The Soybean bZIP Transcription Factor Gene GmbZIP2 Confers Drought and Salt Resistances in Transgenic Plants

Abiotic stresses, such as drought and salt, are major environmental stresses, affecting plant growth and crop productivity. Plant bZIP transcription factors (bZIPs) confer stress resistances in harsh environments and play important roles in each phase of plant growth processes. In this research, 15 soybean bZIP family members were identified from drought-induced de novo transcriptomic sequences of soybean, which were unevenly distributed across 12 soybean chromosomes. Promoter analysis showed that these 15 genes were rich in ABRE, MYB and MYC cis-acting elements which were reported to be involved in abiotic stress responses. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis indicated that 15 GmbZIP genes could be induced by drought and salt stress. GmbZIP2 was significantly upregulated under stress conditions and thus was selected for further study. Subcellular localization analysis revealed that the GmbZIP2 protein was located in the cell nucleus. qRT-PCR results show that GmbZIP2 can be induced by multiple stresses. The overexpression of GmbZIP2 in Arabidopsis and soybean hairy roots could improve plant resistance to drought and salt stresses. The result of differential expression gene analysis shows that the overexpression of GmbZIP2 in soybean hairy roots could enhance the expression of the stress responsive genes GmMYB48, GmWD40, GmDHN15, GmGST1 and GmLEA. These results indicate that soybean bZIPs played pivotal roles in plant resistance to abiotic stresses.

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Revisiting Sulphur—The Once Neglected Nutrient: It’s Roles in Plant Growth, Metabolism, Stress Tolerance and Crop Production

Agriculture ◽

10.3390/agriculture11070626 ◽

2021 ◽

Vol 11 (7) ◽

pp. 626

Author(s):

Tinashe Zenda ◽

Songtao Liu ◽

Anyi Dong ◽

Huijun Duan

Keyword(s):

Plant Growth ◽

Abiotic Stresses ◽

Crop Production ◽

Production Systems ◽

Crop Productivity ◽

Plant Phenotyping ◽

Special Importance ◽

Nutrient Deficiencies ◽

Sulphur Nutrition ◽

Physiological Processes

Sulphur plays crucial roles in plant growth and development, with its functions ranging from being a structural constituent of macro-biomolecules to modulating several physiological processes and tolerance to abiotic stresses. In spite of these numerous sulphur roles being well acknowledged, agriculture has paid scant regard for sulphur nutrition, until only recently. Serious problems related to soil sulphur deficiencies have emerged and the intensification of food, fiber, and animal production is escalating to feed the ever-increasing human population. In the wake of huge demand for high quality cereal and vegetable diets, sulphur can play a key role in augmenting the production, productivity, and quality of crops. Additionally, in light of the emerging problems of soil fertility exhaustion and climate change-exacerbated environmental stresses, sulphur assumes special importance in crop production, particularly under intensively cropped areas. Here, citing several relevant examples, we highlight, in addition to its plant biological and metabolism functions, how sulphur can significantly enhance crop productivity and quality, as well as acclimation to abiotic stresses. By this appraisal, we also aim to stimulate readers interests in crop sulphur research by providing priorities for future pursuance, including bettering our understanding of the molecular processes and dynamics of sulphur availability and utilization in plants, dissecting the role of soil rhizospherical microbes in plant sulphur transformations, enhancing plant phenotyping and diagnosis for nutrient deficiencies, and matching site-specific crop sulphur demands with fertilizer amendments in order to reduce nutrient use inefficiencies in both crop and livestock production systems. This will facilitate the proper utilization of sulphur in crop production and eventually enhance sustainable and environmentally friend food production.

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Genome-wide identification and expression analysis of the VQ gene family in soybean (Glycine max)

10.7287/peerj.preprints.27606v1 ◽

2019 ◽

Author(s):

Yongbin Wang ◽

Zhenfeng Jiang ◽

Zhenxiang Li ◽

Yuanling Zhao ◽

Weiwei Tan ◽

...

Keyword(s):

Glycine Max ◽

Plant Growth ◽

Gene Family ◽

Stress Responses ◽

Pcr Analysis ◽

Rna Seq ◽

Biological Functions ◽

Conserved Domain ◽

Genome Wide ◽

Development Processes

Background. VQ proteins, the plant-specific transcription factors, are involved in the regulation of plant growth, development, and stress responses; however, few articles systematic reported VQ genes in the soybean. Methods. In total, we identified 75 GmVQ genes, which were classified into 7 groups (Ⅰ-Ⅶ). Conserved domain analysis indicated that VQ gene family members all contained the VQ domains. The VQ genes from the same evolutionary branches of soybean shared similar motifs and structures. Promoter analysis revealed cis-elements related to stress responses, phytohormone responses and controlling physical and reproductive growth. Based on the RNA-seq and qRT-PCR analysis, GmVQ genes were expressed in nine tissues suggested their putative function in many aspects of plant growth and development, and response to stresses in Glycine max. Results. The present study provided basic information for further analysis of the biological functions of GmVQ proteins in various development processes.

