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Du L, Kang X, Guo H, Zhu Z, Wu R, Yuan M, Ding C. Cotyledonary somatic embryo is one kind of intermediate material similar to callus in the process of in vitro tissue culture from Rosa hybrida 'John F. Kennedy'. BMC Genomics 2024; 25:362. [PMID: 38609856 PMCID: PMC11010427 DOI: 10.1186/s12864-024-10256-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
BACKGROUND Rose is recognized as an important ornamental plant worldwide, and it is also one of the most widely used flowers in gardens. At present, the improvement of rose traits is still difficult and uncertain, and molecular breeding can provide new ideas for the improvement of modern rose varieties. Somatic embryos are quite good receptors for genetic transformation. However, little is known about the molecular mechanisms underlying during the regeneration process of rose somatic embryos. To elucidate the molecular regulation mechanism of somatic embryo plantlet regeneration, the relationship between the differences in traits of the two different regenerated materials and the significantly differentially expressed genes (DEGs) related to phytohormone pathways in the process of regeneration were be investigated. RESULTS These representative two regenerated samples from single-piece cotyledonary somatic embryo (SPC) culture of Rosa hybrida 'John F. Kennedy', were harvested for transcriptome analysis, with the SPC explants at the initial culture (Day 0) as the control. The differentially expressed genes (DEGs) in the materials from two different types for regeneration approach (SBF type: the regeneration approach type of single bud formed from SPC explants; MBF type: the regeneration approach type of multiple buds formed from SPC explants) were be screened by means of the transcriptome sequencing technology. In this study, a total of about 396.24 million clean reads were obtained, of which 78.95-82.92% were localized to the reference genome, compared with the initial material (CK sample), there were 5594 specific genes in the material of SBF type and 6142 specific genes in the MBF type. The DEGs from the SBF type material were mainly concentrated in the biological processes of GO terms such as phytohormones, substance transport, cell differentiation, and redox reaction. The KEGG enrichment analysis revealed these DEGs were more active in ubiquinone and other terpenoid-quinone biosynthesis, fatty acid elongation, steroid biosynthesis, and glycosphingolipid biosynthesis-globo and isoglobo series. In contrast, the DEGs induced by the MBF type material were mainly associated with the biological processes such as phytohormones, phosphorylation, photosynthesis and signal transduction. According to KEGG analysis, these DEGs of MBF type were significantly enriched in the porphyrin and chlorophyll metabolism, brassinosteroid biosynthesis, carotenoid biosynthesis, and peroxisome. Furthermore, the results from the phytohormone pathways analysis showed that the auxin-responsive factor SAUR and the cell wall modifying enzyme gene XTH were upregulated for expression but the protein phosphatase gene PP2C was downregulated for expression in SBF type; the higher expression of the ethylene receptor ETR, the ethylene transduction genes EBF1/2, the transcription factor EIN3, and the ethylene-responsive transcription factor ERF1/2 were induced by MBF type. CONCLUSIONS According to the GO and KEGG analysis, it indicated the DEGs between two different regenerated materials from somatic embryos were significantly different which might be causing morphological differences. That was somatic embryos from Rosa hybrida 'John F. Kennedy' could regenerate plantlet via both classic somatic embryogenesis (seed-like germination) and organogenesis, cotyledonary somatic embryos should be considered as one kind of intermediate materials similiar to callus, rather than the indicator materials for somatic embryogenesis.
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Affiliation(s)
- Li Du
- Analysis and Test Center, Nanyang Normal University, 473061, Nanyang, China
- Henan Province Engineering Research Center of Rose Germplasm Innovation and Cultivation Technique, Nanyang Normal University, 473061, Nanyang, China
| | - Xiaoling Kang
- Henan Province Engineering Research Center of Rose Germplasm Innovation and Cultivation Technique, Nanyang Normal University, 473061, Nanyang, China
- College of Life Science and Agricultural Engineering, Nanyang Normal University, 473061, Nanyang, China
| | - Haoran Guo
- Henan Province Engineering Research Center of Rose Germplasm Innovation and Cultivation Technique, Nanyang Normal University, 473061, Nanyang, China
- College of Life Science and Agricultural Engineering, Nanyang Normal University, 473061, Nanyang, China
| | - Zhongfeng Zhu
- Henan Province Engineering Research Center of Rose Germplasm Innovation and Cultivation Technique, Nanyang Normal University, 473061, Nanyang, China
- College of Life Science and Agricultural Engineering, Nanyang Normal University, 473061, Nanyang, China
| | - Rui Wu
- Henan Province Engineering Research Center of Rose Germplasm Innovation and Cultivation Technique, Nanyang Normal University, 473061, Nanyang, China
- College of Life Science and Agricultural Engineering, Nanyang Normal University, 473061, Nanyang, China
| | - Meijing Yuan
- Henan Province Engineering Research Center of Rose Germplasm Innovation and Cultivation Technique, Nanyang Normal University, 473061, Nanyang, China
- College of Life Science and Agricultural Engineering, Nanyang Normal University, 473061, Nanyang, China
| | - Chuanyu Ding
- Henan Province Engineering Research Center of Rose Germplasm Innovation and Cultivation Technique, Nanyang Normal University, 473061, Nanyang, China.
- College of Life Science and Agricultural Engineering, Nanyang Normal University, 473061, Nanyang, China.
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Nowak K, Wójcikowska B, Gajecka M, Elżbieciak A, Morończyk J, Wójcik AM, Żemła P, Citerne S, Kiwior-Wesołowska A, Zbieszczyk J, Gaj MD. The improvement of the in vitro plant regeneration in barley with the epigenetic modifier of histone acetylation, trichostatin A. J Appl Genet 2024; 65:13-30. [PMID: 37962803 PMCID: PMC10789698 DOI: 10.1007/s13353-023-00800-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/16/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023]
Abstract
Genotype-limited plant regeneration is one of the main obstacles to the broader use of genetic transformation in barley breeding. Thus, developing new approaches that might improve responses of in vitro recalcitrant genotypes remains at the center of barley biotechnology. Here, we analyzed different barley genotypes, including "Golden Promise," a genotype commonly used in the genetic transformation, and four malting barley cultivars of poor regenerative potential. The expression of hormone-related transcription factor (TF) genes with documented roles in plant regeneration was analyzed in genotypes with various plant-regenerating capacities. The results indicated differential expression of auxin-related TF genes between the barley genotypes in both the explants and the derived cultures. In support of the role of auxin in barley regeneration, distinct differences in the accumulation of free and oxidized auxin were observed in explants and explant-derived callus cultures of barley genotypes. Following the assumption that modifying gene expression might improve plant regeneration in barley, we treated the barley explants with trichostatin A (TSA), which affects histone acetylation. The effects of TSA were genotype-dependent as TSA treatment improved plant regeneration in two barley cultivars. TSA-induced changes in plant regeneration were associated with the increased expression of auxin biosynthesis-involved TFs. The study demonstrated that explant treatment with chromatin modifiers such as TSA might provide a new and effective epigenetic approach to improving plant regeneration in recalcitrant barley genotypes.
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Affiliation(s)
- Katarzyna Nowak
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia, 40-007, Katowice, Poland.
| | - Barbara Wójcikowska
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia, 40-007, Katowice, Poland
| | - Monika Gajecka
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia, 40-007, Katowice, Poland
| | - Anna Elżbieciak
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia, 40-007, Katowice, Poland
| | - Joanna Morończyk
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia, 40-007, Katowice, Poland
| | - Anna M Wójcik
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia, 40-007, Katowice, Poland
| | - Przemysław Żemła
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia, 40-007, Katowice, Poland
- Toxicology Research Group, Łukasiewicz Research Network, Institute of Industrial Organic Chemistry Branch Pszczyna, Doświadczalna 27, 43-200, Pszczyna, Poland
| | - Sylvie Citerne
- Institut Jean-Pierre Bourgin (IJPB), INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
| | - Agnieszka Kiwior-Wesołowska
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia, 40-007, Katowice, Poland
| | - Justyna Zbieszczyk
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia, 40-007, Katowice, Poland
| | - Małgorzata D Gaj
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia, 40-007, Katowice, Poland
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Karami O, de Jong H, Somovilla VJ, Villanueva Acosta B, Sugiarta AB, Ham M, Khadem A, Wennekes T, Offringa R. Structure-activity relationship of 2,4-D correlates auxinic activity with the induction of somatic embryogenesis in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1355-1369. [PMID: 37647363 DOI: 10.1111/tpj.16430] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 07/19/2023] [Accepted: 08/04/2023] [Indexed: 09/01/2023]
Abstract
2,4-dichlorophenoxyacetic acid (2,4-D) is a synthetic analogue of the plant hormone auxin that is commonly used in many in vitro plant regeneration systems, such as somatic embryogenesis (SE). Its effectiveness in inducing SE, compared to the natural auxin indole-3-acetic acid (IAA), has been attributed to the stress triggered by this compound rather than its auxinic activity. However, this hypothesis has never been thoroughly tested. Here we used a library of forty 2,4-D analogues to test the structure-activity relationship with respect to the capacity to induce SE and auxinic activity in Arabidopsis thaliana. Four analogues induced SE as effectively as 2,4-D and 13 analogues induced SE but were less effective. Based on root growth inhibition and auxin response reporter expression, the 2,4-D analogues were classified into different groups, ranging from very active to not active auxin analogues. A halogen at the 4-position of the aromatic ring was important for auxinic activity, whereas a halogen at the 3-position resulted in reduced activity. Moreover, a small substitution at the carboxylate chain was tolerated, as was extending the carboxylate chain with an even number of carbons. The auxinic activity of most 2,4-D analogues was consistent with their simulated TIR1-Aux/IAA coreceptor binding characteristics. A strong correlation was observed between SE induction efficiency and auxinic activity, which is in line with our observation that 2,4-D-induced SE and stress both require TIR1/AFB auxin co-receptor function. Our data indicate that the stress-related effects triggered by 2,4-D and considered important for SE induction are downstream of auxin signalling.
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Affiliation(s)
- Omid Karami
- Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
| | - Hanna de Jong
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomedical Research, Utrecht University, Universiteitsweg 99, 3584CG, Utrecht, The Netherlands
| | - Victor J Somovilla
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramon 182, 20014, Donostia San Sebastián, Spain
| | - Beatriz Villanueva Acosta
- Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
| | - Aldo Bryan Sugiarta
- Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
| | - Marvin Ham
- Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
| | - Azadeh Khadem
- Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
| | - Tom Wennekes
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomedical Research, Utrecht University, Universiteitsweg 99, 3584CG, Utrecht, The Netherlands
| | - Remko Offringa
- Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
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Sun Y, Zang Y, Ma Y, Wang C, Song S, Sun H. Identification and functional analysis of LpNAC37 associated with somatic embryogenesis in Lilium pumilum DC. Fisch. based on transcriptome analysis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 205:107964. [PMID: 37939543 DOI: 10.1016/j.plaphy.2023.107964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 06/16/2023] [Accepted: 08/11/2023] [Indexed: 11/10/2023]
Abstract
Somatic embryogenesis (SE) is important for Lilium bulb propagation, germplasm conservation, and genetic transformation. The transition of somatic cells to embryonic cells is a critical step in SE, but the associated regulatory mechanisms have not been fully elucidated. Lilium pumilum DC. Fisch has a high regenerative capacity, and this study clarifies the critical timing of embryonic cell appearance in Lilium SE. Transcriptome sequencing using RNA-seq technology was performed on 5 representative samples from the early stage of Lilium SE. The 15 established cDNA libraries yielded 91.47 GB of valid data, and a total of 11,155 genes were consistently differentially expressed in the early stages of Lilium SE. GO annotation and KEGG pathway analysis of differentially expressed genes (DEGs) suggested that transcriptional regulation, hormone signaling, and stress response pathways play essential roles in the early stages of Lilium SE. WOX8, WOX11, SHR2, NAC37, AHP2, ANT, PIN1C, LAX2, LBD4, ACS12, YUC4, NFYB3, WRKY28, SAUR50, PYL9, and WRKY39 may be candidate genes for regulating early SE in Lilium. We further cloned LpNAC37, one of the key DEGs obtained from WGCNA and screening. LpNAC37 encodes a protein of 303 amino acids with a conserved NAM structural domain. The protein is a nuclear transcription factor with the highest homology to carrot DcNAC37. Overexpression of LpNAC37 suggested that LpNAC37 promotes embryonic callus formation in Arabidopsis. These results will help reveal the molecular mechanisms of the early stages of Lilium SE and advance the application of SE in Lilium propagation and genetic transformation.
