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Zang Y, Xie L, Su J, Luo Z, Jia X, Ma X. Advances in DNA methylation and demethylation in medicinal plants: a review. Mol Biol Rep 2023; 50:7783-7796. [PMID: 37480509 DOI: 10.1007/s11033-023-08618-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 06/21/2023] [Indexed: 07/24/2023]
Abstract
DNA methylation and demethylation are widely acknowledged epigenetic phenomena which can cause heritable and phenotypic changes in functional genes without changing the DNA sequence. They can thus affect phenotype formation in medicinal plants. However, a comprehensive review of the literature summarizing current research trends in this field is lacking. Thus, this review aims to provide an up-to-date summary of current methods for the detection of 5-mC DNA methylation, identification and analysis of DNA methyltransferases and demethyltransferases, and regulation of DNA methylation in medicinal plants. The data showed that polyploidy and environmental changes can affect DNA methylation levels in medicinal plants. Changes in DNA methylation can thus regulate plant morphogenesis, growth and development, and formation of secondary metabolites. Future research is required to explore the mechanisms by which DNA methylation regulates the accumulation of secondary metabolites in medicinal plants.
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Affiliation(s)
- Yimei Zang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
- Biomedicine College, Beijing City University, Beijing, 100094, China
| | - Lei Xie
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Jiaxian Su
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Zuliang Luo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Xunli Jia
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Xiaojun Ma
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China.
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Gang R, Komakech R, Chung Y, Okello D, Kim WJ, Moon BC, Yim NH, Kang Y. In vitro propagation of Codonopsis pilosula (Franch.) Nannf. using apical shoot segments and phytochemical assessments of the maternal and regenerated plants. BMC PLANT BIOLOGY 2023; 23:33. [PMID: 36642714 PMCID: PMC9841653 DOI: 10.1186/s12870-022-03950-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 11/17/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Codonopsis pilosula (Franch.) Nannf. is a medicinal plant traditionally used in China, Korea, and Japan to treat many diseases including poor gastrointestinal function, low immunity, gastric ulcers, and chronic gastritis. The increasing therapeutic and preventive use of C. pilosula has subsequently led to depletion of the natural populations of this species thus necessitating propagation of this important medicinal plant. Here, we developed an efficient and effective in vitro propagation protocol for C. pilosula using apical shoot segments. We tested various plant tissue culture media for the growth of C. pilosula and evaluated the effects of plant growth regulators on the shoot proliferation and rooting of regenerated C. pilosula plants. Furthermore, the tissues (roots and shoots) of maternal and in vitro-regenerated C. pilosula plants were subjected to Fourier-transform near-infrared (FT-NIR) spectrometry, Gas chromatography-mass spectrometry (GC-MS), and their total flavonoids, phenolics, and antioxidant capacity were determined and compared. RESULTS Full-strength Murashige and Skoog (MS) medium augmented with vitamins and benzylaminopurine (1.5 mg·L-1) regenerated the highest shoot number (12 ± 0.46) per explant. MS medium augmented with indole-3-acetic acid (1.0 mg·L-1) produced the highest root number (9 ± 0.89) and maximum root length (20.88 ± 1.48 mm) from regenerated C. pilosula shoots. The survival rate of in vitro-regenerated C. pilosula plants was 94.00% after acclimatization. The maternal and in vitro-regenerated C. pilosula plant tissues showed similar FT-NIR spectra, total phenolics, total flavonoids, phytochemical composition, and antioxidant activity. Randomly amplified polymorphic DNA (RAPD) test confirmed the genetic fidelity of regenerated C. pilosula plants. CONCLUSIONS The proposed in vitro propagation protocol may be useful for the rapid mass multiplication and production of high quality C. pilosula as well as for germplasm preservation to ensure sustainable supply amidst the ever-increasing demand.
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Affiliation(s)
- Roggers Gang
- Korean Convergence Medical Science Major, University of Science and Technology (UST), Daejeon, 34113, South Korea
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine (KIOM), 111 Geonjae-Ro, Naju-Si, South Korea
- National Agricultural Research Organization (NARO), National Semi-Arid Resources Research Institute (NaSARRI), Soroti, Uganda
| | - Richard Komakech
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine (KIOM), 111 Geonjae-Ro, Naju-Si, South Korea
- Natural Chemotherapeutics Research Institute (NCRI), Ministry of Health, Kampala, Uganda
| | - Yuseong Chung
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine (KIOM), 111 Geonjae-Ro, Naju-Si, South Korea
| | - Denis Okello
- Korean Convergence Medical Science Major, University of Science and Technology (UST), Daejeon, 34113, South Korea
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine (KIOM), 111 Geonjae-Ro, Naju-Si, South Korea
- Department of Biological Sciences, Kabale University, P.O Box 317, Kabale, Uganda
| | - Wook Jin Kim
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine (KIOM), 111 Geonjae-Ro, Naju-Si, South Korea
| | - Byeong Cheol Moon
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine (KIOM), 111 Geonjae-Ro, Naju-Si, South Korea
| | - Nam-Hui Yim
- Korean Medicine Application Center, Korea Institute of Oriental Medicine, 70 Cheomdan-Ro, Dong-Gu, Daegu, 41062, South Korea
| | - Youngmin Kang
- Korean Convergence Medical Science Major, University of Science and Technology (UST), Daejeon, 34113, South Korea.
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine (KIOM), 111 Geonjae-Ro, Naju-Si, South Korea.