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Genome-wide identification and expression profiling of glutathione transferase gene family under multiple stresses and hormone treatments in wheat (Triticum aestivum L.)

BMC Genomics ◽

10.1186/s12864-019-6374-x ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 3

Author(s):

Ruibin Wang ◽

Jingfei Ma ◽

Qian Zhang ◽

Chunlai Wu ◽

Hongyan Zhao ◽

...

Keyword(s):

Stress Responses ◽

Segmental Duplication ◽

Expression Profiling ◽

Abiotic Stresses ◽

Glutathione Transferase ◽

Purifying Selection ◽

Triticum Aestivum L ◽

Wheat Genome ◽

Qrt Pcr ◽

Duplication Events

Abstract Background Glutathione transferases (GSTs), the ancient, ubiquitous and multi-functional proteins, play significant roles in development, metabolism as well as abiotic and biotic stress responses in plants. Wheat is one of the most important crops, but the functions of GST genes in wheat were less studied. Results A total of 330 TaGST genes were identified from the wheat genome and named according to the nomenclature of rice and Arabidopsis GST genes. They were classified into eight classes based on the phylogenetic relationship among wheat, rice, and Arabidopsis, and their gene structure and conserved motif were similar in the same phylogenetic class. The 43 and 171 gene pairs were identified as tandem and segmental duplication genes respectively, and the Ka/Ks ratios of tandem and segmental duplication TaGST genes were less than 1 except segmental duplication gene pair TaGSTU24/TaGSTU154. The 59 TaGST genes were identified to have syntenic relationships with 28 OsGST genes. The expression profiling involved in 15 tissues and biotic and abiotic stresses suggested the different expression and response patterns of the TaGST genes. Furthermore, the qRT-PCR data showed that GST could response to abiotic stresses and hormones extensively in wheat. Conclusions In this study, a large GST family with 330 members was identified from the wheat genome. Duplication events containing tandem and segmental duplication contributed to the expansion of TaGST family, and duplication genes might undergo extensive purifying selection. The expression profiling and cis-elements in promoter region of 330 TaGST genes implied their roles in growth and development as well as adaption to stressful environments. The qRT-PCR data of 14 TaGST genes revealed that they could respond to different abiotic stresses and hormones, especially salt stress and abscisic acid. In conclusion, this study contributed to the further functional analysis of GST genes family in wheat.

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Perturbations of the AMI1 IAM-amidohydrolase expression trigger plant stress responses in Arabidopsis thaliana

10.1101/2020.08.31.275206 ◽

2020 ◽

Author(s):

Marta-Marina Pérez-Alonso ◽

Paloma Ortiz-García ◽

José Moya-Cuevas ◽

Thomas Lehmann ◽

Beatriz Sánchez-Parra ◽

...

Keyword(s):

Plant Growth ◽

Stress Responses ◽

Abiotic Stresses ◽

Plant Stress ◽

Physiological Role ◽

Auxin Homeostasis ◽

Plant Stress Responses ◽

Adaptive Processes ◽

Aba Biosynthesis

ABSTRACTThe evolutionary success of plants relies to a large extent on their extraordinary ability to adapt to changes in their environment. These adaptations require that plants balance their growth with their stress responses. Plant hormones are crucial mediators orchestrating the underlying adaptive processes. However, whether and how the growth-related hormone auxin and the stress-related hormones jasmonic acid (JA), salicylic acid, and abscisic acid (ABA) are coordinated remains largely elusive. Here, we analyze the physiological role of AMIDASE 1 (AMI1) in plant growth and its possible connection to plant adaptations to abiotic stresses. AMI1 contributes to cellular auxin homeostasis by catalyzing the conversion of indole-acetamide into the major plant auxin indole-3-acetic acid. Functional impairment of AMI1 increases the plants’ stress status rendering mutant plants more susceptible to abiotic stresses. Transcriptomic analysis of ami1 mutants disclosed the reprogramming of a considerable number of stress-related genes, including JA and ABA biosynthesis genes. The ami1 mutants exhibit only moderately repressed growth, but an enhanced ABA accumulation, which suggests a role for AMI1 in the crosstalk between auxin and ABA. Altogether, our results suggest that AMI1 is involved in coordinating the trade-off between plant growth and stress responses, balancing auxin with ABA homeostasis.HIGHLIGHTThe IAM amidohydrolase AMI1 catalyzes the conversion of IAM into IAA in vivo. Expression of AMI1 is specifically repressed by osmotic stress conditions, which triggers ABA biosynthesis through the induction of NCED3, thereby linking auxin homeostasis with plant stress responses.

