scholarly journals Whole-genome characterization of Rosa chinensis AP2/ERF transcription factors and analysis of negative regulator RcDREB2B in Arabidopsis

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Wei Li ◽  
Ziwen Geng ◽  
Cuiping Zhang ◽  
Kuiling Wang ◽  
Xinqiang Jiang
Keyword(s):  
Drought Stress ◽  
Gene Structure ◽  
Growth And Development ◽  
Negative Regulator ◽  
Yeast Cells ◽  
Severe Drought ◽  
Rosa Chinensis ◽  
Number Pattern ◽  
Erf Family ◽  
The Rose

Abstract Background Rose (Rosa chinensis) is a traditional famous flower with valuable ornamental characteristics. However, drought stress restricts its growth and development, leading to an abnormal phenotype. One of the main transcription factor (TF) protein groups in the plant kingdom are the APETALA2/ethylene-responsive factor (AP2/ERF) proteins and are potentially involved in the growth and stress responses of various plants. Results Our investigation mainly focused on exploring the genome of rose and thereby we discovered 135 apparent AP2/ERF TFs. Phylogenic analyses revealed that RcAP2/ERF genes are categorized into DREB, Soloist, AP2, and ERF subfamilies, and are further classified these into 17 groups, with the same as Malus domestica and Arabidopsis thaliana. The analysis of the gene structure revealed that the introns ranged from 0 to 9 in number. Pattern examination demonstrated that the RcAP2/ERF predominantly consists of typical AP2 domains, of which the 2nd motif is the most ubiquitous. Distributions of cis-acting elements indicated that members of the AP2/ERF family are frequently involved in growth and development, phytohormone and stress response in rose species. Also, the distribution mapping of the rose chromosomes indicated that AP2/ERF class genes are dispersed among all seven chromosomes. Additionally, we isolated a novel DREB A2 subgroup gene and named it RcDREB2B. Subsequently, the RcDREB2B transcript accumulation was repressed under the mild and severe drought stress in the root samples of rose. RcDREB2B was targeted to the nucleus and exhibited transactivation in yeast cells. The overexpression of RcDREB2B was found to promote sensitivity to a higher salt concentration, ABA, and PEG at the germination and post-germination stages. Twelve putative osmotic and ABA-related genes were impaired in RcDREB2B-overexpressing plants. Conclusions The results provide comprehensive information regarding the gene structure, phylogenic, and distribution of the rose AP2/ERF family and bring insight into the complex transcriptional gene regulation of RcAP2/ERF. Findings in this study would also contribute to further understanding of the RcDREB2B gene in rose.

scholarly journals Whole-genome characterization of Rosa chinensis AP2/ERF transcription factors and analysis of negative regulator RcDREB2B in Arabidopsis

2021 ◽  
Author(s):  
Wei Li ◽  
Ziwen Geng ◽  
Cuiping Zhang ◽  
Kuiling Wang ◽  
Xinqiang Jiang
Keyword(s):  
Drought Stress ◽  
Gene Structure ◽  
Growth And Development ◽  
Negative Regulator ◽  
Yeast Cells ◽  
Severe Drought ◽  
Rosa Chinensis ◽  
Number Pattern ◽  
Erf Family ◽  
The Rose

