Genome-wide identification of TPS genes in sesame and analysis of their expression in response to abiotic stresses

Trehalose and its precursor,trehalose-6-phosphate,play critical roles in plant metabolism and response to abiotic stresses.Trehalose-6-phosphate synthase(TPS)is a key enzyme in the trehalose synthesis pathway.Hence this study identified TPS genes in sesame(SiTPSs)and examined their expression patterns under various abiotic stresses.Totally,ten SiTPSs were identified and comprehensively characterized.SiTPSs were found to be unevenly distributed on five out of 13 sesame chromosomes and were predicted to be localized in chloroplasts and vacuoles of cells.Phylogenetic analysis classified SiTPS proteins into two groups(I and II),which was supported by gene structure and conserved motif analyses.Analysis of cis-acting elements in promoter regions of SiTPSs revealed that they might primarily involve developmental and environmental responses.SiTPSs exhibited different expression patterns in different tissues and under different abiotic stresses.Most group II SiTPS genes(SiTPS4-SiTPS10)were strongly induced by drought,salt,waterlogging,and osmotic stress.Particularly,SiTPS10 was the most significantly up-regulated under various abiotic stresses,indicating it is a candidate gene for improving sesame tolerance to multiple abiotic stresses.Our results provide insight into the TPS gene family in sesame and fundamental resources for genomics studies towards dissecting SiTPS genes’functions.

Defensive Role of Plant Hormones in Advancing Abiotic Stress-Resistant Rice Plants

Consistent climatic perturbations have increased global environmental concerns, especially the impacts of abiotic stresses on crop productivity. Rice is a staple food crop for the majority of the world’s population. Abiotic stresses, including salt, drought, heat, cold and heavy metals, are potential inhibitors of rice growth and yield. Abiotic stresses elicit various acclimation responses that facilitate in stress mitigation. Plant hormones play an important role in mediating the growth and development of rice plants under optimal and stressful environments by activating a multitude of signalling cascades to elicit the rice plant’s adaptive responses. The current review describes the role of plant hormone-mediated abiotic stress tolerance in rice, potential crosstalk between plant hormones involved in rice abiotic stress tolerance and significant advancements in biotechnological initiatives including genetic engineering approach to provide a step forward in making rice resistance to abiotic stress.

Mechanisms of autophagy function and regulation in plant growth,development,and response to abiotic stress

Autophagy is an evolutionarily conserved degradation pathway of lysosomes(in mammals)and vacuoles(in yeasts and plants)from lower yeasts to higher mammals.It wraps unwanted organelles and damaged proteins in a double-membrane structure to transport them to vacuoles for degradation and recycling.In plants,autophagy functions in adaptation to the environment and maintenance of growth and development.This review systematically describes the autophagy process,biological functions,and regulatory mechanisms occurring during plant growth and development and in response to abiotic stresses.It provides a basis for further theoretical research and guidance of agricultural production.

The nuclear export receptor OsXPO1 is required for rice development and involved in abiotic stress responses

The transport of proteins to and from the nucleus is necessary for many cellular processes and is one of the ways plants respond to developmental signals and environmental stresses.Nucleocytoplasmic trafficking of proteins is mediated by the nuclear transport receptor(NTR).Although NTR has been extensively studied in humans and Arabidopsis,it has rarely been identified and functionally characterized in rice.In this study,we identified exportin 1 in rice(OsXPO1)as a nuclear export receptor.OsXPO1shares high protein identity with its functional homologs in Arabidopsis and other organisms.OsXPO1localized to both the nucleus and the cytoplasm,directly interacted with the small GTPases OsRAN1and OsRAN2 in the nucleus,and mediated their nuclear export.Loss-of-function osxpo1 mutations were lethal at the seedling stage.Suppression of OsXPO1 expression in RNA interference lines produced multifaceted developmental defects,including arrested growth,premature senescence,abnormal inflorescence,and brown and mouth-opened spikelets.Overexpression of OsXPO1 in rice reduced plant height and seed-setting rate,but increased plant tolerance in response to PEG-mimicked drought stress and salt stress.These results indicate that OsXPO1 is a nuclear export receptor and acts in regulating plant development and abiotic stress responses.