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Reference Gene Selection for miRNA qRT-PCR Analysis in Lily

10.21203/rs.3.rs-102523/v1 ◽

2020 ◽

Author(s):

Qian Zhang ◽

Xue Gao ◽

Lian-Juan Wang ◽

Yu-Qian Zhao ◽

Gui-Xia Jia

Keyword(s):

Reference Gene ◽

Stress Responses ◽

Reference Genes ◽

Gene Selection ◽

Developmental Stages ◽

Pcr Analysis ◽

Critical Element ◽

Biotic And Abiotic Stress ◽

Experimental Conditions ◽

Qrt Pcr

Abstract Background: The selection of reliable reference genes is a critical element for obtaining accurate gene expression data to assess quantitative real-time polymerase chain reaction (qRT-PCR) performance. It is critical to use suitable reference genes in miRNA qRT-PCR because of short amplification products and large differences in the expression levels of target miRNAs involved in some biological processes. However, in lily, which exhibits a large complex genome but lacks a reference, the available miRNA reference genes for use in qRT-PCR under various treatment conditions are limited, and their reliability has rarely been systematically evaluated.Results: In this study, 8 candidate reference genes, including three classic housekeeping genes and five potential miRNAs from the miRNA library of L. × formolongi, were selected and assessed for expression stability utilizing the BestKeeper, geNorm and Normfinder tools, together with the Delta Ct method, across a diverse set of biotic and abiotic experimental conditions (developmental stages, tissues, heat stress and pathogen defence) to determine the best reference gene(s) for L. × formolongi and L. regale. The final ranking was reordered by using RankAggreg, and the results showed that the novel miRNA PC-3p-67_108977 and the conserved miRNAs miR399a, miR399a and U6 were the most stable genes for L. × formolongi and L. regale, respectively, under all tested experimental conditions. Additionally, PC-3p-67_108977 and U6 were the most suitable genes for qRT-PCR studies in lily.Conclusions: This study provides a comprehensive evaluation of the reliability of reference genes for miRNA studies on development and biotic and abiotic stress responses in different lilies. These results will be beneficial for miRNA identification and functional studies of lilies in the future.

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Genome-Wide Characterization and Identification of Trihelix Transcription Factor and Expression Profiling in Response to Abiotic Stresses in Rice (Oryza sativa L.)

International Journal of Molecular Sciences ◽

10.3390/ijms20020251 ◽

2019 ◽

Vol 20 (2) ◽

pp. 251 ◽

Cited By ~ 7

Author(s):

Jiaming Li ◽

Minghui Zhang ◽

Jian Sun ◽

Xinrui Mao ◽

Jing Wang ◽

...

Keyword(s):

Hydrogen Peroxide ◽

Stress Responses ◽

Abiotic Stresses ◽

Developmental Stages ◽

Oryza Sativa L ◽

Expression Patterns ◽

Rice Genome ◽

High Salt ◽

Pcr Analysis ◽

Signal Molecule

Trihelix transcription factors play a role in plant growth, development and various stress responses. Here, we identified 41 trihelix family genes in the rice genome. These OsMSLs (Myb/SANT-LIKE) were located on twelve chromosomes. Synteny analysis indicated only six duplicated gene pairs in the rice trihelix family. Phylogenetic analysis of these OsMSLs and the trihelix genes from other species divided them into five clusters. OsMSLs from different groups significantly diverged in terms of gene structure and conserved functional domains. However, all OsMSLs contained the same five cis-elements. Some of these were responsive to light and dehydration stress. All OsMSLs expressed in four tissues and six developmental stages of rice but with different expression patterns. Quantitative real-time PCR analysis revealed that the OsMSLs responded to abiotic stresses including drought and high salt stress and stress signal molecule including ABA (abscisic acid), hydrogen peroxide. OsMSL39 were simultaneously expressed under all treatments, while OsMSL28 showed high expression under hydrogen peroxide, drought, and high salt treatments. Moreover, OsMSL16/27/33 displayed significant expression under ABA and drought treatments. Nevertheless, their responses were regulated by light. The expression levels of the 12 chosen OsMSLs differed between light and dark conditions. In conclusion, our results helped elucidate the biological functions of rice trihelix genes and provided a theoretical basis for further characterizing their biological roles in responding to abiotic stresses.

