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Patriota MSS, Bernd RB, de Souza ALX, de Melo LAMP, Scherwinski-Pereira JE. Quantification of DNA Methylation by ELISA in Epigenetic Studies in Plant Tissue Culture: A Theoretical-Practical Guide. Methods Mol Biol 2024; 2827:323-350. [PMID: 38985280 DOI: 10.1007/978-1-0716-3954-2_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
Abstract
This chapter describes a step-by-step protocol for rapid serological quantification of global DNA methylation by enzyme-linked immunosorbent assay (ELISA) in plant tissue culture specimens. As a case study model, we used the coconut palm (Cocos nucifera), from which plumules were subjected to somatic embryogenesis followed by embryogenic calli multiplication. DNA methylation is one of the most common epigenetic markers in the regulation of gene expression. DNA methylation is generally associated with non-expressed genes, that is, gene silencing under certain conditions, and the degree of DNA methylation can be used as a marker of various physiological processes, both in plants and in animal cells. Methylation consists of adding a methyl radical to carbon 5 of the DNA cytosine base. Herein, the global DNA methylation was quantified by ELISA with antibodies against methylated cytosines using a commercial kit (Zymo-Research™). The method allowed the detection of methylation in total DNA extracts from coconut palm embryogenic calli (arising from somatic embryogenesis) cultivated in liquid or solid media by using antibodies against methylated cytosines and enzymatic development with a colorimetric substrate. Control samples of commercially provided Escherichia coli bacterial DNA with previously known methylation percentages were included in the ELISA test to construct an experimental methylation standard curve. The logarithmic regression of this E. coli standard curve allowed methylation quantification in coconut palm samples. The present ELISA methodology, applied to coconut palm tissue culture specimens, is promising for use in other plant species and botanical families. This chapter is presented in a suitable format for use as a step-by-step laboratory procedure manual, with theoretical introduction information, which makes it easy to apply the protocol in samples of any biological nature to evaluate DNA global methylation associated with any physiological process.
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de Araújo Silva-Cardoso IM, Gomes ACMM, Scherwinski-Pereira JE. Cellular responses of oil palm genotypes during somatic embryogenesis involve participation of procambial cells, DNA demethylation, and auxin accumulation. PLANT CELL REPORTS 2022; 41:1875-1893. [PMID: 35776139 DOI: 10.1007/s00299-022-02898-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 06/15/2022] [Indexed: 06/15/2023]
Abstract
Cell markers of somatic embryogenesis initiation from leaf tissues in oil palm involve the participation of procambial cells, DNA demethylation, and auxin accumulation. Low callogenesis and genotype-dependent response have been mentioned in the development of somatic embryogenesis protocols of Elaeis oleifera × E. guineensis elite hybrids, which requires more detailed investigations of the process. Thus, the initial cellular responses of immature leaves of adult genotypes of this hybrid were investigated for the first time, emphasizing histological, epigenetic, and endogenous auxin changes. Leaf segments from two genotypes, one responsive to somatic embryogenesis (B351733) and another non-responsive (B352933), were inoculated in Murashige and Skoog medium with 450 µM of 4-amino-3, 5, 6-trichloropicolinic acid. For anatomical analysis, samples of both genotypes were collected at 0, 20, 90, and 105 days of cultivation. Samples of both genotypes were also taken at different cultivation periods to analyze DNA methylation status (% 5-mC-5 methylcytosine) via ELISA test. Immunolocalization assays were performed with anti-indole-3-acetic acid and anti-5-methyl-deoxycytosine antibodies from samples of hybrid B351733. We distinguished two groups of cells reactive to the induction of embryogenic callogenesis, parenchymatous sheath cells, and procambial cells; however, only the latter are directly involved with the formation of calluses. The data obtained indicate that the formation of calluses in hybrid B351733 is related to DNA hypomethylation, while the non-responsiveness of leaf explants in hybrid B352932 is related to DNA hypermethylation. The in situ immunolocalization enabled the identification of initial markers of the callogenic process, such as IAA accumulation and hypomethylation. Identifying these events brings the possibility of establishing strategies for efficient manipulation of somatic embryogenesis protocols in palm trees.