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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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Asadi-Aghbolaghi M, Dedicova B, Ranade SS, Le KC, Sharifzadeh F, Omidi M, Egertsdotter U. Protocol development for somatic embryogenesis, SSR markers and genetic modification of Stipagrostis pennata (Trin.) De Winter. PLANT METHODS 2021; 17:70. [PMID: 34193231 PMCID: PMC8247082 DOI: 10.1186/s13007-021-00768-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 06/12/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Stipagrostis pennata (Trin.) De Winter is an important species for fixing sand in shifting and semi-fixed sandy lands, for grazing, and potentially as a source of lignocellulose fibres for pulp and paper industry. The seeds have low viability, which limits uses for revegetation. Somatic embryogenesis offers an alternative method for obtaining large numbers of plants from limited seed sources. RESULTS A protocol for plant regeneration from somatic embryos of S. pennata was developed. Somatic embryogenesis was induced on Murashige & Skoog (MS) medium supplemented with 3 mg·L-1 2,4-D subsequently shoots were induced on MS medium and supplemented with 5 mg·L-1 zeatin riboside. The highest shoots induction was obtained when embryogenic callus derived from mature embryos (96%) in combination with MS filter-sterilized medium was used from Khuzestan location. The genetic stability of regenerated plants was analysed using ten simple sequence repeats (SSR) markers from S. pennata which showed no somaclonal variation in regenerated plants from somatic embryos of S. pennata. The regenerated plants of S. pennata showed genetic stability without any somaclonal variation for the four pairs of primers that gave the expected amplicon sizes. This data seems very reliable as three of the PCR products belonged to the coding region of the genome. Furthermore, stable expression of GUS was obtained after Agrobacterium-mediated transformation using a super binary vector carried by a bacterial strain LBA4404. CONCLUSION To our knowledge, the current work is the first attempt to develop an in vitro protocol for somatic embryogenesis including the SSR marker analyses of regenerated plants, and Agrobacterium-mediated transformation of S. pennata that can be used for its large-scale production for commercial purposes.
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Affiliation(s)
- Masoumeh Asadi-Aghbolaghi
- Department of Agronomy and Plant Breeding, College of Agriculture and Natural Resources, University of Tehran, 14174, Karaj, Iran
| | - Beata Dedicova
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 90183, Umeå, Sweden.
| | - Sonali Sachi Ranade
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 90183, Umeå, Sweden
| | - Kim-Cuong Le
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 90183, Umeå, Sweden
| | - Farzad Sharifzadeh
- Department of Agronomy and Plant Breeding, College of Agriculture and Natural Resources, University of Tehran, 14174, Karaj, Iran
| | - Mansoor Omidi
- Department of Agronomy and Plant Breeding, College of Agriculture and Natural Resources, University of Tehran, 14174, Karaj, Iran
| | - Ulrika Egertsdotter
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 90183, Umeå, Sweden
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5
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Tissue culture-induced DNA methylation in crop plants: a review. Mol Biol Rep 2021; 48:823-841. [PMID: 33394224 DOI: 10.1007/s11033-020-06062-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 12/03/2020] [Indexed: 12/15/2022]
Abstract
Plant tissue culture techniques have been extensively employed in commercial micropropagation to provide year-round production. Tissue culture regenerants are not always genotypically and phenotypically similar. Due to the changes in the tissue culture microenvironment, plant cells are exposed to additional stress which induces genetic and epigenetic instabilities in the regenerants. These changes lead to tissue culture-induced variations (TCIV) which are also known as somaclonal variations to categorically specify the inducing environment. TCIV includes molecular and phenotypic changes persuaded in the in vitro culture due to continuous sub-culturing and tissue culture-derived stress. Epigenetic variations such as altered DNA methylation pattern are induced due to the above-mentioned factors. Reportedly, alteration in DNA methylation pattern is much more frequent in the plant genome during the tissue culture process. DNA methylation plays an important role in gene expression and regulation of plant development. Variants originated in tissue culture process due to heritable methylation changes, can contribute to intra-species phenotypic variation. Several molecular techniques are available to detect DNA methylation at different stages of in vitro culture. Here, we review the aspects of TCIV with respect to DNA methylation and its effect on crop improvement programs. It is anticipated that a precise and comprehensive knowledge of molecular basis of in vitro-derived DNA methylation will help to design strategies to overcome the bottlenecks of micropropagation system and maintain the clonal fidelity of the regenerants.
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Yang Y, Tang K, Datsenka TU, Liu W, Lv S, Lang Z, Wang X, Gao J, Wang W, Nie W, Chu Z, Zhang H, Handa AK, Zhu JK, Zhang H. Critical function of DNA methyltransferase 1 in tomato development and regulation of the DNA methylome and transcriptome. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:1224-1242. [PMID: 30652405 DOI: 10.1111/jipb.12778] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 01/14/2019] [Indexed: 05/05/2023]
Abstract
DNA methylation confers epigenetic regulation on gene expression and thereby on various biological processes. Tomato has emerged as an excellent system to study the function of DNA methylation in plant development. To date, regulation and function of DNA methylation maintenance remains unclear in tomato plants. Here, we report the critical function of tomato (Solanum lycopersicum) Methyltransferase 1 (SlMET1) in plant development and DNA methylome and transcriptome regulation. Using CRISPR-Cas9 gene editing, we generated slmet1 mutants and observed severe developmental defects with a frame-shift mutation, including small and curly leaves, defective inflorescence, and parthenocarpy. In leaf tissues, mutations in SlMET1 caused CG hypomethylation and CHH hypermethylation on a whole-genome scale, leading to a disturbed transcriptome including ectopic expression of many RIN target genes such as ACC2 in leaf tissues, which are normally expressed in fruits. Neither the CG hypomethylation nor CHH hypermethylation in the slmet1 mutants is related to tissue culture. Meanwhile, tissue culture induces non-CG hypomethylation, which occurs more frequently at gene regions than at TE regions. Our results depict SlMET1- and tissue culture-dependent tomato DNA methylomes, and that SlMET1 is required for maintaining a normal transcriptome and normal development of tomato.