Identification and Characterization of ZF-HD Genes in Response to Abscisic Acid and Abiotic Stresses in Maize

The zinc finger homeodomain(ZF-HD)genes belong to the homeobox gene family,playing critical roles in flower development and stress response.Despite their importance,however,to date there has been no genome-wide identification and characterization of the ZF-HD genes that are probably involved in stress responses in maize.In this study,24 ZF-HD genes were identified,and their chromosomal locations,protein properties,duplication patterns,structures,conserved motifs and expression patterns were investigated.The results revealed that the ZF-HD genes are unevenly distributed on nine chromosomes and that most of these genes lack introns.Six and two ZF-HD genes have undergone segmental and tandem duplication,respectively,during genome expansion.These 24 ZF-HD transcription factors were classified into six major groups on the basis of protein molecular evolutionary relationship.The expression profiles of these genes in different tissues were evaluated,resulting in producing two distinct clusters.ZF-HD genes are preferentially expressed in reproductive tissues.Furthermore,expression profiles of the 24 ZF-HD genes in response to different kinds of stresses revealed that ten genes were simultaneously up-regulated under ABA,salt and PEG treatments;meanwhile four genes were simultaneously down-regulated.These findings will pave the way for deciphering the function and mechanism of ZF-HD genes on how to implicate in abiotic stress.

Roles of miR319-regulated TCPs in plant development and response to abiotic stress

Elaborate regulation of gene expression is required for plants to maintain normal growth,development,and reproduction.MicroRNAs(miRNAs)and transcription factors are key players that control gene expression in plant regulatory networks.The TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR(TCP)family comprises plantspecific transcription factors that contain a conserved TCP domain of 59 amino acids.Some members of this family are targeted by miR319,one of the most ancient and evolutionarily conserved miRNAs in plants.Accumulating evidence has revealed that miR319-regulated TCP(MRTCP)genes participate extensively in plant development and responses to environmental stress.In this review,the structural characteristics and classifications of TCP transcription factors and the regulatory relationships between TCP transcription factors and miRNAs are introduced.Current knowledge of the regulatory functions of MRTCP genes in multiple biological pathways including leaf development,vascular formation,flowering,hormone signaling,and response to environmental stresses such as cold,salt,and drought is summarized.This review will be beneficial for understanding the roles of the MRTCP-mediated regulatory network and its molecular mechanisms in plant development and stress response,and provides a theoretical basis for plant genetic improvement.

MdDREB2A in apple is involved in the regulation of multiple abiotic stress responses

Abiotic stress has a serious effect on plant growth.The transcription factor DREB2A is a member of the AP2/ERF family,which is widely involved in abiotic stress response.However,the function of apple MdDREB2A has not been systematically investigated.In this study,MdDREB2A was isolated from the cultivar‘Royal Gala’.The open reading frame of MdDREB2A was 1197 bp in length and it encoded a protein of 398 amino acidswithmolecularweight of 43.8 kD.As a transcription factor,MdDREB2Awas located in the nucleus.qRT-PCR analysis showed that MdDREB2A was involved in responses to drought,salt,and ABA stresses.Under these stress treatments,the relative electrical conductivity,superoxide anion and malondialdehyde(MDA)in transgenic materials significantly decreased,and the content of proline increased in MdDREB2A transgenic plants,compared to the controls,indicating that MdDREB2A transgenic apple calli and transgenic Arabidopsis exhibited improved resistance to abiotic stress.This study introduces a candidate gene for the genetic improvement of crop resistance and reveals important function of MdDREB2A in the regulation of abiotic stress response.

Genome-wide identification and transcriptome profiling reveal great expansion of SWEET gene family and their wide-spread responses to abiotic stress in wheat (Triticum aestivum L.)

