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Karami O, Khadem A, Rahimi A, Zagari N, Aigner S, Offringa R. Transient efflux inhibition improves plant regeneration by natural auxins. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:295-303. [PMID: 38361343 DOI: 10.1111/tpj.16682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 01/23/2024] [Accepted: 02/01/2024] [Indexed: 02/17/2024]
Abstract
Plant genome editing and propagation are important tools in crop breeding and production. Both rely heavily on the development of efficient in vitro plant regeneration systems. Two prominent regeneration systems that are widely employed in crop production are somatic embryogenesis (SE) and de novo shoot regeneration. In many of the protocols for SE or shoot regeneration, explants are treated with the synthetic auxin analog 2,4-dichlorophenoxyacetic acid (2,4-D), since natural auxins, such as indole-3-acetic acid (IAA) or 4-chloroindole-3-acetic acid (4-Cl-IAA), are less effective or even fail to induce regeneration. Based on previous reports that 2,4-D, compared to endogenous auxins, is not effectively exported from plant cells, we investigated whether efflux inhibition of endogenous auxins could convert these auxins into efficient inducers of SE in Arabidopsis immature zygotic embryos (IZEs). We show that natural auxins and synthetic analogs thereof become efficient inducers of SE when their efflux is transiently inhibited by co-application of the auxin transport inhibitor naphthylphthalamic acid (NPA). Moreover, IZEs of auxin efflux mutants pin2 or abcb1 abcb19 show enhanced SE efficiency when treated with IAA or efflux-inhibited IAA, confirming that auxin efflux reduces the efficiency of Arabidopsis SE. Importantly, in contrast to the 2,4-D system, where only 50-60% of the embryos converted to seedlings, all SEs induced by transport-inhibited natural auxins converted to seedlings. Efflux-inhibited IAA, like 2,4-D, also efficiently induced SE from carrot suspension cells, whereas IAA alone could not, and efflux-inhibited 4-Cl-IAA significantly improved de novo shoot regeneration in Brassica napus. Our data provides new insights into the action of 2,4-D as an efficient inducer of plant regeneration but also shows that replacing this synthetic auxin for efflux-inhibited natural auxin significantly improves different types of plant regeneration, leading to a more synchronized and homogenous development of the regenerated plants.
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Affiliation(s)
- Omid Karami
- 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
| | - Arezoo Rahimi
- Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
| | - Nicola Zagari
- ENZA Zaden, Haling 1-E, 1602 DB, Enkhuizen, The Netherlands
| | - Simon Aigner
- ENZA Zaden, Haling 1-E, 1602 DB, Enkhuizen, The Netherlands
| | - Remko Offringa
- Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
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Islam MK, Mummadi ST, Liu S, Wei H. Regulation of regeneration in Arabidopsis thaliana. ABIOTECH 2023; 4:332-351. [PMID: 38106435 PMCID: PMC10721781 DOI: 10.1007/s42994-023-00121-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 10/06/2023] [Indexed: 12/19/2023]
Abstract
We employed several algorithms with high efficacy to analyze the public transcriptomic data, aiming to identify key transcription factors (TFs) that regulate regeneration in Arabidopsis thaliana. Initially, we utilized CollaborativeNet, also known as TF-Cluster, to construct a collaborative network of all TFs, which was subsequently decomposed into many subnetworks using the Triple-Link and Compound Spring Embedder (CoSE) algorithms. Functional analysis of these subnetworks led to the identification of nine subnetworks closely associated with regeneration. We further applied principal component analysis and gene ontology (GO) enrichment analysis to reduce the subnetworks from nine to three, namely subnetworks 1, 12, and 17. Searching for TF-binding sites in the promoters of the co-expressed and co-regulated (CCGs) genes of all TFs in these three subnetworks and Triple-Gene Mutual Interaction analysis of TFs in these three subnetworks with the CCGs involved in regeneration enabled us to rank the TFs in each subnetwork. Finally, six potential candidate TFs-WOX9A, LEC2, PGA37, WIP5, PEI1, and AIL1 from subnetwork 1-were identified, and their roles in somatic embryogenesis (GO:0010262) and regeneration (GO:0031099) were discussed, so were the TFs in Subnetwork 12 and 17 associated with regeneration. The TFs identified were also assessed using the CIS-BP database and Expression Atlas. Our analyses suggest some novel TFs that may have regulatory roles in regeneration and embryogenesis and provide valuable data and insights into the regulatory mechanisms related to regeneration. The tools and the procedures used here are instrumental for analyzing high-throughput transcriptomic data and advancing our understanding of the regulation of various biological processes of interest. Supplementary Information The online version contains supplementary material available at 10.1007/s42994-023-00121-9.
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Affiliation(s)
- Md Khairul Islam
- Computational Science and Engineering Program, Michigan Technological University, Houghton, MI 49931 USA
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931 USA
| | - Sai Teja Mummadi
- Computer Science, Michigan Technological University, Houghton, MI 49931 USA
| | - Sanzhen Liu
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506 USA
| | - Hairong Wei
- Computational Science and Engineering Program, Michigan Technological University, Houghton, MI 49931 USA
- Computer Science, Michigan Technological University, Houghton, MI 49931 USA
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931 USA
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Debnath SC, Ghosh A. Phenotypic variation and epigenetic insight into tissue culture berry crops. FRONTIERS IN PLANT SCIENCE 2022; 13:1042726. [PMID: 36600911 PMCID: PMC9806182 DOI: 10.3389/fpls.2022.1042726] [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: 09/12/2022] [Accepted: 11/08/2022] [Indexed: 06/17/2023]
Abstract
Berry crops, a nutrient powerhouse for antioxidant properties, have long been enjoyed as a health-promoting delicious food. Significant progress has been achieved for the propagation of berry crops using tissue culture techniques. Although bioreactor micropropagation has been developed as a cost-effective propagation technology for berry crops, genetic stability can be a problem for commercial micropropagation that can be monitored at morphological, biochemical, and molecular levels. Somaclonal variations, both genetic and epigenetic, in tissue culture regenerants are influenced by different factors, such as donor genotype, explant type and origin, chimeral tissues, culture media type, concentration and combination of plant growth regulators, and culture conditions and period. Tissue culture regenerants in berry crops show increased vegetative growth, rhizome production, and berry yield, containing higher antioxidant activity in fruits and leaves that might be due to epigenetic variation. The present review provides an in-depth study on various aspects of phenotypic variation in micropropagated berry plants and the epigenetic effects on these variations along with the role of DNA methylation, to fill the existing gap in literature.
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Affiliation(s)
- Samir C. Debnath
- St. John’s Research and Development Centre, Agriculture and Agri-Food Canada, St. John’s, NL, Canada
| | - Amrita Ghosh
- Department of Biology, Memorial University of Newfoundland, St. John’s, NL, Canada
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Mohaddab M, El Goumi Y, Gallo M, Montesano D, Zengin G, Bouyahya A, Fakiri M. Biotechnology and In Vitro Culture as an Alternative System for Secondary Metabolite Production. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27228093. [PMID: 36432194 PMCID: PMC9697480 DOI: 10.3390/molecules27228093] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 11/23/2022]
Abstract
Medicinal plants are rich sources of bioactive compounds widely used as medicaments, food additives, perfumes, and agrochemicals. These secondary compounds are produced under stress conditions to carry out physiological tasks in plants. Secondary metabolites have a complex chemical structure with pharmacological properties. The widespread use of these metabolites in a lot of industrial sectors has raised the need to increase the production of secondary metabolites. Biotechnological methods of cell culture allow the conservation of plants, as well as the improvement of metabolite biosynthesis and the possibility to modify the synthesis pathways. The objective of this review is to outline the applications of different in vitro culture systems with previously reported relevant examples for the optimal production of plant-derived secondary metabolites.
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Affiliation(s)
- Marouane Mohaddab
- Laboratory of Agrifood and Health, Faculty of Sciences and Techniques, Hassan First University of Settat, BP 577, Settat 26000, Morocco
| | - Younes El Goumi
- Polyyvalent Team in R&D, Higher School of Technology of Fkih Ben Salah, Sultan Moulay Slimane University, USMS, Beni Mellal 23000, Morocco
| | - Monica Gallo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, via Pansini, 5, 80131 Naples, Italy
- Correspondence: (M.G.); (A.B.)
| | - Domenico Montesano
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Naples, Italy
| | - Gokhan Zengin
- Department of Biology, Science Faculty, Selcuk University, Konya 42130, Turkey
| | - Abdelhakim Bouyahya
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat 10106, Morocco
- Correspondence: (M.G.); (A.B.)
| | - Malika Fakiri
- Laboratory of Agrifood and Health, Faculty of Sciences and Techniques, Hassan First University of Settat, BP 577, Settat 26000, Morocco
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Aguilar ME, Wang XY, Escalona M, Yan L, Huang LF. Somatic embryogenesis of Arabica coffee in temporary immersion culture: Advances, limitations, and perspectives for mass propagation of selected genotypes. FRONTIERS IN PLANT SCIENCE 2022; 13:994578. [PMID: 36275513 PMCID: PMC9582858 DOI: 10.3389/fpls.2022.994578] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 09/16/2022] [Indexed: 06/16/2023]
Abstract
Culture in temporary immersion systems (TIS) is a valuable tool for the semi-automation of high frequency somatic embryogenesis of coffee. This system allows the intermittent exposure of explants to liquid medium in cycles of specific frequency and duration of immersion with renewal of the culture atmosphere in each cycle. TIS have revolutionized somatic embryogenesis of coffee plants as an alternative for scaling up and reducing costs associated with labor-intensive solid media culture. In Central America, somatic embryogenesis is employed on a commercial scale to produce F1 Coffea arabica hybrids. In Asia and Africa, somatic embryogenesis is used for the multiplication of selected genotypes of C. arabica and C.canephora. Somatic embryogenesis of coffee plants is considered a model system for woody species due to its biological versatility and low frequency of somaclonal variation. Nevertheless, the success of somatic embryogenesis for mass propagation of coffee plants depends on the development, optimization, and transfer of complementary technologies. Temporary immersion using the RITA® bioreactor is, so far, the best complementary tool for somatic embryogenesis of Arabica coffee for a single recipient with simple changes in liquid media. Likewise, high volume bioreactors, such as 10-L glass BIT® and 10-L flexible disposable plastic bags, have been successfully used for somatic embryogenesis of other coffee species. These bioreactors allow the manipulation of thousands of embryos under semi-automated conditions. The protocols, advantages, and benefits of this technology have been well documented for organogenesis and somatic embryogenesis pathways. However, adaptation in commercial laboratories requires technical and logistical adjustments based on the biological response of the cultures as well as the costs of implementation and production. This review presents the historical and present background of TIS and its commercial application and, in particular, pertinent information regarding temporary immersion culture for C. arabica somatic embryogenesis. The main limitations of this technology, such as hyperhydricity, asynchrony, and developmental abnormalities, are examined, and a critical analysis of current knowledge regarding physiological, biochemical, and molecular aspects of the plant response to temporary immersion is offered. Further, perspectives are provided for understanding and solving the morpho-physiological problems associated with temporary immersion culture of coffee plants. Systematic Review Registration.
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Affiliation(s)
- María Elena Aguilar
- Biotechnology Laboratories, Tropical Agricultural Research and Higher Education Center (CATIE), Turrialba, Costa Rica
| | - Xiao-yang Wang
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Wanning, China
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture and Rural Affairs, Wanning, China
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Wanning, China
| | - Maritza Escalona
- Plant Tissues Culture Lab, Centro de Bioplantas, Universidad Ciego de Ávila, Ciego de Ávila, Cuba
| | - Lin Yan
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Wanning, China
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture and Rural Affairs, Wanning, China
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Wanning, China
| | - Li-fang Huang
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Wanning, China
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture and Rural Affairs, Wanning, China
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Wanning, China
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In vitro propagation and secondary metabolite production in Gloriosa superba L. Appl Microbiol Biotechnol 2022; 106:5399-5414. [PMID: 35941253 DOI: 10.1007/s00253-022-12094-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 11/02/2022]
Abstract
Gloriosa superba L., commonly known as "gloriosa lily," "glory lily," and "tiger claw," is a perennial climber in the Liliaceae family. This plant is used in African and Southeast Asian cultures as an ayurvedic medicinal herb to treat various health conditions. Its main bioactive component is colchicine, which is responsible for medicinal efficacies as well as poisonous properties of the plant. A high market demand, imprudent harvesting of G. superba from natural habitat, and low seed setting have led scientists to explore micropropagation techniques and in vitro optimization of its phytochemicals. Plant growth regulators have been used to induce callus, root, and shoot organogenesis, and somatic embryogenesis in vitro. This review is aimed at presenting information regarding the occurrence, taxonomic description, phytochemistry, micropropagation, in vitro secondary metabolite, and synthetic seed production. The data collected from the existing literature, along with an analysis of individual study details, outcomes, and variations in the reports, will contribute to the development of biotechnological strategies for conservation and mass propagation of G. superba. KEY POINTS: • Latest literature on micropropagation of Gloriosa superba. • Biotechnological production and optimization of colchicine. • Regeneration, somatic embryogenesis, and synthetic seed production.
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Shi QF, Long JM, Yin ZP, Jiang N, Feng MQ, Zheng B, Guo WW, Wu XM. miR171 modulates induction of somatic embryogenesis in citrus callus. PLANT CELL REPORTS 2022; 41:1403-1415. [PMID: 35381869 DOI: 10.1007/s00299-022-02865-y] [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: 11/30/2021] [Accepted: 03/16/2022] [Indexed: 06/14/2023]
Abstract
Overexpression of miR171 restored SE competence in the recalcitrant citrus callus, and inhibition of miR171 function weakened SE competence in the strongly embryogenic citrus callus. Somatic embryogenesis (SE) is an important way of in vitro regeneration for plants. For perennial woody crops such as citrus, embryogenic callus is usually induced from unfertilized aborted ovules and widely used in biotechnology aided breeding. However, SE capacity always declines in callus during subculture, which makes regeneration difficult and hinders the application of biotechnology. We previously found that miR171 may be a regulator of SE in citrus, based on the abundant expression of csi-miR171c in the embryogenic callus and during SE of citrus. Here, we report that miR171 promotes SE and is required for SE in citrus. Overexpression of miR171 restored SE competence in the recalcitrant callus of 'Guoqing No.1' Satsuma mandarin (G1), whereas inhibition of miR171 function by Short Tandem Target Mimic (STTM) weakened SE competence in the strongly embryogenic callus of 'Valencia' sweet orange (V). The comparative transcriptomic analysis in miR171 overexpressed callus line (OE) and the wild type callus (WT) indicated that overexpression of miR171 decreased the expression level of its SCARECROW-LIKE (CsSCL) targets, and activated stress response related biological processes and metabolic processes that are required for cell differentiation. However, CsSCLs were up-regulated in the OE callus during SE induction process, which activated the cell division and developmental processes that are required for embryogenesis progress. Our results validate the function of miR171 in regulation of SE and reveal the biological responses provoked by miR171 in citrus that may promote SE.