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Conserved miR396b-GRF Regulation Is Involved in Abiotic Stress Responses in Pitaya (Hylocereus polyrhizus)

International Journal of Molecular Sciences ◽

10.3390/ijms20102501 ◽

2019 ◽

Vol 20 (10) ◽

pp. 2501 ◽

Cited By ~ 3

Author(s):

A-Li Li ◽

Zhuang Wen ◽

Kun Yang ◽

Xiao-Peng Wen

Keyword(s):

Abiotic Stress ◽

Drought Stress ◽

Binding Site ◽

Stress Responses ◽

Abiotic Stresses ◽

Molecular Mechanisms ◽

Evolutionary Relationship ◽

Pcr Analysis ◽

Sequencing Analysis ◽

Hylocereus Polyrhizus

MicroRNA396 (miR396) is a conserved microRNA family that targets growth-regulating factors (GRFs), which play significant roles in plant growth and stress responses. Available evidence justifies the idea that miR396-targeted GRFs have important functions in many plant species; however, no genome-wide analysis of the pitaya (Hylocereus polyrhizus) miR396 gene has yet been reported. Further, its biological functions remain elusive. To uncover the regulatory roles of miR396 and its targets, the hairpin sequence of pitaya miR396b and the open reading frame (ORF) of its target, HpGRF6, were isolated from pitaya. Phylogenetic analysis showed that the precursor miR396b (MIR396b) gene of plants might be clustered into three major groups, and, generally, a more recent evolutionary relationship in the intra-family has been demonstrated. The sequence analysis indicated that the binding site of hpo-miR396b in HpGRF6 is located at the conserved motif which codes the conserved “RSRKPVE” amino acid in the Trp–Arg–Cys (WRC) region. In addition, degradome sequencing analysis confirmed that four GRFs (GRF1, c56908.graph_c0; GRF4, c52862.graph_c0; GRF6, c39378.graph_c0 and GRF9, c54658.graph_c0) are hpo-miR396b targets that are regulated by specific cleavage at the binding site between the 10th and 11th nucleotides from the 5′ terminus of hpo-miR396b. Furthermore, quantitative real-time polymerase chain reaction (qRT-PCR) analysis showed that hpo-miR396b is down-regulated when confronted with drought stress (15% polyethylene glycol, PEG), and its expression fluctuates under other abiotic stresses, i.e., low temperature (4 ± 1 °C), high temperature (42 ± 1 °C), NaCl (100 mM), and abscisic acid (ABA; 0.38 mM). Conversely, the expression of HpGRF6 showed the opposite trend to exposure to these abiotic stresses. Taken together, hpo-miR396b plays a regulatory role in the control of HpGRF6, which might influence the abiotic stress response of pitaya. This is the first documentation of this role in pitaya and improves the understanding of the molecular mechanisms underlying the tolerance to drought stress in this fruit.

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Interactive Role of Silicon and Plant–Rhizobacteria Mitigating Abiotic Stresses: A New Approach for Sustainable Agriculture and Climate Change

Plants ◽

10.3390/plants9091055 ◽

2020 ◽

Vol 9 (9) ◽

pp. 1055

Author(s):

Krishan K. Verma ◽

Xiu-Peng Song ◽

Dong-Mei Li ◽

Munna Singh ◽

Vishnu D. Rajput ◽

...

Keyword(s):

Plant Growth ◽

Abiotic Stresses ◽

Crop Production ◽

Plant Growth Promoting Rhizobacteria ◽

Crop Productivity ◽

Agricultural Crop ◽

Plant Growth Promoting ◽

Microbe Interactions ◽

Stimulate Plant Growth ◽

Excess Quantity

Abiotic stresses are the major constraints in agricultural crop production across the globe. The use of some plant–microbe interactions are established as an environment friendly way of enhancing crop productivity, and improving plant development and tolerance to abiotic stresses by direct or indirect mechanisms. Silicon (Si) can also stimulate plant growth and mitigate environmental stresses, and it is not detrimental to plants and is devoid of environmental contamination even if applied in excess quantity. In the present review, we elaborate the interactive application of Si and plant growth promoting rhizobacteria (PGPRs) as an ecologically sound practice to increase the plant growth rate in unfavorable situations, in the presence of abiotic stresses. Experiments investigating the combined use of Si and PGPRs on plants to cope with abiotic stresses can be helpful in the future for agricultural sustainability.

