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Quintana-Escobar AO, Loyola-Vargas VM. Transcriptomic Analysis During the Induction of Somatic Embryogenesis in Coffea canephora. Methods Mol Biol 2024; 2827:363-376. [PMID: 38985282 DOI: 10.1007/978-1-0716-3954-2_24] [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: 07/11/2024]
Abstract
Omic tools have changed the way of doing research in experimental biology. The somatic embryogenesis (SE) study has not been immune to this benefit. The transcriptomic tools have been used to compare the genes expressed during the induction of SE with the genes expressed in zygotic embryogenesis or to compare the development of the different stages embryos go through. It has also been used to compare the expression of genes during the development of calli from which SE is induced, as well as many other applications. The protocol described here is employed in our laboratory to extract RNA and generate several transcriptomes for the study of SE on Coffea canephora.
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Affiliation(s)
- Ana O Quintana-Escobar
- Unidad de Biología Integrativa, Centro de Investigación Científica de Yucatán, Chuburna, Merida, CP, Mexico
| | - Víctor M Loyola-Vargas
- Unidad de Biología Integrativa, Centro de Investigación Científica de Yucatán, Chuburna, Merida, CP, Mexico.
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Fan Y, Tang Z, Wei J, Yu X, Guo H, Li T, Guo H, Zhang L, Fan Y, Zhang C, Zeng F. Dynamic Transcriptome Analysis Reveals Complex Regulatory Pathway Underlying Induction and Dose Effect by Different Exogenous Auxin IAA and 2,4-D During in vitro Embryogenic Redifferentiation in Cotton. FRONTIERS IN PLANT SCIENCE 2022; 13:931105. [PMID: 35845676 PMCID: PMC9278894 DOI: 10.3389/fpls.2022.931105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
Abstract
Plant somatic cells can reprogram into differentiated embryos through somatic embryogenesis (SE) on the condition of plant growth regulators (PGRs). RNA sequencing analysis was performed to investigate transcriptional profiling on cotton redifferentiated callus that was induced by different auxin types (IAA and 2,4-D), different concentrations (0, 0.025, and 0.05 mg L-1), and different incubation times (0, 5, and 20 days). Under the 2,4-D induction effect, signal transduction pathways of plant hormones were significantly enriched in the embryogenic response stage (5 days). These results indicated that auxin signal transduction genes were necessary for the initial response of embryogenic differentiation. In the pre-embryonic initial period (20 days), the photosynthetic pathway was significantly enriched. Most differentially expressed genes (DEGs) were downregulated under the induction of 2,4-D. Upon the dose effect of IAA and 2,4-D, respectively, pathways were significantly enriched in phenylpropanoid biosynthesis, fatty acid metabolism, and carbon metabolic pathways. Therefore, primary and secondary metabolism pathways were critical in cotton SE. These results showed that complex synergistic mechanisms involving multiple cellular pathways were the causes of the induction and dose effect of auxin-induced SE. This study reveals a systematic molecular response to auxin signals and reveals the way that regulates embryogenic redifferentiation during cotton SE.
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Affiliation(s)
- Yupeng Fan
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, China
- College of Life Sciences, Huaibei Normal University, Huaibei City, China
| | - Zhengmin Tang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, China
| | - Junmei Wei
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, China
| | - Xiaoman Yu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, China
| | - Huihui Guo
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, China
| | - Tongtong Li
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, China
| | - Haixia Guo
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, China
| | - Li Zhang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, China
| | - Yijie Fan
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, China
| | - Changyu Zhang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, China
| | - Fanchang Zeng
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, China
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Li Y, Zhu S, Yao J, Fang S, Li T, Li B, Wang X, Wang M, Wu L, Pan J, Feng X, Chen W, Zhang Y. Genome-wide Characterization of the JmjC Domain-Containing Histone Demethylase Gene Family Reveals GhJMJ24 and GhJMJ49 Involving in Somatic Embryogenesis Process in Cotton. Front Mol Biosci 2022; 9:888983. [PMID: 35573733 PMCID: PMC9091307 DOI: 10.3389/fmolb.2022.888983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 04/08/2022] [Indexed: 11/16/2022] Open
Abstract
The Jumonji C (JmjC) domain-containing protein family, an important family of histone demethylase in plants, can directly reverse histone methylation and play important roles in various growth and development processes. In the present study, 51 JmjC genes (GhJMJs) were identified by genome-wide analysis in upland cotton (Gossypium hirsutum), which can be categorized into six distinct groups by phylogenetic analysis. Extensive syntenic relationship events were found between G. hirsutum and Theobroma cacao. We have further explored the putative molecular regulatory mechanisms of the JmjC gene family in cotton. GhJMJ24 and GhJMJ49 were both preferentially expressed in embryogenic callus compared to nonembryogenic callus in cotton tissue culture, which might be regulated by transcription factors and microRNAs to some extent. Further experiments indicated that GhJMJ24 and GhJMJ49 might interact with SUVH4, SUVH6, DDM1, CMT3, and CMT1 in the nucleus, potentially in association with demethylation of H3K9me2. Taken together, our results provide a foundation for future research on the biological functions of GhJMJ genes in cotton, especially in somatic embryogenesis in cotton tissue culture, which is crucial for the regeneration of transgenic plants.