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Affiliation(s)
- Qiao-Fang Shi
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jian-Mei Long
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Zhao-Ping Yin
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Nan Jiang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Meng-Qi Feng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Bo Zheng
- 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
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Xiao-Meng Wu
- 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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Biotechnological Approaches for Production of Artemisinin, an Anti-Malarial Drug from Artemisia annua L. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27093040. [PMID: 35566390 PMCID: PMC9103073 DOI: 10.3390/molecules27093040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/02/2022] [Accepted: 05/03/2022] [Indexed: 11/29/2022]
Abstract
Artemisinin is an anti-malarial sesquiterpene lactone derived from Artemisia annua L. (Asteraceae family). One of the most widely used modes of treatment for malaria is an artemisinin-based combination therapy. Artemisinin and its associated compounds have a variety of pharmacological qualities that have helped achieve economic prominence in recent years. So far, research on the biosynthesis of this bioactive metabolite has revealed that it is produced in glandular trichomes and that the genes responsible for its production must be overexpressed in order to meet demand. Using biotechnological applications such as tissue culture, genetic engineering, and bioreactor-based approaches would aid in the upregulation of artemisinin yield, which is needed for the future. The current review focuses on the tissue culture aspects of propagation of A. annua and production of artemisinin from A. annua L. cell and organ cultures. The review also focuses on elicitation strategies in cell and organ cultures, as well as artemisinin biosynthesis and metabolic engineering of biosynthetic genes in Artemisia and plant model systems.
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Elhiti M, Stasolla C. Transduction of Signals during Somatic Embryogenesis. PLANTS (BASEL, SWITZERLAND) 2022; 11:178. [PMID: 35050066 PMCID: PMC8779037 DOI: 10.3390/plants11020178] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/30/2021] [Accepted: 01/07/2022] [Indexed: 05/05/2023]
Abstract
Somatic embryogenesis (SE) is an in vitro biological process in which bipolar structures (somatic embryos) can be induced to form from somatic cells and regenerate into whole plants. Acquisition of the embryogenic potential in culture is initiated when some competent cells within the explants respond to inductive signals (mostly plant growth regulators, PRGs), and de-differentiate into embryogenic cells. Such cells, "canalized" into the embryogenic developmental pathway, are able to generate embryos comparable in structure and physiology to their in vivo counterparts. Genomic and transcriptomic studies have identified several pathways governing the initial stages of the embryogenic process. In this review, the authors emphasize the importance of the developmental signals required for the progression of embryo development, starting with the de-differentiation of somatic cells and culminating with tissue patterning during the formation of the embryo body. The action and interaction of PGRs are highlighted, along with the participation of master regulators, mostly transcription factors (TFs), and proteins involved in stress responses and the signal transduction required for the initiation of the embryogenic process.
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Affiliation(s)
- Mohamed Elhiti
- Department of Botany, Faculty of Science, Tanta University, Tanta 31527, Egypt;
| | - Claudio Stasolla
- Department of Plant Science, University of Manitoba, Winnipeg, MB R3T2N2, Canada
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10
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Zhang Y, Li J, Li C, Chen S, Tang Q, Xiao Y, Zhong L, Chen Y, Chen B. Gene expression programs during callus development in tissue culture of two Eucalyptus species. BMC PLANT BIOLOGY 2022; 22:1. [PMID: 34979920 PMCID: PMC8722213 DOI: 10.1186/s12870-021-03391-x] [Citation(s) in RCA: 71] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/09/2021] [Indexed: 05/09/2023]
Abstract
BACKGROUND Eucalyptus is a highly diverse genus of the Myrtaceae family and widely planted in the world for timber and pulp production. Tissue culture induced callus has become a common tool for Eucalyptus breeding, however, our knowledge about the genes related to the callus maturation and shoot regeneration is still poor. RESULTS We set up an experiment to monitor the callus induction and callus development of two Eucalyptus species - E. camaldulensis (high embryogenic potential) and E. grandis x urophylla (low embryogenic potential). Then, we performed transcriptome sequencing for primary callus, mature callus, shoot regeneration stage callus and senescence callus. We identified 707 upregulated and 694 downregulated genes during the maturation process of the two Eucalyptus species and most of them were involved in the signaling pathways like plant hormone and MAPK. Next, we identified 135 and 142 genes that might play important roles during the callus development of E. camaldulensis and E. grandis x urophylla, respectively. Further, we found 15 DEGs shared by these two Eucalyptus species during the callus development, including Eucgr.D00640 (stem-specific protein TSJT1), Eucgr.B00171 (BTB/POZ and TAZ domain-containing protein 1), Eucgr.C00948 (zinc finger CCCH domain-containing protein 20), Eucgr.K01667 (stomatal closure-related actinbinding protein 3), Eucgr.C00663 (glutaredoxin-C10) and Eucgr.C00419 (UPF0481 protein At3g47200). Interestingly, the expression patterns of these genes displayed "N" shape in the samples. Further, we found 51 genes that were dysregulated during the callus development of E. camaldulensis but without changes in E. grandis x urophylla, such as Eucgr.B02127 (GRF1-interacting factor 1), Eucgr.C00947 (transcription factor MYB36), Eucgr.B02752 (laccase-7), Eucgr.B03985 (transcription factor MYB108), Eucgr.D00536 (GDSL esterase/lipase At5g45920) and Eucgr.B02347 (scarecrow-like protein 34). These 51 genes might be associated with the high propagation ability of Eucalyptus and 22 might be induced after the dedifferentiation. Last, we performed WGCNA to identify the co-expressed genes during the callus development of Eucalyptus and qRT-PCR experiment to validate the gene expression patterns. CONCLUSIONS This is the first time to globally study the gene profiles during the callus development of Eucalyptus. The results will improve our understanding of gene regulation and molecular mechanisms in the callus maturation and shoot regeneration.
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Affiliation(s)
- Ye Zhang
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002 Guangxi China
| | - Junji Li
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002 Guangxi China
| | - Changrong Li
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002 Guangxi China
| | - Shengkan Chen
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002 Guangxi China
| | - Qinglan Tang
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002 Guangxi China
| | - Yufei Xiao
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002 Guangxi China
| | - Lianxiang Zhong
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002 Guangxi China
| | - Yingying Chen
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002 Guangxi China
| | - Bowen Chen
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002 Guangxi China
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Abstract
Somatic embryogenesis is a natural phenomenon through which somatic embryos are produced from somatic cells although. It is considered the most efficient morphogenic pathways for plant multiplication. One of the key features of somatic embryogenesis is the use of cellular totipotency, where dedifferentiation is induced to foster cell proliferation, followed by the induction of differentiation using plant growth regulators to produce new plants. There is a cell group with the potential to undergo the somatic embryogenesis pathway through adequate stimulation (plant growth regulators, incubation conditions, and supplementation of the culture medium). There are two somatic embryogenesis pathways in plants: direct and indirect embryogenesis. Direct somatic embryogenesis consists of the formation of embryos directly from isolated cells, without the formation of "callous" tissue. Indirect somatic embryogenesis is characterized by the formation of a callus as a stage that precedes the formation of somatic embryos. It should be stressed that not all plant cells have this morphogenic capacity; consequently, determining the type of factors that drive this type of response has been challenging. This book provides the reader with updated available information on the techniques, relevant protocols, and tools to perform somatic embryogenesis in different plant species for economic purposes.
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Affiliation(s)
- Marco A Ramírez-Mosqueda
- Facultad de Ciencias Biológicas y Agropecuarias, Universidad Veracruzana, Amatlán de los Reyes, Veracruz, Mexico.
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Qi S, Zhao R, Yan J, Fan Y, Huang C, Li H, Chen S, Zhang T, Kong L, Zhao J, Zhang J. Global Transcriptome and Coexpression Network Analyses Reveal New Insights Into Somatic Embryogenesis in Hybrid Sweetgum ( Liquidambar styraciflua × Liquidambar formosana). FRONTIERS IN PLANT SCIENCE 2021; 12:751866. [PMID: 34880884 PMCID: PMC8645980 DOI: 10.3389/fpls.2021.751866] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 10/22/2021] [Indexed: 06/13/2023]
Abstract
Somatic embryogenesis (SE) is a process of somatic cells that dedifferentiate to totipotent embryonic stem cells and generate embryos in vitro. Despite recent scientific headway in deciphering the difficulties of somatic embryogenesis, the overall picture of key genes, pathways, and co-expression networks regulating SE is still fragmented. Therefore, deciphering the molecular basis of somatic embryogenesis of hybrid sweetgum remains pertinent. In the present study, we analyzed the transcriptome profiles and gene expression regulation changes via RNA sequencing from three distinct developmental stages of hybrid sweetgum: non-embryogenic callus (NEC), embryogenic callus (EC), and redifferentiation. Comparative transcriptome analysis showed that 19,957 genes were differentially expressed in ten pairwise comparisons of SE. Among these, plant hormone signaling-related genes, especially the auxin and cytokinin signaling components, were significantly enriched in NEC and EC early. The K-means method was used to identify multiple transcription factors, including HB-WOX, B3-ARF, AP2/ERF, and GRFs (growth regulating factors). These transcription factors showed distinct stage- or tissue-specific expression patterns mirroring each of the 12 superclusters to which they belonged. For example, the WOX transcription factor family was expressed only at NEC and EC stages, ARF transcription factor was expressed in EC early, and GRFs was expressed in late SE. It was noteworthy that the AP2/ERF transcription factor family was expressed during the whole SE process, but almost not in roots, stems and leaves. A weighted gene co-expression network analysis (WGCNA) was used in conjunction with the gene expression profiles to recognize the genes and modules that may associate with specific tissues and stages. We constructed co-expression networks and revealed 22 gene modules. Four of these modules with properties relating to embryonic potential, early somatic embryogenesis, and somatic embryo development, as well as some hub genes, were identified for further functional studied. Through a combination analysis of WGCNA and K-means, SE-related genes including AUX22, ABI3, ARF3, ARF5, AIL1, AIL5, AGL15, WOX11, WOX9, IAA29, BBM1, MYB36, LEA6, SMR4 and others were obtained, indicating that these genes play an important role in the processes underlying the progression from EC to somatic embryos (SEs) morphogenesis. The transcriptome information provided here will form the foundation for future research on genetic transformation and epigenetic control of plant embryogenesis at a molecular level. In follow-up studies, these data could be used to construct a regulatory network for SE; Key genes obtained from coexpression network analysis at each critical stage of somatic embryo can be considered as potential candidate genes to verify these networks.
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Affiliation(s)
- Shuaizheng Qi
- College of Biological Science and Biotechnology, Beijing Forestry University, Beijing, China
| | - Ruirui Zhao
- College of Biological Science and Biotechnology, Beijing Forestry University, Beijing, China
| | - Jichen Yan
- College of Biological Science and Biotechnology, Beijing Forestry University, Beijing, China
| | - Yingming Fan
- College of Biological Science and Biotechnology, Beijing Forestry University, Beijing, China
| | - Chao Huang
- College of Biological Science and Biotechnology, Beijing Forestry University, Beijing, China
| | - Hongxuan Li
- College of Biological Science and Biotechnology, Beijing Forestry University, Beijing, China
| | - Siyuan Chen
- College of Biological Science and Biotechnology, Beijing Forestry University, Beijing, China
| | - Ting Zhang
- College of Biological Science and Biotechnology, Beijing Forestry University, Beijing, China
| | - Lisheng Kong
- College of Biological Science and Biotechnology, Beijing Forestry University, Beijing, China
- Department of Biology, Centre for Forest Biology, University of Victoria, Victoria, BC, Canada
| | - Jian Zhao
- College of Biological Science and Biotechnology, Beijing Forestry University, Beijing, China
| | - Jinfeng Zhang
- College of Biological Science and Biotechnology, Beijing Forestry University, Beijing, China
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13
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Yang E, Zheng M, Zou X, Huang X, Yang H, Chen X, Zhang J. Global Transcriptomic Analysis Reveals Differentially Expressed Genes Involved in Embryogenic Callus Induction in Drumstick ( Moringa oleifera Lam.). Int J Mol Sci 2021; 22:ijms222212130. [PMID: 34830008 PMCID: PMC8619801 DOI: 10.3390/ijms222212130] [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: 10/09/2021] [Revised: 11/01/2021] [Accepted: 11/06/2021] [Indexed: 12/25/2022] Open
Abstract
The plant embryogenic callus (EC) is an irregular embryogenic cell mass with strong regenerative ability that can be used for propagation and genetic transformation. However, difficulties with EC induction have hindered the breeding of drumstick, a tree with diverse potential commercial uses. In this study, three drumstick EC cDNA libraries were sequenced using an Illumina NovaSeq 6000 system. A total of 7191 differentially expressed genes (DEGs) for embryogenic callus development were identified, of which 2325 were mapped to the KEGG database, with the categories of plant hormone signal transduction and Plant-pathogen interaction being well-represented. The results obtained suggest that auxin and cytokinin metabolism and several embryogenesis-labeled genes are involved in embryogenic callus induction. Additionally, 589 transcription factors from 20 different families were differentially expressed during EC formation. The differential expression of 16 unigenes related to auxin signaling pathways was validated experimentally by quantitative real time PCR (qRT-PCR) using samples representing three sequential developmental stages of drumstick EC, supporting their apparent involvement in drumstick EC formation. Our study provides valuable information about the molecular mechanism of EC formation and has revealed new genes involved in this process.