Abstract Background: Rose (Rosa chinensis) is a traditional famous flower with valuable ornamental characteristics. However, drought stress restricts its growth and development, leading to an abnormal phenotype. One of the main transcription factor (TF) protein groups in the plant kingdom are the APETALA2/ethylene-responsive factor (AP2/ERF) proteins and are potentially involved in the growth and stress responses of various plants. Results: Our investigation mainly focused on exploring the genome of rose and thereby we discovered 135 apparent AP2/ERF TFs. Phylogenic analyses revealed that RcAP2/ERF genes are categorized into DREB, Soloist, AP2, and ERF subfamilies, and are further classified these into 17 groups, with the same as Malus domestica and Arabidopsis thaliana. The analysis of the gene structure revealed that the introns ranged from 0 to 9 in number. Pattern examination demonstrated that the RcAP2/ERF predominantly consists of typical AP2 domains, of which the 2nd motif is the most ubiquitous. Distributions of cis-acting elements indicated that members of the AP2/ERF family are frequently involved in growth and development, phytohormone and stress response in rose species. Also, the distribution mapping of the rose chromosomes indicated that AP2/ERF class genes are dispersed among all seven chromosomes. Additionally, we isolated a novel DREB A2 subgroup gene and named it RcDREB2B. Subsequently, the RcDREB2B transcript accumulation was repressed under the mild and severe drought stress in the root samples of rose. RcDREB2B was targeted to the nucleus and exhibited transactivation in yeast cells. The overexpression of RcDREB2B was found to promote sensitivity to a higher salt concentration, ABA, and PEG at the germination and post-germination stages. Twelve putative osmotic and ABA-related genes were impaired in RcDREB2B-overexpressing plants. Conclusions: The results provide comprehensive information regarding the gene structure, phylogenic, and distribution of the rose AP2/ERF family and bring insight into the complex transcriptional gene regulation of RcAP2/ERF. Findings in this study would also contribute to further understanding of the RcDREB2B gene in rose.

scholarly journals Whole-genome characterization of Rosa chinensis AP2/ERF transcription factors and analysis of negative regulator RcDREB2B in Arabidopsis

2020 ◽  
Author(s):  
Li Wei ◽  
Ziwen Geng ◽  
Zhang Cuiping ◽  
Wang Kuiling ◽  
Jiang Xinqiang
Keyword(s):  
Drought Stress ◽  
Gene Structure ◽  
Growth And Development ◽  
Negative Regulator ◽  
Yeast Cells ◽  
Severe Drought ◽  
Rosa Chinensis ◽  
Number Pattern ◽  
Erf Family ◽  
The Rose

Abstract Background: Rose (Rosa chinensis) is a traditional famous flower with valuable ornamental characteristics. However, drought stress restricts its growth and development, leading to an abnormal phenotype. One of the main transcription factor (TF) protein groups in the plant kingdom are the APETALA2/ethylene-responsive factor (AP2/ERF) proteins and are potentially involved in the growth and stress responses of various plants. Results: Our investigation mainly focused on exploring the genome of rose and thereby we discovered 135 apparent AP2/ERF TFs. Phylogenic analyses revealed that RcAP2/ERF genes are categorized into DREB, Soloist, AP2, and ERF subfamilies, and are further classified these into 17 groups, with the same as Malus domestica and Arabidopsis thaliana. The analysis of the gene structure revealed that the introns ranged from 0 to 9 in number. Pattern examination demonstrated that the RcAP2/ERF predominantly consists of typical AP2 domains, of which the 2nd motif is the most ubiquitous. Distributions of cis-acting elements indicated that members of the AP2/ERF family are frequently involved in growth and development, phytohormone and stress response in rose species. Also, the distribution mapping of the rose chromosomes indicated that AP2/ERF class genes are dispersed among all seven chromosomes. Additionally, we isolated a novel DREB A2 subgroup gene and named it RcDREB2B. Subsequently, the RcDREB2B transcript accumulation was repressed under the mild and severe drought stress in the root samples of rose. RcDREB2B was targeted to the nucleus and exhibited transactivation in yeast cells. The overexpression of RcDREB2B was found to promote sensitivity to a higher salt concentration, ABA, and PEG at the germination and post-germination stages. Twelve putative osmotic and ABA-related genes were impaired in RcDREB2B-overexpressing plants. Conclusions: The results provide comprehensive information regarding the gene structure, phylogenic, and distribution of the rose AP2/ERF family and bring insight into the complex transcriptional gene regulation of RcAP2/ERF. Findings in this study would also contribute to further understanding of the RcDREB2B gene in rose.

scholarly journals Whole-Genome Characterization of Rosa Chinensis AP2/ERF Transcription Factors and Analysis of Negative Regulator RcDREB2B in Arabidopsis

2020 ◽  
Author(s):  
Li Wei ◽  
Ziwen Geng ◽  
Zhang Cuiping ◽  
Wang Kuiling ◽  
Jiang Xinqiang
Keyword(s):  
Drought Stress ◽  
Gene Structure ◽  
Stress Responses ◽  
Negative Regulator ◽  
Yeast Cells ◽  
Severe Drought ◽  
Transcript Accumulation ◽  
Rosa Chinensis ◽  
Number Pattern ◽  
Erf Family