The Sugars Will Eventually be Exported Jransporter(SWEET)gene family,identified as sugar transporters,has been demonstrated to play key roles in phloem loading,grain filling,pollen nutrition,and plant-pathogen interactions.To date,the study of SWEET genes in response to abiotic stress is very limited.In this study,we performed a genome-wide identification of the SWEET gene family in wheat and examined their expression profiles under mutiple abiotic stresses.We identified a total of 105 wheat SWEET genes,and phylogenic analysis revealed that they fall into five clades,with clade V specific to wheat and its closely related species.Of the 105 wheat SWEET genes,59%exhibited significant expression changes after stress treatments,including drought,heat,heat combined with drought,and salt stresses,and more up-regulated genes were found in response to drought and salt stresses.Further hierarchical clustering analysis revealed that SWEET genes exhibited differential expression patterns in response to different stress treatments or in different wheat cultivars.Moreover,different phylogenetic clades also showed distinct response to abiotic stress treatments.Finally,we found that homoeologous SWEET genes from different wheat subgenomes exhibited differential expression patterns in response to different abiotic stress treatments.The genome-wide analysis revealed the great expansion of SWEET gene family in wheat and their wide participation in abiotic stress response.The expression partitioning of SWEET homoeologs under abiotic stress conditions may confer greater flexibility for hexaploid wheat to adapt to ever changing environments.

Differential Expression of Two Cytosolic Ascorbate Peroxidases and Two Superoxide Dismutase Genes in Response to Abiotic Stress in Rice

Superoxide dismutase (SOD) and ascorbate peroxidase (APX) play central roles in the pathway for scavenging reactive oxygen species in plants, thereby contributing to the tolerance against abiotic stress. Here we report the responses of cytosolic SOD (cSOD; sodCc1 and sodCc2) and cytosolic APX (cAPX; OsAPX1 and OsAPX2) genes to oxidative and abiotic stress in rice. RNA blot analyses revealed that methyl viologen treatment caused a more prominent induction of cAPXs compared with cSODs, and hydrogen peroxide treatment induced the expression of cAPXs whereas cSODs were not affected. These results suggest that cAPXs play more important roles in defense against oxidative stress compared with cSODs. It is noted that cSODs and cAPXs showed coordinate response to abscisic acid treatment which induced both sodCc1 and OsAPX2. However, cSODs and cAPXs responded differentially to drought, salt and chilling stress, which indicates that cSOD and cAPX genes are expressed differentially in response to oxidative and abiotic stress in rice.

TaSnRK2.4 is a vital regulator in control of thousand-kernel weight and response to abiotic stress in wheat

Sucrose non-fermenting 1-related protein kinase 2(Sn RK2) is a plant-specific serine/threonine kinase involved in response to adverse environmental stimuli. Previous studies showed that Ta Sn RK2.4 was involved in response to abiotic stresses and conferred enhanced tolerance to multiple stresses in Arabidopsis. Further experiments were performed to decipher the underlying mechanisms and discover new functions. The genomic sequences of Ta Sn RK2.4 s locating on chromosome 3 A, 3 B and 3 D were obtained. Sequencing identified one and 13 variations of Ta Sn RK2.4-3 A and Ta Sn RK2.4-3 B, respectively, but no variation was detected in Ta Sn RK2.4-3 D. The markers 2.4 AM1, 2.4 BM1 and 2.4 BM2 were developed based on three variations. Association analysis showed that both Ta Sn RK2.4-3 A and Ta Sn RK2.4-3 B were significantly associated with thousand-kernel weight(TKW), and that SNP3 A-T and SNP3 B-C were favorable alleles for higher TKW. Yeast two-hybrid and split luciferase assays showed that Ta Sn RK2.4 physically interacted with abiotic stress responsive protein Ta LTP3, suggesting that Ta Sn RK2.4 enhanced abiotic stress tolerance by activating Ta LTP3. Our studies suggested that Ta Sn RK2.4 have potential in improving TKW and response to abiotic stress.

Systematic Identification of Rice ABC1 Gene Family and Its Response to Abiotic Stress