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Affiliation(s)
- Endian Yang
- Department of Forestry, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (E.Y.); (M.Z.); (X.Z.); (X.H.); (H.Y.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
- Guangdong Province Research Center of Woody Forage Engineering Technology, Guangzhou 510642, China
| | - Mingyang Zheng
- Department of Forestry, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (E.Y.); (M.Z.); (X.Z.); (X.H.); (H.Y.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
- Guangdong Province Research Center of Woody Forage Engineering Technology, Guangzhou 510642, China
| | - Xuan Zou
- Department of Forestry, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (E.Y.); (M.Z.); (X.Z.); (X.H.); (H.Y.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
- Guangdong Province Research Center of Woody Forage Engineering Technology, Guangzhou 510642, China
| | - Xiaoling Huang
- Department of Forestry, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (E.Y.); (M.Z.); (X.Z.); (X.H.); (H.Y.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
| | - Heyue Yang
- Department of Forestry, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (E.Y.); (M.Z.); (X.Z.); (X.H.); (H.Y.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
| | - Xiaoyang Chen
- Department of Forestry, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (E.Y.); (M.Z.); (X.Z.); (X.H.); (H.Y.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
- Guangdong Province Research Center of Woody Forage Engineering Technology, Guangzhou 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Correspondence: (X.C.); (J.Z.)
| | - Junjie Zhang
- Department of Forestry, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (E.Y.); (M.Z.); (X.Z.); (X.H.); (H.Y.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
- Guangdong Province Research Center of Woody Forage Engineering Technology, Guangzhou 510642, China
- Correspondence: (X.C.); (J.Z.)
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Sasidharan V, Sánchez Alvarado A. The Diverse Manifestations of Regeneration and Why We Need to Study Them. Cold Spring Harb Perspect Biol 2021; 14:a040931. [PMID: 34750171 PMCID: PMC9438785 DOI: 10.1101/cshperspect.a040931] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
For hundreds of years, the question of why some organisms can regenerate missing body parts while others cannot has remained poorly understood. This has been due in great part to the inability to genetically, molecularly, and cellularly dissect this problem for most of the history of the field. It has only been in the past 20-30 years that important mechanistic advances have been made in methodologies that introduce loss and gain of gene function in animals that can regenerate. However, we still have a very incomplete understanding of how broadly regenerative abilities may be dispersed across species and whether or not such properties share a common evolutionary origin, which may have emerged independently or both. Understanding regeneration, therefore, will require rigorously practiced fundamental, curiosity-driven, discovery research. Expanding the number of research organisms used to study regeneration allows us to uncover aspects of this problem we may not yet know exist and simultaneously increases our chances of solving this long-standing problem of biology.
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Current Proteomic and Metabolomic Knowledge of Zygotic and Somatic Embryogenesis in Plants. Int J Mol Sci 2021; 22:ijms222111807. [PMID: 34769239 PMCID: PMC8583726 DOI: 10.3390/ijms222111807] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/13/2021] [Accepted: 10/27/2021] [Indexed: 11/16/2022] Open
Abstract
Embryogenesis is the primary developmental program in plants. The mechanisms that underlie the regulation of embryogenesis are an essential research subject given its potential contribution to mass in vitro propagation of profitable plant species. Somatic embryogenesis (SE) refers to the use of in vitro techniques to mimic the sexual reproduction program known as zygotic embryogenesis (ZE). In this review, we synthesize the current state of research on proteomic and metabolomic studies of SE and ZE in angiosperms (monocots and dicots) and gymnosperms. The most striking finding was the small number of studies addressing ZE. Meanwhile, the research effort focused on SE has been substantial but disjointed. Together, these research gaps may explain why the embryogenic induction stage and the maturation of the somatic embryo continue to be bottlenecks for efficient and large-scale regeneration of plants. Comprehensive and integrative studies of both SE and ZE are needed to provide the molecular foundation of plant embryogenesis, information which is needed to rationally guide experimental strategies to solve SE drawbacks in each species.
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16
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Qin Z, Li J, Zhang Y, Xiao Y, Zhang X, Zhong L, Liu H, Chen B. Genome-wide identification of microRNAs involved in the somatic embryogenesis of Eucalyptus. G3-GENES GENOMES GENETICS 2021; 11:6163290. [PMID: 33693674 PMCID: PMC8049409 DOI: 10.1093/g3journal/jkab070] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 02/24/2021] [Accepted: 02/27/2021] [Indexed: 11/13/2022]
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs (18-24 nt) and function in many biological processes in plants. Although Eucalyptus trees are widely planted across the world, our understanding of the miRNA regulation in the somatic embryogenesis (SE) of Eucalyptus is still poor. Here we reported, for the first time, the miRNA profiles of differentiated and dedifferentiated tissues of two Eucalyptus species and identified miRNAs involved in SE of Eucalyptus. Stem and tissue culture-induced callus were obtained from the subculture seedlings of E. camaldulensis and E. grandis x urophylla and were used as differentiated and dedifferentiated samples, respectively. Small RNA sequencing generated 304.2 million clean reads for the Eucalyptus samples (n = 3) and identified 888 miRNA precursors (197 known and 691 novel) for Eucalyptus. These miRNAs were mainly distributed in chromosomes Chr03, Chr05, and Chr08 and can produce 46 miRNA clusters. Then, we identified 327 and 343 differentially expressed miRNAs (DEmiRs) in the dedifferentiation process of E. camaldulensis and E. grandis x urophylla, respectively. DEmiRs shared by the two Eucalyptus species might be involved in the development of embryonic callus, such as MIR156, MIR159, MIR160, MIR164, MIR166, MIR169, MIR171, MIR399, and MIR482. Notably, we identified 81 upregulated and 67 downregulated miRNAs specific to E. camaldulensis, which might be associated with the high embryogenic potential. Target prediction and functional analysis showed that they might be involved in longevity regulating and plant hormone signal transduction pathways. Further, using the gene expression profiles, we observed the negative regulation of miRNA-target pairs, such as MIR160~ARF18, MIR396~GRF6, MIR166~ATHB15/HD-ZIP, and MIR156/MIR157~SPL1. Interestingly, transcription factors such as WRKY, MYB, GAMYB, TCP4, and PIL1 were found to be regulated by the DEmiRs. The genes encoding PIL1 and RPS21C, regulated by upregulated miRNAs (e.g., egd-N-miR63-5p, egd-N-miR63-5p, and MIR169,) were downregulated exclusively in the dedifferentiation of E. camaldulensis. This is the first time to study the miRNA regulation in the dedifferentiation process of Eucalyptus and it will provide a valuable resource for future studies. More importantly, it will improve our understanding of miRNA regulation during the somatic embryogenesis of Eucalyptus and benefit the Eucalyptus breeding program.
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Affiliation(s)
- Zihai Qin
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, Nanning 530002, China
| | - Junji Li
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, Nanning 530002, China
| | - Ye Zhang
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, Nanning 530002, China
| | - Yufei Xiao
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, Nanning 530002, China
| | - Xiaoning Zhang
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, Nanning 530002, China
| | - Lianxiang Zhong
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, Nanning 530002, China
| | - Hailong Liu
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, Nanning 530002, China
| | - Bowen Chen
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, Nanning 530002, China
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Comparative transcriptome analysis during developmental stages of direct somatic embryogenesis in Tilia amurensis Rupr. Sci Rep 2021; 11:6359. [PMID: 33737673 PMCID: PMC7973583 DOI: 10.1038/s41598-021-85886-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 03/04/2021] [Indexed: 12/13/2022] Open
Abstract
Tilia species are valuable woody species due to their beautiful shape and role as honey trees. Somatic embryogenesis can be an alternative method for mass propagation of T. amurensis. However, the molecular mechanisms of T. amurensis somatic embryogenesis are yet to be known. Here, we conducted comparative transcriptional analysis during somatic embryogenesis of T. amurensis. RNA-Seq identified 1505 differentially expressed genes, including developmental regulatory genes. Auxin related genes such as YUC, AUX/IAA and ARF and signal transduction pathway related genes including LEA and SERK were differentially regulated during somatic embryogenesis. Also, B3 domain family (LEC2, FUS3), VAL and PKL, the regulatory transcription factors, were differentially expressed by somatic embryo developmental stages. Our results could provide plausible pathway of signaling somatic embryogenesis of T. amurensis, and serve an important resource for further studies in direct somatic embryogenesis in woody plants.
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18
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Li T, Yuan W, Qiu S, Shi J. Selection of reference genes for gene expression analysis in Liriodendron hybrids' somatic embryogenesis and germinative tissues. Sci Rep 2021; 11:4957. [PMID: 33654231 PMCID: PMC7925589 DOI: 10.1038/s41598-021-84518-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 02/15/2021] [Indexed: 01/29/2023] Open
Abstract
The differential expression of genes is crucial for plant somatic embryogenesis (SE), and the accurate quantification of gene expression levels relies on choosing appropriate reference genes. To select the most suitable reference genes for SE studies, 10 commonly used reference genes were examined in synchronized somatic embryogenic and subsequent germinative cultures of Liriodendron hybrids by using quantitative real-time reverse transcription PCR. Four popular normalization algorithms: geNorm, NormFinder, Bestkeeper and Delta-Ct were used to select and validate the suitable reference genes. The results showed that elongation factor 1-gamma, histone H1 linker protein, glyceraldehyde-3-phosphate dehydrogenase and α-tubulin were suitable for SE tissues, while elongation factor 1-gamma and actin were best for the germinative organ tissues. Our work will benefit future studies of gene expression and functional analyses of SE in Liriodendron hybrids. It is also serves as a guide of reference gene selection in early embryonic gene expression analyses for other woody plant species.
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Affiliation(s)
- Tingting Li
- Zhejiang Academy of Forestry, Hangzhou, 310023, China.
| | - Weigao Yuan
- Zhejiang Academy of Forestry, Hangzhou, 310023, China
| | - Shuai Qiu
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.,Research and Development Center, Hangzhou Landscaping Incorporated, Hangzhou, 310020, China
| | - Jisen Shi
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
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19
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Kępczyńska E, Orłowska A. Profiles of endogenous ABA, bioactive GAs, IAA and their metabolites in Medicago truncatula Gaertn. non-embryogenic and embryogenic tissues during induction phase in relation to somatic embryo formation. PLANTA 2021; 253:67. [PMID: 33586054 PMCID: PMC7882586 DOI: 10.1007/s00425-021-03582-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 01/30/2021] [Indexed: 05/02/2023]
Abstract
During the 3-week-long induction phase, when M. truncatula cells leaf explants from non-embryogenic genotype (M9) and embryogenic variant (M9-10a) were forming the callus, biosynthesis and degradation of ABA, Gas and IAA proceeded at different levels. Induction of embryo formation is related to a lower ABA content, compared to the content of IAA and that of total bioactive GAs. Endogenous phytohormones are involved in the regulation of zygotic embryogenesis, but their role, especially of ABA, a plant growth inhibitor, in inducing somatic embryogenesis (SE) in angiosperms is still incompletely known. To arrive a better understanding of the ABA role in the process, we analyzed simultaneously and in detail changes in the contents of both ABA and five bioactive GAs (GA4, GA7, GA1, GA3, GA6) and IAA in M. truncatula non-embryogenic M9 (NE) and embryogenic M9-10a (E) genotypes. The initial leaf explants of both genotypes, and particularly NE, contained many times more ABA compared to the total bioactive GAs or IAA. In tissues during the entire 21-day induction all the hormones mentioned and their metabolites or conjugates were present; however, their contents were found to differ between the lines tested. The ABA level in primary explants of NE genotype was more than two times higher than that in E genotype. An even larger difference in the ABA content was found on the last day (day 21) of the induction phase (IP); the ABA content in E callus was over six times lower than in NE callus. In contrast, the IAA and GAs contents in primary explants of both genotypes in relation to ABA were low, but the contents of IAA and GAs exceeded that of ABA in the M9-10a tissues on the last day of IP. It is shown for the first time that endogenous ABA together with endogenous bioactive GAs and IAA is involved in acquisition of embryogenic competence in Medicago truncatula leaf somatic cells. These findings have a strong functional implication as they allow to improve the SE induction protocol.
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Affiliation(s)
- Ewa Kępczyńska
- Institute of Biology, University of Szczecin, Wąska 13, 71-415, Szczecin, Poland.
| | - Anna Orłowska
- Institute of Biology, University of Szczecin, Wąska 13, 71-415, Szczecin, Poland
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Gulzar B, Mujib A, Rajam MV, Zafar N, Mamgain J, Malik M, Syeed R, Ejaz B. Shotgun label-free proteomic and biochemical study of somatic embryos (cotyledonary and maturation stage) in Catharanthus roseus (L.) G. Don. 3 Biotech 2021; 11:86. [PMID: 33505840 PMCID: PMC7817727 DOI: 10.1007/s13205-021-02649-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 01/08/2021] [Indexed: 10/22/2022] Open
Abstract
Somatic embryogenesis is an important and wonderful biotechnological tool used to develop whole plant from a single or a group of somatic cells. The differentiated somatic cells become totipotent stem cells by drastic reprogramming of a wide range of cellular activities, leading to the acquisition of embryogenic competence. After acquiring competence, the cells pass through globular, heart, torpedo and cotyledonary stages of embryo; however, all advanced embryos do not convert into full plant, produce adventive embryos or callus instead, thus reverses the programming. This is a big limitation in propagation of many plants. Understanding and unraveling the proteins at this 'embryo to plantlet' transition stage will help to get more numbers of plants. Thus, our study was aimed at an identification of differentially abundant proteins between two important advanced stages, i.e. cotyledonary-(T1) and maturation stage (T2) of somatic embryos in Catharanthus roseus. A total of 2949 and 3030 proteins were identified in cotyledonary and maturation stage, respectively. Of these, 1129 proteins were common to both. Several proteins were found to be differentially accumulated in two different embryo stages in which over 60 proteins were most accumulated during somatic embryo maturation time. More chlorophyll accumulation was noted at this time under the influence of gibberellic acid (GA3). Proteins like Mg-protoporphyrin IX chelatase, chlorophyll a-b-binding protein, photosystem I iron-sulfur center, photosystem II Psb, photosystem II subunit P-1, P-II domain-containing protein, RuBisCO large chain, RuBisCO small chain, RuBisCO activase, RuBisCO large subunit-binding proteins were synthesized. Some of the identified proteins are linked to chlorophyll synthesis, carbohydrate metabolism and stress. The identified proteins are categorized into different groups on the basis of their cellular location, role and other metabolic processes. Biochemical attributes like protein, sugar, proline, antioxidant enzyme (APX, SOD and CAT) activities were high in T2 as compared to T1. The proteins like peroxidases, pathogenesis-related proteins, the late-embryogenesis abundant proteins, argonaute, germin and others have been discussed in C. roseus somatic embryo maturation process.