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Affiliation(s)
- Yue Sun
- Key Laboratory of Protected Horticulture of Education Ministry, College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yuqing Zang
- Key Laboratory of Protected Horticulture of Education Ministry, College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yue Ma
- Key Laboratory of Protected Horticulture of Education Ministry, College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Chunxia Wang
- Key Laboratory of Protected Horticulture of Education Ministry, College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Shengli Song
- Key Laboratory of Protected Horticulture of Education Ministry, College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China.
| | - Hongmei Sun
- Key Laboratory of Protected Horticulture of Education Ministry, College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China; National and Local Joint Engineering Research Center of Northern Horticultural Facilities Design and Application Technology, Shenyang, 110866, China.
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5
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Jiang L, Li R, Yang J, Yao Z, Cao S. Ethylene response factor ERF022 is involved in regulating Arabidopsis root growth. PLANT MOLECULAR BIOLOGY 2023; 113:1-17. [PMID: 37553544 DOI: 10.1007/s11103-023-01373-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 07/05/2023] [Indexed: 08/10/2023]
Abstract
Ethylene response factors (ERFs) are involved in the regulation of plant development processes and stress responses. In this study, we provide evidence for the role of ERF022, a member of the ERF transcription factor group III, in regulating Arabidopsis root growth. We found that ERF022-loss-of-function mutants exhibited increased primary root length and lateral root numbers, and also morphological growth advantages compared to wild-type. Further studies showed that mutants had enhanced cell size in length in the root elongation zones. These results were accompanied by significant increase in the expression of cell elongation and cell wall expansion related genes SAUR10, GASA14, LRX2, XTH19 in mutants. Moreover, ERF022-mediated root growth was associated with the enhanced endogenous auxin and gibberellins levels. Our results suggest that loss-of-function of ERF022 up-regulated the expression of cell elongation and cell wall related genes through auxin and gibberellins signal in the regulation of root growth. Unexpectedly, ERF022 overexpression lines also showed longer primary roots and more lateral roots compared to wild-type, and had longer root apical meristematic zone with increased cell numbers. Overexpression of ERF022 significantly up-regulated cell proliferation, organ growth and auxin biosynthesis genes EXO, HB2, GALK2, LBD26, YUC5, which contribute to enhanced root growth. Altogether, our results provide genetic evidence that ERF022 plays an important role in regulating root growth in Arabidopsis thaliana.
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Affiliation(s)
- Li Jiang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China.
| | - Ruyin Li
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Juan Yang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Zhicheng Yao
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Shuqing Cao
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
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Zhang X, Liang S, Luo B, Zhou Z, Bao J, Fang R, Wang F, Song X, Liao Z, Chen G, Wang Y, Xu F, Teng Y, Li W, Xu S, Lin FC. Transcriptomic and Metabolomic Investigation on Leaf Necrosis Induced by ZmWus2 Transient Overexpression in Nicotiana benthamiana. Int J Mol Sci 2023; 24:11190. [PMID: 37446367 DOI: 10.3390/ijms241311190] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/02/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023] Open
Abstract
WUSCHEL (WUS) is a crucial transcription factor in regulating plant stem cell development, and its expression can also improve genetic transformation. However, the ectopic expression of WUS always causes pleiotropic effects during genetic transformation, making it important to understand the regulatory mechanisms underlying these phenomena. In our study, we found that the transient expression of the maize WUS ortholog ZmWus2 caused severe leaf necrosis in Nicotiana benthamiana. We performed transcriptomic and non-target metabolomic analyses on tobacco leaves during healthy to wilted states after ZmWus2 transient overexpression. Transcriptomic analysis revealed that ZmWus2 transformation caused active metabolism of inositol trisphosphate and glycerol-3-phosphate, while also upregulating plant hormone signaling and downregulating photosystem and protein folding pathways. Metabolomic analysis mainly identified changes in the synthesis of phenylpropanoid compounds and various lipid classes, including steroid synthesis. In addition, transcription factors such as ethylene-responsive factors (ERFs), the basic helix-loop-helix (bHLH) factors, and MYBs were found to be regulated by ZmWus2. By integrating these findings, we developed a WUS regulatory model that includes plant hormone accumulation, stress responses, lipid remodeling, and leaf necrosis. Our study sheds light on the mechanisms underlying WUS ectopic expression causing leaf necrosis and may inform the development of future genetic transformation strategies.
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Affiliation(s)
- Xianwen Zhang
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Shuang Liang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Biao Luo
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- Hunan Engineering Laboratory for Good Agricultural Practice and Comprehensive Utilization of Famous-Region Medicinal Plants, Hunan Agricultural University, Changsha 410128, China
| | - Zhongjing Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jiandong Bao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Ruiqiu Fang
- Institute of Maize and Featured Upland Crops, Zhejiang Academy of Agricultural Sciences, Dongyang 322100, China
| | - Fang Wang
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xijiao Song
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Zhenfeng Liao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Guang Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Yan Wang
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Fei Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Yi Teng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Wanchang Li
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Shengchun Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- Xianghu Laboratory, Hangzhou 311231, China
| | - Fu-Cheng Lin
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
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Khadem A, Moshtaghi N, Bagheri A. Regulatory networks of hormone-involved transcription factors and their downstream pathways during somatic embryogenesis of Arabidopsis thaliana. 3 Biotech 2023; 13:132. [PMID: 37091499 PMCID: PMC10115918 DOI: 10.1007/s13205-023-03546-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 03/28/2023] [Indexed: 04/25/2023] Open
Abstract
Somatic embryogenesis (SE) depends on a variety of developmental pathways that are influenced by several environmental factors. Therefore, it is important to understand the relationship between environmental and genetic factors by identifying the gene networks involved in SE through gene set enrichment analysis (GSEA). For determination of SE effective transcription factors, upstream sequences of core-enriched genes were analyzed. The results indicated that response to hormones is one of the biological pathways activated by the enriched TFs at all stages of somatic embryogenesis and about half of the hormonal pathways were enriched. On the fifth day after 2,4-Dichlorophenoxyacetic acid (2,4-D) treatment, the activity of hormone-affecting genes reached its maximum. At this time, more transcription factors regulated the enriched genes compared to the other stages of somatic embryogenesis. MYBs, AT-HOOKs, and HSFs are the main families of transcription factors which affect core-enriched genes during SE. CCA1, PRR7, and TOC1 and their related genes at the center of protein-protein interaction of SE-key transcription factors, involved in the regulation of the circadian clock. Gene expression analysis of CCA1, PRR7, and TOC1 revealed that the genes involved in circadian clock reached their maximum activity when embryonic cells formed. Also, auxin response elements were identified at the upstream of SE-circadian clock transcription factors, indicating that they might mediate between auxin signaling and SE-related hormonal pathways as well as SE marker genes such as AGL15, BBM, and LECs. Based on these results, it is possible that the cellular circadian rhythm activates various developmental pathways under the influence of auxin signal transduction and their interactions determine the induction of somatic embryogenesis. According to the results of this study, modifying pathways affected by SE-related transcription factors such as circadian rhythm may result in cell reprogramming and increase somatic embryogenesis efficiency. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03546-7.
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Affiliation(s)
- Azadeh Khadem
- Department of Biotechnology and Plant Breeding, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Nasrin Moshtaghi
- Department of Biotechnology and Plant Breeding, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Abdolreza Bagheri
- Department of Biotechnology and Plant Breeding, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
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Ya R, Li J, Zhang N, Yu Q, Xu W. Phenotypically abnormal cotyledonary Vitis vinifera embryos differ in anatomy, endogenous hormone levels and transcriptome profiles. TREE PHYSIOLOGY 2023; 43:467-485. [PMID: 36331330 DOI: 10.1093/treephys/tpac129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 10/05/2022] [Accepted: 10/25/2022] [Indexed: 05/03/2023]
Abstract
In many perennial fruit species, including grapevine (Vitis vinifera L.), the highly complex process of somatic embryogenesis (SE) can result in the formation of a deformed embryo, although the underlying reasons are still poorly understood. Here, V. vinifera cv. 'Chardonnay' cotyledonary embryos with distinct morphologies were used to address this issue. Normal cotyledonary embryos (NCEs) and elongated cotyledonary embryos (ECEs) were observed to have better-developed vasculature and shoot meristems than the vitrified cotyledonary embryos (VCEs) and fused cotyledonary embryos (FCEs), but ECEs were less developed. We determined that the morphological differences in these phenotypically abnormal embryos were likely associated with endogenous hormone levels, since concentrations of the phytohormones indoleacetic acid (IAA) and abscisic acid (ABA) in NCEs were higher than in the other three types. Comparative transcriptome analysis revealed large differences in gene expression of the hormone signaling pathways in normal and abnormal cotyledonary embryos. Weighted gene co-expression network analysis of the different cotyledonary types allowed the identification of co-regulated gene modules associated with SE, suggesting a role for ERF family genes and other transcription factors (TFs) in regulating morphology. Moreover, an analysis of morphology-specific gene expression indicated that the activation of a specific protein kinase, small heat shock proteins (sHSPs) and certain TFs was closely associated with the formation of normal cotyledonary embryos. Our comparative analyses provide insights into the gene networks regulating somatic cotyledon development and open new avenues for research into plant regeneration and functional genomic studies of malformed embryos.
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Affiliation(s)
- Rong Ya
- School of Agronomy, Ningxia University, No. 489 Helanshan West Road, Yinchuan, Ningxia 750021, China
- Engineering Research Center of Grape and Wine, Ministry of Education, Ningxia University, No. 489 Helanshan West Road, Yinchuan, Ningxia 750021, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, No. 489 Helanshan West Road,Yinchuan, Ningxia 750021, China
| | - Junduo Li
- School of Agronomy, Ningxia University, No. 489 Helanshan West Road, Yinchuan, Ningxia 750021, China
- Engineering Research Center of Grape and Wine, Ministry of Education, Ningxia University, No. 489 Helanshan West Road, Yinchuan, Ningxia 750021, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, No. 489 Helanshan West Road,Yinchuan, Ningxia 750021, China
| | - Ningbo Zhang
- Engineering Research Center of Grape and Wine, Ministry of Education, Ningxia University, No. 489 Helanshan West Road, Yinchuan, Ningxia 750021, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, No. 489 Helanshan West Road,Yinchuan, Ningxia 750021, China
- School of Food & Wine, Ningxia University, No. 489 Helanshan West Road, Yinchuan, Ningxia 750021, China
| | - Qinhan Yu
- School of Agronomy, Ningxia University, No. 489 Helanshan West Road, Yinchuan, Ningxia 750021, China
- Engineering Research Center of Grape and Wine, Ministry of Education, Ningxia University, No. 489 Helanshan West Road, Yinchuan, Ningxia 750021, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, No. 489 Helanshan West Road,Yinchuan, Ningxia 750021, China
| | - Weirong Xu
- School of Agronomy, Ningxia University, No. 489 Helanshan West Road, Yinchuan, Ningxia 750021, China
- Engineering Research Center of Grape and Wine, Ministry of Education, Ningxia University, No. 489 Helanshan West Road, Yinchuan, Ningxia 750021, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, No. 489 Helanshan West Road,Yinchuan, Ningxia 750021, China
- School of Food & Wine, Ningxia University, No. 489 Helanshan West Road, Yinchuan, Ningxia 750021, China
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9
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Awada R, Lepelley M, Breton D, Charpagne A, Campa C, Berry V, Georget F, Breitler JC, Léran S, Djerrab D, Martinez-Seidel F, Descombes P, Crouzillat D, Bertrand B, Etienne H. Global transcriptome profiling reveals differential regulatory, metabolic and hormonal networks during somatic embryogenesis in Coffea arabica. BMC Genomics 2023; 24:41. [PMID: 36694132 PMCID: PMC9875526 DOI: 10.1186/s12864-022-09098-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 12/22/2022] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Somatic embryogenesis (SE) is one of the most promising processes for large-scale dissemination of elite varieties. However, for many plant species, optimizing SE protocols still relies on a trial and error approach. We report the first global scale transcriptome profiling performed at all developmental stages of SE in coffee to unravel the mechanisms that regulate cell fate and totipotency. RESULTS RNA-seq of 48 samples (12 developmental stages × 4 biological replicates) generated 90 million high quality reads per sample, approximately 74% of which were uniquely mapped to the Arabica genome. First, the statistical analysis of transcript data clearly grouped SE developmental stages into seven important phases (Leaf, Dedifferentiation, Primary callus, Embryogenic callus, Embryogenic cell clusters, Redifferentiation and Embryo) enabling the identification of six key developmental phase switches, which are strategic for the overall biological efficiency of embryo regeneration. Differential gene expression and functional analysis showed that genes encoding transcription factors, stress-related genes, metabolism-related genes and hormone signaling-related genes were significantly enriched. Second, the standard environmental drivers used to control SE, i.e. light, growth regulators and cell density, were clearly perceived at the molecular level at different developmental stages. Third, expression profiles of auxin-related genes, transcription factor-related genes and secondary metabolism-related genes were analyzed during SE. Gene co-expression networks were also inferred. Auxin-related genes were upregulated during dedifferentiation and redifferentiation while transcription factor-related genes were switched on from the embryogenic callus and onward. Secondary metabolism-related genes were switched off during dedifferentiation and switched back on at the onset of redifferentiation. Secondary metabolites and endogenous IAA content were tightly linked with their respective gene expression. Lastly, comparing Arabica embryogenic and non-embryogenic cell transcriptomes enabled the identification of biological processes involved in the acquisition of embryogenic capacity. CONCLUSIONS The present analysis showed that transcript fingerprints are discriminating signatures of cell fate and are under the direct influence of environmental drivers. A total of 23 molecular candidates were successfully identified overall the 12 developmental stages and can be tested in many plant species to optimize SE protocols in a rational way.