Members of the activity of bc1 complex (ABC1) family are protein kinases that are widely found in prokaryotes and eukaryotes. Previous studies showed that several plant ABC1 genes participated in the abiotic stress response. Here, we present the systematic identification of rice and Arabidopsis ABC1 genes and the expression analysis of rice ABC1 genes. A total of 15 and 17 ABC1 genes from the rice and Arabidopsis genomes, respectively, were identified using a bioinformatics approach. Phylogenetic analyses of these proteins suggested that the divergence of this family had occurred and their main characteristics were established before the monocot-dicot split. Indeed, species-specific expansion contributed to the evolution of this family in rice and Arabidopsis after the monocot-dicot split. Intron/exon structure analysis indicated that most of the orthologous genes had similar exon sizes, but diverse intron sizes, and the rice genes contained larger introns, moreover, intron gain was an important event accompanying the recent evolution of the rice ABC1 family. Multiple sequence alignment revealed one conserved amino acid segment and four conserved amino acids in the ABC1 domain. Online subcellular localization predicted that nine rice ABC1 proteins were localized in chloroplasts. Real-time RT-PCR established that the rice ABC1 genes were primarily expressed in leaves and the expression could be modulated by a broad range of abiotic factors such as H2O2, abscisic acid, low temperature, drought, darkness and high salinity. These results reveal that the rice ABC1 gene family plays roles in the environmental stress response and specific biological processes of rice.

Morpho-Physiological,Biochemical and Molecular Adaptation of Millets to Abiotic Stresses:A Review

Abiotic stresses such as drought,heat,cold,nutrient deficiency,excess salt and hazardous metals can hamper plantgrowth and development.Intensive agriculture of only a few major staple food crops that are sensitive and intolerant to environmental stresses has led to an agrarian crisis.On the other hand,nutritionally rich,gluten free and stress tolerant plants like millets are neglected and underutilized.Millets sustain about one-third of the world’s population and show exceptional tolerance to various abiotic and biotic stresses.Millets are C4 plants that are adapted to marginal and dry lands of arid and semi-arid regions,and survive low rainfall and poor soils.Abiotic stresses significantly affect plant growth which ultimately results in reduced crop yields.However,various adaptation mechanisms have evolved in millets to withstand different stresses.This review aims at exploring various of these morphophysiological,biochemical and molecular aspects of mechanisms in millets.Morphological adaptations include short life span,smallplant height and leaf area,dense root system,adjusted flowering time,increased root and decreased shoot lengths,high tillering,and leaf folding.A high accumulation of various osmoprotectants(proline,soluble sugars,proteins)improves hyperosmolarity and enhances the activity of antioxidant enzymes(e.g.,Ascorbate peroxidase,Superoxide dismutase,Catalase,Peroxidase)providing defense against oxidative damage.Physiologically,plants show low photosynthetic and stomatal conductance rates,and root respiration which help them to escape from water stress.Molecular adaptations include the upregulation of stress-related transcriptional factors,signalling genes,ion transporters,secondary metabolite pathways,receptor kinases,phytohormone biosynthesis and antioxidative enzymes.Lack of genetic resources hampers improvement of millets.However,several identified and characterized genes for stress tolerance can be exploited for further development of millet resilience.This will provide them with an extra characteristic plant resistance to withstand environmental pressures,besides their excellent nutritional value over the conventional staple crops like rice,wheat and maize.

Reference Gene Selection for Quantitative Real-Time PCR Analyses of Acer palmatum under Abiotic Stress

Quantitative real-time reverse transcriptase PCR(qRT-PCR)technology has been extensively used to estimate gene expression levels,and the selection of appropriate reference genes for qRT-PCR analysis is critically important for obtaining authentic normalized data.Acer palmatum is an important colorful leaf ornamental tree species,and reference genes suitable for normalization of the qRT-PCR data obtained from this species have not been investigated.In this study,the expression stability of ten candidate reference genes,namely,Actin3,Actin6,Actin9,EF1α,PP2A,SAMDC,TIP41,TUBα,TUBβand UBQ10,in two distinct tissues(leaves and roots)of A.palmatum under four different abiotic stress conditions(cold,heat,salt and drought)were investigated and assessed using three statistical methods(GeNorm,NormFinder and BestKeeper).The combinations of reference genes that showed stability in the different stressed samples differed.Specifically,Actin6,UBQ10 and Actin9 were the most stable reference genes in all the samples,and Actin3 and Actin6 wexre stably expressed in cold-stressed leaves and roots.Actin3,Actin6 and UBQ10 were identified as an appropriate combination of reference genes for the analysis of heat-stressed leaves and roots,whereas the combination of Actin9,UBQ10 and Actin6 was deemed the most suitable for the analysis of salt-stressed leaves and roots.Similarly,Actin6 and UBQ10 exhibited stable expression in drought-stressed leaves and roots.Furthermore,the expression levels of CBF,Cu/Zn-SOD and HsfA1 were estimated to determine the reliability of the reference genes assessed in this study.This study revealed stable reference genes in A.palmatum that might be used for the normalization of qRT-PCR data obtained under various abiotic stresses.