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Affiliation(s)
- Yu Yang
- Shanghai Center for Plant Stress Biology, the Chinese Academy of Sciences, Shanghai, 201602, China
| | - Kai Tang
- Shanghai Center for Plant Stress Biology, the Chinese Academy of Sciences, Shanghai, 201602, China
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, USA
| | - Tatsiana U Datsenka
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, USA
| | - Wenshan Liu
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, USA
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400715, China
| | - Suhui Lv
- Shanghai Center for Plant Stress Biology, the Chinese Academy of Sciences, Shanghai, 201602, China
| | - Zhaobo Lang
- Shanghai Center for Plant Stress Biology, the Chinese Academy of Sciences, Shanghai, 201602, China
| | - Xingang Wang
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, USA
| | - Jinghui Gao
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, USA
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, China
| | - Wei Wang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
- Shanghai Chenshan Plant Science Research Center, the Chinese Academy of Sciences, Shanghai, 201602, China
| | - Wenfeng Nie
- Shanghai Center for Plant Stress Biology, the Chinese Academy of Sciences, Shanghai, 201602, China
| | - Zhaoqing Chu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
- Shanghai Chenshan Plant Science Research Center, the Chinese Academy of Sciences, Shanghai, 201602, China
| | - Heng Zhang
- Shanghai Center for Plant Stress Biology, the Chinese Academy of Sciences, Shanghai, 201602, China
| | - Avtar K Handa
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, USA
| | - Jian-Kang Zhu
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, USA
- Shanghai Center for Plant Stress Biology, CAS Center of Excellence in Molecular Plant Sciences, the Chinese Academy of Sciences, Shanghai 200032, China
| | - Huiming Zhang
- Shanghai Center for Plant Stress Biology, CAS Center of Excellence in Molecular Plant Sciences, the Chinese Academy of Sciences, Shanghai 200032, China
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Genetic stability assessment of Taraxacum pieninicum plantlets after long-term slow growth storage using ISSR and SCoT markers. Biologia (Bratisl) 2019. [DOI: 10.2478/s11756-019-00377-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Hao DC, Xiao PG. Deep in shadows: Epigenetic and epigenomic regulations of medicinal plants. CHINESE HERBAL MEDICINES 2018. [DOI: 10.1016/j.chmed.2018.02.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
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Coronel CJ, González AI, Ruiz ML, Polanco C. Analysis of somaclonal variation in transgenic and regenerated plants of Arabidopsis thaliana using methylation related metAFLP and TMD markers. PLANT CELL REPORTS 2018; 37:137-152. [PMID: 29038910 DOI: 10.1007/s00299-017-2217-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 10/04/2017] [Indexed: 05/14/2023]
Abstract
We provide evidence that nucleotide sequence and methylation status changes occur in the Arabidopsis genome during in vitro tissue culture at a frequency high enough to represent an important source of variation. Somaclonal variation is a general consequence of the tissue culture process that has to be analyzed specifically when regenerated plants are obtained in any plant species. Currently, there are few studies about the variability comprising sequence changes and methylation status at the DNA level, generated by the culture of A. thaliana cells and tissues. In this work, two types of highly reproducible molecular markers, modified methylation sensitive AFLP (metAFLP) and transposon methylation display (TMD) have been used for the first time in this species to analyze the nucleotide and cytosine methylation changes induced by transformation and tissue culture protocols. We found significantly higher average methylation values (7.5%) in regenerated and transgenic plants when compared to values obtained from seed derived plants (3.2%) and that the main component of the somaclonal variation present in Arabidopsis clonal plants is genetic rather than epigenetic. However, we have found that the Arabidopsis regenerated and transgenic plants had a higher number of non-fully methylated sites flanking transposable elements than the control plants, and therefore, their mobilization can be facilitated. These data provide further evidence that changes in nucleotide sequence and methylation status occur in the Arabidopsis genome during in vitro tissue culture frequently enough to be an important source of variation in this species.
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Affiliation(s)
- Carlos J Coronel
- Área de Genética, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24071, León, Spain
| | - Ana I González
- Área de Genética, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24071, León, Spain
| | - María L Ruiz
- Área de Genética, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24071, León, Spain
| | - Carlos Polanco
- Área de Genética, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24071, León, Spain.
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Gao R, Wang H, Dong B, Yang X, Chen S, Jiang J, Zhang Z, Liu C, Zhao N, Chen F. Morphological, Genome and Gene Expression Changes in Newly Induced Autopolyploid Chrysanthemum lavandulifolium (Fisch. ex Trautv.) Makino. Int J Mol Sci 2016; 17:E1690. [PMID: 27735845 PMCID: PMC5085722 DOI: 10.3390/ijms17101690] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 09/26/2016] [Accepted: 09/29/2016] [Indexed: 12/13/2022] Open
Abstract
Autopolyploidy is widespread in higher plants and plays an important role in the process of evolution. The present study successfully induced autotetraploidys from Chrysanthemum lavandulifolium by colchicine. The plant morphology, genomic, transcriptomic, and epigenetic changes between tetraploid and diploid plants were investigated. Ligulate flower, tubular flower and leaves of tetraploid plants were greater than those of the diploid plants. Compared with diploid plants, the genome changed as a consequence of polyploidization in tetraploid plants, namely, 1.1% lost fragments and 1.6% novel fragments occurred. In addition, DNA methylation increased after genome doubling in tetraploid plants. Among 485 common transcript-derived fragments (TDFs), which existed in tetraploid and diploid progenitors, 62 fragments were detected as differentially expressed TDFs, 6.8% of TDFs exhibited up-regulated gene expression in the tetraploid plants and 6.0% exhibited down-regulation. The present study provides a reference for further studying the autopolyploidization role in the evolution of C. lavandulifolium. In conclusion, the autopolyploid C. lavandulifolium showed a global change in morphology, genome and gene expression compared with corresponding diploid.
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Affiliation(s)
- Ri Gao
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
- Department of Horticulture, Agricultural College Yanbian University, Park Road 977, Yanji 133002, China.
| | - Haibin Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Bin Dong
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Xiaodong Yang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Sumei Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Jiafu Jiang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Zhaohe Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Chen Liu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Nan Zhao
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Fadi Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
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Krishna H, Alizadeh M, Singh D, Singh U, Chauhan N, Eftekhari M, Sadh RK. Somaclonal variations and their applications in horticultural crops improvement. 3 Biotech 2016; 6:54. [PMID: 28330124 PMCID: PMC4752953 DOI: 10.1007/s13205-016-0389-7] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 10/20/2015] [Indexed: 01/07/2023] Open
Abstract
The advancements made in tissue culture techniques has made it possible to regenerate various horticultural species in vitro as micropropagation protocols for commercial scale multiplication are available for a wide range of crops. Clonal propagation and preservation of elite genotypes, selected for their superior characteristics, require high degree of genetic uniformity amongst the regenerated plants. However, plant tissue culture may generate genetic variability, i.e., somaclonal variations as a result of gene mutation or changes in epigenetic marks. The occurrence of subtle somaclonal variation is a drawback for both in vitro cloning as well as germplasm preservation. Therefore, it is of immense significance to assure the genetic uniformity of in vitro raised plants at an early stage. Several strategies have been followed to ascertain the genetic fidelity of the in vitro raised progenies comprising morpho-physiological, biochemical, cytological and DNA-based molecular markers approaches. Somaclonal variation can pose a serious problem in any micropropagation program, where it is highly desirable to produce true-to-type plant material. On the other hand, somaclonal variation has provided a new and alternative tool to the breeders for obtaining genetic variability relatively rapidly and without sophisticated technology in horticultural crops, which are either difficult to breed or have narrow genetic base. In the present paper, sources of variations induced during tissue culture cycle and strategies to ascertain and confirm genetic fidelity in a variety of in vitro raised plantlets and potential application of variants in horticultural crop improvement are reviewed.