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Affiliation(s)
- Rayan Awada
- Nestlé Research - Plant Science Research Unit, Tours, France ,grid.8183.20000 0001 2153 9871UMR DIADE, CIRAD, Montpellier, France ,grid.121334.60000 0001 2097 0141UMR DIADE, Université de Montpellier, CIRAD, Montpellier, IRD France
| | - Maud Lepelley
- Nestlé Research - Plant Science Research Unit, Tours, France
| | - David Breton
- Nestlé Research - Plant Science Research Unit, Tours, France
| | - Aline Charpagne
- grid.419905.00000 0001 0066 4948Nestlé Research, Société Des Produits Nestlé SA, Lausanne, Switzerland ,grid.511382.c0000 0004 7595 5223Sophia Genetics, Genève, Switzerland
| | - Claudine Campa
- grid.121334.60000 0001 2097 0141UMR DIADE, Université de Montpellier, CIRAD, Montpellier, IRD France ,grid.4399.70000000122879528UMR DIADE, IRD, Montpellier, France
| | - Victoria Berry
- Nestlé Research - Plant Science Research Unit, Tours, France
| | - Frédéric Georget
- grid.8183.20000 0001 2153 9871UMR DIADE, CIRAD, Montpellier, France ,grid.121334.60000 0001 2097 0141UMR DIADE, Université de Montpellier, CIRAD, Montpellier, IRD France
| | - Jean-Christophe Breitler
- grid.8183.20000 0001 2153 9871UMR DIADE, CIRAD, Montpellier, France ,grid.121334.60000 0001 2097 0141UMR DIADE, Université de Montpellier, CIRAD, Montpellier, IRD France
| | - Sophie Léran
- grid.8183.20000 0001 2153 9871UMR DIADE, CIRAD, Montpellier, France ,grid.121334.60000 0001 2097 0141UMR DIADE, Université de Montpellier, CIRAD, Montpellier, IRD France
| | - Doâa Djerrab
- grid.8183.20000 0001 2153 9871UMR DIADE, CIRAD, Montpellier, France ,grid.121334.60000 0001 2097 0141UMR DIADE, Université de Montpellier, CIRAD, Montpellier, IRD France
| | - Federico Martinez-Seidel
- grid.418390.70000 0004 0491 976XMax Planck Institute for Molecular Plant Physiology, Golm, Germany ,grid.1008.90000 0001 2179 088XSchool of BioSciences, The University of Melbourne, Parkville, VIC Australia
| | - Patrick Descombes
- grid.419905.00000 0001 0066 4948Nestlé Research, Société Des Produits Nestlé SA, Lausanne, Switzerland
| | | | - Benoît Bertrand
- grid.8183.20000 0001 2153 9871UMR DIADE, CIRAD, Montpellier, France ,grid.121334.60000 0001 2097 0141UMR DIADE, Université de Montpellier, CIRAD, Montpellier, IRD France
| | - Hervé Etienne
- grid.8183.20000 0001 2153 9871UMR DIADE, CIRAD, Montpellier, France ,grid.121334.60000 0001 2097 0141UMR DIADE, Université de Montpellier, CIRAD, Montpellier, IRD France
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10
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Hao JF, Wang C, Gu CR, Xu DX, Zhang L, Zhang HG. Anatomical observation and transcriptome analysis of buds reveal the association between the AP2 gene family and reproductive induction in hybrid larch (Larix kaempferi × Larix olgensis). TREE PHYSIOLOGY 2023; 43:118-129. [PMID: 36150026 PMCID: PMC9833870 DOI: 10.1093/treephys/tpac111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 09/11/2022] [Indexed: 06/16/2023]
Abstract
Hybrid larch is an excellent afforestation species in northern China. The instability of seed yield is an urgent problem to be solved. The biological characteristics related to seed setting in larch are different from those in angiosperms and other gymnosperms. Studying the developmental mechanism of the larch sporophyll can deepen our understanding of conifer reproductive development and help to ensure an adequate supply of seeds in the seed orchard. The results showed that the formation of microstrobilus primordia in hybrid larch could be observed in anatomical sections collected in the middle of July. The contents of endogenous gibberellin 3 (GA3) and abscisic acid (ABA) were higher and the contents of GA4, GA7, jasmonic acid and salicylic acid were lower in multiseeded larch. Transcriptome analysis showed that transcription factors were significantly enriched in the AP2 family. There were 23 differentially expressed genes in the buds of the multiseeded and less-seeded types, and the expression of most of these genes was higher in the buds than in the needles. We conclude that mid-July is the early stage of reproductive organ development in hybrid larch and is suitable for the study of reproductive development. GA3 and ABA may be helpful for improving seed setting in larch, and 23 AP2/EREBP family genes are involved in the regulation of reproductive development in larch.
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Affiliation(s)
- Jun-Fei Hao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, No. 51 Hexing Road, Xiangfang District, Harbin 150040, China
| | - Chen Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, No. 51 Hexing Road, Xiangfang District, Harbin 150040, China
| | - Chen-Rui Gu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, No. 51 Hexing Road, Xiangfang District, Harbin 150040, China
| | - Dai-Xi Xu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, No. 51 Hexing Road, Xiangfang District, Harbin 150040, China
| | - Lei Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, No. 51 Hexing Road, Xiangfang District, Harbin 150040, China
| | - Han-Guo Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, No. 51 Hexing Road, Xiangfang District, Harbin 150040, China
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11
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Sivanesan I, Nayeem S, Venkidasamy B, Kuppuraj SP, RN C, Samynathan R. Genetic and epigenetic modes of the regulation of somatic embryogenesis: a review. Biol Futur 2022; 73:259-277. [DOI: 10.1007/s42977-022-00126-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 06/16/2022] [Indexed: 01/17/2023]
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Huang Y, Liu L, Hu H, Tang N, Shi L, Xu F, Wang S. Arabidopsis ERF012 Is a Versatile Regulator of Plant Growth, Development and Abiotic Stress Responses. Int J Mol Sci 2022; 23:ijms23126841. [PMID: 35743283 PMCID: PMC9224505 DOI: 10.3390/ijms23126841] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/12/2022] [Accepted: 06/16/2022] [Indexed: 02/04/2023] Open
Abstract
The AP2/ERF transcription factors are widely involved in the regulation of plant growth, development and stress responses. Arabidopsis ERF012 is differentially responsive to various stresses; however, its potential regulatory role remains elusive. Here, we show that ERF012 is predominantly expressed in the vascular bundles, lateral root primordium and vein branch points. ERF012 overexpression inhibits root growth, whereas it promotes root hair development and leaf senescence. In particular, ERF012 may downregulate its target genes AtC4H and At4CL1, key players in phenylpropanoid metabolism and cell wall formation, to hinder auxin accumulation and thereby impacting root growth and leaf senescence. Consistent with this, exogenous IAA application effectively relieves the effect of ERF012 overexpression on root growth and leaf senescence. Meanwhile, ERF012 presumably activates ethylene biosynthesis to promote root hair development, considering that the ERF012-mediated root hair development can be suppressed by the ethylene biosynthetic inhibitor. In addition, ERF012 overexpression displays positive and negative effects on low- and high-temperature responses, respectively, while conferring plant resistance to drought, salinity and heavy metal stresses. Taken together, this study provides a comprehensive evaluation of the functional versatility of ERF012 in plant growth, development and abiotic stress responses.
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Affiliation(s)
- Yupu Huang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (Y.H.); (L.L.); (L.S.); (F.X.)
- Microelement Research Center, College of Resources & Environment, Huazhong Agricultural University, Wuhan 430070, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng 475001, China; (H.H.); (N.T.)
| | - Ling Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (Y.H.); (L.L.); (L.S.); (F.X.)
- Microelement Research Center, College of Resources & Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Haitao Hu
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng 475001, China; (H.H.); (N.T.)
| | - Ning Tang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng 475001, China; (H.H.); (N.T.)
| | - Lei Shi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (Y.H.); (L.L.); (L.S.); (F.X.)
- Microelement Research Center, College of Resources & Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Fangsen Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (Y.H.); (L.L.); (L.S.); (F.X.)
- Microelement Research Center, College of Resources & Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Sheliang Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (Y.H.); (L.L.); (L.S.); (F.X.)
- Microelement Research Center, College of Resources & Environment, Huazhong Agricultural University, Wuhan 430070, China
- Correspondence:
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13
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Liu B, Sun G, Liu C, Liu S. LEAFY COTYLEDON 2: A Regulatory Factor of Plant Growth and Seed Development. Genes (Basel) 2021; 12:genes12121896. [PMID: 34946844 PMCID: PMC8701892 DOI: 10.3390/genes12121896] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/18/2021] [Accepted: 11/23/2021] [Indexed: 11/16/2022] Open
Abstract
Transcription factors are key molecules in the regulation of gene expression in all organisms. The transcription factor LEAFY COTYLEDON 2 (LEC2), which belongs to the DNA-binding protein family, contains a B3 domain. The transcription factor is involved in the regulation of important plant biological processes such as embryogenesis, somatic embryo formation, seed storage protein synthesis, fatty acid metabolism, and other important biological processes. Recent studies have shown that LEC2 regulates the formation of lateral roots and influences the embryonic resetting of the parental vernalization state. The orthologs of LEC2 and their regulatory effects have also been identified in some crops; however, their regulatory mechanism requires further investigation. Here, we summarize the most recent findings concerning the effects of LEC2 on plant growth and seed development. In addition, we discuss the potential molecular mechanisms of the action of the LEC2 gene during plant development.