Genome-wide identification and characterization of the JAZ gene family and its expression patterns under various abiotic stresses in Sorghum bicolor

The jasmonate ZIM domain(JAZ)protein belongs to the TIFY((TIF[F/Y]XG)domain protein)family,which is composed of several plant-specific proteins that play important roles in plant growth,development,and defense responses.However,the mechanism of the sorghum JAZ family in response to abiotic stress remains unclear.In the present study,a total of 17 JAZ genes were identified in sorghum using a Hidden Markov Model search.In addition,real-time quantification polymerase chain reaction(RT-qPCR)was used to analyze the gene expression patterns under abiotic stress.Based on phylogenetic tree analysis,the sorghum JAZ proteins were mainly divided into nine subfamilies.A promoter analysis revealed that the SbJAZ family contains diverse types of promoter cis-acting elements,indicating that JAZ proteins function in multiple pathways upon stress stimulation in plants.According to RT-qPCR,SbJAZ gene expression is tissuespecific.Additionally,under cold,hot,polyethylene glycol,jasmonic acid,abscisic acid,and gibberellin treatments,the expression patterns of SbJAZ genes were distinctly different,indicating that the expression of SbJAZ genes may be coordinated with different stresses.Furthermore,the overexpression of SbJAZ1 in Escherichia coli was found to promote the growth of recombinant cells under abiotic stresses,such as PEG 6000,NaCl,and 40℃ treatments.Altogether,our findings help us to better understand the potential molecular mechanisms of the SbJAZ family in sorghum in response to abiotic stresses.

A rice XANTHINE DEHYDROGENASE gene regulates leaf senescence and response to abiotic stresses

Xanthine dehydrogenase, a member of the molybdenum enzyme family, participates in purine metabolism and catalyzes the generation of ureides from xanthine and hypoxanthine. However, the mechanisms by which xanthine dehydrogenase affects rice growth and development are poorly understood. In the present study, we identified a mutant with early leaf senescence and reduced tillering that we named early senescence and less-tillering 1(esl1). Map-based cloning revealed that ESL1 encodes a xanthine dehydrogenase, and it was expressed in all tissues. Chlorophyll content was reduced and chloroplast maldevelopment was severe in the esl1 mutant. Mutation of ESL1 led to decreases in allantoin, allantoate, and ABA contents. Further analysis revealed that the accumulation of reactive oxygen species in esl1 resulted in decreased photosynthesis and impaired chloroplast development, along with increased sensitivity to abscisic acid and abiotic stresses. Ttranscriptome analysis showed that the ESL1 mutation altered the expression of genes involved in the photosynthesis process and reactive oxygen species metabolism.Our results suggest that ESL1 is involved in purine metabolism and the induction of leaf senescence.These findings reveal novel molecular mechanisms of ESL1 gene-mediated plant growth and leaf senescence.

Advances in the functional study of glutamine synthetase in plant abiotic stress tolerance response

Plant glutamine synthetase(GS,EC6.3.1.2)catalyzes the synthesis of glutamine from glutamate and ammonium ions and acts as a key enzyme in the nitrogen metabolic pathway in organisms.Nitrogen is an essential element for plant growth and development and plays an important role in crop yield and quality formation.Therefore,GS is crucial in many physiological processes in plants.Currently,nitrogen regulation by GS in plants is well-studied in terms of its effect on plant growth and development.This article reviews the regulatory role of plant GS and its molecular mechanism in mitigating stress injury,such as low or high temperature,salinity,drought and oxidation.The function of plant GS in stress tolerance response is focused.The review aims to provide a reference for the utilization of plant GS in crop stress tolerance breeding.