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Affiliation(s)
- Basit Gulzar
- Cellular Differentiation and Molecular Genetics Section, Department of Botany, Jamia Hamdard, New Delhi, India
| | - Abdul Mujib
- Cellular Differentiation and Molecular Genetics Section, Department of Botany, Jamia Hamdard, New Delhi, India
| | | | - Nadia Zafar
- Cellular Differentiation and Molecular Genetics Section, Department of Botany, Jamia Hamdard, New Delhi, India
| | - Jyoti Mamgain
- Cellular Differentiation and Molecular Genetics Section, Department of Botany, Jamia Hamdard, New Delhi, India
| | - Moien Malik
- Cellular Differentiation and Molecular Genetics Section, Department of Botany, Jamia Hamdard, New Delhi, India
| | - Rukaya Syeed
- Cellular Differentiation and Molecular Genetics Section, Department of Botany, Jamia Hamdard, New Delhi, India
| | - Bushra Ejaz
- Cellular Differentiation and Molecular Genetics Section, Department of Botany, Jamia Hamdard, New Delhi, India
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21
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Nalapalli S, Tunc-Ozdemir M, Sun Y, Elumalai S, Que Q. Morphogenic Regulators and Their Application in Improving Plant Transformation. Methods Mol Biol 2021; 2238:37-61. [PMID: 33471323 DOI: 10.1007/978-1-0716-1068-8_3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Generation of plant lines with transgene or edited gene variants is the desired outcome of transformation technology. Conventional DNA-based plant transformation methods are the most commonly used technology but these approaches are limited to a small number of plant species with efficient transformation systems. The ideal transformation technologies are those that allow biotechnology applications across wide genetic background, especially within elite germplasm of major crop species. This chapter will briefly review key regulatory genes involved in plant morphogenesis with a focus on in vitro somatic embryogenesis and their application in improving plant transformation.
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Affiliation(s)
- Samson Nalapalli
- Seeds Research, Syngenta Crop Protection LLC, Research Triangle Park, NC, USA.
| | | | - Yuejin Sun
- Seeds Research, Syngenta Crop Protection LLC, Research Triangle Park, NC, USA
| | - Sivamani Elumalai
- Seeds Research, Syngenta Crop Protection LLC, Research Triangle Park, NC, USA
| | - Qiudeng Que
- Seeds Research, Syngenta Crop Protection LLC, Research Triangle Park, NC, USA
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22
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Subban P, Kutsher Y, Evenor D, Belausov E, Zemach H, Faigenboim A, Bocobza S, Timko MP, Reuveni M. Shoot Regeneration Is Not a Single Cell Event. PLANTS 2020; 10:plants10010058. [PMID: 33383798 PMCID: PMC7823732 DOI: 10.3390/plants10010058] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 12/20/2020] [Accepted: 12/24/2020] [Indexed: 11/24/2022]
Abstract
Shoot regeneration is a key tool of modern plant biotechnology. While many researchers use this process empirically, very little is known about the early molecular genetic factors and signaling events that lead to shoot regeneration. Using tobacco as a model system, we found that the inductive events required for shoot regeneration occur in the first 4–5 days following incubation on regeneration medium. Leaf segments placed on regeneration medium did not produce shoots if removed from the medium before four days indicating this time frame is crucial for the induction of shoot regeneration. Leaf segments placed on regeneration medium for longer than five days maintain the capacity to produce shoots when removed from the regeneration medium. Analysis of gene expression during the early days of incubation on regeneration medium revealed many changes occurring with no single expression pattern evident among major gene families previously implicated in developmental processes. For example, expression of Knotted gene family members increased during the induction period, whereas transcription factors from the Wuschel gene family were unaltered during shoot induction. Expression levels of genes involved in cell cycle regulation increased steadily on regeneration medium while expression of NAC genes varied. No obvious possible candidate genes or developmental processes could be identified as a target for the early events (first few days) in the induction of shoot regeneration. On the other hand, observations during the early stages of regeneration pointed out that regeneration does not occur from a single cell but a group of cells. We observed that while cell division starts just as leaf segments are placed on regeneration medium, only a group of cells could become shoot primordia. Still, these primordia are not identifiable during the first days.
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Affiliation(s)
- Patharajan Subban
- Institute of Plant Sciences, ARO Volcani Center, P.O. Box 15159, Rishon LeZion 7528809, Israel; (P.S.); (Y.K.); (D.E.); (E.B.); (H.Z.); (A.F.); (S.B.)
| | - Yaarit Kutsher
- Institute of Plant Sciences, ARO Volcani Center, P.O. Box 15159, Rishon LeZion 7528809, Israel; (P.S.); (Y.K.); (D.E.); (E.B.); (H.Z.); (A.F.); (S.B.)
| | - Dalia Evenor
- Institute of Plant Sciences, ARO Volcani Center, P.O. Box 15159, Rishon LeZion 7528809, Israel; (P.S.); (Y.K.); (D.E.); (E.B.); (H.Z.); (A.F.); (S.B.)
| | - Eduard Belausov
- Institute of Plant Sciences, ARO Volcani Center, P.O. Box 15159, Rishon LeZion 7528809, Israel; (P.S.); (Y.K.); (D.E.); (E.B.); (H.Z.); (A.F.); (S.B.)
| | - Hanita Zemach
- Institute of Plant Sciences, ARO Volcani Center, P.O. Box 15159, Rishon LeZion 7528809, Israel; (P.S.); (Y.K.); (D.E.); (E.B.); (H.Z.); (A.F.); (S.B.)
| | - Adi Faigenboim
- Institute of Plant Sciences, ARO Volcani Center, P.O. Box 15159, Rishon LeZion 7528809, Israel; (P.S.); (Y.K.); (D.E.); (E.B.); (H.Z.); (A.F.); (S.B.)
| | - Samuel Bocobza
- Institute of Plant Sciences, ARO Volcani Center, P.O. Box 15159, Rishon LeZion 7528809, Israel; (P.S.); (Y.K.); (D.E.); (E.B.); (H.Z.); (A.F.); (S.B.)
| | - Michael P. Timko
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA;
| | - Moshe Reuveni
- Institute of Plant Sciences, ARO Volcani Center, P.O. Box 15159, Rishon LeZion 7528809, Israel; (P.S.); (Y.K.); (D.E.); (E.B.); (H.Z.); (A.F.); (S.B.)
- Correspondence:
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Chen X, Huang S, Jiang M, Chen Y, XuHan X, Zhang Z, Lin Y, Lai Z. Genome-wide identification and expression analysis of the SR gene family in longan (Dimocarpus longan Lour.). PLoS One 2020; 15:e0238032. [PMID: 32841304 PMCID: PMC7447046 DOI: 10.1371/journal.pone.0238032] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 08/07/2020] [Indexed: 12/05/2022] Open
Abstract
Longan (Dimocarpus longan Lour.) is an important commercial fruit tree in southern China. The embryogenesis of longan affects the quality and yield of fruit. A large number of alternative splicing events occurs during somatic embryogenesis (SE), which is regulated by serine/arginine-rich (SR) proteins. However, the functions of SR proteins in longan are poorly understood. In this study, 21 Dlo-SR gene family members belonging to six subfamilies were identified, among which Dlo-RSZ20a, Dlo-SR30, Dlo-SR17, Dlo-SR53 and Dlo-SR32 were localized in the nucleus, Dlo-RSZ20b, Dlo-RSZ20c, Dlo-RSZ20d, Dlo-SC18, Dlo-RS2Z29, Dlo-SCL41, and Dlo-SR33 were localized in chloroplasts, and Dlo-RS43, Dlo-SC33, Dlo-SC37, Dlo-RS2Z33, Dlo-RS2Z16, Dlo-RS2Z24, Dlo-SCL43, Dlo-SR112, and Dlo-SR59 were localized in the nucleus and chloroplasts. The Dlo-SR genes exhibited differential expression patterns in different tissues of longan. The transcript levels of Dlo-RSZ20a, Dlo-SC18, Dlo-RS2Z29, DLo-SR59, Dlo-SR53, and Dlo-SR17 were low in all analyzed tissues, whereas Dlo-RS43, Dlo-RS2Z16, Dlo-RS2Z24, and Dlo-SR30 were highly expressed in all tissues. To clarify their function during SE, the transcript levels of Dlo-SR genes were analyzed at different four stages of SE, comprising non-embryonic callus (NEC), friable-embryogenic callus (EC), incomplete compact pro-embryogenic culture (ICpEC) and globular embryo (GE). Interestingly, the transcript levels of Dlo-RS2Z29 and Dlo-SR112 were increased in embryogenic cells compared with the NEC stage, whereas transcript levels of Dlo-RSZ20a, Dlo-RS43, Dlo-SC37, and Dlo-RS2Z16 were especially increased at the GE stage compared with the other stages. Alternative splicing events of Dlo-SR mRNA precursors (pre-mRNAs) was detected during SE, with totals of 41, 29, 35, and 44 events detected during NEC, EC, ICpEC, and GE respectively. Protein–protein interaction analysis showed that SR proteins were capable of interaction with each other. The results indicate that the alternative splicing of Dlo-SR pre-mRNAs occurs during SE and that Dlo-SR proteins may interact to regulate embryogenesis of longan.
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Affiliation(s)
- Xiaodong Chen
- Institute of horticultural biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shuqi Huang
- Institute of horticultural biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mengqi Jiang
- Institute of horticultural biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yukun Chen
- Institute of horticultural biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xu XuHan
- Institute of horticultural biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute de la Recherche Interdisciplinaire de Toulouse, Toulouse, France
| | - Zihao Zhang
- Institute of horticultural biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuling Lin
- Institute of horticultural biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
- * E-mail: (YL); (ZL)
| | - Zhongxiong Lai
- Institute of horticultural biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
- * E-mail: (YL); (ZL)
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Hesami M, Naderi R, Tohidfar M, Yoosefzadeh-Najafabadi M. Development of support vector machine-based model and comparative analysis with artificial neural network for modeling the plant tissue culture procedures: effect of plant growth regulators on somatic embryogenesis of chrysanthemum, as a case study. PLANT METHODS 2020; 16:112. [PMID: 32817755 PMCID: PMC7424974 DOI: 10.1186/s13007-020-00655-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 08/08/2020] [Indexed: 05/12/2023]
Abstract
BACKGROUND Optimizing the somatic embryogenesis protocol can be considered as the first and foremost step in successful gene transformation studies. However, it is usually difficult to achieve an optimized embryogenesis protocol due to the cost and time-consuming as well as the complexity of this process. Therefore, it is necessary to use a novel computational approach, such as machine learning algorithms for this aim. In the present study, two machine learning algorithms, including Multilayer Perceptron (MLP) as an artificial neural network (ANN) and support vector regression (SVR), were employed to model somatic embryogenesis of chrysanthemum, as a case study, and compare their prediction accuracy. RESULTS The results showed that SVR (R2 > 0.92) had better performance accuracy than MLP (R2 > 0.82). Moreover, the Non-dominated Sorting Genetic Algorithm-II (NSGA-II) was also applied for the optimization of the somatic embryogenesis and the results showed that the highest embryogenesis rate (99.09%) and the maximum number of somatic embryos per explant (56.24) can be obtained from a medium containing 9.10 μM 2,4-dichlorophenoxyacetic acid (2,4-D), 4.70 μM kinetin (KIN), and 18.73 μM sodium nitroprusside (SNP). According to our results, SVR-NSGA-II was able to optimize the chrysanthemum's somatic embryogenesis accurately. CONCLUSIONS SVR-NSGA-II can be employed as a reliable and applicable computational methodology in future plant tissue culture studies.
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Affiliation(s)
- Mohsen Hesami
- Department of Plant Agriculture, University of Guelph, Guelph, ON Canada
| | - Roohangiz Naderi
- Department of Horticultural Science, Faculty of Agriculture, University of Tehran, Karaj, Iran
| | - Masoud Tohidfar
- Department of Plant Biotechnology, Faculty of Science and Biotechnology, Shahid Beheshti University, G.C., Tehran, Iran
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Full-Length Transcriptome Analysis of the ABCB, PIN/PIN-LIKES, and AUX/LAX Families Involved in Somatic Embryogenesis of Lilium pumilum DC. Fisch. Int J Mol Sci 2020; 21:ijms21020453. [PMID: 31936841 PMCID: PMC7014436 DOI: 10.3390/ijms21020453] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 01/07/2020] [Accepted: 01/08/2020] [Indexed: 12/13/2022] Open
Abstract
Plant cell totipotency is one of the 25 major topics in current scientific research, and somatic embryos are good experimental material for studying cell totipotency. Polar auxin transport plays an important regulatory role in somatic embryogenesis (SE). However, little is known about the auxin transport genes and their regulatory mechanisms in Lilium SE. In this study, we applied single-molecule real-time (SMRT) sequencing to Lilium pumilum DC. Fisch. for the first time and obtained a total of 119,649 transcripts, of which 14 encoded auxin transport genes. Correlation analyses between somatic embryo induction and gene expression under different treatments revealed that auxin transport genes, especially ATP-binding cassette (ABC) transporter B family member 21 (ABCB21) and PIN-FORMED (PIN) LIKES 7 (PILS7), may be key players in SE, and the necessary duration of picloram (PIC) treatment to induce SE is as short as 3 days. Our research provides valuable genetic information on Lilium pumilum, elucidating the candidate auxin transport genes involved in SE and their influencing factors. This study lays a foundation for elucidating the regulatory mechanism of auxin transport in SE.
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Dynamic Transcriptome Analysis Reveals Uncharacterized Complex Regulatory Pathway Underlying Dose IBA-Induced Embryogenic Redifferentiation in Cotton. Int J Mol Sci 2020; 21:ijms21020426. [PMID: 31936561 PMCID: PMC7013799 DOI: 10.3390/ijms21020426] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 01/03/2020] [Accepted: 01/07/2020] [Indexed: 11/17/2022] Open
Abstract
The somatic embryogenesis (SE) process of plants is regulated by exogenous hormones. During the SE, different genes sensitively respond to hormone signals through complex regulatory networks to exhibit plant totipotency. When cultured in indole-3-butyric acid (IBA) concentration gradient medium supplemented with 0 mg dm-3, 0.025 mg dm-3, and 0.05 mg dm-3 IBA, the callus differentiation rate first increased then decreased in cotton. To characterize the molecular basis of IBA-induced regulating SE, transcriptome analysis was conducted on embryogenic redifferentiation. Upon the examination of the IBA's embryogenic inductive effect, it was revealed that pathways related to plant hormone signal transduction and alcohol degradation were significantly enriched in the embryogenic responsive stage (5 days). The photosynthesis, alcohol metabolism and cell cycle pathways were specifically regulated in the pre-embryonic initial period (20 days). Upon the effect of the IBA dose, in the embryogenic responsive stage (5 days), the metabolism of xenobiotics by the cytochrome P450 pathway and secondary metabolism pathways of steroid, flavonoid, and anthocyanin biosynthesis were significantly enriched. The phenylpropanoid, brassinosteroid, and anthocyanin biosynthesis pathways were specifically associated in the pre-embryonic initial period (20 days). At different developmental stages of embryogenic induction, photosynthesis, flavonoid biosynthesis, phenylpropanoid biosynthesis, mitogen-activated protein kinase (MAPK) signaling, xenobiotics metabolism by cytochrome P450, and brassinosteroid biosynthesis pathways were enriched at low a IBA concentration. Meanwhile, at high IBA concentration, the carbon metabolism, alcohol degradation, circadian rhythm and biosynthesis of amino acids pathways were significantly enriched. The results reveal that complex regulating pathways participate in the process of IBA-induced redifferentiation in cotton somatic embryogenesis. In addition, collections of potential essential signaling and regulatory genes responsible for dose IBA-induced efficient embryogenic redifferentiation were identified. Quantitative real-time PCR (qRT-PCR) was performed on the candidate genes with different expression patterns, and the results are basically consistent with the RNA-seq data. The results suggest that the complicated and concerted IBA-induced mechanisms involving multiple cellular pathways are responsible for dose-dependent plant growth regulator-induced SE. This report represents a systematic study and provides new insight into molecular signaling and regulatory basis underlying the process of dose IBA-induced embryogenic redifferentiation during SE.