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14
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Neves M, Correia S, Cavaleiro C, Canhoto J. Modulation of Organogenesis and Somatic Embryogenesis by Ethylene: An Overview. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10061208. [PMID: 34198660 PMCID: PMC8232195 DOI: 10.3390/plants10061208] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/07/2021] [Accepted: 06/09/2021] [Indexed: 05/13/2023]
Abstract
Ethylene is a plant hormone controlling physiological and developmental processes such as fruit maturation, hairy root formation, and leaf abscission. Its effect on regeneration systems, such as organogenesis and somatic embryogenesis (SE), has been studied, and progress in molecular biology techniques have contributed to unveiling the mechanisms behind its effects. The influence of ethylene on regeneration should not be overlooked. This compound affects regeneration differently, depending on the species, genotype, and explant. In some species, ethylene seems to revert recalcitrance in genotypes with low regeneration capacity. However, its effect is not additive, since in genotypes with high regeneration capacity this ability decreases in the presence of ethylene precursors, suggesting that regeneration is modulated by ethylene. Several lines of evidence have shown that the role of ethylene in regeneration is markedly connected to biotic and abiotic stresses as well as to hormonal-crosstalk, in particular with key regeneration hormones and growth regulators of the auxin and cytokinin families. Transcriptional factors of the ethylene response factor (ERF) family are regulated by ethylene and strongly connected to SE induction. Thus, an evident connection between ethylene, stress responses, and regeneration capacity is markedly established. In this review the effect of ethylene and the way it interacts with other players during organogenesis and somatic embryogenesis is discussed. Further studies on the regulation of ERF gene expression induced by ethylene during regeneration can contribute to new insights on the exact role of ethylene in these processes. A possible role in epigenetic modifications should be considered, since some ethylene signaling components are directly related to histone acetylation.
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Affiliation(s)
- Mariana Neves
- Center for Functional Ecology, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal; (M.N.); (S.C.)
| | - Sandra Correia
- Center for Functional Ecology, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal; (M.N.); (S.C.)
| | - Carlos Cavaleiro
- CIEPQPF, Faculty of Pharmacy, University of Coimbra, Pólo das Ciências da Saúde, Azinhaga de Santa Comba, 3000-548 Coimbra, Portugal;
| | - Jorge Canhoto
- Center for Functional Ecology, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal; (M.N.); (S.C.)
- Correspondence:
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15
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Ranade SS, Egertsdotter U. In silico characterization of putative gene homologues involved in somatic embryogenesis suggests that some conifer species may lack LEC2, one of the key regulators of initiation of the process. BMC Genomics 2021; 22:392. [PMID: 34039265 PMCID: PMC8157724 DOI: 10.1186/s12864-021-07718-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 05/12/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Somatic embryogenesis (SE) is the process in which somatic embryos develop from somatic tissue in vitro on medium in most cases supplemented with growth regulators. Knowledge of genes involved in regulation of initiation and of development of somatic embryos is crucial for application of SE as an efficient tool to enable genetic improvement across genotypes by clonal propagation. RESULTS Current work presents in silico identification of putative homologues of central regulators of SE initiation and development in conifers focusing mainly on key transcription factors (TFs) e.g. BBM, LEC1, LEC1-LIKE, LEC2 and FUSCA3, based on sequence similarity using BLASTP. Protein sequences of well-characterised candidates genes from Arabidopsis thaliana were used to query the databases (Gymno PLAZA, Congenie, GenBank) including whole-genome sequence data from two representative species from the genus Picea (Picea abies) and Pinus (Pinus taeda), for finding putative conifer homologues, using BLASTP. Identification of corresponding conifer proteins was further confirmed by domain search (Conserved Domain Database), alignment (MUSCLE) with respective sequences of Arabidopsis thaliana proteins and phylogenetic analysis (Phylogeny.fr). CONCLUSIONS This in silico analysis suggests absence of LEC2 in Picea abies and Pinus taeda, the conifer species whose genomes have been sequenced. Based on available sequence data to date, LEC2 was also not detected in the other conifer species included in the study. LEC2 is one of the key TFs associated with initiation and regulation of the process of SE in angiosperms. Potential alternative mechanisms that might be functional in conifers to compensate the lack of LEC2 are discussed.
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Affiliation(s)
- Sonali Sachin Ranade
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Center (UPSC), Swedish University of Agricultural Science (SLU), 901 83, Umeå, Sweden.
| | - Ulrika Egertsdotter
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Center (UPSC), Swedish University of Agricultural Science (SLU), 901 83, Umeå, Sweden
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16
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De Clercq I, Van de Velde J, Luo X, Liu L, Storme V, Van Bel M, Pottie R, Vaneechoutte D, Van Breusegem F, Vandepoele K. Integrative inference of transcriptional networks in Arabidopsis yields novel ROS signalling regulators. NATURE PLANTS 2021; 7:500-513. [PMID: 33846597 DOI: 10.1038/s41477-021-00894-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 03/04/2021] [Indexed: 05/12/2023]
Abstract
Gene regulation is a dynamic process in which transcription factors (TFs) play an important role in controlling spatiotemporal gene expression. To enhance our global understanding of regulatory interactions in Arabidopsis thaliana, different regulatory input networks capturing complementary information about DNA motifs, open chromatin, TF-binding and expression-based regulatory interactions were combined using a supervised learning approach, resulting in an integrated gene regulatory network (iGRN) covering 1,491 TFs and 31,393 target genes (1.7 million interactions). This iGRN outperforms the different input networks to predict known regulatory interactions and has a similar performance to recover functional interactions compared to state-of-the-art experimental methods. The iGRN correctly inferred known functions for 681 TFs and predicted new gene functions for hundreds of unknown TFs. For regulators predicted to be involved in reactive oxygen species (ROS) stress regulation, we confirmed in total 75% of TFs with a function in ROS and/or physiological stress responses. This includes 13 ROS regulators, previously not connected to any ROS or stress function, that were experimentally validated in our ROS-specific phenotypic assays of loss- or gain-of-function lines. In conclusion, the presented iGRN offers a high-quality starting point to enhance our understanding of gene regulation in plants by integrating different experimental data types.
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Affiliation(s)
- Inge De Clercq
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- VIB Center for Plant Systems Biology, Ghent, Belgium.
| | - Jan Van de Velde
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Xiaopeng Luo
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Li Liu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Veronique Storme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Michiel Van Bel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Robin Pottie
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Dries Vaneechoutte
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- VIB Center for Plant Systems Biology, Ghent, Belgium.
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium.
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Amaral-Silva PM, Clarindo WR, Guilhen JHS, de Jesus Passos ABR, Sanglard NA, Ferreira A. Global 5-methylcytosine and physiological changes are triggers of indirect somatic embryogenesis in Coffea canephora. PROTOPLASMA 2021; 258:45-57. [PMID: 32895735 DOI: 10.1007/s00709-020-01551-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 08/28/2020] [Indexed: 05/27/2023]
Abstract
Indirect somatic embryogenesis (ISE) establishment for Coffea species started in the 1970s. Since then, intraspecific variations in the morphogenic pathway have been reported, even in the common environmental condition in vitro. Several authors have suggested that these variations are the result of genetic, epigenetic, and/or physiological events, highlighting the need for investigations to know the causes. Along these lines, this study aimed to investigate and describe, for the first time, the global 5-methylcytosine and physiological changes that occur in the cells of the aggregate suspensions of Coffea canephora during proliferation and somatic embryo regeneration steps. The cell proliferation step was characterized by increase in cell mass in all subcultures; relatively low mean values of global 5-methylcytosine (5-mC%), abscisic acid (ABA), and indole-3-acetic acid (IAA); high mean value of 1-aminocyclopropane-1-carboxylic acid (ACC, an ethylene precursor); and increase followed by decrease in spermidine (Spd, a polyamine) level. Therefore, these epigenetic and physiologic aspects promoted the cell proliferation, which is fundamental for ISE. In turn, the somatic embryo regeneration was correlated with global 5-mC% and physiological changes. The competence acquisition, determination, and cell differentiation steps were marked by increases in mean values of 5-mC%, IAA and ABA, and decreases in ACC and Spd, evincing that these changes are the triggers for regeneration and maturation of somatic embryos. Therefore, dynamic and coordinated epigenetic and physiologic changes occur in the cells of the aggregate suspensions during the C. canephora ISE in liquid system.
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Affiliation(s)
- Paulo Marcos Amaral-Silva
- Laboratório de Citogenética e Cultura de Tecidos Vegetais, Centro de Ciências Agrárias e Engenharias, Universidade Federal do Espírito Santo, Alegre, ES, 29500-000, Brazil
| | - Wellington Ronildo Clarindo
- Laboratório de Citogenética e Citometria, Departamento de Biologia Geral, Centro de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil.
| | - José Henrique Soler Guilhen
- Laboratório de Biometria, Centro de Ciências Agrárias e Engenharias, Universidade Federal do Espírito Santo, Alegre, ES, 29500-000, Brazil
| | - Ana Beatriz Rocha de Jesus Passos
- Laboratório de Biometria, Centro de Ciências Agrárias e Engenharias, Universidade Federal do Espírito Santo, Alegre, ES, 29500-000, Brazil
- Laboratório de Genética e Melhoramento, Centro de Ciências Agrárias e Engenharias, Universidade Federal do Espírito Santo, Alegre, ES, 29500-000, Brazil
| | - Natália Arruda Sanglard
- Laboratório de Citogenética e Cultura de Tecidos Vegetais, Centro de Ciências Agrárias e Engenharias, Universidade Federal do Espírito Santo, Alegre, ES, 29500-000, Brazil
| | - Adésio Ferreira
- Laboratório de Biometria, Centro de Ciências Agrárias e Engenharias, Universidade Federal do Espírito Santo, Alegre, ES, 29500-000, Brazil
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18
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Ding M, Dong H, Xue Y, Su S, Wu Y, Li S, Liu H, Li H, Han J, Shan X, Yuan Y. Transcriptomic analysis reveals somatic embryogenesis-associated signaling pathways and gene expression regulation in maize (Zea mays L.). PLANT MOLECULAR BIOLOGY 2020; 104:647-663. [PMID: 32910317 DOI: 10.1007/s11103-020-01066-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 08/31/2020] [Indexed: 06/11/2023]
Abstract
Transcriptome analysis of maize embryogenic callus and somatic embryos reveals associated genes reprogramming, hormone signaling pathways and transcriptional regulation involved in somatic embryogenesis in maize. Somatic embryos are widely utilized in propagation and genetic engineering of crop plants. In our laboratory, an elite maize inbred line Y423 that could generate intact somatic embryos was obtained and applied to genetic transformation. To enhance our understanding of regulatory mechanisms during maize somatic embryogenesis, we used RNA-based sequencing (RNA-seq) to characterize the transcriptome of immature embryo (IE), embryogenic callus (EC) and somatic embryo (SE) from maize inbred line Y423. The number of differentially expressed genes (DEGs) in three pairwise comparisons (IE-vs-EC, IE-vs-SE and EC-vs-SE) was 5767, 7084 and 1065, respectively. The expression patterns of DEGs were separated into eight major clusters. Somatic embryogenesis associated genes were mainly grouped into cluster A or B with an expression trend toward up-regulation during dedifferentiation. GO annotation and KEGG pathway analysis revealed that DEGs were implicated in plant hormone signal transduction, stress response and metabolic process. Among the differentially expressed transcription factors, the most frequently represented families were associated with the common stress response or related to cell differentiation, embryogenic patterning and embryonic maturation processes. Genes include hormone response/transduction and stress response, as well as several transcription factors were discussed in this study, which may be potential candidates for further analyses regarding their roles in somatic embryogenesis. Furthermore, the temporal expression patterns of candidate genes were analyzed to reveal their roles in somatic embryogenesis. This transcriptomic data provide insights into future functional studies, which will facilitate further dissections of the molecular mechanisms that control maize somatic embryogenesis.
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Affiliation(s)
- Meiqi Ding
- College of Plant Science, Jilin University, Changchun, 130062, China
| | - Haixiao Dong
- College of Plant Science, Jilin University, Changchun, 130062, China
| | - Yingjie Xue
- College of Plant Science, Jilin University, Changchun, 130062, China
| | - Shengzhong Su
- College of Plant Science, Jilin University, Changchun, 130062, China
| | - Ying Wu
- College of Plant Science, Jilin University, Changchun, 130062, China
| | - Shipeng Li
- College of Plant Science, Jilin University, Changchun, 130062, China
| | - Hongkui Liu
- College of Plant Science, Jilin University, Changchun, 130062, China
| | - He Li
- College of Plant Science, Jilin University, Changchun, 130062, China
| | - Junyou Han
- College of Plant Science, Jilin University, Changchun, 130062, China
| | - Xiaohui Shan
- College of Plant Science, Jilin University, Changchun, 130062, China.
| | - Yaping Yuan
- College of Plant Science, Jilin University, Changchun, 130062, China.