Abstract Background: Rose (Rosa chinensis) is a traditional famous flower with valuable ornamental characteristics. However, drought stress restricts its growth and development, leading to abnormal phenotype. APETALA2/ethylene-responsive factor (AP2/ERF) proteins are a kind of transcription factor (TF) protein groups in the plant kingdom, which are crucially involved in the growth and stress responses of most plants. Results: Our investigation focused on exploring the genome of rose and we discovered 135 apparent AP2/ERF TFs. Phylogenic analyses revealed that RcAP2/ERF genes are categorized into DREB, Soloist, AP2, and ERF subfamilies, and further classified these into 17 groups. Analysis of the gene structure revealed that the introns ranged from 0 to 9 in number. Pattern examination demonstrated that the RcAP2/ERF predominantly had typical AP2 domains, of which the 2nd motif is the most ubiquitous. Distributions of cis-acting elements showed members of the AP2/ERF family are involved in growth development and stress response in rose species. We carried out a distribution mapping of the seven rose chromosomes which revealed that AP2/ERF class genes are dispersed among all seven chromosomes. Additionally, we isolated a novel DREB A-2 subgroup gene and named it RcDREB2B. RcDREB2B transcript accumulation was repressed under mild drought and severe drought stress in the root samples of rose. RcDREB2B was targeted to the nucleus and exhibited transactivation in yeast cells. Overexpression of RcDREB2B resulted in enhanced sensitivity to high salt concentration, ABA, and PEG at the germination and post-germination stages. Twelve putative osmotic and ABA-related genes were impaired in RcDREB2B-overexpressing plants. Conclusion: The results provide comprehensive information regarding the gene structure, phylogenic, and distribution of rose AP2/ERF family and shed insight into the complex transcriptional gene regulation of RcAP2/ERF. Findings in this study would also contribute to further understanding of the RcDREB2B gene in rose.

scholarly journals Genome-wide investigation of the AP2/ERF gene family in ginger: evolution and expression profiling during development and abiotic stresses

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Haitao Xing ◽  
Yusong Jiang ◽  
Yong Zou ◽  
Xiaoling Long ◽  
Xiaoli Wu ◽  
...  
Keyword(s):  
Gene Structure ◽  
Abiotic Stresses ◽  
Growth And Development ◽  
Expression Profiles ◽  
Rna Seq ◽  
Qrt Pcr ◽  
Genome Wide ◽  
Evolutionary Features ◽  
Erf Family

Abstract Background AP2/ERF transcription factors (TFs) constitute one of the largest TF families in plants, which play crucial roles in plant metabolism, growth, and development as well as biotic and abiotic stresses responses. Although the AP2/ERF family has been thoroughly identified in many plant species and several AP2/ERF TFs have been functionally characterized, little is known about this family in ginger (Zingiber officinale Roscoe), an important affinal drug and diet vegetable. Recent completion of the ginger genome sequencing provides an opportunity to investigate the expression profiles of AP2/ERF genes in ginger on a genome-wide basis. Results A total of 163 AP2/ERF genes were obtained in the Z.officinale genome and renamed according to the chromosomal distribution of the ZoAP2/ERF genes. Phylogenetic analysis divided them into three subfamilies, of which 35 belonged to the AP2 subfamily, 120 to ERF, three to RAV, and five to Sololist, respectively, which is in accordance with the number of conserved domains and gene structure analysis. A total of 10 motifs were detected in ZoAP2/ERF genes, and some of the unique motifs were found to be important for the function of ZoAP2/ERF genes. The chromosomal localization, gene structure, and conserved protein motif analyses, as well as the characterization of gene duplication events provided deep insight into the evolutionary features of these ZoAP2/ERF genes. The expression profiles derived from the RNA-seq data and quantitative reserve transcription (qRT-PCR) analysis of ZoAP2/ERFs during development and responses to abiotic stresses were investigated in ginger. Conclusion A comprehensive analysis of the AP2/ERF gene expression patterns in various tissues by RNA-seq and qRT-PCR showed that they played an important role in the growth and development of ginger, and genes that might regulate rhizome and flower development were preliminary identified. In additionally, the ZoAP2/ERF family genes that responded to abiotic stresses were also identified. This study is the first time to identify the ZoAP2/ERF family, which contributes to research on evolutionary characteristics and better understanding the molecular basis for development and abiotic stress response, as well as further functional characterization of ZoAP2/ERF genes with an aim of ginger crop improvement.

