (GB-) based biostimulant (Vegetal B60, ED&F Man) was tested and distributed at a rate of 6 kg/ha. Exogenous application of GB, a widely accumulated and documented stress adaptor molecule in plants, has been demonstrated to enhance the plant abiotic stress tolerance, including drought. Trials were conducted on tomato plants during the flowering stage in a greenhouse. The experiment was designed as a factorial combination of irrigation (water-stressed and well-watered) and biostimulant treatment (treated and control) and adopted a mixed phenotyping-omics approach. The efficacy of a continuous whole-canopy multichamber system coupled with generalized additive mixed modeling (GAMM) was evaluated to discriminate between water-stressed plants under the biostimulant treatment. Photosynthetic performance was evaluated by using GAMM, and was then correlated to metabolic profile. The results confirmed a higher photosynthetic efficiency of the treated plants, which is correlated to biostimulant-mediated drought tolerance. Furthermore, metabolomic analyses demonstrated the priming effect of the biostimulant for stress tolerance and detoxification and stabilization of photosynthetic machinery. In support of this, the overaccumulation of carotenoids was particularly relevant, given their photoprotective role in preventing the overexcitation of photosystem II. Metabolic profile and photosynthetic performance findings suggest an increased effective use of water (EUW) through the overaccumulation of lipids and leaf thickening. The positive effect of GB on water stress resistance could be attributed to both the delayed onset of stress and the elicitation of stress priming through the induction of H2O2-mediated antioxidant mechanisms. Overall, the mixed approach supported by a GAMM analysis could prove a valuable contribution to high-throughput biostimulant testing.

<p><strong>Molecular cloning and <em>in</em> <em>silico</em> analysis of heat stress responsive gene <em>ClpB</em>1 </strong><strong>from <em>Ziziphus nummularia </em>genotypes</strong></p>

Heat stress is one of the most destructive abiotic stresses which adversely affect crop plants, resulting in reduced potential yield. Plants that are able to tolerate heat stress possess an intrinsic mechanism which needs to be unravelled at molecular level so as to decipher the role of gene and metabolic pathways involved in heat stress tolerance. To understand the molecular mechanism of heat stress tolerance, studies on isolation and characterization of gene for abiotic stress tolerance, ClpB1 were performed in Ziziphus nummularia (Burm. f.) Wight & Arn, an inherently abiotic stress tolerant plant. Differential expression studies of gene ClpB1 by qRT-PCR in contrasting genotypes of Z. nummularia (genotype Jaisalmer: heat tolerant and genotype Godhra: heat sensitive) was carried out. CDS (Coding DNA sequence) of gene ClpB1 from the genotypes Z. nummularia J and Z. nummularia G were cloned and characterized. These genes ZnJClpB1 (ACNO: MN398267) and ZnGClpB1 (ACNO: MN398268) showed 1.09 and 2.3% dissimilarity at nucleotide and amino acid level, respectively. Computational based analysis revealed the presence of larger functional AAA lid 9 domains in ZnJClpB1 as compared to ZnGClpB1. Phylogenetic relationship and structure modeling was performed to understand isoform type and basic molecular functioning and of gene ZnClpB1 from Z. nummularia genotypes. Possibly, it is the first report on cloning, characterization and comparative in silico based analysis of gene ZnClpB1 in Z. nummularia. Gene ZnClpB1 would be a prospective resource for developing abiotic stress tolerant crops by transgenic or breeding approach.

The Effects of Plant-Associated Bacterial Exopolysaccharides on Plant Abiotic Stress Tolerance

Plant growth-promoting rhizobacteria (PGPR) are beneficial soil microorganisms that can stimulate plant growth and increase tolerance to biotic and abiotic stresses. Some PGPR are capable of secreting exopolysaccharides (EPS) to protect themselves and, consequently, their plant hosts against environmental fluctuations and other abiotic stresses such as drought, salinity, or heavy metal pollution. This review focuses on the enhancement of plant abiotic stress tolerance by bacterial EPS. We provide a comprehensive summary of the mechanisms through EPS to alleviate plant abiotic stress tolerance, including salinity, drought, temperature, and heavy metal toxicity. Finally, we discuss how these abiotic stresses may affect bacterial EPS production and its role during plant-microbe interactions.

Nitric oxide, crosstalk with stress regulators and plant abiotic stress tolerance.