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Grzybkowska D, Nowak K, Gaj MD. Hypermethylation of Auxin-Responsive Motifs in the Promoters of the Transcription Factor Genes Accompanies the Somatic Embryogenesis Induction in Arabidopsis. Int J Mol Sci 2020; 21:E6849. [PMID: 32961931 PMCID: PMC7555384 DOI: 10.3390/ijms21186849] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/09/2020] [Accepted: 09/16/2020] [Indexed: 12/17/2022] Open
Abstract
The auxin-induced embryogenic reprogramming of plant somatic cells is associated with extensive modulation of the gene expression in which epigenetic modifications, including DNA methylation, seem to play a crucial role. However, the function of DNA methylation, including the role of auxin in epigenetic regulation of the SE-controlling genes, remains poorly understood. Hence, in the present study, we analysed the expression and methylation of the TF genes that play a critical regulatory role during SE induction (LEC1, LEC2, BBM, WUS and AGL15) in auxin-treated explants of Arabidopsis. The results showed that auxin treatment substantially affected both the expression and methylation patterns of the SE-involved TF genes in a concentration-dependent manner. The auxin treatment differentially modulated the methylation of the promoter (P) and gene body (GB) sequences of the SE-involved genes. Relevantly, the SE-effective auxin treatment (5.0 µM of 2,4-D) was associated with the stable hypermethylation of the P regions of the SE-involved genes and a significantly higher methylation of the P than the GB fragments was a characteristic feature of the embryogenic culture. The presence of auxin-responsive (AuxRE) motifs in the hypermethylated P regions suggests that auxin might substantially contribute to the DNA methylation-mediated control of the SE-involved genes.
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Affiliation(s)
| | | | - Małgorzata D. Gaj
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Jagiellońska 28, 40-032 Katowice, Poland; (D.G.); (K.N.)
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20
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Nowak K, Morończyk J, Wójcik A, Gaj MD. AGL15 Controls the Embryogenic Reprogramming of Somatic Cells in Arabidopsis through the Histone Acetylation-Mediated Repression of the miRNA Biogenesis Genes. Int J Mol Sci 2020; 21:ijms21186733. [PMID: 32937992 PMCID: PMC7554740 DOI: 10.3390/ijms21186733] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/09/2020] [Accepted: 09/11/2020] [Indexed: 12/24/2022] Open
Abstract
The embryogenic transition of somatic cells requires an extensive reprogramming of the cell transcriptome. Relevantly, the extensive modulation of the genes that have a regulatory function, in particular the genes encoding the transcription factors (TFs) and miRNAs, have been indicated as controlling somatic embryogenesis (SE) that is induced in vitro in the somatic cells of plants. Identifying the regulatory relationships between the TFs and miRNAs during SE induction is of central importance for understanding the complex regulatory interplay that fine-tunes a cell transcriptome during the embryogenic transition. Hence, here, we analysed the regulatory relationships between AGL15 (AGAMOUS-LIKE 15) TF and miR156 in an embryogenic culture of Arabidopsis. Both AGL15 and miR156 control SE induction and AGL15 has been reported to target the MIR156 genes in planta. The results showed that AGL15 contributes to the regulation of miR156 in an embryogenic culture at two levels that involve the activation of the MIR156 transcription and the containment of the abundance of mature miR156 by repressing the miRNA biogenesis genes DCL1 (DICER-LIKE1), SERRATE and HEN1 (HUA-ENHANCER1). To repress the miRNA biogenesis genes AGL15 seems to co-operate with the TOPLESS co-repressors (TPL and TPR1-4), which are components of the SIN3/HDAC silencing complex. The impact of TSA (trichostatin A), an inhibitor of the HDAC histone deacetylases, on the expression of the miRNA biogenesis genes together with the ChIP results implies that histone deacetylation is involved in the AGL15-mediated repression of miRNA processing. The results indicate that HDAC6 and HDAC19 histone deacetylases might co-operate with AGL15 in silencing the complex that controls the abundance of miR156 during embryogenic induction. This study provides new evidence about the histone acetylation-mediated control of the miRNA pathways during the embryogenic reprogramming of plant somatic cells and the essential role of AGL15 in this regulatory mechanism.
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21
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Marimuthu K, Subbaraya U, Suthanthiram B, Marimuthu SS. Molecular analysis of somatic embryogenesis through proteomic approach and optimization of protocol in recalcitrant Musa spp. PHYSIOLOGIA PLANTARUM 2019; 167:282-301. [PMID: 30883793 DOI: 10.1111/ppl.12966] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 02/23/2019] [Accepted: 03/11/2019] [Indexed: 05/12/2023]
Abstract
Somatic embryogenesis (SE) is a complex stress related process regulated by numerous biological factors. SE is mainly applicable to mass propagation and genetic improvement of plants through gene transfer technology and induced mutations. In banana, SE is highly genome dependent as the efficiency varies with cultivars. To understand the molecular mechanism of SE, a proteomics approach was carried out to identify proteins expressed during embryogenic calli (EC) induction, regeneration and germination of somatic embryos in the banana cultivar cv. Rasthali (AAB). In total, 70 spots were differentially expressed in various developmental stages of SE, of which 16 were uniquely expressed and 17 were highly abundant in EC compared to non-embryogenic calli and explants. Also, four spots were uniquely expressed in germinating somatic embryos. The functional annotation of identified proteins revealed that calcium signaling along with stress and endogenous hormones related proteins played a vital role in EC induction and germination of somatic embryos. Thus, based on this outcome, the callus induction media was modified and tested in five cultivars. Among them, cultivars Grand Naine (AAA), Monthan (ABB) and Ney Poovan (AB) showed a better response in tryptophan added media, whereas Red Banana (AAA) and Karpuravalli (ABB) showed maximum EC induction in kinetin and CaCl2 supplemented media respectively. Simultaneously, germination media were modified to induce proteins responsible for germination. In cv. Rasthali, media supplemented with 10 mM CaCl2 showed a maximum increase in germination (51.79%) over control plants. Thus, the present study revealed that media modification based on proteomic analysis can induce SE in recalcitrant cultivars and also enhance germination in cultivars amenable for SE.
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Affiliation(s)
- Kumaravel Marimuthu
- Crop Improvement Division, ICAR-National Research Centre for Banana, Tiruchirappalli, India
| | - Uma Subbaraya
- Crop Improvement Division, ICAR-National Research Centre for Banana, Tiruchirappalli, India
| | | | - Saraswathi S Marimuthu
- Crop Improvement Division, ICAR-National Research Centre for Banana, Tiruchirappalli, India
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22
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Awada R, Campa C, Gibault E, Déchamp E, Georget F, Lepelley M, Abdallah C, Erban A, Martinez-Seidel F, Kopka J, Legendre L, Léran S, Conéjéro G, Verdeil JL, Crouzillat D, Breton D, Bertrand B, Etienne H. Unravelling the Metabolic and Hormonal Machinery During Key Steps of Somatic Embryogenesis: A Case Study in Coffee. Int J Mol Sci 2019; 20:ijms20194665. [PMID: 31547069 PMCID: PMC6802359 DOI: 10.3390/ijms20194665] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 09/17/2019] [Accepted: 09/18/2019] [Indexed: 12/11/2022] Open
Abstract
Somatic embryogenesis (SE) is one of the most promising processes for large-scale dissemination of elite varieties. However, for many plant species, optimizing SE protocols still relies on a trial-and-error approach. Using coffee as a model plant, we report here the first global analysis of metabolome and hormone dynamics aiming to unravel mechanisms regulating cell fate and totipotency. Sampling from leaf explant dedifferentiation until embryo development covered 15 key stages. An in-depth statistical analysis performed on 104 metabolites revealed that massive re-configuration of metabolic pathways induced SE. During initial dedifferentiation, a sharp decrease in phenolic compounds and caffeine levels was also observed while auxins, cytokinins and ethylene levels were at their highest. Totipotency reached its highest expression during the callus stages when a shut-off in hormonal and metabolic pathways related to sugar and energetic substance hydrolysis was evidenced. Abscisic acid, leucine, maltotriose, myo-inositol, proline, tricarboxylic acid cycle metabolites and zeatin appeared as key metabolic markers of the embryogenic capacity. Combining metabolomics with multiphoton microscopy led to the identification of chlorogenic acids as markers of embryo redifferentiation. The present analysis shows that metabolite fingerprints are signatures of cell fate and represent a starting point for optimizing SE protocols in a rational way.
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Affiliation(s)
- Rayan Awada
- Nestlé Research-Plant Science Unit, 101 avenue Gustave Eiffel, F-37097 Tours CEDEX 2, France.
- CIRAD (Centre de coopération internationale en recherche agronomique pour le développement), UMR IPME, F-34398 Montpellier, France.
- UMR IPME (Interactions Plantes Microorganismes Environnement), University of Montpellier, CIRAD, IRD, F-34398 Montpellier, France.
| | - Claudine Campa
- UMR IPME (Interactions Plantes Microorganismes Environnement), University of Montpellier, CIRAD, IRD, F-34398 Montpellier, France.
- IRD (Institut de recherche pour le développement), UMR IPME, F-34398 Montpellier, France.
| | - Estelle Gibault
- Nestlé Research-Plant Science Unit, 101 avenue Gustave Eiffel, F-37097 Tours CEDEX 2, France.
| | - Eveline Déchamp
- CIRAD (Centre de coopération internationale en recherche agronomique pour le développement), UMR IPME, F-34398 Montpellier, France.
- UMR IPME (Interactions Plantes Microorganismes Environnement), University of Montpellier, CIRAD, IRD, F-34398 Montpellier, France.
| | - Frédéric Georget
- CIRAD (Centre de coopération internationale en recherche agronomique pour le développement), UMR IPME, F-34398 Montpellier, France.
- UMR IPME (Interactions Plantes Microorganismes Environnement), University of Montpellier, CIRAD, IRD, F-34398 Montpellier, France.
| | - Maud Lepelley
- Nestlé Research-Plant Science Unit, 101 avenue Gustave Eiffel, F-37097 Tours CEDEX 2, France.
| | - Cécile Abdallah
- UMR IPME (Interactions Plantes Microorganismes Environnement), University of Montpellier, CIRAD, IRD, F-34398 Montpellier, France.
- IRD (Institut de recherche pour le développement), UMR IPME, F-34398 Montpellier, France.
| | - Alexander Erban
- Max Planck Institute for Molecular Plant Physiology, Am Muehlenberg 1, D-14476 Golm, Germany.
| | | | - Joachim Kopka
- Max Planck Institute for Molecular Plant Physiology, Am Muehlenberg 1, D-14476 Golm, Germany.
| | - Laurent Legendre
- Université de Lyon (Université Lyon 1, CNRS, UMR5557, Ecologie Microbienne, INRA, UMR1418), F-69622 Lyon, France.
| | - Sophie Léran
- CIRAD (Centre de coopération internationale en recherche agronomique pour le développement), UMR IPME, F-34398 Montpellier, France.
- UMR IPME (Interactions Plantes Microorganismes Environnement), University of Montpellier, CIRAD, IRD, F-34398 Montpellier, France.
| | - Geneviève Conéjéro
- Histocytology and Plant Cell Imaging platform PHIV, UMR AGAP (CIRAD, INRA, SupAgro)-UMR B&PMP (INRA, CNRS, SupAgro, University of Montpellier), F-34095 Montpellier, France.
| | - Jean-Luc Verdeil
- Histocytology and Plant Cell Imaging platform PHIV, UMR AGAP (CIRAD, INRA, SupAgro)-UMR B&PMP (INRA, CNRS, SupAgro, University of Montpellier), F-34095 Montpellier, France.
| | - Dominique Crouzillat
- Nestlé Research-Plant Science Unit, 101 avenue Gustave Eiffel, F-37097 Tours CEDEX 2, France.
| | - David Breton
- Nestlé Research-Plant Science Unit, 101 avenue Gustave Eiffel, F-37097 Tours CEDEX 2, France.
| | - Benoît Bertrand
- CIRAD (Centre de coopération internationale en recherche agronomique pour le développement), UMR IPME, F-34398 Montpellier, France.