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Affiliation(s)
- Yan Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Shouhong Zhu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jinbo Yao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Shengtao Fang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Tengyu Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Bei Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xinyu Wang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Mingyang Wang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Lanxin Wu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jingwen Pan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xuemei Feng
- Shandong Denghai Shengfeng Seed Industry Co., Ltd., Jining, china
| | - Wei Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- *Correspondence: Wei Chen, ; Yongshan Zhang,
| | - Yongshan Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- *Correspondence: Wei Chen, ; Yongshan Zhang,
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Bharadwaj R, Noceda C, Mohanapriya G, Kumar SR, Thiers KLL, Costa JH, Macedo ES, Kumari A, Gupta KJ, Srivastava S, Adholeya A, Oliveira M, Velada I, Sircar D, Sathishkumar R, Arnholdt-Schmitt B. Adaptive Reprogramming During Early Seed Germination Requires Temporarily Enhanced Fermentation-A Critical Role for Alternative Oxidase Regulation That Concerns Also Microbiota Effectiveness. FRONTIERS IN PLANT SCIENCE 2021; 12:686274. [PMID: 34659277 PMCID: PMC8518632 DOI: 10.3389/fpls.2021.686274] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 08/10/2021] [Indexed: 05/05/2023]
Abstract
Plants respond to environmental cues via adaptive cell reprogramming that can affect whole plant and ecosystem functionality. Microbiota constitutes part of the inner and outer environment of the plant. This Umwelt underlies steady dynamics, due to complex local and global biotic and abiotic changes. Hence, adaptive plant holobiont responses are crucial for continuous metabolic adjustment at the systems level. Plants require oxygen-dependent respiration for energy-dependent adaptive morphology, such as germination, root and shoot growth, and formation of adventitious, clonal, and reproductive organs, fruits, and seeds. Fermentative paths can help in acclimation and, to our view, the role of alternative oxidase (AOX) in coordinating complex metabolic and physiological adjustments is underestimated. Cellular levels of sucrose are an important sensor of environmental stress. We explored the role of exogenous sucrose and its interplay with AOX during early seed germination. We found that sucrose-dependent initiation of fermentation during the first 12 h after imbibition (HAI) was beneficial to germination. However, parallel upregulated AOX expression was essential to control negative effects by prolonged sucrose treatment. Early downregulated AOX activity until 12 HAI improved germination efficiency in the absence of sucrose but suppressed early germination in its presence. The results also suggest that seeds inoculated with arbuscular mycorrhizal fungi (AMF) can buffer sucrose stress during germination to restore normal respiration more efficiently. Following this approach, we propose a simple method to identify organic seeds and low-cost on-farm perspectives for early identifying disease tolerance, predicting plant holobiont behavior, and improving germination. Furthermore, the research strengthens the view that AOX can serve as a powerful functional marker source for seed hologenomes.