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Affiliation(s)
- Hare Krishna
- ICAR-Central Institute for Arid Horticulture, Beechwal, Bikaner, Rajasthan, 334 006, India.
| | - Mahdi Alizadeh
- Department of Horticulture, Faculty of Agriculture, Gorgan University of Agricultural Sciences and Natural Resources (GUASNR), Golestan, Gorgan, Iran
| | - Dhurendra Singh
- ICAR-Central Institute for Arid Horticulture, Beechwal, Bikaner, Rajasthan, 334 006, India
| | - Udayvir Singh
- ICAR-Central Institute for Arid Horticulture, Beechwal, Bikaner, Rajasthan, 334 006, India
| | - Nitesh Chauhan
- ICAR-Central Institute for Arid Horticulture, Beechwal, Bikaner, Rajasthan, 334 006, India
| | - Maliheh Eftekhari
- Department of Horticulture, Faculty of Agriculture, Gorgan University of Agricultural Sciences and Natural Resources (GUASNR), Golestan, Gorgan, Iran
| | - Radha Kishan Sadh
- ICAR-Central Institute for Arid Horticulture, Beechwal, Bikaner, Rajasthan, 334 006, India
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Wang QM, Wang L, Zhou Y, Cui J, Wang Y, Zhao C. Leaf patterning of Clivia miniata var. variegata is associated with differential DNA methylation. PLANT CELL REPORTS 2016; 35:167-84. [PMID: 26466593 DOI: 10.1007/s00299-015-1877-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Revised: 09/21/2015] [Accepted: 09/29/2015] [Indexed: 05/15/2023]
Abstract
Leaf patterns (yellow, green and striped) of Clivia miniata var. variegata might be caused by differential DNA methylation in CCGG sites in response to heterogeneous environmental pressure. Clivia miniata is an important ornamental plant.Clivia miniata var. variegata (Cmvv) is a variegated leaf mutant of C. miniata. Typical Cmvv has attractive green and yellow-stripped leaves. The study has revealed that an explant of Cmvv, even a full-green explant, could regenerate plants of three different types: yellow, green, ands triped; normal-appearing chloroplasts were found in guard cells but not in mesophyll cells of all the three types of Cmvv using confocal laser scanning microscopy (CLSM).Thus, we speculated that cells of the three types of Cmvv had an identical mutation and the mutation might disturb mesophyll cell chloroplast biogenesis after symplastic isolation of guard cells. Using CLSM and methylation sensitive amplification polymorphism (MSAP), we found that (a) striped leaves of Cmvv are due to sectorial decreases in chlorophyll levels and the decreases are associated with CG hypermethylation; (b) extent of epigenetic divergence among the three types of Cmvv leaves is positively correlated with intensity of leaf-color difference; and (c) green stripes of two plants are clustered in one group based on the MSAP profiles, but green and yellow stripes of a plant are not. Sequencing analysis indicated that CG hypermethylation in gene bodies of CPSAR1 and ycf2 might lead to gene silencing and yellow leaves/stripes of Cmvv. All together, it is possible that cytosine methylation involved regulating leaf color of Cmvv, also striped pattern of Cmvv might be caused by differential DNA methylation in response to heterogeneous environmental pressure. Furthermore, a novel leaf-color epigenetic hypothesis was proposed in this article.
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Machczyńska J, Zimny J, Bednarek PT. Tissue culture-induced genetic and epigenetic variation in triticale (× Triticosecale spp. Wittmack ex A. Camus 1927) regenerants. PLANT MOLECULAR BIOLOGY 2015; 89:279-92. [PMID: 26337939 PMCID: PMC4579263 DOI: 10.1007/s11103-015-0368-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 08/22/2015] [Indexed: 05/26/2023]
Abstract
Plant regeneration via in vitro culture can induce genetic and epigenetic variation; however, the extent of such changes in triticale is not yet understood. In the present study, metAFLP, a variation of methylation-sensitive amplified fragment length polymorphism analysis, was used to investigate tissue culture-induced variation in triticale regenerants derived from four distinct genotypes using androgenesis and somatic embryogenesis. The metAFLP technique enabled identification of both sequence and DNA methylation pattern changes in a single experiment. Moreover, it was possible to quantify subtle effects such as sequence variation, demethylation, and de novo methylation, which affected 19, 5.5, 4.5% of sites, respectively. Comparison of variation in different genotypes and with different in vitro regeneration approaches demonstrated that both the culture technique and genetic background of donor plants affected tissue culture-induced variation. The results showed that the metAFLP approach could be used for quantification of tissue culture-induced variation and provided direct evidence that in vitro plant regeneration could cause genetic and epigenetic variation.
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Affiliation(s)
- Joanna Machczyńska
- Department of Plant Physiology and Biochemistry, Plant Breeding and Acclimatization Institute-National Research Institute, 05-870, Błonie, Radzików, Poland
| | - Janusz Zimny
- Department of Plant Biotechnology and Cytogenetics, Plant Breeding and Acclimatization Institute-National Research Institute, 05-870, Błonie, Radzików, Poland
| | - Piotr Tomasz Bednarek
- Department of Plant Physiology and Biochemistry, Plant Breeding and Acclimatization Institute-National Research Institute, 05-870, Błonie, Radzików, Poland.
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14
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Yang C, Wei H. Designing microarray and RNA-Seq experiments for greater systems biology discovery in modern plant genomics. MOLECULAR PLANT 2015; 8:196-206. [PMID: 25680773 DOI: 10.1016/j.molp.2014.11.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Revised: 10/31/2014] [Accepted: 11/02/2014] [Indexed: 05/07/2023]
Abstract
Microarray and RNA-seq experiments have become an important part of modern genomics and systems biology. Obtaining meaningful biological data from these experiments is an arduous task that demands close attention to many details. Negligence at any step can lead to gene expression data containing inadequate or composite information that is recalcitrant for pattern extraction. Therefore, it is imperative to carefully consider experimental design before launching a time-consuming and costly experiment. Contemporarily, most genomics experiments have two objectives: (1) to generate two or more groups of comparable data for identifying differentially expressed genes, gene families, biological processes, or metabolic pathways under experimental conditions; (2) to build local gene regulatory networks and identify hierarchically important regulators governing biological processes and pathways of interest. Since the first objective aims to identify the active molecular identities and the second provides a basis for understanding the underlying molecular mechanisms through inferring causality relationships mediated by treatment, an optimal experiment is to produce biologically relevant and extractable data to meet both objectives without substantially increasing the cost. This review discusses the major issues that researchers commonly face when embarking on microarray or RNA-seq experiments and summarizes important aspects of experimental design, which aim to help researchers deliberate how to generate gene expression profiles with low background noise but with more interaction to facilitate novel biological discoveries in modern plant genomics.