- UMR IPME (Interactions Plantes Microorganismes Environnement), University of Montpellier, CIRAD, IRD, F-34398 Montpellier, France.
| | - Hervé Etienne
- CIRAD (Centre de coopération internationale en recherche agronomique pour le développement), UMR IPME, F-34398 Montpellier, France.
- UMR IPME (Interactions Plantes Microorganismes Environnement), University of Montpellier, CIRAD, IRD, F-34398 Montpellier, France.
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Solanki M, Sinha A, Shukla LI. Optimization of in vitro culture media for improvement in yield of Navara ancient Indian medicinal rice. 3 Biotech 2019; 9:270. [DOI: 10.1007/s13205-019-1797-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 06/06/2019] [Indexed: 10/26/2022] Open
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Srivastava D, Verma G, Chauhan AS, Pande V, Chakrabarty D. Rice (Oryza sativa L.) tau class glutathione S-transferase (OsGSTU30) overexpression in Arabidopsis thaliana modulates a regulatory network leading to heavy metal and drought stress tolerance. Metallomics 2019; 11:375-389. [PMID: 30516767 DOI: 10.1039/c8mt00204e] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
OsGSTU30 increases the abiotic stress tolerance in plants either by its catalytic activity or by modulating the expression of stress responsive genes.
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Affiliation(s)
- Dipali Srivastava
- Genetics and Molecular Biology Division
- CSIR-National Botanical Research Institute
- India
- Department of Biotechnology
- Kumaun University
| | - Giti Verma
- Genetics and Molecular Biology Division
- CSIR-National Botanical Research Institute
- India
| | | | - Veena Pande
- Department of Biotechnology
- Kumaun University
- India
| | - Debasis Chakrabarty
- Genetics and Molecular Biology Division
- CSIR-National Botanical Research Institute
- India
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25
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Pais MS. Somatic Embryogenesis Induction in Woody Species: The Future After OMICs Data Assessment. FRONTIERS IN PLANT SCIENCE 2019; 10:240. [PMID: 30984207 PMCID: PMC6447717 DOI: 10.3389/fpls.2019.00240] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 02/12/2019] [Indexed: 05/15/2023]
Abstract
Very early somatic embryogenesis has been recognized as a powerful method to propagate plants in vitro. For some woody species and in particular for some coniferous trees, somatic embryogenesis induction has become a routine procedure. For the majority, the application of this technology presents yet many limitations especially due to the genotype, the induction conditions, the number of embryos produced, maturation, and conversion, among other factors that compromise the systematic use of somatic embryogenesis for commercial purposes especially of woody species and forest trees in particular. The advancements obtained on somatic embryogenesis in Arabidopsis and the development of OMIC technologies allowed the characterization of genes and the corresponding proteins that are conserved in woody species. This knowledge will help in understanding the molecular mechanisms underlying the complex regulatory networks that control somatic embryogenesis in woody plants. In this revision, we report on developments of OMICs (genomics, transcriptomics, metabolomics, and proteomics) applied to somatic embryogenesis induction and its contribution for understanding the change of fate giving rise to the expression of somatic embryogenesis competence.
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26
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Huen A, Bally J, Smith P. Identification and characterisation of microRNAs and their target genes in phosphate-starved Nicotiana benthamiana by small RNA deep sequencing and 5'RACE analysis. BMC Genomics 2018; 19:940. [PMID: 30558535 PMCID: PMC6296076 DOI: 10.1186/s12864-018-5258-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 11/16/2018] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Phosphorus is an important macronutrient that is severely lacking in soils. In plants, specific microRNAs (miRNAs) essential for nutrient management and the regulation of stress responses are responsible for the control of many phosphate starvation responses. Further understanding of conserved and species-specific microRNA species has potential implications for the development of crops tolerant to soils with low phosphate. RESULTS This study identified and characterised phosphate starvation-responsive miRNAs in the native Australian tobacco Nicotiana benthamiana. Small RNA libraries were constructed and sequenced from phosphate-starved plant leaves, stems and roots. Twenty-four conserved miRNA families and 36 species-specific miRNAs were identified. The majority of highly phosphate starvation-responsive miRNAs were highly conserved, comprising of members from the miR399, miR827, and miR2111 families. In addition, two miRNA-star species were identified to be phosphate starvation-responsive. A total of seven miRNA targets were confirmed using RLM-5'RACE to be cleaved by five miRNA families, including two confirmed cleavage targets for Nbe-miR399 species, one for Nbe-miR2111, and two for Nbe-miR398. A number of N. benthamiana-specific features for conserved miRNAs were identified, including species-specific miRNA targets predicted or confirmed for miR399, miR827, and miR398. CONCLUSIONS Our results give an insight into the phosphate starvation-responsive miRNAs of Nicotiana benthamiana, and indicate that the phosphate starvation response pathways in N. benthamiana contain both highly conserved and species-specific components.
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Affiliation(s)
- Amanda Huen
- School of Life and Environmental Sciences, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Julia Bally
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, QLD, Brisbane, 4000, Australia
| | - Penelope Smith
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, 3086, Australia.
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27
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Liu Z, Ge XX, Qiu WM, Long JM, Jia HH, Yang W, Dutt M, Wu XM, Guo WW. Overexpression of the CsFUS3 gene encoding a B3 transcription factor promotes somatic embryogenesis in Citrus. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 277:121-131. [PMID: 30466577 DOI: 10.1016/j.plantsci.2018.10.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 10/15/2018] [Accepted: 10/16/2018] [Indexed: 06/09/2023]
Abstract
In citrus, genetic improvement via biotechnology is challenging due to insufficient understanding of molecular barriers that prevent regeneration by somatic embryogenesis (SE). Our previous study indicated that LEC genes were involved in SE in citrus, but their regulatory roles remain to be elucidated. Here, we cloned one of the LEC genes, CsFUS3, and show that it is preferentially expressed during SE and in the embryogenic callus (EC) derived from citrus varieties with strong embryogenic competence. The overexpression of CsFUS3 in recalcitrant citrus callus restored embryogenic competence. Complementation of the loss-of-function Arabidopsis fus3 mutant with the CsFUS3 gene restored normal late embryogenesis, which is consistent with the CsFUS3 and AtFUS3 proteins contributing to the same regulatory network in Arabidopsis. Transcriptome profiling revealed that the expression of particular TFs that promote SE was up-regulated in the citrus overexpression (OE) line. The 104 differentially expressed genes associated with hormone biosynthesis, catabolism, and signaling are particularly noteworthy. The dynamic change in the ratio of ABA to GA during SE in wild-type callus mirrored the expression pattern of CsFUS3. In contrast, in the OE line, the ratio of ABA to GA was higher and the capacity for SE was greater when the OE line was separately treated with ABA and GA biosynthesis inhibitors. Taken together, our results demonstrate that the overexpression of CsFUS3 appears to establish a cellular environment favorable to SE, at least in part by promoting a high ABA to GA ratio and by regulating the expression of TFs that promote SE.
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Affiliation(s)
- Zheng Liu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China; Fruit and Tea Research Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China.
| | - Xiao-Xia Ge
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China; Center of Applied Biotechnology, Wuhan University of Bioengineering, Wuhan 430415, China.
| | - Wen-Ming Qiu
- Fruit and Tea Research Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; Citrus Research and Education Center, University of Florida, Lake Alfred, FL 33850, USA.
| | - Jian-Mei Long
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China.
| | - Hui-Hui Jia
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China.
| | - Wei Yang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China.
| | - Manjul Dutt
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL 33850, USA.
| | - Xiao-Meng Wu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China.
| | - Wen-Wu Guo
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China.
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28
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Li W, Nishiyama R, Watanabe Y, Van Ha C, Kojima M, An P, Tian L, Tian C, Sakakibara H, Tran LSP. Effects of overproduced ethylene on the contents of other phytohormones and expression of their key biosynthetic genes. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 128:170-177. [PMID: 29783182 DOI: 10.1016/j.plaphy.2018.05.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 05/08/2018] [Accepted: 05/08/2018] [Indexed: 05/12/2023]
Abstract
Ethylene is involved in regulation of various aspects of plant growth and development. Physiological and genetic analyses have indicated the existence of crosstalk between ethylene and other phytohormones, including auxin, cytokinin (CK), abscisic acid (ABA), gibberellin (GA), salicylic acid (SA), jasmonic acid (JA), brassinosteroid (BR) and strigolactone (SL) in regulation of different developmental processes. However, the effects of ethylene on the biosynthesis and contents of these hormones are not fully understood. Here, we investigated how overproduction of ethylene may affect the contents of other plant hormones using the ethylene-overproducing mutant ethylene-overproducer 1 (eto1-1). The contents of various hormones and transcript levels of the associated biosynthetic genes in the 10-day-old Arabidopsis eto1-1 mutant and wild-type (WT) plants were determined and compared. Higher levels of CK and ABA, while lower levels of auxin, SA and GA were observed in eto1-1 plants in comparison with WT, which was supported by the up- or down-regulation of their biosynthetic genes. Although we could not quantify the BR and SL contents in Arabidopsis, we observed that the transcript levels of the potential rate-limiting BR and SL biosynthetic genes were increased in the eto1-1 versus WT plants, suggesting that BR and SL levels might be enhanced by ethylene overproduction. JA level was not affected by overproduction of ethylene, which might be explained by unaltered expression level of the proposed rate-limiting JA biosynthetic gene allene oxide synthase. Taken together, our results suggest that ET affects the levels of auxin, CK, ABA, SA and GA, and potentially BR and SL, by influencing the expression of genes involved in the rate-limiting steps of their biosynthesis.
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Affiliation(s)
- Weiqiang Li
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Rie Nishiyama
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Yasuko Watanabe
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Chien Van Ha
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Mikiko Kojima
- Plant Productivity Systems Research Group, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Ping An
- Arid Land Research Center, Tottori University, 1390 Hamasaka, Tottori 680-0001, Japan
| | - Lei Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 4888, Shengbei Street, Changchun 130102, China
| | - Chunjie Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 4888, Shengbei Street, Changchun 130102, China
| | - Hitoshi Sakakibara
- Plant Productivity Systems Research Group, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Lam-Son Phan Tran
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan; Institute of Research and Development, Duy Tan University, 03 Quang Trung, Da Nang, Vietnam.
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Ajengui A, Bertolini E, Ligorio A, Chebil S, Ippolito A, Sanzani SM. Comparative transcriptome analysis of two citrus germplasms with contrasting susceptibility to Phytophthora nicotianae provides new insights into tolerance mechanisms. PLANT CELL REPORTS 2018; 37:483-499. [PMID: 29290008 DOI: 10.1007/s00299-017-2244-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 12/26/2017] [Indexed: 06/07/2023]
Abstract
Host perception of Phytophthora nicotianae switching to necrotrophy is fundamental for disease tolerance of citrus. It involves an HR-like response, strengthening of the cell wall structure and hormonal signaling. Stem rot caused by P. nicotianae is a worldwide disease of several important crops, including citrus. Given the growing awareness of chemical fungicides drawbacks, genetic improvement of citrus rootstocks remains the best alternative. However, the molecular basis underlying the successful response of resistant and/or tolerant genotypes remains poorly understood. Therefore, we performed a transcriptomic analysis to examine the differential defense response to P. nicotianae of two germplasms-tolerant sour orange (SO, Citrus aurantium) and susceptible Madam Vinous (MV, C. sinensis)-in both the biotrophic and necrotrophic phases of host-pathogen interaction. Our results revealed the necrotrophic phase as a decisive turning point, since it included stronger modulation of a number of genes implicated in pathogen perception, signal transduction, HR-like response, transcriptional reprogramming, hormone signaling, and cell wall modifications. In particular, the pathogen perception category reflected the ability of SO to perceive the pathogen even after its switch to necrotrophy, and thus to cope successfully with the infection, while MV failed. The concomitant changes in genes involved in the remaining functional categories seemed to prevent pathogen spread. This investigation provided further understanding of the successful defense mechanisms of C. aurantium against P. nicotianae, which might be exploited in post-genomic strategies to develop resistant Citrus genotypes.