Nitric oxide is a dynamic gaseous molecule involved in signalling, crosstalk with stress regulators, and plant abiotic-stress responses. It has great exploratory potentials for engineering abiotic stress tolerance in crops. Nitric oxide (NO), a redox-active gaseous signalling molecule, though present uniformly through the eukaryotes, maintain its specificity in plants with respect to its formation, signalling, and functions. Its cellular concentrations are decisive for its function, as a signalling molecule at lower concentrations, but triggers nitro-oxidative stress and cellular damage when produced at higher concentrations. Besides, it also acts as a potent stress alleviator. Discovered in animals as neurotransmitter, NO has come a long way to being a stress radical and growth regulator in plants. As a key redox molecule, it exhibits several key cellular and molecular interactions including with reactive chemical species, hydrogen sulphide, and calcium. Apart from being a signalling molecule, it is emerging as a key player involved in regulations of plant growth, development and plant-environment interactions. It is involved in crosstalk with stress regulators and is thus pivotal in these stress regulatory mechanisms. NO is getting an unprecedented attention from research community, being investigated and explored for its multifaceted roles in plant abiotic stress tolerance. Through this review, we intend to present the current knowledge and updates on NO biosynthesis and signalling, crosstalk with stress regulators, and how biotechnological manipulations of NO pathway are leading towards developing transgenic crop plants that can withstand environmental stresses and climate change. The targets of various stress responsive miRNA signalling have also been discussed besides giving an account of current approaches used to characterise and detect the NO.

Current Understanding of bHLH Transcription Factors in Plant Abiotic Stress Tolerance.

Named for the characteristic basic helix-loop-helix (bHLH) region in their protein structure, bHLH proteins are a widespread transcription factor class in eukaryotes. bHLHs transcriptionally regulate their target genes by binding to specific positions on their promoters and thereby direct a variety of plant developmental and metabolic processes, such as photomorphogenesis, flowering induction, shade avoidance, and secondary metabolite biosynthesis, which are important for promoting plant tolerance or adaptation to adverse environments. In this review, we discuss the vital roles of bHLHs in plant responses to abiotic stresses, such as drought, salinity, cold, and iron deficiency. We suggest directions for future studies into the roles of bHLH genes in plant and discuss their potential applications in crop breeding.

Beneficial Effects of Exogenous Melatonin on Overcoming Salt Stress in Sugar Beets (Beta vulgaris L.).

Melatonin has been regarded as a promising substance that enhances the abiotic stress tolerance of plants. However, few studies have devoted attention to the role of melatonin in improving salt tolerance in sugar beets. Here, the effects of different application methods (foliar application (100 μM), root application (100 μM), and combined foliar and root application) of melatonin on the morphological and physiological traits of sugar beets exposed to salt stress were investigated. The results showed that melatonin improved the growth of sugar beet seedlings, root yield and sugar content, synthesis of chlorophyll, photosystem II (PS II) activity, and gas exchange parameters under salt stress conditions. Moreover, melatonin enhanced the capacity of osmotic adjustment by increasing the accumulation of osmolytes (betaine, proline, and soluble sugar). At the same time, melatonin increased the H+-pump activities in the roots, thus promoting Na+ efflux and K+ influx, which maintained K+/Na+ homeostasis and mitigated Na+ toxicity. In addition, melatonin strengthened the antioxidant defense system by enhancing the activities of antioxidant enzymes, modulating the ASA-GSH cycle, and mediating the phenylalanine pathway, which removed superoxide anions (O2•−) and hydrogen peroxide (H2O2) and maintained cell membrane integrity. These positive effects were more pronounced when melatonin was applied by combined foliar and root application. To summarize, this study clarifies the potential roles of melatonin in mitigating salt stress in sugar beets by improving photosynthesis, water status, ion homeostasis, and the antioxidant defense system.

A Versatile Peroxidase from the Fungus Bjerkandera adusta Confers Abiotic Stress Tolerance in Transgenic Tobacco Plants.

White-rot fungi are efficient lignin degraders due to the secretion of lignin peroxidase, manganese peroxidase, laccase, and versatile peroxidase (VP) on decayed wood. The VP is a high-redox-potential enzyme and could be used to detoxify reactive oxygen species (ROS), which accumulate in plants during biotic and abiotic stresses. We cloned the VP gene and expressed it via the Agrobacterium transformation procedure in transgenic tobacco plants to assay their tolerance to different abiotic stress conditions. Thirty independent T2 transgenic VP lines overexpressing the fungal Bjerkandera adusta VP gene were selected on kanamycin. The VP22, VP24, and VP27 lines showed significant manganese peroxidase (MnP) activity. The highest was VP22, which showed 10.87-fold more manganese peroxidase activity than the wild-type plants and led to a 34% increase in plant height and 28% more biomass. The VP22, VP24, and VP27 lines showed enhanced tolerance to drought, 200 mM NaCl, and 400 mM sorbitol. Also, these transgenics displayed significant tolerance to methyl viologen, an active oxygen-generating compound. The present data indicate that overproducing the VP gene in plants increases significantly their biomass and the abiotic stress tolerance. The VP enzyme is an effective biotechnological tool to protect organisms against ROS. In transgenic tobacco plants, it improves drought, salt, and oxidative stress tolerance. Thus, the VP gene represents a great potential for obtaining stress-tolerant crops.