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Affiliation(s)
- Chuanping Yang
- State Key Laboratory of Forest Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang 150040, China
| | - Hairong Wei
- State Key Laboratory of Forest Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang 150040, China; Biotechnology Research Center, School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA.
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Wang H, Dong B, Jiang J, Fang W, Guan Z, Liao Y, Chen S, Chen F. Characterization of in vitro haploid and doubled haploid Chrysanthemum morifolium plants via unfertilized ovule culture for phenotypical traits and DNA methylation pattern. FRONTIERS IN PLANT SCIENCE 2014; 5:738. [PMID: 25566305 PMCID: PMC4273617 DOI: 10.3389/fpls.2014.00738] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 12/04/2014] [Indexed: 05/19/2023]
Abstract
Chrysanthemum is one of important ornamental species in the world. Its highly heterozygous state complicates molecular analysis, so it is of interest to derive haploid forms. A total of 2579 non-fertilized chrysanthemum ovules pollinated by Argyranthemum frutescens were cultured in vitro to isolate haploid progeny. One single regenerant emerged from each of three of the 105 calli produced. Chromosome counts and microsatellite fingerprinting showed that only one of the regenerants was a true haploid. Nine doubled haploid derivatives were subsequently generated by colchicine treatment of 80 in vitro cultured haploid nodal segments. Morphological screening showed that the haploid plant was shorter than the doubled haploids, and developed smaller leaves, flowers, and stomata. An in vitro pollen germination test showed that few of the haploid's pollen were able to germinate and those which did so were abnormal. Both the haploid and the doubled haploids produced yellow flowers, whereas those of the maternal parental cultivar were mauve. Methylation-sensitive amplification polymorphism (MSAP) profiling was further used to detect alterations in cytosine methylation caused by the haploidization and/or the chromosome doubling processes. While 52.2% of the resulting amplified fragments were cytosine methylated in the maternal parent's genome, the corresponding proportions for the haploid's and doubled haploids' genomes were, respectively, 47.0 and 51.7%, demonstrating a reduction in global cytosine methylation caused by haploidization and a partial recovery following chromosome doubling.
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Affiliation(s)
- Haibin Wang
- College of Horticulture, Nanjing Agricultural UniversityNanjing, China
- Jiangsu Province Engineering Lab for Modern Facility Agriculture Technology & EquipmentNanjing, China
| | - Bin Dong
- College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Jiafu Jiang
- College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Weimin Fang
- College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Zhiyong Guan
- College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Yuan Liao
- College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Sumei Chen
- College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Fadi Chen
- College of Horticulture, Nanjing Agricultural UniversityNanjing, China
- Jiangsu Province Engineering Lab for Modern Facility Agriculture Technology & EquipmentNanjing, China
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16
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Liu TJ, Sun LF, Shan XH, Wu Y, Su SZ, Li SP, Liu HK, Han JY, Yuan YP. Analysis of DNA methylation patterns and levels in maize hybrids and their parents. GENETICS AND MOLECULAR RESEARCH : GMR 2014. [PMID: 25366740 DOI: 10.1007/s10535-015-0490-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Heterosis is the superior performance of heterozygous individuals and has been widely exploited in plant breeding, although the underlying regulatory mechanisms still remain largely elusive. To understand the molecular basis of heterosis in maize, in this study, roots and leaves at the seedling stage and embryos and endosperm tissues 15 days after fertilization of 2 elite hybrids and their parental lines were used to estimate the levels and patterns of cytosine methylation by the methylation-sensitive amplification polymorphism method. The relative total methylation levels were lower in all the tissues of all hybrids than their corresponding mid-parent values, and the number of demethylation events was higher in the hybrids. These results implied that the decreasing trend and demethylation in hybrids relative to their parents may enable the derepression and possibly expression of many genes that were associated with the phenotypic variation in hybrids. To further analyze the observed methylation pattern changes, a total of 63 differentially displayed DNA fragments were successfully sequenced. Basic Local Alignment Search Tool analysis showed that 11 fragments shared similarity with known functional proteins in maize or other plant species, including metabolism, transposon/retrotransposon, development, stress response, and signal transduction, which indicated that these genes might play a significant role in maize hybrid vigor.
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Affiliation(s)
- T J Liu
- College of Plant Science, Jilin University, Changchun, China
| | - L F Sun
- College of Plant Science, Jilin University, Changchun, China
| | - X H Shan
- College of Plant Science, Jilin University, Changchun, China
| | - Y Wu
- College of Plant Science, Jilin University, Changchun, China
| | - S Z Su
- College of Plant Science, Jilin University, Changchun, China
| | - S P Li
- College of Plant Science, Jilin University, Changchun, China
| | - H K Liu
- College of Plant Science, Jilin University, Changchun, China
| | - J Y Han
- College of Plant Science, Jilin University, Changchun, China
| | - Y P Yuan
- College of Plant Science, Jilin University, Changchun, China
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17
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Wang H, Jiang J, Chen S, Qi X, Fang W, Guan Z, Teng N, Liao Y, Chen F. Rapid genetic and epigenetic alterations under intergeneric genomic shock in newly synthesized Chrysanthemum morifolium x Leucanthemum paludosum hybrids (Asteraceae). Genome Biol Evol 2014; 6:247-59. [PMID: 24407856 PMCID: PMC3914698 DOI: 10.1093/gbe/evu008] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The Asteraceae family is at the forefront of the evolution due to frequent hybridization. Hybridization is associated with the induction of widespread genetic and epigenetic changes and has played an important role in the evolution of many plant taxa. We attempted the intergeneric cross Chrysanthemum morifolium × Leucanthemum paludosum. To obtain the success in cross, we have to turn to ovule rescue. DNA profiling of the amphihaploid and amphidiploid was investigated using amplified fragment length polymorphism, sequence-related amplified polymorphism, start codon targeted polymorphism, and methylation-sensitive amplification polymorphism (MSAP). Hybridization induced rapid changes at the genetic and the epigenetic levels. The genetic changes mainly involved loss of parental fragments and gaining of novel fragments, and some eliminated sequences possibly from the noncoding region of L. paludosum. The MSAP analysis indicated that the level of DNA methylation was lower in the amphiploid (∼45%) than in the parental lines (51.5-50.6%), whereas it increased after amphidiploid formation. Events associated with intergeneric genomic shock were a feature of C. morifolium × L. paludosum hybrid, given that the genetic relationship between the parental species is relatively distant. Our results provide genetic and epigenetic evidence for understanding genomic shock in wide crosses between species in Asteraceae and suggest a need to expand our current evolutionary framework to encompass a genetic/epigenetic dimension when seeking to understand wide crosses.