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Affiliation(s)
- Arwa Ajengui
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj-Cédria, 2050, Hammam-Lif, Tunisia
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari "Aldo Moro", Via Amendola 165/A, 70126, Bari, Italy
- Faculté des Sciences de Tunis, LR03ES03 Laboratoire Microorganismes et Biomolécules Actives, Université Tunis El Manar, 2092, Tunis, Tunisia
| | - Edoardo Bertolini
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy
| | - Angela Ligorio
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari "Aldo Moro", Via Amendola 165/A, 70126, Bari, Italy
| | - Samir Chebil
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj-Cédria, 2050, Hammam-Lif, Tunisia
| | - Antonio Ippolito
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari "Aldo Moro", Via Amendola 165/A, 70126, Bari, Italy
| | - Simona Marianna Sanzani
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari "Aldo Moro", Via Amendola 165/A, 70126, Bari, Italy.
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30
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Garcia C, Britto D, Marelli JP. Transcription Factors: Their Role in the Regulation of Somatic Embryogenesis in Theobroma cacao L. and Other Species. Methods Mol Biol 2018; 1815:385-396. [PMID: 29981137 DOI: 10.1007/978-1-4939-8594-4_27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Transcription factors are proteins that help with the control and regulation in the transcription of the DNA to mRNA by binding to special DNA sequences. With the aim to understand more about gene transcription regulation in Theobroma cacao L., this review outlines the principal transcription factors that were reported in other plants especially Arabidopsis thaliana and attempts at looking for the homologies with transcription factors in T. cacao. The information cited in this work is about the initiation, development, and maturation of the cacao somatic embryos and other crops. It is important to underline that there are very few publications in T. cacao discussing transcription factors that control the somatic embryogenesis process, but there is some information about transcription factors in other crops that we have used as a guide to try to understand this process.
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Arro J, Cuenca J, Yang Y, Liang Z, Cousins P, Zhong GY. A transcriptome analysis of two grapevine populations segregating for tendril phyllotaxy. HORTICULTURE RESEARCH 2017; 4:17032. [PMID: 28713572 PMCID: PMC5506248 DOI: 10.1038/hortres.2017.32] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 05/16/2017] [Accepted: 06/07/2017] [Indexed: 06/01/2023]
Abstract
The shoot structure of cultivated grapevine Vitis vinifera L. typically exhibits a three-node modular repetitive pattern, two sequential leaf-opposed tendrils followed by a tendril-free node. In this study, we investigated the molecular basis of this pattern by characterizing differentially expressed genes in 10 bulk samples of young tendril tissue from two grapevine populations showing segregation of mutant or wild-type shoot/tendril phyllotaxy. One population was the selfed progeny and the other one, an outcrossed progeny of a Vitis hybrid, 'Roger's Red'. We analyzed 13 375 expressed genes and carried out in-depth analyses of 324 of them, which were differentially expressed with a minimum of 1.5-fold changes between the mutant and wild-type bulk samples in both selfed and cross populations. A significant portion of these genes were direct cis-binding targets of 14 transcription factor families that were themselves differentially expressed. Network-based dependency analysis further revealed that most of the significantly rewired connections among the 10 most connected hub genes involved at least one transcription factor. TCP3 and MYB12, which were known important for plant-form development, were among these transcription factors. More importantly, TCP3 and MYB12 were found in this study to be involved in regulating the lignin gene PRX52, which is important to plant-form development. A further support evidence for the roles of TCP3-MYB12-PRX52 in contributing to tendril phyllotaxy was the findings of two other lignin-related genes uniquely expressed in the mutant phyllotaxy background.
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Affiliation(s)
- Jie Arro
- USDA-Agricultural Research Service, Grape Genetics Research Unit, Geneva, NY 14456, USA
| | - Jose Cuenca
- USDA-Agricultural Research Service, Grape Genetics Research Unit, Geneva, NY 14456, USA
| | - Yingzhen Yang
- USDA-Agricultural Research Service, Grape Genetics Research Unit, Geneva, NY 14456, USA
| | - Zhenchang Liang
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resource, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, People’s Republic of China
| | | | - Gan-Yuan Zhong
- USDA-Agricultural Research Service, Grape Genetics Research Unit, Geneva, NY 14456, USA
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Wójcikowska B, Gaj MD. Expression profiling of AUXIN RESPONSE FACTOR genes during somatic embryogenesis induction in Arabidopsis. PLANT CELL REPORTS 2017; 36:843-858. [PMID: 28255787 PMCID: PMC5486788 DOI: 10.1007/s00299-017-2114-3] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 02/01/2017] [Indexed: 05/18/2023]
Abstract
Extensive modulation of numerous ARF transcripts in the embryogenic culture of Arabidopsis indicates a substantial role of auxin signaling in the mechanism of somatic embryogenesis induction. Somatic embryogenesis (SE) is induced by auxin in plants and auxin signaling is considered to play a key role in the molecular mechanism that controls the embryogenic transition of plant somatic cells. Accordingly, the expression of AUXIN RESPONSE FACTOR (ARF) genes in embryogenic culture of Arabidopsis was analyzed. The study revealed that 14 of the 22 ARFs were transcribed during SE in Arabidopsis. RT-qPCR analysis indicated that the expression of six ARFs (ARF5, ARF6, ARF8, ARF10, ARF16, and ARF17) was significantly up-regulated, whereas five other genes (ARF1, ARF2, ARF3, ARF11, and ARF18) were substantially down-regulated in the SE-induced explants. The activity of ARFs during SE was also monitored with GFP reporter lines and the ARFs that were expressed in areas of the explants engaged in SE induction were detected. A functional test of ARFs transcribed during SE was performed and the embryogenic potential of the arf mutants and overexpressor lines was evaluated. ARFs with a significantly modulated expression during SE coupled with an impaired embryogenic response of the relevant mutant and/or overexpressor line, including ARF1, ARF2, ARF3, ARF5, ARF6, ARF8, and ARF11 were indicated as possibly being involved in SE induction. The study provides evidence that embryogenic induction strongly depends on ARFs, which are key regulators of the auxin signaling. Some clues on the possible functions of the candidate ARFs, especially ARF5, in the mechanism of embryogenic transition are discussed. The results provide guidelines for further research on the auxin-related functional genomics of SE and the developmental plasticity of somatic cells.
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Affiliation(s)
- Barbara Wójcikowska
- Department of Genetics, University of Silesia, ul. Jagiellońska 28, 40-032, Katowice, Poland
| | - Małgorzata D Gaj
- Department of Genetics, University of Silesia, ul. Jagiellońska 28, 40-032, Katowice, Poland.
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Zhang J, Xue B, Gai M, Song S, Jia N, Sun H. Small RNA and Transcriptome Sequencing Reveal a Potential miRNA-Mediated Interaction Network That Functions during Somatic Embryogenesis in Lilium pumilum DC. Fisch. FRONTIERS IN PLANT SCIENCE 2017; 8:566. [PMID: 28473835 PMCID: PMC5397531 DOI: 10.3389/fpls.2017.00566] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 03/29/2017] [Indexed: 05/23/2023]
Abstract
Plant somatic embryos are widely used in the fields of germplasm conservation, breeding for genetic engineering and artificial seed production. MicroRNAs (miRNAs) play pivotal roles in somatic embryogenesis (SE) regulation. However, their regulatory roles during various stages of SE remain unclear. In this study, six types of embryogenic samples of Lilium pumilum DC. Fisch., including organogenic callus, embryogenic callus induced for 4 weeks, embryogenic callus induced for 6 weeks, globular embryos, torpedo embryos and cotyledon embryos, were prepared for small RNA sequencing. The results revealed a total of 2,378,760 small RNA reads, among which the most common size was 24 nt. Four hundred and fifty-two known miRNAs, belonging to more than 86 families, 57 novel miRNAs and 40 miRNA*s were identified. The 86 known miRNA families were sorted according to an alignment with their homologs across 24 land plants into the following four categories: 23 highly conserved, 4 moderately conserved, 15 less conserved and 44 species-specific miRNAs. Differentially expressed known miRNAs were identified during various stages of SE. Subsequently, the expression levels of 12 differentially expressed miRNAs and 4 targets were validated using qRT-PCR. In addition, six samples were mixed in equal amounts for transcript sequencing, and the sequencing data were used as transcripts for miRNA target prediction. A total of 66,422 unigenes with an average length of 800 bp were assembled from 56,258,974 raw reads. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment indicated that 38,004 and 15,497 unigenes were successfully assigned to GO terms and KEGG pathways, respectively. Among the unigenes, 2,182 transcripts were predicted to be targets for 396 known miRNAs. The potential targets of the identified miRNAs were mostly classified into the following GO terms: cell, binding and metabolic process. Enriched KEGG analysis demonstrated that carbohydrate metabolism was the predominant pathway in Lilium SE. Thus, we performed systemic characterization, homology comparisons and profiling of miRNA expression, and we constructed an miRNA-target network during Lilium SE for the first time. Our findings establish a foundation for the further exploration of critical genes and elucidation of SE in Lilium.
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Affiliation(s)
| | | | | | | | | | - Hongmei Sun
- Key Laboratory of Protected Horticulture of Education Ministry and Liaoning Province, College of Horticulture, Shenyang Agricultural UniversityShenyang, China
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Yu Y, Yang D, Zhou S, Gu J, Wang F, Dong J, Huang R. The ethylene response factor OsERF109 negatively affects ethylene biosynthesis and drought tolerance in rice. PROTOPLASMA 2017; 254:401-408. [PMID: 27040682 DOI: 10.1007/s00709-016-0960-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 03/07/2016] [Indexed: 05/24/2023]
Abstract
Drought is an important factor limiting plant development and crop production. Dissecting the factors involved in this process is the key for enhancement of plant tolerance to drought stress by genetic approach. Here, we evaluated the regulatory function of a novel rice ethylene response factor (ERF) OsERF109 in drought stress. Expression of OsERF109 was rapidly induced by stress and phytohormones. Subcellular localization and transactivation assay demonstrated that OsERF109 was localized in nucleus and possessed transactivation activity. Transgenic plants overexpressing (OE) and knockdown with RNA interfering (RI) OsERF109 exhibited significantly reduced and improved drought resistance, respectively, indicating that OsERF109 negatively regulates drought resistance in rice. Furthermore, measurement by gas chromatography showed that ethylene contents were less in OE while more in RI lines than these in wild types, supporting the data of drought tolerance and water loss in transgenic lines. Quantitative real-time PCR analysis also proved the regulation of OsERF109 in the expression of OSACS6, OSACO2, and OsERF3, which have been identified to play important roles in ethylene biosynthesis. Based on these results, our data evidence that OsERF109 regulates drought resistance by affecting the ethylene biosynthesis in rice. Overall, our study reveals the negative role of OsERF109 in ethylene biosynthesis and drought tolerance in rice.
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Affiliation(s)
- Yanwen Yu
- College of Life Sciences, Agricultural University of Hebei, Baoding, 071001, China
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Dexin Yang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shirong Zhou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Juntao Gu
- College of Life Sciences, Agricultural University of Hebei, Baoding, 071001, China
| | - Fengru Wang
- College of Life Sciences, Agricultural University of Hebei, Baoding, 071001, China
| | - Jingao Dong
- College of Life Sciences, Agricultural University of Hebei, Baoding, 071001, China.
| | - Rongfeng Huang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
- National Key Facility of Crop Gene Resources and Genetic Improvement, Beijing, 100081, China.