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Affiliation(s)
- Revuru Bharadwaj
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
| | - Carlos Noceda
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Cell and Molecular Biology of Plants (BIOCEMP)/Industrial Biotechnology and Bioproducts, Departamento de Ciencias de la Vida y de la Agricultura, Universidad de las Fuerzas Armadas-ESPE, Sangolquí, Ecuador
| | - Gunasekharan Mohanapriya
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
| | - Sarma Rajeev Kumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
| | - Karine Leitão Lima Thiers
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Functional Genomics and Bioinformatics Group, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Brazil
| | - José Hélio Costa
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Functional Genomics and Bioinformatics Group, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Brazil
| | - Elisete Santos Macedo
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
| | - Aprajita Kumari
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- National Institute of Plant Genome Research, New Delhi, India
| | - Kapuganti Jagadis Gupta
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- National Institute of Plant Genome Research, New Delhi, India
| | - Shivani Srivastava
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Centre for Mycorrhizal Research, Sustainable Agriculture Division, The Energy and Resources Institute (TERI), TERI Gram, Gurugram, India
| | - Alok Adholeya
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Centre for Mycorrhizal Research, Sustainable Agriculture Division, The Energy and Resources Institute (TERI), TERI Gram, Gurugram, India
| | - Manuela Oliveira
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Department of Mathematics and CIMA - Center for Research on Mathematics and Its Applications, Universidade de Évora, Évora, Portugal
| | - Isabel Velada
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- MED—Mediterranean Institute for Agriculture, Environment and Development, Instituto de Investigação e Formação Avançada, Universidade de Évora, Évora, Portugal
| | - Debabrata Sircar
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Ramalingam Sathishkumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
| | - Birgit Arnholdt-Schmitt
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Functional Genomics and Bioinformatics Group, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Brazil
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Arnholdt-Schmitt B, Mohanapriya G, Bharadwaj R, Noceda C, Macedo ES, Sathishkumar R, Gupta KJ, Sircar D, Kumar SR, Srivastava S, Adholeya A, Thiers KL, Aziz S, Velada I, Oliveira M, Quaresma P, Achra A, Gupta N, Kumar A, Costa JH. From Plant Survival Under Severe Stress to Anti-Viral Human Defense - A Perspective That Calls for Common Efforts. Front Immunol 2021; 12:673723. [PMID: 34211468 PMCID: PMC8240590 DOI: 10.3389/fimmu.2021.673723] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 05/13/2021] [Indexed: 12/11/2022] Open
Abstract
Reprogramming of primary virus-infected cells is the critical step that turns viral attacks harmful to humans by initiating super-spreading at cell, organism and population levels. To develop early anti-viral therapies and proactive administration, it is important to understand the very first steps of this process. Plant somatic embryogenesis (SE) is the earliest and most studied model for de novo programming upon severe stress that, in contrast to virus attacks, promotes individual cell and organism survival. We argued that transcript level profiles of target genes established from in vitro SE induction as reference compared to virus-induced profiles can identify differential virus traits that link to harmful reprogramming. To validate this hypothesis, we selected a standard set of genes named 'ReprogVirus'. This approach was recently applied and published. It resulted in identifying 'CoV-MAC-TED', a complex trait that is promising to support combating SARS-CoV-2-induced cell reprogramming in primary infected nose and mouth cells. In this perspective, we aim to explain the rationale of our scientific approach. We are highlighting relevant background knowledge on SE, emphasize the role of alternative oxidase in plant reprogramming and resilience as a learning tool for designing human virus-defense strategies and, present the list of selected genes. As an outlook, we announce wider data collection in a 'ReprogVirus Platform' to support anti-viral strategy design through common efforts.
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Affiliation(s)
- Birgit Arnholdt-Schmitt
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), Coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Functional Genomics and Bioinformatics Group, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Brazil
| | - Gunasekaran Mohanapriya
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), Coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
| | - Revuru Bharadwaj
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), Coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
| | - Carlos Noceda
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), Coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Cell and Molecular Biotechnology of Plants (BIOCEMP)/Industrial Biotechnology and Bioproducts, Departamento de Ciencias de la Vida y de la Agricultura, Universidad de las Fuerzas Armadas-ESPE, Sangolquí, Ecuador
| | - Elisete Santos Macedo
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), Coordinated from Foros de Vale de Figueira, Alentejo, Portugal
| | - Ramalingam Sathishkumar
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), Coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
| | - Kapuganti Jagadis Gupta
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), Coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Debabrata Sircar
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), Coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Department of Biotechnology, Indian Institute of Technology, Roorkee, Uttarakhand, India
| | - Sarma Rajeev Kumar
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), Coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