Identification of phytohormone changes and its related genes under abiotic stresses in transgenic rice

Abiotic stresses,such as drought and salinity,adversely affect plant growth and productivity.Comparison between non transgenic and transgenic rice harboring CaMsrB2 gene,which induces tolerance to abiotic stress,is important to observe response of gene under abiotic stress.Phytohormone showed a tendency to increase under the drought stress or salinity stress in the transgenic plant.RT-PCR analysis showed that gene expression and phytohormone levels under abiotic stress,to be closely related.The CaMsrB2 gene is related to the expression of JA and ABA hormones.Therefore,the level of expression of these genes and hormones was observed.The transcription levels of LOX2 and OsWRKY45 were substantially higher in the wild type rice in comparison to the transformants,which suggested that phytohormone are also required for the regulation of leaf and root.Comparison between control and transgenic rice overexpressing a CaMsrB2 gene,resulted in different pattern of ABA,JA levels under different stress condition.In both drought and salinity stresses,the expression of OsWRKY45 gene was similar in both treatments with time.These results suggest that gene involved in the plant physiology response in mechanism to abiotic stress.

Responses of leaf stomatal and mesophyll conductance to abiotic stress factors

Plant photosynthesis assimilates CO_(2)from the atmosphere,and CO_(2)diffusion efficiency is mainly constrained by stomatal and mesophyll resistance.The stomatal and mesophyll conductance of plants are sensitive to abiotic stress factors,which affect the CO_(2)concentrations at carboxylation sites to control photosynthetic rates.Early studies conducted relevant reviews on the responses of stomatal conductance to the environment and the limitations of mesophyll conductance by internal structure and biochemical factors.However,reviews on the abiotic stress factors that systematically regulate plant CO_(2)diffusion are rare.Therefore,in this review,the rapid and long-term responses of stomatal and mesophyll conductance to abiotic stress factors(such as light intensity,drought,CO_(2)concentration and temperature)and their physiological mechanisms are summarized.Finally,future research trends are also investigated.

Omics Studies and Systems Biology Perspective towards Abiotic Stress Response in Plants

Plant abiotic stress responses are vital yield-restricting aspect in agriculture. Recent technology in plant biology allows research of such stress responses at a molecular scale in plants. Network analysis provides in-depth knowledge regarding omics information visualisation as it reduces the intrinsic intricacy of such data. The use of integrated functional genomics helps to understand the relationship between the genomic profile and the phenotypic profile in different environmental conditions of an organism. Plants’ responses to abiotic stress are often considered as a complex process. Systems biology approaches allow visualising and understanding how plant life works to overcome abiotic stress. The combination of integrated functional genomics along with bioinformatics will put a hand in additional in-depth research knowledge on stress tolerance to plants by exploiting available genetic information and continuously improving techniques and strategies. Most of the omics technologies are high throughput with very rapid data generation rates and humongous outputs. These technologies have made noticeable contributions to the modern-day improvements in our knowledge of plant biology. So, in this review, omics studies and the system biology approach towards abiotic stress tolerance in plants are highlighted.

Heterogeneous expression of Osa-MIR156bc increases abiotic stress resistance and forage quality of alfalfa

Alfalfa (Medicago sativa L.) is the most widely cultivated perennial leguminous forage crop woldwide.Micro RNA156 (miR156) precursor genes from dicotyledonous species are reportedly useful for improving alfalfa plant architecture and abiotic stress resistance.However,there has been no report on whether a miR156 precursor gene from a monocotyledonous species functions in alfalfa.We introduced two tandem precursor genes of miR156,rice Osa-MIR156b and Osa-MIR156c (Osa-MIR156bc),into alfalfa.The expression of miR156 in the transgenic (TG) alfalfa was significantly elevated.Compared to wild-type plants,the TG plants overexpressing miR156 had more branches and leaves and showed improved salt and drought tolerance.Overexpression of miR156 slightly reduced plant height,but the biomass yield of TG plants grown in flowerpots was still increased.Forage quality of TG plants was markedly improved by reduction of acid detergent lignin (ADL) content and increase in crude protein content.The expression of the putative miR156 target genes Ms SPL6,Ms SPL12,and Ms SPL13 in TG plants was repressed by miR156overexpression,and that of all tested Ms SPLs would be sharply increased under drought or salt stress.RNA sequencing revealed that overexpression of miR156 affected the expression of genes associated with abiotic stress resistance and plant development in multiple pathways.This first report of overexpression of monocot miR156 precursors in alfalfa sheds light on the function of mi RNA156 precursors from the monocot species rice that could be used for genetic improvement of the dicot forage crop alfalfa.