scholarly journals Comparative Transcriptome and Weighted Gene Co-expression Network Analysis Identify Key Transcription Factors of Rosa chinensis ‘Old Blush’ After Exposure to a Gradual Drought Stress Followed by Recovery

2021 ◽  
Vol 12 ◽  
Author(s):  
Xin Jia ◽  
Hui Feng ◽  
Yanhua Bu ◽  
Naizhe Ji ◽  
Yingmin Lyu ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Drought Stress ◽  
Network Analysis ◽  
Physiological Traits ◽  
Drought Response ◽  
Rosa Chinensis ◽  
Primary And Secondary Metabolism ◽  
Term Enrichment ◽  
High Degree ◽  
The Rose

Rose is one of the most fundamental ornamental crops, but its yield and quality are highly limited by drought. The key transcription factors (TFs) and co-expression networks during rose’s response to drought stress and recovery after drought stress are still limited. In this study, the transcriptomes of leaves of 2-year-old cutting seedlings of Rosa chinensis ‘Old Blush’ from three continuous droughted stages (30, 60, 90 days after full watering) and rewatering were analyzed using RNA sequencing. Weighted gene co-expression network analysis (WGCNA) was used to construct a co-expression network, which was associated with the physiological traits of drought response to discovering the hub TFs involved in drought response. More than 45 million high-quality clean reads were generated from the sample and used for comparison with the rose reference genome. A total of 46433 differentially expressed genes (DEGs) were identified. Gene Ontology (GO) term enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that drought stress caused significant changes in signal transduction, plant hormones including ABA, auxin, brassinosteroid (BR), cytokinin, ethylene (ET), jasmonic acid (JA) and salicylic acid (SA), primary and secondary metabolism, and a certain degree of recovery after rewatering. Gene co-expression analysis identified 18 modules, in which four modules showed a high degree of correlation with physiological traits. In addition, 42 TFs including members of NACs, WRKYs, MYBs, AP2/ERFs, ARFs, and bHLHs with high connectivity in navajowhite1 and blue modules were screened. This study provides the transcriptome sequencing report of R. chinensis ‘Old Blush’ during drought stress and rewatering process. The study also identifies the response of candidate TFs to drought stress, providing guidelines for improving the drought tolerance of the rose through molecular breeding in the future.

scholarly journals Comparative Transcriptome Analysis Reveals Molecular Mechanism and Regulatory Network of Rosa Chinensis ‘Old Blush’ Leaves in Response to Drought Stress

2020 ◽  
Author(s):  
Xin Jia ◽  
Hui Feng ◽  
Yanhua Bu ◽  
Yingmin Lu ◽  
Naizhe Ji ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Drought Stress ◽  
Molecular Mechanism ◽  
Physiological Traits ◽  
Drought Response ◽  
Rosa Chinensis ◽  
Primary And Secondary Metabolism ◽  
Term Enrichment ◽  
Stress Related Genes ◽  
The Rose

Abstract Background: Rose is one of the most important ornamental crops, but drought limits its yield and quality seriously. Although serval abiotic stress related genes have been identified, the molecular mechanism during rose’s responding to drought stress is still limited. In this study, the transcriptomes of leaves of two-year-old cutting seedlings of Rosa chinensis ’Old Blush’ from three continuous droughted stages (30, 60, 90 days after full watering) and rewatering were analyzed using RNA sequencing. Meanwhile, weighted gene co-expression network analysis (WGCNA) was used to construct a co-expression network associated with the physiological traits of drought response to discover the hub transcription factors involved in drought response.Results: More than 45 million high-quality clean reads were generated from samples and used for comparison with the rose reference genome. A total of 46433 differentially expressed genes were identified. Gene ontology (GO) term enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that drought stress caused significant changes in signal transduction, plant hormones, primary and secondary metabolism, and a certain degree of recovery after rewatering. Gene co-expression analysis identified 18 modules, in which four modules have highly degree of correlation with physiological traits. In addition, twenty-two transcription factors including members of NACs, WRKYs, MYBs, ERFs, ARFs and bHLHs with high connectivity in these four modules were screened. Conclusions: The results of this study provided the first transcriptome sequencing report of the drought stress in R.chinensis, and also provided candidate transcription factors in response to drought stress, providing clues for improving the drought tolerance of the rose through molecular breeding in the future.