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Affiliation(s)
- Haibin Wang
- College of Horticulture, Nanjing Agricultural University, China
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18
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Sun S, Zhong J, Li S, Wang X. Tissue culture-induced somaclonal variation of decreased pollen viability in torenia (Torenia fournieri Lind.). BOTANICAL STUDIES 2013; 54:36. [PMID: 28510883 PMCID: PMC5432822 DOI: 10.1186/1999-3110-54-36] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 09/13/2013] [Indexed: 05/22/2023]
Abstract
BACKGROUND Phenotypic and genotypic variations, collectively called somaclonal variations, are induced during tissue culture. RESULTS We studied the phenotypic variation in pollen viability of regenerants of torenia after subculturing for one to nine generations. We found that pollen viability of regenerants continuously decreased with increasing subculture time. High concentrations of plant growth regulators applied to the Murashige and Skoog (MS) medium also resulted in diminished pollen viability. Furthermore, antibiotic application during gene transformation also decreased pollen viability of the transformants. However, the process of long-term culture did not significantly change pollen viability. The mean methylation level of regenerants showed a 0.28% to 3.95% decrease in seedlings subcultured in vitro for nine generations. Moreover, when the ninth subcultured regenerants with reduced pollen vibility were recovered in soil to get seeds, the pollen viability of seed-derive plants was similar to that of the wild type. CONCLUSIONS The results show that plant growth regulators, antibiotics, and the number of subculture generations influence somaclonal variations in torenia. The somaclonal variations in torenia may results from epigenetic changes.
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Affiliation(s)
- ShuLan Sun
- Guangdong Key Lab of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou, Guangdong, 510631 People’s Republic of China
| | - JianQiang Zhong
- Guangdong Key Lab of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou, Guangdong, 510631 People’s Republic of China
| | - ShuHua Li
- Guangdong Key Lab of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou, Guangdong, 510631 People’s Republic of China
| | - XiaoJing Wang
- Guangdong Key Lab of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou, Guangdong, 510631 People’s Republic of China
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19
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Bobadilla Landey R, Cenci A, Georget F, Bertrand B, Camayo G, Dechamp E, Herrera JC, Santoni S, Lashermes P, Simpson J, Etienne H. High genetic and epigenetic stability in Coffea arabica plants derived from embryogenic suspensions and secondary embryogenesis as revealed by AFLP, MSAP and the phenotypic variation rate. PLoS One 2013; 8:e56372. [PMID: 23418563 PMCID: PMC3572038 DOI: 10.1371/journal.pone.0056372] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 01/08/2013] [Indexed: 01/30/2023] Open
Abstract
Embryogenic suspensions that involve extensive cell division are risky in respect to genome and epigenome instability. Elevated frequencies of somaclonal variation in embryogenic suspension-derived plants were reported in many species, including coffee. This problem could be overcome by using culture conditions that allow moderate cell proliferation. In view of true-to-type large-scale propagation of C. arabica hybrids, suspension protocols based on low 2,4-D concentrations and short proliferation periods were developed. As mechanisms leading to somaclonal variation are often complex, the phenotypic, genetic and epigenetic changes were jointly assessed so as to accurately evaluate the conformity of suspension-derived plants. The effects of embryogenic suspensions and secondary embryogenesis, used as proliferation systems, on the genetic conformity of somatic embryogenesis-derived plants (emblings) were assessed in two hybrids. When applied over a 6 month period, both systems ensured very low somaclonal variation rates, as observed through massive phenotypic observations in field plots (0.74% from 200,000 plant). Molecular AFLP and MSAP analyses performed on 145 three year-old emblings showed that polymorphism between mother plants and emblings was extremely low, i.e. ranges of 0-0.003% and 0.07-0.18% respectively, with no significant difference between the proliferation systems for the two hybrids. No embling was found to cumulate more than three methylation polymorphisms. No relation was established between the variant phenotype (27 variants studied) and a particular MSAP pattern. Chromosome counting showed that 7 of the 11 variant emblings analyzed were characterized by the loss of 1-3 chromosomes. This work showed that both embryogenic suspensions and secondary embryogenesis are reliable for true-to-type propagation of elite material. Molecular analyses revealed that genetic and epigenetic alterations are particularly limited during coffee somatic embryogenesis. The main change in most of the rare phenotypic variants was aneuploidy, indicating that mitotic aberrations play a major role in somaclonal variation in coffee.