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Chen Y, Xu X, Liu Z, Zhang Z, XuHan X, Lin Y, Lai Z. Global scale transcriptome analysis reveals differentially expressed genes involve in early somatic embryogenesis in Dimocarpus longan Lour. BMC Genomics 2020; 21:4. [PMID: 31898486 PMCID: PMC6941269 DOI: 10.1186/s12864-019-6393-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 12/12/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Somatic embryogenesis (SE) is a process of somatic cells that dedifferentiate to totipotent embryonic stem cells and generate embryos in vitro. Longan SE has been established and wildly used as model system for studying embryogenesis in woody plants, SE-related genes had been characterized. In spite of that, a comprehensive overview of SE at a molecular level is still absent. To understand the molecular mechanisms during longan SE, we examined the transcriptome changes by using Illumina HiSeq from the four distinct developmental stages, including non-embryogenic callus (NEC), embryogenic callus (EC), incomplete compact pro-embryogenic cultures (ICpEC), globular embryos (GE). RESULTS RNA-seq of the four samples generated a total of 243.78 million high quality reads, approximately 81.5% of the data were mapped to longan genome. The cDNA libraries of NEC, EC, ICpEC and GE, generated 22,743, 19,745, 21,144, 21,102 expressed transcripts, 1935, 1710, 1816, 1732 novel transcripts, 2645, 366, 505, 588 unique genes, respectively. Comparative transcriptome analysis showed that a total of 10,642, 4180, 5846 and 1785 genes were differentially expressed in the pairwise comparisons of NEC_vs_EC, EC_vs_ICpEC, EC_vs_GE, ICpEC_vs_GE, respectively. Among them, plant hormones signalling related genes were significantly enriched, especially the auxin and cytokinin signalling components. The transcripts of flavonoid biosynthesis related genes were mainly expressed in NEC, while fatty acid biosynthesis related genes mainly accumulated in early SE. In addition, the extracelluar protein encoding genes LTP, CHI, GLP, AGP, EP1 were related to longan SE. Combined with the FPKM value of longan nine tissues transcription, 27 SE specific or preferential genes (LEC1, LEC1-like, PDF1.3, GH3.6, AGL80, PIN1, BBM, WOX9, WOX2, ABI3, et al.) and 28 NEC preferential genes (LEA5, CNOT3, DC2.15, PR1-1, NsLTP2, DIR1, PIP1, PIP2.1, TIP2-1, POD-P7 and POD5 et al.) were characterized as molecular markers for longan early SE. qRT-PCR validation of SE-related genes showed a high correlation between RNA-seq and qRT-PCR data. CONCLUSION This study provides new insights into the role of the transcriptome during early SE in longan. Differentially expressed genes reveal that plant hormones signalling, flavonoid and fatty acid biosynthesis, and extracelluar protein related genes were involved in longan early SE. It could serve as a valuable platform resource for further functional studies addressing embryogenesis in woody plants.
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Affiliation(s)
- Yukun Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xiaoping Xu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Zhuanxia Liu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Zihao Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xu XuHan
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Institut de la Recherche Interdisciplinaire de Toulouse, IRIT-ARI, 31300 Toulouse, France
| | - Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Zhongxion Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
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28
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Chen JC, Tong CG, Lin HY, Fang SC. Phalaenopsis LEAFY COTYLEDON1-Induced Somatic Embryonic Structures Are Morphologically Distinct From Protocorm-Like Bodies. FRONTIERS IN PLANT SCIENCE 2019; 10:1594. [PMID: 31850050 PMCID: PMC6896055 DOI: 10.3389/fpls.2019.01594] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 11/13/2019] [Indexed: 05/27/2023]
Abstract
Somatic embryogenesis is commonly used for clonal propagation of a wide variety of plant species. Induction of protocorm-like-bodies (PLBs), which are capable of developing into individual plants, is a routine tissue culture-based practice for micropropagation of orchid plants. Even though PLBs are often regarded as somatic embryos, our recent study provides molecular evidence to argue that PLBs are not derived from somatic embryogenesis. Here, we report and characterize the somatic embryonic tissues induced by Phalaenopsis aphrodite LEAFY COTYLEDON1 (PaLEC1) in Phalaenopsis equestris. We found that PaLEC1-induced somatic tissues are morphologically different from PLBs, supporting our molecular study that PLBs are not of somatic embryonic origin. The embryonic identity of PaLEC1-induced embryonic tissues was confirmed by expression of the embryonic-specific transcription factors FUSCA3 (FUS3) and ABSCISIC ACID INSENSITIVE3 (ABI3), and seed storage proteins 7S GLOBULIN and OLEOSIN. Moreover, PaLEC1-GFP protein was found to be associated with the Pa7S-1 and PaFUS3 promoters containing the CCAAT element, supporting that PaLEC1 directly regulates embryo-specific processes to activate the somatic embryonic program in P. equestris. Despite diverse embryonic structures, PaLEC1-GFP-induced embryonic structures are pluripotent and capable of generating new shoots. Our study resolves the long-term debate on the developmental identity of PLB and suggests that somatic embryogenesis may be a useful approach to clonally propagate orchid seedlings.
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Affiliation(s)
- Jhun-Chen Chen
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Chii-Gong Tong
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Hsiang-Yin Lin
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Su-Chiung Fang
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
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29
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Rodrigues AS, Chaves I, Costa BV, Lin YC, Lopes S, Milhinhos A, Van de Peer Y, Miguel CM. Small RNA profiling in Pinus pinaster reveals the transcriptome of developing seeds and highlights differences between zygotic and somatic embryos. Sci Rep 2019; 9:11327. [PMID: 31383905 PMCID: PMC6683148 DOI: 10.1038/s41598-019-47789-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 07/24/2019] [Indexed: 02/07/2023] Open
Abstract
Regulation of seed development by small non-coding RNAs (sRNAs) is an important mechanism controlling a crucial phase of the life cycle of seed plants. In this work, sRNAs from seed tissues (zygotic embryos and megagametophytes) and from somatic embryos of Pinus pinaster were analysed to identify putative regulators of seed/embryo development in conifers. In total, sixteen sRNA libraries covering several developmental stages were sequenced. We show that embryos and megagametophytes express a large population of 21-nt sRNAs and that substantial amounts of 24-nt sRNAs were also detected, especially in somatic embryos. A total of 215 conserved miRNAs, one third of which are conifer-specific, and 212 high-confidence novel miRNAs were annotated. MIR159, MIR171 and MIR394 families were found in embryos, but were greatly reduced in megagametophytes. Other families, like MIR397 and MIR408, predominated in somatic embryos and megagametophytes, suggesting their expression in somatic embryos is associated with in vitro conditions. Analysis of the predicted miRNA targets suggests that miRNA functions are relevant in several processes including transporter activity at the cotyledon-forming stage, and sulfur metabolism across several developmental stages. An important resource for studying conifer embryogenesis is made available here, which may also provide insightful clues for improving clonal propagation via somatic embryogenesis.
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Affiliation(s)
- Andreia S Rodrigues
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901, Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. República, 2780-157, Oeiras, Portugal
| | - Inês Chaves
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901, Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. República, 2780-157, Oeiras, Portugal
| | - Bruno Vasques Costa
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901, Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. República, 2780-157, Oeiras, Portugal
- INESC-ID, Instituto Superior Técnico, Universidade de Lisboa, Rua Alves Redol 9, Lisboa, 1000-029, Portugal
| | - Yao-Cheng Lin
- Biotechnology Center in Southern Taiwan and Agricultural Biotechnology Research Center, Academia Sinica, Tainan, Taiwan
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
| | - Susana Lopes
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901, Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. República, 2780-157, Oeiras, Portugal
| | - Ana Milhinhos
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901, Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. República, 2780-157, Oeiras, Portugal
| | - Yves Van de Peer
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
| | - Célia M Miguel
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901, Oeiras, Portugal.
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. República, 2780-157, Oeiras, Portugal.
- BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal.
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Guo H, Guo H, Zhang L, Fan Y, Fan Y, Zeng F. SELTP-assembled battery drives totipotency of somatic plant cell. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1188-1190. [PMID: 30844118 PMCID: PMC6576022 DOI: 10.1111/pbi.13107] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/27/2019] [Accepted: 03/04/2019] [Indexed: 05/28/2023]
Affiliation(s)
- Huihui Guo
- State Key Laboratory of Crop BiologyCollege of AgronomyShandong Agricultural UniversityTai'anChina
| | - Haixia Guo
- State Key Laboratory of Crop BiologyCollege of AgronomyShandong Agricultural UniversityTai'anChina
| | - Li Zhang
- State Key Laboratory of Crop BiologyCollege of AgronomyShandong Agricultural UniversityTai'anChina
| | - Yijie Fan
- State Key Laboratory of Crop BiologyCollege of AgronomyShandong Agricultural UniversityTai'anChina
| | - Yupeng Fan
- State Key Laboratory of Crop BiologyCollege of AgronomyShandong Agricultural UniversityTai'anChina
| | - Fanchang Zeng
- State Key Laboratory of Crop BiologyCollege of AgronomyShandong Agricultural UniversityTai'anChina
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31
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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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Homeologous regulation of Frigida-like genes provides insights on reproductive development and somatic embryogenesis in the allotetraploid Coffea arabica. Sci Rep 2019; 9:8446. [PMID: 31186437 PMCID: PMC6560031 DOI: 10.1038/s41598-019-44666-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 05/22/2019] [Indexed: 01/10/2023] Open
Abstract
Coffea arabica is an allotetraploid of high economic importance. C. arabica transcriptome is a combination of the transcripts of two parental genomes (C. eugenioides and C. canephora) that gave rise to the homeologous genes of the species. Previous studies have reported the transcriptional dynamics of C. arabica. In these reports, the ancestry of homeologous genes was identified and the overall regulation of homeologous differential expression (HDE) was explored. One of these genes is part of the FRIGIDA-like family (FRL), which includes the Arabidopsis thaliana flowering-time regulation protein, FRIGIDA (FRI). As nonfunctional FRI proteins give rise to rapid-cycling summer annual ecotypes instead of vernalization-responsive winter-annuals, allelic variation in FRI can modulate flowering time in A. thaliana. Using bioinformatics, genomic analysis, and the evaluation of gene expression of homeologs, we characterized the FRL gene family in C. arabica. Our findings indicate that C. arabica expresses 10 FRL homeologs, and that, throughout flower and fruit development, these genes are differentially transcribed. Strikingly, in addition to confirming the expression of FRL genes during zygotic embryogenesis, we detected FRL expression during direct somatic embryogenesis, a novel finding regarding the FRL gene family. The HDE profile of FRL genes suggests an intertwined homeologous gene regulation. Furthermore, we observed that FLC gene of C. arabica has an expression profile similar to that of CaFRL genes.
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Correia S, Alhinho AT, Casimiro B, Miguel CM, Oliveira M, Veríssimo P, Canhoto J. NEP-TC a rRNA Methyltransferase Involved on Somatic Embryogenesis of Tamarillo ( Solanum betaceum Cav.). FRONTIERS IN PLANT SCIENCE 2019; 10:438. [PMID: 31024602 PMCID: PMC6459958 DOI: 10.3389/fpls.2019.00438] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 03/22/2019] [Indexed: 05/23/2023]
Abstract
Somatic embryogenesis (SE) is an important biotechnological tool for large-scale clonal propagation and for embryogenesis research. Moreover, genetic transformation and cryopreservation procedures in many species rely on efficient SE protocols. We have been studying different aspects related to SE induction and somatic embryo development in tamarillo (Solanum betaceum Cav.), a small tree from the Solanaceae family. Previous proteomic analyses identified a protein (NEP-TC, 26.5 kDa) consistently present in non-embryogenic calluses of tamarillo, but absent in the embryogenic ones. In this work, the role of NEP-TC during SE was assessed by gene expression analysis and immunolocalization. The results obtained demonstrated that NEP-TC is a putative member of the SpoU rRNA methylase family. This protein, present in the cytoplasm and nucleus, is expressed in non-embryogenic cells and not expressed in embryogenic cells. Slightly enhanced SE induction levels in tamarillo plants with NEP-TC down-regulated levels also supports the role of this protein on SE induction. Heterologous expression was used to confirm NEP-TC rRNA methyltransferase activity, with enhanced activity levels when rRNA was used as a substrate. These data relate a putative member of the SpoU methylase family with plant morphogenesis, in particular with SE induction.
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Affiliation(s)
- Sandra Correia
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
- Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Ana T. Alhinho
- Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Bruno Casimiro
- Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Célia M. Miguel
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-UNL), Oeiras, Portugal
| | - Margarida Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-UNL), Oeiras, Portugal
| | - Paula Veríssimo
- Department of Life Sciences, University of Coimbra, Coimbra, Portugal
- Centro de Neurociências e Biologia Celular (CNBC/UC), Edifiício da Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal
| | - Jorge Canhoto
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
- Department of Life Sciences, University of Coimbra, Coimbra, Portugal
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Isah T. Proteome study of somatic embryogenesis in Nothapodytes nimmoniana (J. Graham) Mabberly. 3 Biotech 2019; 9:119. [PMID: 30854279 DOI: 10.1007/s13205-019-1637-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 02/14/2019] [Indexed: 01/02/2023] Open
Abstract
Somatic embryogenesis (SE) is the most suitable biotechnological tool for the rapid clonal propagation of endangered woody plants, but many bottlenecks limit understanding its molecular and physiological processes in Nothapodytes nimmoniana. Combinations of two-dimensional electrophoresis (2-DE) and mass spectrometry (MaSp) were used to study proteomic expression changes during SE of the forest tree. Callus was induced from mature seed embryos, and embryogenic callus (EC) obtained at very low frequency after about 6 month culture. Globular embryos were induced from the seed embryo-derived EC and the subsequent stages of the SE. Analysis of the extracted proteins from globular, heart/torpedo-shaped, and maturing embryo stages resolved in the 2-DE gels showed increased protein expression across developmental stages of the somatic embryos. The mass spectrometric analysis with database search aided identification of 55 out of 100 and 54 selected protein spots. Identified proteins classified by the cellular role which they perform are involved in aspects of stress responses, energy metabolism, carbon fixation, secondary metabolism, and other metabolic functions, while three proteins are of unknown cellular role. The putative role of the expressed proteins during SE provided insight into the physiology of somatic embryo development in N. nimmoniana.