EkFLS overexpression promotes flavonoid accumulation and abiotic stress tolerance in plant.

Flavonoids with great medicinal value play an important role in plant individual growth and stress resistance. Flavonol synthetase (FLS) is one of the key enzymes to synthesize flavonoids. However, the role of the FLS gene in flavonoid accumulation and tolerance to abiotic stresses, as well as its mechanism has not yet been investigated systematically in plants. The aim of this research is to evaluate the effect of FLS overexpression on the accumulation of active ingredients and stress resistance in Euphorbia kansui Liou. The results showed that when the EkFLS gene was overexpressed in Arabidopsis thaliana, the accumulation of flavonoids was improved. In addition, when the wild-type and EkFLS overexpressed Arabidopsis plants were treated with ABA and MeJA, compared with WT Arabidopsis, EkFLS overexpressed Arabidopsis promoted stomatal aperture to influence photosynthesis of the plants, which in turn can promote stress resistance. Meanwhile, under MeJA, NaCl, and PEG treatment, EkFLS overexpressed in Arabidopsis induced higher accumulation of flavonoids, which significantly enhanced peroxidase (POD) and superoxide dismutase (SOD) activities that can scavenge reactive oxygen species in cells to protect the plant. These results indicated that EkFLS overexpression is strongly correlated to the increase of flavonoid synthesis and therefore the tolerance to abiotic stresses in plants, providing a theoretical basis for further improving the quality of medicinal plants and their resistance to abiotic stresses simultaneously.

The Multiple Roles of Ascorbate in the Abiotic Stress Response of Plants: Antioxidant, Cofactor, and Regulator.

Ascorbate (ASC) plays a critical role in plant stress response. The antioxidant role of ASC has been well-studied, but there are still several confusing questions about the function of ASC in plant abiotic stress response. ASC can scavenge reactive oxygen species (ROS) and should be helpful for plant stress tolerance. But in some cases, increasing ASC content impairs plant abiotic stress tolerance, whereas, inhibiting ASC synthesis or regeneration enhances plant stress tolerance. This confusing phenomenon indicates that ASC may have multiple roles in plant abiotic stress response not just as an antioxidant, though many studies more or less ignored other roles of ASC in plant. In fact, ACS also can act as the cofactor of some enzymes, which are involved in the synthesis, metabolism, and modification of a variety of substances, which has important effects on plant stress response. In addition, ASC can monitor and effectively regulate cell redox status. Therefore, we believe that ASC has atleast triple roles in plant abiotic stress response: as the antioxidant to scavenge accumulated ROS, as the cofactor to involve in plant metabolism, or as the regulator to coordinate the actions of various signal pathways under abiotic stress. The role of ASC in plant abiotic stress response is important and complex. The detail role of ASC in plant abiotic stress response should be analyzed according to specific physiological process in specific organ. In this review, we discuss the versatile roles of ASC in the response of plants to abiotic stresses.

TaASR1-D confers abiotic stress resistance by affecting ROS accumulation and ABA signalling in transgenic wheat.

Cultivating new crop cultivars with multiple abiotic stress tolerances is important for crop production. The abscisic acid‐stress‐ripening (ASR) protein has been shown to confer abiotic stress tolerance in plants. However, the mechanisms of ASR function under stress condition remain largely unclear. In this study, we characterized all ASR family members in common wheat and constitutively overexpressed TaASR1‐D in a commercial hexaploid wheat cultivar Zhengmai 9023. The transgenic wheat plants exhibited increased tolerance to multiple abiotic stresses and increased grain yields under salt stress condition. Overexpression of TaASR1‐D conferred enhanced antioxidant capacity and ABA sensitivity in transgenic wheat plants. Further, RNA in situ hybridization results showed that TaASR1‐D had higher expression levels in the vascular tissues of leaves and the parenchyma cells around the vascular tissues of roots and stems. Yeast one‐hybrid and electrophoretic mobility shift assays revealed that TaASR1‐D could directly bind the specific cis‐elements in the promoters of TaNCED1 and TaGPx1‐D. In conclusion, our findings suggest that TaASR1‐D can be used to breed new wheat cultivars with increased multiple abiotic stress tolerances, and TaASR1‐D enhances abiotic stress tolerances by reinforcing antioxidant capacity and ABA signalling.