scholarly journals Role of Suillus placidus in Improving the Drought Tolerance of Masson Pine (Pinus massoniana Lamb.) Seedlings

Forests ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 332
Author(s):  
Min Li ◽  
Haoyun Wang ◽  
Xizhou Zhao ◽  
Zhongke Lu ◽  
Xueguang Sun ◽  
...  
Keyword(s):  
Drought Stress ◽  
Defense Mechanism ◽  
Southern China ◽  
Dry Weight ◽  
Pinus Massoniana ◽  
Photosynthetic Performance ◽  
Ectomycorrhizal Fungus ◽  
Severe Drought ◽  
Masson Pine ◽  
Pine Seedlings

Masson pine is an important afforestation species in southern China, where seasonal drought is common. The present study focused on the effects of Suillus placidus, an ectomycorrhizal fungus, inoculation on the growth and physiological and biochemical performance of masson pine seedlings under four different watering treatments (well-watered, mild drought, moderate drought, and severe drought) to evaluate the symbiotic relationship between S. placidus and masson pine seedlings. Ectomycorrhizal-inoculated (ECM) and non-inoculated (NM) seedlings were grown in pots and maintained for 60 days using the weighing method. Results showed that seedlings’ growth, dry weight, RWC, chlorophyll content, PSII efficiency, and photosynthesis decreased as drought stress intensified in both ECM and NM plants. This suggests that drought stress significantly limits the growth and photosynthetic performance of masson pine seedlings. Nevertheless, increased An/gs and proline contents in both NM and ECM prevented oxidative damage caused by drought stress. In addition, increased peroxidase (POD) activity is an essential defense mechanism of ECM seedling under drought stress. Compared with NM, ECM seedlings showed faster growth, higher RWC, and photosynthetic performance, and lower lipid peroxidation in cell membranes under drought stress, as indicated by higher POD activity and lower proline and malondialdehyde (MDA). Our experiment found that S. placidus inoculation can enhance the drought resistance of masson pine seedlings by increasing antioxidant enzyme activity, water use efficiency, and proline content, thereby enhancing growth under water-deficiency conditions. S. placidus can be used to cultivate high-quality seedlings and improve their survival in regions that experience seasonal droughts.

scholarly journals Arabidopsis MADS-box factor AGL16 negatively regulates drought resistance via stomatal density and stomatal movement

2020 ◽  
Vol 71 (19) ◽  
pp. 6092-6106 ◽  
Author(s):  
Ping-Xia Zhao ◽  
Zi-Qing Miao ◽  
Jing Zhang ◽  
Si-Yan Chen ◽  
Qian-Qian Liu ◽  
...  
Keyword(s):  
Drought Stress ◽  
Drought Resistance ◽  
Molecular Mechanisms ◽  
Stomatal Density ◽  
Stomatal Closure ◽  
Negative Regulator ◽  
Stomatal Development ◽  
Mads Box ◽  
Mobility Shift ◽  
Aba Metabolism