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Affiliation(s)
- Tasiu Isah
- Department of Botany, School of Chemical and Life Sciences, Hamdard University, New Delhi, 110 062 India
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Brand A, Quimbaya M, Tohme J, Chavarriaga-Aguirre P. Arabidopsis LEC1 and LEC2 Orthologous Genes Are Key Regulators of Somatic Embryogenesis in Cassava. FRONTIERS IN PLANT SCIENCE 2019; 10:673. [PMID: 31191582 PMCID: PMC6541005 DOI: 10.3389/fpls.2019.00673] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Accepted: 05/03/2019] [Indexed: 05/22/2023]
Abstract
High genotype-dependent variation in friable embryogenic callus (FEC) induction and subsequent somaclonal variation constitute bottlenecks for the application and scaling of genetic transformation (GT) technology to more farmer- and industry-preferred cassava varieties. The understanding and identification of molecular factors underlying embryogenic development in cassava may help to overcome these constraints. Here, we described the Arabidopsis thaliana LEAFY COTYLEDON (LEC) LEC1 and LEC2 orthologous genes in cassava, designated as MeLEC1 and MeLEC2, respectively. Expression analyses showed that both, MeLEC1 and MeLEC2, are expressed at higher levels in somatic embryogenic (SE) tissues in contrast with differentiated mature tissues. The rapid expression increase of MeLEC genes at early SE induction times strongly suggests that they are involved in the transition from a somatic to an embryonic state, and probably, in the competence acquisition for SE development in cassava. The independent overexpression of the MeLEC genes resulted in different regenerated events with embryogenic characteristics such as MeLEC1OE plants with cotyledon-like leaves and MeLEC2OE plants with somatic-like embryos that emerged over the surface of mature leaves. Transcript increases of other embryo-specific regulating factors were also detected in MeLECOE plants, supporting their mutual interaction in the embryo development coordination. The single overexpression of MeLEC2 was enough to reprogram the vegetative cells and induce direct somatic embryogenesis, which converts this gene into a tool that could improve the recovery of transformed plants of recalcitrant genotypes. The identification of MeLEC genes contributes not only to improve our understanding of SE process in cassava, but also provides viable alternatives to optimize GT and advance in gene editing in this crop, through the development of genotype-independent protocols.
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Affiliation(s)
- Alejandro Brand
- International Center for Tropical Agriculture, Cali, Colombia
| | - Mauricio Quimbaya
- Department of Natural Sciences and Mathematics, Pontificia Universidad Javeriana Cali, Cali, Colombia
| | - Joe Tohme
- International Center for Tropical Agriculture, Cali, Colombia
| | - Paul Chavarriaga-Aguirre
- International Center for Tropical Agriculture, Cali, Colombia
- *Correspondence: Paul Chavarriaga-Aguirre,
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High-Efficiency Somatic Embryogenesis from Seedlings of Koelreuteria paniculata Laxm. FORESTS 2018. [DOI: 10.3390/f9120769] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Research Highlights: In the current study, we established a method for plant regeneration via somatic embryogenesis (SE) in Koelreuteria paniculata Laxm. for the first time. Background and Objectives: K. paniculata is an important ornamental and medicinal plant in China. However, the plant has difficulty with asexual reproduction, which imposes a limitation on large-scale propagation. Materials and Methods: Embryogenic calluses were induced from stems of aseptic seedlings on induction media. The effects of different media types and concentrations of N6-benzyladenine (BA), α-naphthaleneacetic acid (NAA), and 2,4-dichlorophenoxyacetic acid (2,4-D) on callus induction were examined. Embryogenic calluses were then transferred to Driver-Kuniyuki Walnut (DKW) media containing NAA (0.1–0.2 mg L−1) or 2,4-D (0.5–2.0 mg L−1) to develop somatic embryos. Cotyledon embryos were cultured on DKW media containing NAA (0.1–0.2 mg L−1) until maturation, and were then transferred to 1/2 DKW medium supplemented with 1.0 mg L−1 indole-3-butyric acid (IBA) to produce complete plants. The effects of IBA and NAA on rhizogenesis were then examined by clonal culture. Results: The maximum callus induction frequency (80.25%) was obtained on DKW medium supplemented by 0.5 mg L−1 BA, 0.25 mg L−1 NAA, and 1.5 mg L−1 2,4-D. NAA had a more pronounced effect on somatic embryo growth than did 2,4-D, with a maximum SE frequency (54.75%) observed with 0.1 mg L−1 NAA added to DKW medium. For clonal culture, the highest rooting rate (52%) was observed on 1/4 DKW medium containing 1.5 mg L−1 IBA. Histology studies confirmed the presence of embryogenic calluses and somatic embryos in different stages. Conclusions: This protocol provides a novel method for large-scale propagation of K. paniculata, and creates opportunities for genetic engineering in this species.
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Ghosh A, Igamberdiev AU, Debnath SC. Thidiazuron-induced somatic embryogenesis and changes of antioxidant properties in tissue cultures of half-high blueberry plants. Sci Rep 2018; 8:16978. [PMID: 30451961 PMCID: PMC6242952 DOI: 10.1038/s41598-018-35233-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 10/29/2018] [Indexed: 12/19/2022] Open
Abstract
An efficient protocol of somatic embryogenesis (SE) has been developed for the first time in four half-high blueberry (Vaccinium corymbosum L. × V. angustifolium Ait.) cultivars. Thidiazuron (TDZ), a plant growth regulator with potential activities for shoot regeneration and shoot proliferation, was found most effective for somatic embryo formation when added to a nutrient medium at high concentration (9 µM). Although TDZ was also best for embryo germination at low concentration (2.3 µM), it was followed by zeatin at 4.6 µM for the same. Plantlets developed from SE were removed from the nutrient medium and transferred on a peat: perlite medium where 100% survival rate was acquired following the acclimatization process in a greenhouse. The concentrations of total phenolic and flavonoid contents were higher in greenhouse-grown conventionally cutting-propagated donor mother plants than those of respective SE plants for 'St. Cloud', 'Patriot' and 'Northblue' but not for 'Chippewa'. The effect of propagation method and/or the older age of donor mother plants were clearly visible exclusively as the 15-year-old donor plants showed higher level of 2,2-diphenyl-1-picrylhydrazyl scavenging activity than the eight-weeks-old SE plants in all four cultivars.
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Affiliation(s)
- Amrita Ghosh
- Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
- St. John's Research and Development Centre, Agriculture and Agri-Food Canada, St. John's, Newfoundland and Labrador, Canada
| | - Abir U Igamberdiev
- Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | - Samir C Debnath
- St. John's Research and Development Centre, Agriculture and Agri-Food Canada, St. John's, Newfoundland and Labrador, Canada.
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Partial maintenance of organ-specific epigenetic marks during plant asexual reproduction leads to heritable phenotypic variation. Proc Natl Acad Sci U S A 2018; 115:E9145-E9152. [PMID: 30201727 PMCID: PMC6166847 DOI: 10.1073/pnas.1805371115] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
While clonally propagated individuals should share identical genomes, there is often substantial phenotypic variation among them. Both genetic and epigenetic modifications induced during regeneration have been associated with this phenomenon. Here we investigated the fate of the epigenome after asexual propagation by generating clonal individuals from differentiated somatic cells through the manipulation of a zygotic transcription factor. We found that phenotypic novelty in clonal progeny was linked to epigenetic imprints that reflect the organ used for regeneration. Some of these organ-specific imprints can be maintained during the cloning process and subsequent rounds of meiosis. Our findings are fundamental for understanding the significance of epigenetic variability arising from asexual reproduction and have significant implications for future biotechnological applications. Plants differ from animals in their capability to easily regenerate fertile adult individuals from terminally differentiated cells. This unique developmental plasticity is commonly observed in nature, where many species can reproduce asexually through the ectopic initiation of organogenic or embryogenic developmental programs. While organ-specific epigenetic marks are not passed on during sexual reproduction, the fate of epigenetic marks during asexual reproduction and the implications for clonal progeny remain unclear. Here we report that organ-specific epigenetic imprints in Arabidopsis thaliana can be partially maintained during asexual propagation from somatic cells in which a zygotic program is artificially induced. The altered marks are inherited even over multiple rounds of sexual reproduction, becoming fixed in hybrids and resulting in heritable molecular and physiological phenotypes that depend on the identity of the founder tissue. Consequently, clonal plants display distinct interactions with beneficial and pathogenic microorganisms. Our results demonstrate how novel phenotypic variation in plants can be unlocked through altered inheritance of epigenetic marks upon asexual propagation.
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Seed-Specific Gene MOTHER of FT and TFL1(MFT) Involved in Embryogenesis, Hormones and Stress Responses in Dimocarpus longan Lour. Int J Mol Sci 2018; 19:ijms19082403. [PMID: 30110985 PMCID: PMC6122071 DOI: 10.3390/ijms19082403] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 08/09/2018] [Accepted: 08/10/2018] [Indexed: 11/30/2022] Open
Abstract
Mother of FT and TFL1 (MFT) belongs to phosphatidylethanolamine-binding protein (PEBP) family, which plays an important role in flowering time regulation, seed development, and germination. To gain insight into the molecular function of DlMFT in Dimocarpus longan Lour., we isolated DlMFT and its promoter sequence from longan embryogenic callus (EC). Bioinformatic analysis indicated that the promoter contained multiphytohormones and light responsive regulatory elements. Subcellular localization showed that the given the DlMFT signal localized in the nucleus, expression profiling implied that DlMFT showed significant upregulation during somatic embryogenesis (SE) and zygotic embryogenesis (ZE), and particular highly expressed in late or maturation stages. The accumulation of DlMFT was mainly detected in mature fruit and seed, while it was undetected in abortive seeds, and notably decreased during seed germination. DlMFT responded differentially to exogenous hormones in longan EC. Auxins, salicylic acid (SA) and methyl jasmonate (MeJa) suppressed its expression, however, abscisic acid (ABA), brassinosteroids (BR) showed the opposite function. Meanwhile, DlMFT differentially responded to various abiotic stresses. Our study revealed that DlMFT might be a key regulator of longan somatic and zygotic embryo development, and in seed germination, it is involved in complex plant hormones and abiotic stress signaling pathways.
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Parrilla J, Gaillard C, Verbeke J, Maucourt M, Aleksandrov RA, Thibault F, Fleurat-Lessard P, Gibon Y, Rolin D, Atanassova R. Comparative metabolomics and glycolysis enzyme profiling of embryogenic and nonembryogenic grape cells. FEBS Open Bio 2018; 8:784-798. [PMID: 29744293 PMCID: PMC5929931 DOI: 10.1002/2211-5463.12415] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 03/06/2018] [Accepted: 03/07/2018] [Indexed: 11/06/2022] Open
Abstract
A novel biological model was created for the comparison of grapevine embryogenic cells (EC) and nonembryogenic cells (NEC) sharing a common genetic background but distinct phenotypes, when cultured on their respective most appropriate media. Cytological characterization, 1H-NMR analysis of intracellular metabolites, and glycolytic enzyme activities provided evidence for the marked metabolic differences between EC and NEC. The EC were characterized by a moderate and organized cell proliferation, coupled with a low flux through glycolysis, high capacity of phosphoenolpyruvate carboxylase and glucokinase, and high oxygen consumption. The NEC displayed strong anarchic growth, and their high rate of glycolysis due to the low energetic efficiency of the fermentative metabolism is confirmed by increased enolase capacity and low oxygen consumption.