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Affiliation(s)
- Roberto Bobadilla Landey
- Unité Mixte de Recherche Résistance des Plantes aux Bioagresseurs, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Montpellier, France
| | - Alberto Cenci
- Unité Mixte de Recherche Résistance des Plantes aux Bioagresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - Frédéric Georget
- Unité Mixte de Recherche Résistance des Plantes aux Bioagresseurs, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Montpellier, France
| | - Benoît Bertrand
- Unité Mixte de Recherche Résistance des Plantes aux Bioagresseurs, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Montpellier, France
| | - Gloria Camayo
- Centro Nacional de Investigaciones de Café, Manizales, Colombia
| | - Eveline Dechamp
- Unité Mixte de Recherche Résistance des Plantes aux Bioagresseurs, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Montpellier, France
| | | | - Sylvain Santoni
- Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Tropicales et Méditerranéennes, Institut National de la Recherche Agronomique, Montpellier, France
| | - Philippe Lashermes
- Unité Mixte de Recherche Résistance des Plantes aux Bioagresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - June Simpson
- Department of Plant Genetic Engineering, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, Mexico
| | - Hervé Etienne
- Unité Mixte de Recherche Résistance des Plantes aux Bioagresseurs, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Montpellier, France
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Wang QM, Wang L. An evolutionary view of plant tissue culture: somaclonal variation and selection. PLANT CELL REPORTS 2012; 31:1535-47. [PMID: 22610486 DOI: 10.1007/s00299-012-1281-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Revised: 04/30/2012] [Accepted: 04/30/2012] [Indexed: 05/20/2023]
Abstract
Plants regenerated from in vitro cultures possess an array of genetic and epigenetic changes. This phenomenon is known as 'somaclonal variation' and the frequency of somaclonal variation (SV) is usually elevated far beyond that expected in nature. Initially, the relationship between time in culture and detected SV was found to support the widespread belief that SV accumulates with culture age. However, a few studies indicated that older cultures yielded regenerants with less SV. What leads to this seemed contradiction? In this article, we have proposed a novel in vitro callus selection hypothesis, differentiation bottleneck (D-bottleneck) and dedifferentiation bottleneck (Dd-bottleneck), which consider natural selection theory to be fit for cell population in vitro. The results of multiplication races between the cells with the true-to-type phenotype and the deleterious cells determine the increase/decrease of SV frequencies in calli or regenerants as in vitro culture time goes on. The possibility of interpreting the complex situation of time-related SV by the evolutionary theory is discussed in this paper. In addition, the SV threshold, space-determined hypothesis and D-bottleneck are proposed to interpret the loss of the regenerability through a long period of plant tissue culture (PTC).
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Affiliation(s)
- Qin-Mei Wang
- Institute of Genetics and Cytology, Northeast Normal University, Changchun, 130024, People's Republic of China.
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Wang QM, Wang YZ, Sun LL, Gao FZ, Sun W, He J, Gao X, Wang L. Direct and indirect organogenesis of Clivia miniata and assessment of DNA methylation changes in various regenerated plantlets. PLANT CELL REPORTS 2012; 31:1283-96. [PMID: 22532007 DOI: 10.1007/s00299-012-1248-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2011] [Revised: 02/15/2012] [Accepted: 03/15/2012] [Indexed: 05/09/2023]
Abstract
UNLABELLED Clivia miniata is an important indoor ornamental plant and has been reported to have medicinal value. We developed an efficient in vitro micropropagation protocol from young leaves (indirect organogenesis), young petals (indirect organogenesis) and shoot tips (direct organogenesis) of this plant. Using young leaves and shoot tips as explants, the regeneration frequencies were much higher than those in previous investigation and the regeneration was dependent upon less nutrition. We speculated that the leaf-derived callus can generate amino acids necessary for protein synthesis by itself. We employed the methylation-sensitive amplified polymorphism (MSAP) method to assess cytosine methylation variation in various regenerated plantlets and between organs. The MSAP profiles indicated that the frequency of somaclonal variation in the form of cytosine methylation was highest in petal-derived plantlets followed by secondary leaf-derived, primary leaf-derived and shoot tip-derived plantlets, but the methylation variation in petal-derived plantlets was lower than between petals and leaves of a single plant. The results indicated that the methylation variation in regenerated plantlets was related to the types of explants, regeneration pathways and number of regeneration generations. Two possible factors for the highest somaclonal variation rate in petal-derived plantlets are the callus phase and petal-specific set of epigenetic regulators. The property of meristem integrity can account for the lowest variation rate in shoot tip-derived plantlets. Moreover, the secondary plantlets underwent a longer total period of in vitro culture, which can explain why the methylation variation rate in the secondary plantlets is higher than in the primary ones. KEY MESSAGE Methylation variation in regenerated plantlets of C. miniata was found to be related to the types of explants, regeneration pathways and number of regeneration generations.
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Affiliation(s)
- Qin-Mei Wang
- Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, People's Republic of China
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Ravindra NS, Ramesh SI, Gupta MK, Jhang T, Shukla AK, Darokar MP, Kulkarni RN. Evaluation of somaclonal variation for genetic improvement of patchouli (Pogostemon patchouli), an exclusively vegetatively propagated aromatic plant. ACTA ACUST UNITED AC 2012. [DOI: 10.1007/s12892-011-0068-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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Neelakandan AK, Wang K. Recent progress in the understanding of tissue culture-induced genome level changes in plants and potential applications. PLANT CELL REPORTS 2012; 31:597-620. [PMID: 22179259 DOI: 10.1007/s00299-011-1202-z] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Revised: 11/30/2011] [Accepted: 12/01/2011] [Indexed: 05/23/2023]
Abstract
In vitro cell and tissue-based systems have tremendous potential in fundamental research and for commercial applications such as clonal propagation, genetic engineering and production of valuable metabolites. Since the invention of plant cell and tissue culture techniques more than half a century ago, scientists have been trying to understand the morphological, physiological, biochemical and molecular changes associated with tissue culture responses. Establishment of de novo developmental cell fate in vitro is governed by factors such as genetic make-up, stress and plant growth regulators. In vitro culture is believed to destabilize the genetic and epigenetic program of intact plant tissue and can lead to chromosomal and DNA sequence variations, methylation changes, transposon activation, and generation of somaclonal variants. In this review, we discuss the current status of understanding the genomic and epigenomic changes that take place under in vitro conditions. It is hoped that a precise and comprehensive knowledge of the molecular basis of these variations and acquisition of developmental cell fate would help to devise strategies to improve the totipotency and embryogenic capability in recalcitrant species and genotypes, and to address bottlenecks associated with clonal propagation.
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Jaligot E, Adler S, Debladis É, Beulé T, Richaud F, Ilbert P, Finnegan EJ, Rival A. Epigenetic imbalance and the floral developmental abnormality of the in vitro-regenerated oil palm Elaeis guineensis. ANNALS OF BOTANY 2011; 108:1453-62. [PMID: 21224269 PMCID: PMC3219487 DOI: 10.1093/aob/mcq266] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Accepted: 11/19/2010] [Indexed: 05/24/2023]
Abstract
BACKGROUND The large-scale clonal propagation of oil palm (Elaeis guineensis) is being stalled by the occurrence of the mantled somaclonal variation. Indeed, this abnormality which presents a homeotic-like conversion of male floral organs into carpelloid structures, hampers oil production since the supernumerary female organs are either sterile or produce fruits with poor oil yields. SCOPE In the last 15 years, the prevailing point of view on the origin of the mantled floral phenotype has evolved from a random mutation event triggered by in vitro culture to a hormone-dependent dysfunction of gene regulation processes. In this review, we retrace the history of the research on the mantled variation in the light of the parallel advances made in the understanding of plant development regulation in model systems and more specifically in the role of epigenetic mechanisms. An overview of the current state of oil palm genomic and transcriptomic resources, which are key to any comparison with model organisms, is given. We show that, while displaying original characteristics, the mantled phenotype of oil palm is morphologically, and possibly molecularly, related to MADS-box genes mutants described in model plants. We also discuss the occurrence of comparable floral phenotypes in other palm species. CONCLUSIONS Beyond its primary interest in the search for discriminating markers against an economically crippling phenotype, the study of the mantled abnormality also provides a unique opportunity to investigate the regulation of reproductive development in a perennial tropical palm. On the basis of recent results, we propose that future efforts should concentrate on the epigenetic regulation targeting MADS-box genes and transposable elements of oil palm, since both types of sequences are most likely to be involved in the mantled variant phenotype.