Abstract Drought is one of the most important environmental factors limiting plant growth and productivity. The molecular mechanisms underlying plant drought resistance are complex and not yet fully understood. Here, we show that the Arabidopsis MADS-box transcription factor AGL16 acts as a negative regulator in drought resistance by regulating stomatal density and movement. Loss-of-AGL16 mutants were more resistant to drought stress and had higher relative water content, which was attributed to lower leaf stomatal density and more sensitive stomatal closure due to higher leaf ABA levels compared with the wild type. AGL16-overexpressing lines displayed the opposite phenotypes. AGL16 is preferentially expressed in guard cells and down-regulated in response to drought stress. The expression of CYP707A3 and AAO3 in ABA metabolism and SDD1 in stomatal development was altered in agl16 and overexpression lines, making them potential targets of AGL16. Using chromatin immunoprecipitation, transient transactivation, yeast one-hybrid, and electrophoretic mobility shift assays, we demonstrated that AGL16 was able to bind the CArG motifs in the promoters of the CYP707A3, AAO3, and SDD1 and regulate their transcription, leading to altered leaf stomatal density and ABA levels. Taking our findings together, AGL16 acts as a negative regulator of drought resistance by modulating leaf stomatal density and ABA accumulation.

scholarly journals Spermine: Its Emerging Role in Regulating Drought Stress Responses in Plants

Cells ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 261
Author(s):  
Md. Mahadi Hasan ◽  
Milan Skalicky ◽  
Mohammad Shah Jahan ◽  
Md. Nazmul Hossain ◽  
Zunaira Anwar ◽  
...  
Keyword(s):  
Drought Stress ◽  
Drought Tolerance ◽  
Stress Responses ◽  
Abiotic Stresses ◽  
Defense Mechanisms ◽  
Antioxidant Defense ◽  
Severe Drought ◽  
New Information ◽  
Effects Of Drought

In recent years, research on spermine (Spm) has turned up a lot of new information about this essential polyamine, especially as it is able to counteract damage from abiotic stresses. Spm has been shown to protect plants from a variety of environmental insults, but whether it can prevent the adverse effects of drought has not yet been reported. Drought stress increases endogenous Spm in plants and exogenous application of Spm improves the plants’ ability to tolerate drought stress. Spm’s role in enhancing antioxidant defense mechanisms, glyoxalase systems, methylglyoxal (MG) detoxification, and creating tolerance for drought-induced oxidative stress is well documented in plants. However, the influences of enzyme activity and osmoregulation on Spm biosynthesis and metabolism are variable. Spm interacts with other molecules like nitric oxide (NO) and phytohormones such as abscisic acid, salicylic acid, brassinosteroids, and ethylene, to coordinate the reactions necessary for developing drought tolerance. This review focuses on the role of Spm in plants under severe drought stress. We have proposed models to explain how Spm interacts with existing defense mechanisms in plants to improve drought tolerance.

Mapping QTLs for yield components and chlorophyll a fluorescence parameters in wheat under three levels of water availability

2011 ◽  
Vol 9 (2) ◽  
pp. 291-295 ◽  
Author(s):  
Ilona Czyczyło-Mysza ◽  
Izabela Marcińska ◽  
Edyta Skrzypek ◽  
Małgorzata Chrupek ◽  
Stanisław Grzesiak ◽  
...  
Keyword(s):  
Drought Stress ◽  
Chlorophyll A ◽  
Chlorophyll A Fluorescence ◽  
Wheat Yield ◽  
Dry Weight ◽  
Interval Mapping ◽  
Main Stem ◽  
Severe Drought ◽  
Single Marker Analysis ◽  
Fluorescence Parameters

Drought is one of the major factors limiting wheat yield in many developing countries worldwide. Parameters of chlorophyll a fluorescence kinetics under drought stress conditions have been used to characterize dehydration tolerance in wheat. In the present study, a set of 94 doubled haploid lines obtained from Chinese Spring × SQ1 (CSDH), mapped with 450 markers, was evaluated for yield (grain dry weight/main stem ear), number of grains/main stem ear (NG) and chlorophyll a fluorescence parameters (FC) under moderate and severe drought stress, and compared with results for well-watered plants. quantitative trait loci (QTLs) were identified using Windows QTLCartographer version 2.5 software and the results were analysed using single-marker analysis (SMA) and composite interval mapping (CIM). Analysis using SMA and CIM showed mostly similar QTLs for all traits, though more QTLs were identified by SMA than by CIM. The genetic control of yield, NG and FC varied considerably between drought-stressed and non-stressed plants. Although no major QTL co-locations were found for yield and FC using CIM, the co-location of QTLs for NG, yield and Fv/Fm in drought-stressed plants was observed on chromosome 5A using SMA.

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