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Affiliation(s)
- Jonathan Parrilla
- Laboratoire EBI- Ecologie et Biologie des Interactions Équipe SEVE-Sucres et Échanges Végétaux-Environnement UMR 7267 Centre National de la Recherche Scientifique Université de Poitiers France
| | - Cécile Gaillard
- Laboratoire EBI- Ecologie et Biologie des Interactions Équipe SEVE-Sucres et Échanges Végétaux-Environnement UMR 7267 Centre National de la Recherche Scientifique Université de Poitiers France
| | - Jérémy Verbeke
- Laboratoire EBI- Ecologie et Biologie des Interactions Équipe SEVE-Sucres et Échanges Végétaux-Environnement UMR 7267 Centre National de la Recherche Scientifique Université de Poitiers France.,GReD. UMR CNRS 6293 - INSERM U1103 Université Clermont-Auvergne CRBC Faculté de médecine Clermont-Ferrand France
| | - Mickaël Maucourt
- Laboratoire Biologie du Fruit et Pathologie UMR 1332 Institut National de la Recherche Agronomique Université de Bordeaux Villenave d'Ornon France.,Plateforme Métabolome du Centre de Génomique Fonctionnelle Bordeaux MetaboHUB Institut National de la Recherche Agronomique Villenave d'Ornon France
| | - Radoslav A Aleksandrov
- Laboratoire EBI- Ecologie et Biologie des Interactions Équipe SEVE-Sucres et Échanges Végétaux-Environnement UMR 7267 Centre National de la Recherche Scientifique Université de Poitiers France.,Institute of Molecular Biology Bulgarian Academy of Sciences Acad Sofia Bulgaria
| | - Florence Thibault
- Laboratoire EBI- Ecologie et Biologie des Interactions Équipe SEVE-Sucres et Échanges Végétaux-Environnement UMR 7267 Centre National de la Recherche Scientifique Université de Poitiers France
| | - Pierrette Fleurat-Lessard
- Laboratoire EBI- Ecologie et Biologie des Interactions Équipe SEVE-Sucres et Échanges Végétaux-Environnement UMR 7267 Centre National de la Recherche Scientifique Université de Poitiers France
| | - Yves Gibon
- Laboratoire Biologie du Fruit et Pathologie UMR 1332 Institut National de la Recherche Agronomique Université de Bordeaux Villenave d'Ornon France.,Plateforme Métabolome du Centre de Génomique Fonctionnelle Bordeaux MetaboHUB Institut National de la Recherche Agronomique Villenave d'Ornon France
| | - Dominique Rolin
- Laboratoire Biologie du Fruit et Pathologie UMR 1332 Institut National de la Recherche Agronomique Université de Bordeaux Villenave d'Ornon France.,Plateforme Métabolome du Centre de Génomique Fonctionnelle Bordeaux MetaboHUB Institut National de la Recherche Agronomique Villenave d'Ornon France
| | - Rossitza Atanassova
- Laboratoire EBI- Ecologie et Biologie des Interactions Équipe SEVE-Sucres et Échanges Végétaux-Environnement UMR 7267 Centre National de la Recherche Scientifique Université de Poitiers France
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Xiao Y, Chen Y, Ding Y, Wu J, Wang P, Yu Y, Wei X, Wang Y, Zhang C, Li F, Ge X. Effects of GhWUS from upland cotton (Gossypium hirsutum L.) on somatic embryogenesis and shoot regeneration. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 270:157-165. [PMID: 29576069 DOI: 10.1016/j.plantsci.2018.02.018] [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: 11/29/2017] [Revised: 01/15/2018] [Accepted: 02/18/2018] [Indexed: 05/28/2023]
Abstract
The WUSCHEL (WUS) gene encodes a plant-specific homeodomain-containing transcriptional regulator, which plays important roles during embryogenesis, as well as in the formation of shoot and flower meristems. Here, we isolated two homologues of Arabidopsis thaliana WUS (AtWUS), GhWUS1a_At and GhWUS1b_At, from upland cotton (Gossypium hirsutum). Domain analysis suggested that the two putative GhWUS proteins contained a highly conserved DNA-binding HOX domain and a WUS-box. Expression profile analysis showed that GhWUSs were predominantly expressed during the embryoid stage. Ectopic expression of GhWUSs in Arabidopsis could induce somatic embryo and shoot formation from seedling root tips. Furthermore, in the absence of exogenous hormone, overexpression of GhWUSs in Arabidopsis could promote shoot regeneration from excised roots, and in the presence of exogenous auxin, excised roots expressing GhWUS could be induced to produce somatic embryo. In addition, expression of the chimeric GhWUS repressor in cotton callus inhibited embryogenic callus formation. Our results show that GhWUS is an important regulator of somatic embryogenesis and shoot regeneration.
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Affiliation(s)
- Yanqing Xiao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000 Henan, China
| | - Yanli Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000 Henan, China
| | - Yanpeng Ding
- Hebei Agricultural University, Baoding, 071001 Hebei, China
| | - Jie Wu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000 Henan, China
| | - Peng Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000 Henan, China
| | - Ya Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000 Henan, China
| | - Xi Wei
- Shenyang Agricultural University, Shenyang 110866, China
| | - Ye Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000 Henan, China
| | - Chaojun Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000 Henan, China
| | - Fuguang Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000 Henan, China.
| | - Xiaoyang Ge
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000 Henan, China.
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Mamedes-Rodrigues TC, Batista DS, Vieira NM, Matos EM, Fernandes D, Nunes-Nesi A, Cruz CD, Viccini LF, Nogueira FTS, Otoni WC. Regenerative potential, metabolic profile, and genetic stability of Brachypodium distachyon embryogenic calli as affected by successive subcultures. PROTOPLASMA 2018; 255:655-667. [PMID: 29080994 DOI: 10.1007/s00709-017-1177-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Accepted: 10/17/2017] [Indexed: 06/07/2023]
Abstract
Brachypodium distachyon, a model species for forage grasses and cereal crops, has been used in studies seeking improved biomass production and increased crop yield for biofuel production purposes. Somatic embryogenesis (SE) is the morphogenetic pathway that supports in vitro regeneration of such species. However, there are gaps in terms of studies on the metabolic profile and genetic stability along successive subcultures. The physiological variables and the metabolic profile of embryogenic callus (EC) and embryogenic structures (ES) from successive subcultures (30, 60, 90, 120, 150, 180, 210, 240, and 360-day-old subcultures) were analyzed. Canonical discriminant analysis separated EC into three groups: 60, 90, and 120 to 240 days. EC with 60 and 90 days showed the highest regenerative potential. EC grown for 90 days and submitted to SE induction in 2 mg L-1 of kinetin-supplemented medium was the highest ES producer. The metabolite profiles of non-embryogenic callus (NEC), EC, and ES submitted to principal component analysis (PCA) separated into two groups: 30 to 240- and 360-day-old calli. The most abundant metabolites for these groups were malonic acid, tryptophan, asparagine, and erythrose. PCA of ES also separated ages into groups and ranked 60- and 90-day-old calli as the best for use due to their high levels of various metabolites. The key metabolites that distinguished the ES groups were galactinol, oxaloacetate, tryptophan, and valine. In addition, significant secondary metabolites (e.g., caffeoylquinic, cinnamic, and ferulic acids) were important in the EC phase. Ferulic, cinnamic, and phenylacetic acids marked the decreases in the regenerative capacity of ES in B. distachyon. Decreased accumulations of the amino acids aspartic acid, asparagine, tryptophan, and glycine characterized NEC, suggesting that these metabolites are indispensable for the embryogenic competence in B. distachyon. The genetic stability of the regenerated plants was evaluated by flow cytometry, showing that ploidy instability in regenerated plants from B. distachyon calli is not correlated with callus age. Taken together, our data indicated that the loss of regenerative capacity in B. distachyon EC occurs after 120 days of subcultures, demonstrating that the use of EC can be extended to 90 days.
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Affiliation(s)
- T C Mamedes-Rodrigues
- Laboratório de Cultura de Tecidos/BIOAGRO, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Campus Universitário, Avenida Peter Henry Rolfs s/n, Viçosa, MG, 36570-900, Brazil
| | - D S Batista
- Laboratório de Cultura de Tecidos/BIOAGRO, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Campus Universitário, Avenida Peter Henry Rolfs s/n, Viçosa, MG, 36570-900, Brazil
| | - N M Vieira
- Departamento de Microbiologia/Núcleo de Análises de Biomoléculas-NUBIOMOL, Universidade Federal de Viçosa, Av. P.H. Rolfs, s/n, Viçosa, MG, 36570-900, Brazil
| | - E M Matos
- Laboratório de Cultura de Tecidos/BIOAGRO, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Campus Universitário, Avenida Peter Henry Rolfs s/n, Viçosa, MG, 36570-900, Brazil
| | - D Fernandes
- Laboratório de Cultura de Tecidos/BIOAGRO, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Campus Universitário, Avenida Peter Henry Rolfs s/n, Viçosa, MG, 36570-900, Brazil
| | - A Nunes-Nesi
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Av. P.H. Rolfs, s/n, Viçosa, MG, 36570-900, Brazil
| | - C D Cruz
- Laboratório de Bioinformática/BIOAGRO, Departamento de Biologia Geral, Universidade Federal de Viçosa, Av. P.H. Rolfs, s/n, Viçosa, MG, 35670-900, Brazil
| | - L F Viccini
- Laboratório de Genética e Biotecnologia, Departamento de Ciências Biológicas, Universidade Federal de Juiz de Fora, Rua José Lourenço Kelmer, s/n, Martelos, Juiz de Fora, MG, 36036-330, Brazil
| | - F T S Nogueira
- Laboratório de Genética Molecular do Desenvolvimento Vegetal (LGMDV), Universidade de São Paulo / ESALQ, Av. Pádua Dias, Piracicaba, SP, 13418-900, Brazil
| | - W C Otoni
- Laboratório de Cultura de Tecidos/BIOAGRO, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Campus Universitário, Avenida Peter Henry Rolfs s/n, Viçosa, MG, 36570-900, Brazil.
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Zhu HG, Cheng WH, Tian WG, Li YJ, Liu F, Xue F, Zhu QH, Sun YQ, Sun J. iTRAQ-based comparative proteomic analysis provides insights into somatic embryogenesis in Gossypium hirsutum L. PLANT MOLECULAR BIOLOGY 2018; 96:89-102. [PMID: 29214424 PMCID: PMC5778175 DOI: 10.1007/s11103-017-0681-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 11/08/2017] [Indexed: 05/22/2023]
Abstract
KEY MESSAGE: iTRAQ based proteomic identified key proteins and provided new insights into the molecular mechanisms underlying somatic embryogenesis in cotton. Somatic embryogenesis, which involves cell dedifferentiation and redifferentiation, has been used as a model system for understanding molecular events of plant embryo development in vitro. In this study, we performed comparative proteomics analysis using samples of non-embryogenic callus (NEC), embryogenic callus (EC) and somatic embryo (SE) using the isobaric tags for relative and absolute quantitation (iTRAQ) technology. In total, 5892 proteins were identified amongst the three samples. The majority of these proteins (93.4%) were found to have catalytic activity, binding activity, transporter activity or structural molecular activity. Of these proteins, 1024 and 858 were differentially expressed in NEC versus EC and EC versus SE, respectively. Compared to NEC, EC had 452 and 572 down- and up-regulated proteins, respectively, and compared to EC, SE had 647 and 221 down- and up-regulated proteins, respectively. KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis indicated that genetic information transmission, plant hormone transduction, glycolysis, fatty acid biosynthesis and metabolism, galactose metabolism were the top pathways involved in somatic embryogenesis. Our proteomics results not only confirmed our previous transcriptomic results on the role of the polyamine metabolic pathways and stress responses in cotton somatic embryogenesis, but identified key proteins important for cotton somatic embryogenesis and provided new insights into the molecular mechanisms underlying somatic embryogenesis in cotton.
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Affiliation(s)
- Hua-Guo Zhu
- College of Agriculture/The Key Laboratory of Oasis Eco-Agriculture, Shihezi University, Shihezi, 832000 Xinjiang China
| | - Wen-Han Cheng
- College of Agriculture/The Key Laboratory of Oasis Eco-Agriculture, Shihezi University, Shihezi, 832000 Xinjiang China
- Jingchu University of Technology, Jingmen, 448000 Hubei China
| | - Wen-Gang Tian
- College of Agriculture/The Key Laboratory of Oasis Eco-Agriculture, Shihezi University, Shihezi, 832000 Xinjiang China
| | - Yang-Jun Li
- College of Agriculture/The Key Laboratory of Oasis Eco-Agriculture, Shihezi University, Shihezi, 832000 Xinjiang China
| | - Feng Liu
- College of Agriculture/The Key Laboratory of Oasis Eco-Agriculture, Shihezi University, Shihezi, 832000 Xinjiang China
| | - Fei Xue
- College of Agriculture/The Key Laboratory of Oasis Eco-Agriculture, Shihezi University, Shihezi, 832000 Xinjiang China
| | - Qian-Hao Zhu
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT 2601 Australia
| | - Yu-Qiang Sun
- College of Agriculture/The Key Laboratory of Oasis Eco-Agriculture, Shihezi University, Shihezi, 832000 Xinjiang China
- College of Life Sciences, Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou, 310018 Zhejiang China
| | - Jie Sun
- College of Agriculture/The Key Laboratory of Oasis Eco-Agriculture, Shihezi University, Shihezi, 832000 Xinjiang China
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Wójcik AM, Mosiolek M, Karcz J, Nodine MD, Gaj MD. Whole Mount in situ Localization of miRNAs and mRNAs During Somatic Embryogenesis in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2018; 9:1277. [PMID: 30233621 PMCID: PMC6131960 DOI: 10.3389/fpls.2018.01277] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 08/15/2018] [Indexed: 05/11/2023]
Abstract
Somatic embryogenesis (SE) results from the transition of differentiated plant somatic cells into embryogenic cells that requires the extensive reprogramming of the somatic cell transcriptome. Commonly, the SE-involved genes are identified by analyzing the heterogeneous population of explant cells and thus, it is necessary to validate the expression of the candidate genes in the cells that are competent for embryogenic transition. Here, we optimized and implemented the whole mount in situ hybridization (WISH) method (Bleckmann and Dresselhaus, 2016; Dastidar et al., 2016) in order to analyze the spatiotemporal localization of miRNAs (miR156, miR166, miR390, miR167) and mRNAs such as WOX5 and PHABULOSA-target of miR165/166 during the SE that is induced in Arabidopsis explants. This study presents a detailed step-by-step description of the WISH procedure in which DIG-labeled LNA and RNA probes were used to detect miRNAs and mRNAs, respectively. The usefulness of the WISH in the functional analysis of the SE-involved regulatory pathways is demonstrated and the advantages of this method are highlighted: (i) the ability to analyze intact non-sectioned plant tissue; (ii) the specificity of transcript detection; (iii) the detection of miRNA; and (iv) a semi-quantitative assessment of the RNA abundance.
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Affiliation(s)
- Anna M. Wójcik
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Magdalena Mosiolek
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria
| | - Jagna Karcz
- Scanning Electron Microscopy Laboratory, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Michael D. Nodine
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria
| | - Małgorzata D. Gaj
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
- *Correspondence: Małgorzata D. Gaj,
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Lowe K, La Rota M, Hoerster G, Hastings C, Wang N, Chamberlin M, Wu E, Jones T, Gordon-Kamm W. Rapid genotype "independent" Zea mays L. (maize) transformation via direct somatic embryogenesis. IN VITRO CELLULAR & DEVELOPMENTAL BIOLOGY. PLANT : JOURNAL OF THE TISSUE CULTURE ASSOCIATION 2018; 54:240-252. [PMID: 29780216 PMCID: PMC5954046 DOI: 10.1007/s11627-018-9905-2] [Citation(s) in RCA: 144] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 03/26/2018] [Indexed: 05/18/2023]
Abstract
Constitutive expression of the Zea mays L. (maize) morphogenic transcription factors Baby Boom (Bbm) and Wuschel2 (Wus2) in maize can not only greatly increase transformation efficiency but can also induce phenotypic abnormalities and sterility. In an effort to alleviate the pleiotropic effects of constitutive expression, a genome wide search was undertaken to find suitable maize promoters to drive tissue and timing-specific expression of the transformation enhancing genes Bbm and Wus2. A promoter from a maize phospholipid transferase protein gene (Zm-PLTPpro ) was identified based on its expression in leaves, embryos, and callus while being downregulated in roots, meristems, and reproductive tissues. When Zm-PLTPpro driving Bbm was transformed into immature maize embryos along with a Wus2 expression cassette driven by the nopaline synthase promoter (Nospro ::Wus2) abundant somatic embryos rapidly formed on the scutella. These embryos were individual and uniformly transformed and could be directly germinated into plants without a callus phase. Transformed plants could be sent to the greenhouse in as little as 1 mo and regenerated plants matched the seed-derived phenotype for the inbred and were fertile. However, T1 seed from these plants had poor germination. Replacing Nospro with a maize auxin-inducible promoter (Zm-Axig1pro ) in combination with Zm-PLTPpro ::Bbm, allowed healthy, fertile plants to be regenerated. Single-copy T1 seed germinated normally and had a predominantly wild-type inbred phenotype. For maize, this callus-free transformation process has worked in all inbred lines tested.