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Reference gene selection for qRT-PCR assays inStellera chamaejasmesubjected to abiotic stresses and hormone treatments based on transcriptome datasets

PeerJ ◽

10.7717/peerj.4535 ◽

2018 ◽

Vol 6 ◽

pp. e4535 ◽

Cited By ~ 10

Author(s):

Xin Liu ◽

Huirui Guan ◽

Min Song ◽

Yanping Fu ◽

Xiaomin Han ◽

...

Keyword(s):

Gene Expression ◽

Internal Control ◽

Abiotic Stresses ◽

Target Genes ◽

Expression Patterns ◽

Control Measures ◽

Rapid Expansion ◽

Pcr Analysis ◽

Data Normalization ◽

Qrt Pcr

BackgroundStellera chamaejasmeLinn, an important poisonous plant of the China grassland, is toxic to humans and livestock. The rapid expansion ofS. chamaejasmehas greatly damaged the grassland ecology and, consequently, seriously endangered the development of animal husbandry. To draft efficient prevention and control measures, it has become more urgent to carry out research on its adaptive and expansion mechanisms in different unfavorable habitats at the genetic level. Quantitative real-time polymerase chain reaction (qRT-PCR) is a widely used technique for studying gene expression at the transcript level; however, qRT-PCR requires reference genes (RGs) as endogenous controls for data normalization and only through appropriate RG selection and qRT-PCR can we guarantee the reliability and robustness of expression studies and RNA-seq data analysis. Unfortunately, little research on the selection of RGs for gene expression data normalization inS. chamaejasmehas been reported.MethodIn this study, 10 candidate RGs namely,18S,60S,CYP,GAPCP1,GAPDH2,EF1B,MDH,SAND,TUA1, andTUA6, were singled out from the transcriptome database ofS. chamaejasme, and their expression stability under three abiotic stresses (drought, cold, and salt) and three hormone treatments (abscisic acid, ABA; gibberellin, GA; ethephon, ETH) were estimated with the programs geNorm, NormFinder, and BestKeeper.ResultOur results showed thatGAPCP1andEF1Bwere the best combination for the three abiotic stresses, whereasTUA6andSAND,TUA1andCYP,GAPDH2and60Swere the best choices for ABA, GA, and ETH treatment, respectively. Moreover,GAPCP1and60Swere assessed to be the best combination for all samples, and18Swas the least stable RG for use as an internal control in all of the experimental subsets. The expression patterns of two target genes (P5CS2andGI) further verified that the RGs that we selected were suitable for gene expression normalization.DiscussionThis work is the first attempt to comprehensively estimate the stability of RGs inS. chamaejasme. Our results provide suitable RGs for high-precision normalization in qRT-PCR analysis, thereby making it more convenient to analyze gene expression under these experimental conditions.

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S1-bZIP Transcription Factors Play Important Roles in the Regulation of Fruit Quality and Stress Response

Frontiers in Plant Science ◽

10.3389/fpls.2021.802802 ◽

2022 ◽

Vol 12 ◽

Author(s):

Hong Wang ◽

Yunting Zhang ◽

Ayla Norris ◽

Cai-Zhong Jiang

Keyword(s):

Stress Response ◽

Plant Growth ◽

Fruit Quality ◽

Stress Responses ◽

Growth And Development ◽

Leucine Zipper ◽

Sugar Metabolism ◽

Bzip Transcription Factor ◽

Biological Functions ◽

Plant Growth And Development

Sugar metabolism not only determines fruit sweetness and quality but also acts as signaling molecules to substantially connect with other primary metabolic processes and, therefore, modulates plant growth and development, fruit ripening, and stress response. The basic region/leucine zipper motif (bZIP) transcription factor family is ubiquitous in eukaryotes and plays a diverse array of biological functions in plants. Among the bZIP family members, the smallest bZIP subgroup, S1-bZIP, is a unique one, due to the conserved upstream open reading frames (uORFs) in the 5′ leader region of their mRNA. The translated small peptides from these uORFs are suggested to mediate Sucrose-Induced Repression of Translation (SIRT), an important mechanism to maintain sucrose homeostasis in plants. Here, we review recent research on the evolution, sequence features, and biological functions of this bZIP subgroup. S1-bZIPs play important roles in fruit quality, abiotic and biotic stress responses, plant growth and development, and other metabolite biosynthesis by acting as signaling hubs through dimerization with the subgroup C-bZIPs and other cofactors like SnRK1 to coordinate the expression of downstream genes. Direction for further research and genetic engineering of S1-bZIPs in plants is suggested for the improvement of quality and safety traits of fruit.

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