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Affiliation(s)
| | | | - Jonny Everson Scherwinski-Pereira
- Laboratório de Microscopia, Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil.
- Laboratório de Cultura de Tecidos e Genética Vegetal, Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil.
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Bull T, Michelmore R. Molecular Determinants of in vitro Plant Regeneration: Prospects for Enhanced Manipulation of Lettuce ( Lactuca sativa L.). FRONTIERS IN PLANT SCIENCE 2022; 13:888425. [PMID: 35615120 PMCID: PMC9125155 DOI: 10.3389/fpls.2022.888425] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 03/31/2022] [Indexed: 05/12/2023]
Abstract
In vitro plant regeneration involves dedifferentiation and molecular reprogramming of cells in order to regenerate whole organs. Plant regeneration can occur via two pathways, de novo organogenesis and somatic embryogenesis. Both pathways involve intricate molecular mechanisms and crosstalk between auxin and cytokinin signaling. Molecular determinants of both pathways have been studied in detail in model species, but little is known about the molecular mechanisms controlling de novo shoot organogenesis in lettuce. This review provides a synopsis of our current knowledge on molecular determinants of de novo organogenesis and somatic embryogenesis with an emphasis on the former as well as provides insights into applying this information for enhanced in vitro regeneration in non-model species such as lettuce (Lactuca sativa L.).
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Affiliation(s)
- Tawni Bull
- The Genome Center, University of California, Davis, Davis, CA, United States
- Graduate Group in Horticulture and Agronomy, University of California, Davis, Davis, CA, United States
| | - Richard Michelmore
- The Genome Center, University of California, Davis, Davis, CA, United States
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
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Yan J, Buer H, Wang YP, Zhula G, Bai YE. Transcriptomic Time-Series Analyses of Gene Expression Profile During Zygotic Embryo Development in Picea mongolica. Front Genet 2021; 12:738649. [PMID: 34659359 PMCID: PMC8513737 DOI: 10.3389/fgene.2021.738649] [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: 07/09/2021] [Accepted: 09/01/2021] [Indexed: 11/13/2022] Open
Abstract
Zygotic embryogenesis is a critical process during seed development in gymnosperms. However, knowledge on the genome-wide transcriptional activation that guides this process in conifers is limited, especially in Picea mongolica. This tree species is endemic to semiarid habitats of Inner Mongolia in China. To extend what is known about the molecular events underpinning its zygotic embryogenesis, comparative transcriptomic analyses of gene expression in zygotic embryos were performed by RNA sequencing in P. mongolica. Our results showed that most changes in transcript levels occurred in the early embryonic pattering determination and formation of mature embryos. Transcripts related to embryogenic competence, cell division pattern, hormones, and stress response genes were identified during embryogenesis. Auxin is essential for early embryo patterning and pre-cotyledon embryonic formation. However, ABA is a major regulator of embryo maturation. Moreover, we found that methylation-related gene expression is associated with activation of early-stage embryos, late embryogenesis abundant proteins, and storage/energy-related genes with late and mature embryos. Furthermore, network analysis revealed stage-specific and multistage gene expression clusters during embryogenesis. WOX, MYB, AP2, and HLH transcription factors seem more relevant to embryogenesis in different stages. Our results provide large-scale and comprehensive transcriptome data for embryo development in P. mongolica. These data will lay a foundation for the protection and utilization of P. mongolica resources.