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Affiliation(s)
| | | | | | | | | | | | - Emily Wu
- DuPont Pioneer, Johnston, IA USA
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Chu Z, Chen J, Sun J, Dong Z, Yang X, Wang Y, Xu H, Zhang X, Chen F, Cui D. De novo assembly and comparative analysis of the transcriptome of embryogenic callus formation in bread wheat (Triticum aestivum L.). BMC PLANT BIOLOGY 2017; 17:244. [PMID: 29258440 PMCID: PMC5735865 DOI: 10.1186/s12870-017-1204-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 12/06/2017] [Indexed: 05/26/2023]
Abstract
BACKGROUND During asexual reproduction the embryogenic callus can differentiate into a new plantlet, offering great potential for fostering in vitro culture efficiency in plants. The immature embryos (IMEs) of wheat (Triticum aestivum L.) are more easily able to generate embryogenic callus than mature embryos (MEs). To understand the molecular process of embryogenic callus formation in wheat, de novo transcriptome sequencing was used to generate transcriptome sequences from calli derived from IMEs and MEs after 3d, 6d, or 15d of culture (DC). RESULTS In total, 155 million high quality paired-end reads were obtained from the 6 cDNA libraries. Our de novo assembly generated 142,221 unigenes, of which 59,976 (42.17%) were annotated with a significant Blastx against nr, Pfam, Swissprot, KOG, KEGG, GO and COG/KOG databases. Comparative transcriptome analysis indicated that a total of 5194 differentially expressed genes (DEGs) were identified in the comparisons of IME vs. ME at the three stages, including 3181, 2085 and 1468 DEGs at 3, 6 and 15 DC, respectively. Of them, 283 overlapped in all the three comparisons. Furthermore, 4731 DEGs were identified in the comparisons between stages in IMEs and MEs. Functional analysis revealed that 271transcription factor (TF) genes (10 overlapped in all 3 comparisons of IME vs. ME) and 346 somatic embryogenesis related genes (SSEGs; 35 overlapped in all 3 comparisons of IME vs. ME) were differentially expressed in at least one comparison of IME vs. ME. In addition, of the 283 overlapped DEGs in the 3 comparisons of IME vs. ME, excluding the SSEGs and TFs, 39 possessed a higher rate of involvement in biological processes relating to response to stimuli, in multi-organism processes, reproductive processes and reproduction. Furthermore, 7 were simultaneously differentially expressed in the 2 comparisons between the stages in IMEs, but not MEs, suggesting that they may be related to embryogenic callus formation. The expression levels of genes, which were validated by qRT-PCR, showed a high correlation with the RNA-seq value. CONCLUSIONS This study provides new insights into the role of the transcriptome in embryogenic callus formation in wheat, and will serve as a valuable resource for further studies addressing embryogenic callus formation in plants.
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Affiliation(s)
- Zongli Chu
- Agronomy College/Collaborative Innovation Center of Henan Grain Crops/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 15 Longzihu College District, Zhengzhou, 450046 People’s Republic of China
- Xinyang Agriculture and Forestry University, Xinyang, 464000 China
| | - Junying Chen
- Agronomy College/Collaborative Innovation Center of Henan Grain Crops/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 15 Longzihu College District, Zhengzhou, 450046 People’s Republic of China
| | - Junyan Sun
- Xinyang Agriculture and Forestry University, Xinyang, 464000 China
| | - Zhongdong Dong
- Agronomy College/Collaborative Innovation Center of Henan Grain Crops/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 15 Longzihu College District, Zhengzhou, 450046 People’s Republic of China
| | - Xia Yang
- Agronomy College/Collaborative Innovation Center of Henan Grain Crops/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 15 Longzihu College District, Zhengzhou, 450046 People’s Republic of China
| | - Ying Wang
- Agronomy College/Collaborative Innovation Center of Henan Grain Crops/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 15 Longzihu College District, Zhengzhou, 450046 People’s Republic of China
| | - Haixia Xu
- Agronomy College/Collaborative Innovation Center of Henan Grain Crops/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 15 Longzihu College District, Zhengzhou, 450046 People’s Republic of China
| | - Xiaoke Zhang
- Agronomy College, North West Agriculture and Forestry University, Yangling, 712100 China
| | - Feng Chen
- Agronomy College/Collaborative Innovation Center of Henan Grain Crops/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 15 Longzihu College District, Zhengzhou, 450046 People’s Republic of China
| | - Dangqun Cui
- Agronomy College/Collaborative Innovation Center of Henan Grain Crops/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 15 Longzihu College District, Zhengzhou, 450046 People’s Republic of China
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Chemical Compositions, Somatic Embryogenesis, and Somaclonal Variation in Cumin. BIOMED RESEARCH INTERNATIONAL 2017; 2017:7283806. [PMID: 29234682 PMCID: PMC5694991 DOI: 10.1155/2017/7283806] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 08/16/2017] [Accepted: 10/09/2017] [Indexed: 11/18/2022]
Abstract
This is the first report evaluating the relationship between the chemical compositions of cumin seeds (based on the analysis of the content of catalase, ascorbate peroxidase, proline, protein, terpenic compounds, alcohol/phenols, aldehydes, and epoxides) and the induction efficiency of somatic embryogenesis in two Iranian superior cumin landraces (Golestan and North Khorasan). Cotyledons isolated from Golestan landrace seeds cultivated on MS medium supplemented with 0.1 mg/L kinetin proved to be the best primary explant for the induction of somatic embryogenesis as well as the regeneration of the whole plantlet. Results indicated that different developmental stages of somatic embryos were simultaneously observed on a callus with embryogenic potential. The high content of catalase, ascorbate peroxidase, proline, and terpenic hydrocarbons and low content of alcoholic and phenolic compositions had a stimulatory effect on somatic embryogenesis. Band patterns of RAPD markers in regenerated plants were different from those of the mother plants. This may be related to somaclonal variations or pollination system of cumin. Generally, measurement of chemical compositions can be used as a marker for evaluating the occurrence of somatic embryogenesis in cumin. Also, somaclonal variations of regenerated plants can be applied by the plant breeders in breeding programs.
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Oliveira EJ, Koehler AD, Rocha DI, Vieira LM, Pinheiro MVM, de Matos EM, da Cruz ACF, da Silva TCR, Tanaka FAO, Nogueira FTS, Otoni WC. Morpho-histological, histochemical, and molecular evidences related to cellular reprogramming during somatic embryogenesis of the model grass Brachypodium distachyon. PROTOPLASMA 2017; 254:2017-2034. [PMID: 28290060 DOI: 10.1007/s00709-017-1089-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Accepted: 02/13/2017] [Indexed: 05/25/2023]
Abstract
The wild grass species Brachypodium distachyon (L.) has been proposed as a new model for temperate grasses. Among the biotechnological tools already developed for the species, an efficient induction protocol of somatic embryogenesis (SE) using immature zygotic embryos has provided the basis for genetic transformation studies. However, a systematic work to better understanding the basic cellular and molecular mechanisms that underlie the SE process of this grass species is still missing. Here, we present new insights at the morpho-histological, histochemical, and molecular aspects of B. distachyon SE pathway. Somatic embryos arose from embryogenic callus formed by cells derived from the protodermal-dividing cells of the scutellum. These protodermal cells showed typical meristematic features and high protein accumulation which were interpreted as the first observable steps towards the acquisition of a competent state. Starch content decreased along embryogenic callus differentiation supporting the idea that carbohydrate reserves are essential to morphogenetic processes. Interestingly, starch accumulation was also observed at late stages of SE process. Searches in databanks revealed three sequences available annotated as BdSERK, being two copies corresponding to SERK1 and one showing greater identity to SERK2. In silico analysis confirmed the presence of characteristic domains in a B. distachyon Somatic Embryogenesis Receptor Kinase genes candidates (BdSERKs), which suggests SERK functions are conserved in B. distachyon. In situ hybridization demonstrated the presence of transcripts of BdSERK1 in all development since globular until scutellar stages. The results reported in this study convey important information about the morphogenetic events in the embryogenic pathway which has been lacking in B. distachyon. This study also demonstrates that B. distachyon provides a useful model system for investigating the genetic regulation of SE in grass species.
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Affiliation(s)
- Evelyn Jardim Oliveira
- Laboratório de Cultura de Tecidos/BIOAGRO, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Avenida P. H. Rolfs s/n, 36570-900, Viçosa, MG, Brazil
| | - Andréa Dias Koehler
- Laboratório de Cultura de Tecidos/BIOAGRO, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Avenida P. H. Rolfs s/n, 36570-900, Viçosa, MG, Brazil
| | - Diego Ismael Rocha
- Instituto de Biociências, Universidade Federal de Goiás, Regional Jataí, BR 364, km 195, 75801-615, Jataí, GO, Brazil
| | - Lorena Melo Vieira
- Laboratório de Cultura de Tecidos/BIOAGRO, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Avenida P. H. Rolfs s/n, 36570-900, Viçosa, MG, Brazil
| | - Marcos Vinícius Marques Pinheiro
- Laboratório de Cultura de Tecidos/BIOAGRO, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Avenida P. H. Rolfs s/n, 36570-900, Viçosa, MG, Brazil
| | - Elyabe Monteiro de Matos
- Laboratório de Cultura de Tecidos/BIOAGRO, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Avenida P. H. Rolfs s/n, 36570-900, Viçosa, MG, Brazil
| | - Ana Claudia Ferreira da Cruz
- Laboratório de Cultura de Tecidos/BIOAGRO, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Avenida P. H. Rolfs s/n, 36570-900, Viçosa, MG, Brazil
| | - Thais Cristina Ribeiro da Silva
- Laboratório de Cultura de Tecidos/BIOAGRO, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Avenida P. H. Rolfs s/n, 36570-900, Viçosa, MG, Brazil
| | - Francisco André Ossamu Tanaka
- Departamento de Fitopatologia e Nematologia, Universidade de São Paulo/ESALQ, Av. Pádua Dias, 13418-900, Piracicaba, SP, Brazil
| | - Fabio Tebaldi Silveira Nogueira
- Laboratorio de Genética Molecular do Desenvolvimento Vegetal (LGMDV), Universidade de São Paulo/ESALQ, Av. Pádua Dias, 13418-900, Piracicaba, SP, Brazil.
| | - Wagner Campos Otoni
- Laboratório de Cultura de Tecidos/BIOAGRO, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Avenida P. H. Rolfs s/n, 36570-900, Viçosa, MG, Brazil.
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Tikhenko N, Rutten T, Senula A, Rubtsova M, Keller ERJ, Börner A. The changes in the reproductive barrier between hexaploid wheat (Triticum aestivum L.) and rye (Secale cereale L.): different states lead to different fates. PLANTA 2017; 246:377-388. [PMID: 28424873 DOI: 10.1007/s00425-017-2694-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 04/12/2017] [Indexed: 06/07/2023]
Abstract
The changes in the reproductive barrier between hexaploid wheat ( Triticum aestivum L.) and rye ( Secale cereale L.) can be induced using in situ embryo rescue of abnormal embryos, yielding stable fertile amphidiploid plants. In intergeneric crosses between hexaploid wheat (Triticum aestivum L.) and rye (Secale cereale L.), postzygotic barriers may occur at different stages of hybrid development. One such mechanism is embryo lethality, which is genetically determined by the interaction and expression of two incompatible genes in wheat (Eml-A1) and rye (Eml-R1). Using in vitro culture methods as stressors, we overcame this hybrid lethality. Normal and abnormal embryos were observed to build embryogenic calli and produce regenerated plantlets in a similar manner. The high regenerative capacity of the abnormal embryos led us to conclude that the reproductive barrier in these intergeneric hybrids may have an epigenetic origin that can be easily overcome by culturing immature embryos via callus induction. After colchicine treatment during callus culture, amphidiploid plants were obtained. However, most of these plants did not produce seeds, due mainly to sterility of the pollen but also of the embryo sacs. These findings demonstrate that hybrid sterility affects both male and female gametophytes in plants obtained from abnormal embryos. The key roles of double fertilization and stress factors in the implementation of the apical meristem formation program in embryos from incompatible intergeneric crosses between hexaploid wheat and rye during in vitro culture are discussed. We also propose a hypothetical model for a wheat-rye lethality system involving differential expression of incompatible wheat Eml-A1 and rye Eml-R1b alleles in an identical genetic background.
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Affiliation(s)
- Natalia Tikhenko
- SPb Branch Vavilov Institute of General Genetics, RAS, 199034, St. Petersburg, Russia
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, 06466, Stadt Seeland OT Gatersleben, Germany
| | - Twan Rutten
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, 06466, Stadt Seeland OT Gatersleben, Germany
| | - Angelika Senula
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, 06466, Stadt Seeland OT Gatersleben, Germany
| | - Myroslava Rubtsova
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, 06466, Stadt Seeland OT Gatersleben, Germany
| | - E R Joachim Keller
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, 06466, Stadt Seeland OT Gatersleben, Germany
| | - Andreas Börner
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, 06466, Stadt Seeland OT Gatersleben, Germany.
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Somatic embryogenesis in guava (Psidium guajava L.): current status and future perspectives. 3 Biotech 2017; 7:203. [PMID: 28667644 DOI: 10.1007/s13205-017-0844-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 05/17/2017] [Indexed: 10/19/2022] Open
Abstract
Guava (Psidium guajava L.) is a highly perishable fruit crop comparable to mango owing to its high medicinal value and intense aroma. The presence of high genetic variability limits the chances of further expansion of guava improvement using biotechnological interventions. Conventional methods of guava improvement encountered with restricted achievement in progress of disease resistant varieties because of existing high genetic variability in the germplasm. There is a considerable demand for the establishment of successful and efficient regeneration protocols via somatic embryogenesis. Plants regenerated through somatic embryogenesis could be more useful than plants obtained through organogenesis because, in most cases, somatic embryos are of single-cell origin, and have a low frequency of chimeras and a high number of regenerations. This review is a snapshot of the recent status of somatic embryogenesis as a basis for expanding genetic improvement in guava for quality traits and future perspectives using advanced technologies.
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