CRISPR-Cas genome-editing tool in plant abiotic stress-tolerance

Adverse ambience caused by abiotic stresses affect the plant growth and increase the chances of low yield and resulting economic loss. To resolve this issue, several measures have been taken. Use of CRISPR/Cas gene-editing system to develop stress-resistant plant varieties has gained attention at present. Versatility of this user-friendly system has made it popular to the researchers. The DNA sequence family “CRISPR” and the endonuclease “Cas” work together in the gene-editing process following the direction by specific guide RNA. CRISPR/Cas system is applied in a number of plant species. Cas9 is frequently used in most of the cases. Several reports of the improvement of abiotic stress-tolerance in plants using CRISPR/Cas9 technology has been documented. Genome-editing efficiency of CRISPR/Cas9 system depends on some factors like Cas9 expression, RNA polymerase specificity, guide RNA expression, promoter sequence, types of transformation vectors etc. Sometimes, a few modifications of this system is needed to get expected outcomes. CRISPR/Cas9 system can be utilized in some prospective programmes like mutant library generation, reduction of agrochemical supplementation during cultivation, gene regulation, plant domestication etc. Basic and applied plant biology might be enriched through the further progress of CRISPR/Cas9 technology. The present review encompasses the applications of CRISPR-Cas genome-editing toolkit against abiotic stress-tolerance in many model as well as commercially important plants with notes on their genetic regulations. In addition, the article also outlines the existing shortcomings in past research with notes on future prospective.

Knockout of the entire family of AITR genes in Arabidopsis leads to enhanced drought and salinity tolerance without fitness costs

BackgorundEnvironmental stresses including abiotic stresses and biotic stresses limit yield of plants. Stress-tolerant breeding is an efficient way to improve plant yield under stress conditions. Genome editing by CRISPR/Cas9 can be used in molecular breeding to improve agronomic traits in crops, but in most cases, with fitness costs. The plant hormone ABA regulates plant responses to abiotic stresses via signaling transduction. We previously identified AITRs as a family of novel transcription factors that play a role in regulating plant responses to ABA and abiotic stresses. We found that abiotic stress tolerance was increased in the single, double and triple aitr mutants. However, it is unclear if the increased abiotic stress tolerance in the mutants may have fitness costs.ResultsWe report here the characterization of AITRs as suitable candidate genes for CRISPR/Cas9 editing to improve plant stress tolerance. By using CRISPR/Cas9 to target AITR3 and AITR4 simultaneously in the aitr256 triple and aitr1256 quadruple mutants respectively, we generated Cas9-free aitr23456 quintuple and aitr123456 sextuple mutants. We found that reduced sensitivities to ABA and enhanced tolerance to drought and salt were observed in these mutants. Most importantly, plant growth and development was not affected even in the aitr123456 sextuple mutants, in whom the entire AITR family genes have been knocked out, and the aitr123456 sextuple mutants also showed a wild type response to the pathogen infection.ConclusionsOur results suggest that knockout of the AITR family genes in Arabidopsis enhanced abiotic stress tolerance without fitness costs. Considering that knock-out a few AITRs will lead to enhanced abiotic stress tolerance, that AITRs are widely distributed in angiosperms with multiple encoding genes, AITRs may be targeted for molecular breeding to improve abiotic stress tolerance in plants including crops.

Beyond gene ontology (GO): using biocuration approach to improve the gene nomenclature and functional annotation of rice S-domain kinase subfamily

The S-domain subfamily of receptor-like kinases (SDRLKs) in plants is poorly characterized. Most members of this subfamily are currently assigned gene function based on the S-locus Receptor Kinase from Brassica that acts as the female determinant of self-incompatibility (SI). However, Brassica like SI mechanisms does not exist in most plants. Thus, automated Gene Ontology (GO) pipelines are not sufficient for functional annotation of SDRLK subfamily members and lead to erroneous association with the GO biological process of SI. Here, we show that manual bio-curation can help to correct and improve the gene annotations and association with relevant biological processes. Using publicly available genomic and transcriptome datasets, we conducted a detailed analysis of the expansion of the rice (Oryza sativa) SDRLK subfamily, the structure of individual genes and proteins, and their expression.The 144-member SDRLK family in rice consists of 82 receptor-like kinases (RLKs) (67 full-length, 15 truncated),12 receptor-like proteins, 14 SD kinases, 26 kinase-like and 10 GnK2 domain-containing kinases and RLKs. Except for nine genes, all other SDRLK family members are transcribed in rice, but they vary in their tissue-specific and stress-response expression profiles. Furthermore, 98 genes show differential expression under biotic stress and 98 genes show differential expression under abiotic stress conditions, but share 81 genes in common.Our analysis led to the identification of candidate genes likely to play important roles in plant development, pathogen resistance, and abiotic stress tolerance. We propose a nomenclature for 144 SDRLK gene family members based on gene/protein conserved structural features, gene expression profiles, and literature review. Our biocuration approach, rooted in the principles of findability, accessibility, interoperability and reusability, sets forth an example of how manual annotation of large-gene families can fill in the knowledge gap that exists due to the implementation of automated GO projections, thereby helping to improve the quality and contents of public databases.