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Yue X, Li XG, Gao XQ, Zhao XY, Dong YX, Zhou C. The Arabidopsis phytohormone crosstalk network involves a consecutive metabolic route and circular control units of transcription factors that regulate enzyme-encoding genes. BMC SYSTEMS BIOLOGY 2016; 10:87. [PMID: 27590055 PMCID: PMC5009710 DOI: 10.1186/s12918-016-0333-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 08/25/2016] [Indexed: 01/26/2023]
Abstract
Background Phytohormone synergies and signaling interdependency are important topics in plant developmental biology. Physiological and genetic experimental evidence for phytohormone crosstalk has been accumulating and a genome-scale enzyme correlation model representing the Arabidopsis metabolic pathway has been published. However, an integrated molecular characterization of phytohormone crosstalk is still not available. Results A novel modeling methodology and advanced computational approaches were used to construct an enzyme-based Arabidopsis phytohormone crosstalk network (EAPCN) at the biosynthesis level. The EAPCN provided the structural connectivity architecture of phytohormone biosynthesis pathways and revealed a surprising result; that enzymes localized at the highly connected nodes formed a consecutive metabolic route. Furthermore, our analysis revealed that the transcription factors (TFs) that regulate enzyme-encoding genes in the consecutive metabolic route formed structures, which we describe as circular control units operating at the transcriptional level. Furthermore, the downstream TFs in phytohormone signal transduction pathways were found to be involved in the circular control units that included the TFs regulating enzyme-encoding genes. In addition, multiple functional enzymes in the EAPCN were found to be involved in ion and pH homeostasis, environmental signal perception, cellular redox homeostasis, and circadian clocks. Last, publicly available transcriptional profiles and a protein expression map of the Arabidopsis root apical meristem were used as a case study to validate the proposed framework. Conclusions Our results revealed multiple scales of coupled mechanisms in that hormonal crosstalk networks that play a central role in coordinating internal developmental processes with environmental signals, and give a broader view of Arabidopsis phytohormone crosstalk. We also uncovered potential key regulators that can be further analyzed in future studies. Electronic supplementary material The online version of this article (doi:10.1186/s12918-016-0333-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xun Yue
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China. .,State Key Laboratory of Crop Biology, College of Information Sciences and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China.
| | - Xing Guo Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Xin-Qi Gao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Xiang Yu Zhao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Yu Xiu Dong
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Chao Zhou
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
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Manan S, Chen B, She G, Wan X, Zhao J. Transport and transcriptional regulation of oil production in plants. Crit Rev Biotechnol 2016; 37:641-655. [DOI: 10.1080/07388551.2016.1212185] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Sehrish Manan
- National Key Laboratory for Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Beibei Chen
- National Key Laboratory for Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Guangbiao She
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Xiaochun Wan
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Jian Zhao
- National Key Laboratory for Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
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Hopper DW, Ghan R, Schlauch KA, Cramer GR. Transcriptomic network analyses of leaf dehydration responses identify highly connected ABA and ethylene signaling hubs in three grapevine species differing in drought tolerance. BMC PLANT BIOLOGY 2016; 16:118. [PMID: 27215785 PMCID: PMC4877820 DOI: 10.1186/s12870-016-0804-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 05/17/2016] [Indexed: 05/03/2023]
Abstract
BACKGROUND Grapevine is a major food crop that is affected by global climate change. Consistent with field studies, dehydration assays of grapevine leaves can reveal valuable information of the plant's response at physiological, transcript, and protein levels. There are well-known differences in grapevine rootstocks responses to dehydration. We used time-series transcriptomic approaches combined with network analyses to elucidate and identify important physiological processes and network hubs that responded to dehydration in three different grapevine species differing in their drought tolerance. RESULTS Transcriptomic analyses of the leaves of Cabernet Sauvignon, Riparia Gloire, and Ramsey were evaluated at different times during a 24-h controlled dehydration. Analysis of variance (ANOVA) revealed that approximately 11,000 transcripts changed significantly with respect to the genotype x treatment interaction term and approximately 6000 transcripts changed significantly according to the genotype x treatment x time interaction term indicating massive differential changes in gene expression over time. Standard analyses determined substantial effects on the transcript abundance of genes involved in the metabolism and signaling of two known plant stress hormones, abscisic acid (ABA) and ethylene. ABA and ethylene signaling maps were constructed and revealed specific changes in transcript abundance that were associated with the known drought tolerance of the genotypes including genes such as VviABI5, VviABF2, VviACS2, and VviWRKY22. Weighted-gene coexpression network analysis (WGCNA) confirmed these results. In particular, WGCNA identified 30 different modules, some of which had highly enriched gene ontology (GO) categories for photosynthesis, phenylpropanoid metabolism, ABA and ethylene signaling. The ABA signaling transcription factors, VviABI5 and VviABF2, were highly connected hubs in two modules, one being enriched in gaseous transport and the other in ethylene signaling. VviABI5 was distinctly correlated with an early response and high expression for the drought tolerant Ramsey and with little response from the drought sensitive Riparia Gloire. These ABA signaling transcription factors were highly connected to VviSnRK1 and other gene hubs associated with sugar, ethylene and ABA signaling. CONCLUSION A leaf dehydration assay provided transcriptomic evidence for differential leaf responses to dehydration between genotypes differing in their drought tolerance. WGCNA proved to be a powerful network analysis approach; it identified 30 distinct modules (networks) with highly enriched GO categories and enabled the identification of gene hubs in these modules. Some of these genes were highly connected hubs in both the ABA and ethylene signaling pathways, supporting the hypothesis that there is substantial crosstalk between the two hormone pathways. This study identifies solid gene candidates for future investigations of drought tolerance in grapevine.
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Affiliation(s)
- Daniel W Hopper
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA
| | - Ryan Ghan
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA
| | - Karen A Schlauch
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA
| | - Grant R Cramer
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA.
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Nowak K, Gaj MD. Stress-related function of bHLH109 in somatic embryo induction in Arabidopsis. JOURNAL OF PLANT PHYSIOLOGY 2016; 193:119-26. [PMID: 26973252 DOI: 10.1016/j.jplph.2016.02.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 02/19/2016] [Accepted: 02/22/2016] [Indexed: 05/11/2023]
Abstract
The bHLH109 gene of the bHLH family was identified among the transcription factor encoding genes that were differentially expressed in an embryogenic culture of Arabidopsis. A strong activation of bHLH109 expression was found to be associated with somatic embryogenesis (SE) induction. Several pieces of evidence suggested the involvement of bHLH109 in SE, including the high stimulation of the gene expression in SE-induced explants, which contrasts to the drastically lower level of the gene transcripts in the non-embryogenic callus and in tissue that is induced towards shoot regeneration via organogenesis. Moreover, in contrast to the overexpression of bHLH109, which has been indicated to enhance SE induction in a culture, the bhlh109 knock-out mutation was found to impair the embryogenic potential of explants. In order to identify the genes interacting with the bHLH109, the candidate co-expressed genes were identified in a yeast one hybrid assay. The in vitro regulatory interactions that were identified were verified through mutant and expression analysis. The results suggest that in SE bHLH109 acts as an activator of ECP63, a member of the LEA (LATE EMBRYOGENESIS ABUNDANT) family. Among the potential regulators of bHLH109, three candidates (At5g61620, bZIP4 and bZIP43) were indicated to possibly control bHLH109. The functions of all of the genes that are assumed to interact with bHLH109 are annotated to stress responses. Collectively, the results of the study provide new evidence that cell responses to stress that is imposed under in vitro conditions underlies the promotion of SE. bHLH109 may play a central role in the stress-related mechanism of SE induction via an increased accumulation of the LEA protein (ECP63), which results in the enhanced tolerance of the cells to stress.
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Affiliation(s)
- Katarzyna Nowak
- Department of Genetics, University of Silesia, Jagiellonska 28, 40-032 Katowice, Poland.
| | - Małgorzata D Gaj
- Department of Genetics, University of Silesia, Jagiellonska 28, 40-032 Katowice, Poland
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Rattanakon S, Ghan R, Gambetta GA, Deluc LG, Schlauch KA, Cramer GR. Abscisic acid transcriptomic signaling varies with grapevine organ. BMC PLANT BIOLOGY 2016; 16:72. [PMID: 27001301 PMCID: PMC4802729 DOI: 10.1186/s12870-016-0763-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 03/15/2016] [Indexed: 05/03/2023]
Abstract
BACKGROUND Abscisic acid (ABA) regulates various developmental processes and stress responses over both short (i.e. hours or days) and longer (i.e. months or seasons) time frames. To elucidate the transcriptional regulation of early responses of grapevine (Vitis vinifera) responding to ABA, different organs of grape (berries, shoot tips, leaves, roots and cell cultures) were treated with 10 μM (S)-(+)-ABA for 2 h. NimbleGen whole genome microarrays of Vitis vinifera were used to determine the effects of ABA on organ-specific mRNA expression patterns. RESULTS Transcriptomic analysis revealed 839 genes whose transcript abundances varied significantly in a specific organ in response to ABA treatment. No single gene exhibited the same changes in transcript abundance across all organs in response to ABA. The biochemical pathways affected by ABA were identified using the Cytoscape program with the BiNGO plug-in software. The results indicated that these 839 genes were involved in several biological processes such as flavonoid metabolism, response to reactive oxygen species, response to light, and response to temperature stimulus. ABA affected ion and water transporters, particularly in the root. The protein amino acid phosphorylation process was significantly overrepresented in shoot tips and roots treated with ABA. ABA affected mRNA abundance of genes (CYP707As, UGTs, and PP2Cs) associated with ABA degradation, conjugation, and the ABA signaling pathway. ABA also significantly affected the expression of several transcription factors (e.g. AP2/ERF, MYC/MYB, and bZIP/AREB). The greatest number of significantly differentially expressed genes was observed in the roots followed by cell cultures, leaves, berries, and shoot tips, respectively. Each organ had a unique set of gene responses to ABA. CONCLUSIONS This study examined the short-term effects of ABA on different organs of grapevine. The responses of each organ were unique indicating that ABA signaling varies with the organ. Understanding the ABA responses in an organ-specific manner is crucial to fully understand hormone action and plant responses to water deficit.
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Affiliation(s)
- Supakan Rattanakon
- />Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557 USA
| | - Ryan Ghan
- />Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557 USA
| | - Gregory A. Gambetta
- />Bordeaux Sciences Agro, Institut des Sciences de la Vigne et du Vin (ISVV), EGFV, UMR 1287, F-33140 Villenave d’Ornon, France
| | - Laurent G. Deluc
- />Department of Horticulture, Oregon State University, Corvallis, OR 97331 USA
| | - Karen A. Schlauch
- />Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557 USA
| | - Grant R. Cramer
- />Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557 USA
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Tao L, Zhao Y, Wu Y, Wang Q, Yuan H, Zhao L, Guo W, You X. Transcriptome profiling and digital gene expression by deep sequencing in early somatic embryogenesis of endangered medicinal Eleutherococcus senticosus Maxim. Gene 2015; 578:17-24. [PMID: 26657036 DOI: 10.1016/j.gene.2015.11.050] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 11/21/2015] [Accepted: 11/30/2015] [Indexed: 11/19/2022]
Abstract
Somatic embryogenesis (SE) has been studied as a model system to understand molecular events in physiology, biochemistry, and cytology during plant embryo development. In particular, it is exceedingly difficult to access the morphological and early regulatory events in zygotic embryos. To understand the molecular mechanisms regulating early SE in Eleutherococcus senticosus Maxim., we used high-throughput RNA-Seq technology to investigate its transcriptome. We obtained 58,327,688 reads, which were assembled into 75,803 unique unigenes. To better understand their functions, the unigenes were annotated using the Clusters of Orthologous Groups, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes databases. Digital gene expression libraries revealed differences in gene expression profiles at different developmental stages (embryogenic callus, yellow embryogenic callus, global embryo). We obtained a sequencing depth of >5.6 million tags per sample and identified many differentially expressed genes at various stages of SE. The initiation of SE affected gene expression in many KEGG pathways, but predominantly that in metabolic pathways, biosynthesis of secondary metabolites, and plant hormone signal transduction. This information on the changes in the multiple pathways related to SE induction in E. senticosus Maxim. embryogenic tissue will contribute to a more comprehensive understanding of the mechanisms involved in early SE. Additionally, the differentially expressed genes may act as molecular markers and could play very important roles in the early stage of SE. The results are a comprehensive molecular biology resource for investigating SE of E. senticosus Maxim.
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Affiliation(s)
- Lei Tao
- College of Life Sciences, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Yue Zhao
- College of Life Sciences, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Ying Wu
- College of Life Sciences, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Qiuyu Wang
- College of Life Sciences, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Hongmei Yuan
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China
| | - Lijuan Zhao
- Crop Breeding Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China
| | - Wendong Guo
- Institute of Natural Resources and Ecology, Heilongjiang Academy of Sciences, Harbin 150040, China
| | - Xiangling You
- College of Life Sciences, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China.
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