| | - Shivani Srivastava
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), Coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Centre for Mycorrhizal Research, Sustainable Agriculture Division, The Energy and Resources Institute (TERI), TERI Gram, Gual Pahari, Gurugram, India
| | - Alok Adholeya
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), Coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Centre for Mycorrhizal Research, Sustainable Agriculture Division, The Energy and Resources Institute (TERI), TERI Gram, Gual Pahari, Gurugram, India
| | - KarineLeitão Lima Thiers
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), Coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Functional Genomics and Bioinformatics Group, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Brazil
| | - Shahid Aziz
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), Coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Functional Genomics and Bioinformatics Group, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Brazil
| | - Isabel Velada
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), Coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- MED—Mediterranean Institute for Agriculture, Environment and Development, Instituto de Investigação e Formação Avançada, Universidade de Évora, Évora, Portugal
| | - Manuela Oliveira
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), Coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Department of Mathematics and CIMA - Center for Research on Mathematics and its Applications, Universidade de Évora, Évora, Portugal
| | - Paulo Quaresma
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), Coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- NOVA LINCS – Laboratory for Informatics and Computer Science, University of Évora, Évora, Portugal
| | - Arvind Achra
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), Coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Department of Microbiology, Atal Bihari Vajpayee Institute of Medical Sciences & Dr Ram Manohar Lohia Hospital, New Delhi, India
| | - Nidhi Gupta
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), Coordinated from Foros de Vale de Figueira, Alentejo, Portugal
| | - Ashwani Kumar
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), Coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Hargovind Khorana Chair, Jayoti Vidyapeeth Womens University, Jaipur, India
| | - José Hélio Costa
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), Coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Functional Genomics and Bioinformatics Group, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Brazil
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6
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Guo H, Guo H, Zhang L, Fan Y, Wu J, Tang Z, Zhang Y, Fan Y, Zeng F. Dynamic Transcriptome Analysis Reveals Uncharacterized Complex Regulatory Pathway Underlying Genotype-Recalcitrant Somatic Embryogenesis Transdifferentiation in Cotton. Genes (Basel) 2020; 11:E519. [PMID: 32392816 PMCID: PMC7290922 DOI: 10.3390/genes11050519] [Citation(s) in RCA: 8] [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: 03/10/2020] [Revised: 04/21/2020] [Accepted: 05/05/2020] [Indexed: 11/27/2022] Open
Abstract
As a notable illustration of totipotency and plant regeneration, somatic embryogenesis (SE) is the developmental reprogramming of somatic cells toward the embryogenesis pathway, the key step for genetic engineering. Investigations examining the totipotency process are of great fundamental and practical importance in crop biotechnology. However, high-frequency regeneration of cotton via SE has been limited due to genotype-dependent response. The molecular basis deciphering SE genotype recalcitrance remains largely unexplored in cotton. In the current study, to comprehensively investigate the dynamic transcriptional profiling and gene regulatory patterns involved in SE process, a genome-wide RNA sequencing analysis was performed in two cotton genotypes with distinct embryogenic abilities, the highly embryogenic genotype Yuzao 1 (YZ) and the recalcitrant genotype Lumian 1 (LM). Three typical developmental staged cultures of early SE-hypocotyls (HY), nonembryogenic calli (NEC) and primary embryogenic calli (PEC)-were selected to establish the transcriptional profiles. Our data revealed that a total of 62,562 transcripts were present amongst different developmental stages in the two genotypes. Of these, 18,394 and 26,514 differentially expressed genes (DEGs) were identified during callus dedifferentiation (NEC-VS-HY) and embryogenic transdifferentiation (PEC-VS-NEC), respectively in the recalcitrant genotype, 21,842 and 22,343 DEGs in the highly embryogenic genotype. Furthermore, DEGs were clustered into six expression patterns during cotton SE process in the two genotypes. Moreover, functional enrichment analysis revealed that DEGs were significantly enriched in fatty acid, tryptophan and pyruvate metabolism in the highly embryogenic genotype and in DNA conformation change otherwise in the recalcitrant genotype. In addition, critical SE-associated expressed transcription factors, as well as alternative splicing events, were notably and preferentially activated during embryogenic transdifferentiation in the highly embryogenic genotype compared with the recalcitrant genotype. Taken together, by systematically comparing two genotypes with distinct embryogenic abilities, the findings in our study revealed a comprehensive overview of the dynamic gene regulatory patterns and uncharacterized complex regulatory pathways during cotton SE genotype-dependent response. Our work provides insights into the molecular basis and important gene resources for understanding the underlying genotype recalcitrance during SE process and plant regeneration, thereby holding great promise for accelerating the application of biotechnology to cotton for improving its breeding efficiency.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Fanchang Zeng
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an 271018, China; (H.G.); (H.G.); (L.Z.); (Y.F.); (J.W.); (Z.T.); (Y.Z.); (Y.F.)
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