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Affiliation(s)
- Jia Yan
- Institute of Forest Tree Genetic Breeding, Forestry College, Inner Mongolia Agricultural University, Hohhot, China.,Life Science of College, Inner Mongolia University, Hohhot, China
| | - Ha Buer
- Institute of Forest Tree Genetic Breeding, Forestry College, Inner Mongolia Agricultural University, Hohhot, China
| | - Ya Ping Wang
- Institute of Forest Tree Genetic Breeding, Forestry College, Inner Mongolia Agricultural University, Hohhot, China
| | - Gegen Zhula
- Institute of Forest Tree Genetic Breeding, Forestry College, Inner Mongolia Agricultural University, Hohhot, China
| | - Yu E Bai
- Institute of Forest Tree Genetic Breeding, Forestry College, Inner Mongolia Agricultural University, Hohhot, China
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Kalaipandian S, Mu Z, Kong EYY, Biddle J, Cave R, Bazrafshan A, Wijayabandara K, Beveridge FC, Nguyen Q, Adkins SW. Cloning Coconut via Somatic Embryogenesis: A Review of the Current Status and Future Prospects. PLANTS (BASEL, SWITZERLAND) 2021; 10:2050. [PMID: 34685859 PMCID: PMC8538321 DOI: 10.3390/plants10102050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 09/17/2021] [Accepted: 09/17/2021] [Indexed: 11/30/2022]
Abstract
Coconut [Cocos nucifera L.] is often called "the tree of life" because of its many uses in the food, beverage, medicinal, and cosmetic industries. Currently, more than 50% of the palms grown throughout the world are senile and need to be replanted immediately to ensure production levels meet the present and increasing demand for coconut products. Mass replanting will not be possible using traditional propagation methods from seed. Recent studies have indicated that in vitro cloning via somatic embryogenesis is the most promising alternative for the large-scale production of new coconut palms. This paper provides a review on the status and prospects for the application of somatic embryogenesis to mass clonal propagation of coconut.
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Affiliation(s)
- Sundaravelpandian Kalaipandian
- School of Agriculture and Food Sciences, The University of Queensland, Gatton, QLD 4343, Australia; (Z.M.); (E.Y.Y.K.); (J.B.); (R.C.); (A.B.); (K.W.); (F.C.B.); (S.W.A.)
| | - Zhihua Mu
- School of Agriculture and Food Sciences, The University of Queensland, Gatton, QLD 4343, Australia; (Z.M.); (E.Y.Y.K.); (J.B.); (R.C.); (A.B.); (K.W.); (F.C.B.); (S.W.A.)
| | - Eveline Yee Yan Kong
- School of Agriculture and Food Sciences, The University of Queensland, Gatton, QLD 4343, Australia; (Z.M.); (E.Y.Y.K.); (J.B.); (R.C.); (A.B.); (K.W.); (F.C.B.); (S.W.A.)
| | - Julianne Biddle
- School of Agriculture and Food Sciences, The University of Queensland, Gatton, QLD 4343, Australia; (Z.M.); (E.Y.Y.K.); (J.B.); (R.C.); (A.B.); (K.W.); (F.C.B.); (S.W.A.)
- Australian Centre for International Agricultural Research, Canberra, ACT 2617, Australia
| | - Robyn Cave
- School of Agriculture and Food Sciences, The University of Queensland, Gatton, QLD 4343, Australia; (Z.M.); (E.Y.Y.K.); (J.B.); (R.C.); (A.B.); (K.W.); (F.C.B.); (S.W.A.)
| | - Amirhossein Bazrafshan
- School of Agriculture and Food Sciences, The University of Queensland, Gatton, QLD 4343, Australia; (Z.M.); (E.Y.Y.K.); (J.B.); (R.C.); (A.B.); (K.W.); (F.C.B.); (S.W.A.)
| | - Kusinara Wijayabandara
- School of Agriculture and Food Sciences, The University of Queensland, Gatton, QLD 4343, Australia; (Z.M.); (E.Y.Y.K.); (J.B.); (R.C.); (A.B.); (K.W.); (F.C.B.); (S.W.A.)
| | - Fernanda Caro Beveridge
- School of Agriculture and Food Sciences, The University of Queensland, Gatton, QLD 4343, Australia; (Z.M.); (E.Y.Y.K.); (J.B.); (R.C.); (A.B.); (K.W.); (F.C.B.); (S.W.A.)
| | - Quang Nguyen
- Applied Biotechnology for Crop Development Research Unit, The International University, Ho Chi Minh City 700000, Vietnam;
| | - Steve W. Adkins
- School of Agriculture and Food Sciences, The University of Queensland, Gatton, QLD 4343, Australia; (Z.M.); (E.Y.Y.K.); (J.B.); (R.C.); (A.B.); (K.W.); (F.C.B.); (S.W.A.)
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