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Affiliation(s)
- Estelle Jaligot
- UMR DIADE (IRD, UM2), IRD/CIRAD Palm Development Group, 911 avenue Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France.
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25
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Miguel C, Marum L. An epigenetic view of plant cells cultured in vitro: somaclonal variation and beyond. JOURNAL OF EXPERIMENTAL BOTANY 2011; 62:3713-25. [PMID: 21617249 DOI: 10.1093/jxb/err155] [Citation(s) in RCA: 152] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Epigenetic mechanisms are highly dynamic events that modulate gene expression. As more accurate and powerful tools for epigenetic analysis become available for application in a broader range of plant species, analysis of the epigenetic landscape of plant cell cultures may turn out to be crucial for understanding variant phenotypes. In vitro plant cell and tissue culture methodologies are important for many ongoing plant propagation and breeding programmes as well as for cutting-edge research in several plant model species. Although it has long been known that in vitro conditions induce variation at several levels, most studies using such conditions rely on the assumption that in vitro cultured plant cells/tissues mostly conform genotypically and phenotypically. However, when large-scale clonal propagation is the aim, there has been a concern in confirming true-to-typeness using molecular markers for evaluating stability. While in most reports genetic variation has been found to occur at relatively modest frequencies, variation in DNA methylation patterns seems to be much more frequent and in some cases it has been directly implicated in phenotypic variation. Recent advances in the field of epigenetics have uncovered highly dynamic mechanisms of chromatin remodelling occurring during cell dedifferentiation and differentiation processes on which in vitro adventitious plant regeneration systems are based. Here, an overview of recent findings related to developmental switches occurring during in vitro culture is presented. Additionally, an update on the detection of epigenetic variation in plant cell cultures will be provided and discussed in the light of recent progress in the plant epigenetics field.
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Affiliation(s)
- Célia Miguel
- Instituto de Tecnologia Química e Biológica-Universidade Nova de Lisboa, Oeiras, Portugal.
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26
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Rai MK, Kalia RK, Singh R, Gangola MP, Dhawan A. Developing stress tolerant plants through in vitro selection—An overview of the recent progress. ENVIRONMENTAL AND EXPERIMENTAL BOTANY 2011. [PMID: 0 DOI: 10.1016/j.envexpbot.2010.10.021] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
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27
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Dann AL, Wilson CR. Comparative assessment of genetic and epigenetic variation among regenerants of potato (Solanum tuberosum) derived from long-term nodal tissue-culture and cell selection. PLANT CELL REPORTS 2011; 30:631-9. [PMID: 21210276 DOI: 10.1007/s00299-010-0983-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Revised: 12/03/2010] [Accepted: 12/13/2010] [Indexed: 05/08/2023]
Abstract
Three long-term nodal tissued cultured Russet Burbank potato clones and nine thaxtomin A-treated regenerant lines, derived from the nodal lines, were assessed for genetic and epigenetic (in the form of DNA methylation) differences by AFLP and MSAP. The treated regenerant lines were originally selected for superior resistance to common scab disease and acceptable tuber yield in pot and field trials. The long-term, tissue culture clone lines exhibited genetic (8.75-15.63% polymorphisms) and epigenetic (12.56-26.13% polymorphisms) differences between them and may represent a stress response induced by normal plant growth disruption. The thaxtomin A-treated regenerant lines exhibited much higher significant (p < 0.05) genetic (2-29.38%) and epigenetic (45.22-51.76%) polymorphisms than the nodal cultured parent clones. Methylation-sensitive mutations accumulated within the regenerant lines are significantly correlated (p < 0.05) to disease resistance. However, linking phenotypic differences that could be of benefit to potato growers, to single gene sequence polymorphisms in a tetraploid plant such as the potato would be extremely difficult since it is assumed many desirable traits are under polygenic control.
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Affiliation(s)
- Alison L Dann
- Tasmanian Institute of Agricultural Research, University of Tasmania, New Town Research Laboratories, 13 St Johns Ave, New Town, TAS 7008, Australia
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Kour G, Kour B, Kaul S, Dhar MK. Genetic and epigenetic instability of amplification-prone sequences of a novel B chromosome induced by tissue culture in Plantago lagopus L. PLANT CELL REPORTS 2009; 28:1857-1867. [PMID: 19847437 DOI: 10.1007/s00299-009-0789-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2009] [Revised: 09/19/2009] [Accepted: 10/05/2009] [Indexed: 05/28/2023]
Abstract
Gene amplification is prevalent in many eukaryotes and has been found linked to various phenomena such as ontogenesis, carcinogenesis, in vitro culturing, neoplasia and drug resistance. Earlier, we reported a novel B chromosome in Plantago lagopus L., which was found to have arisen as a result of massive amplification of 5S rDNA. In addition, the chromosome is also composed of 45S rDNA and transposable elements. While the importance of gene amplification cannot be underestimated, its mechanism of origin is still unclear. Therefore, the aim of the present study was to determine whether amplification can be reactivated in the novel B chromosome. For this purpose, in vitro culture was used as stress. Three modes of tissue culture, i.e., direct, indirect and somatic embryogenesis were used for raising in vitro cultures. The variations due to genetic and epigenetic mechanisms were assessed in regenerants using molecular techniques, namely, PCR-RFLP, SSAP and MSAP. The retrotransposon-based molecular markers were applied to detect the polymorphism within transposable elements of in vitro regenerated and mother plants. We detected the variations that may be due to genetic changes either because of element recombination or activation of transposable elements which can lead to increase in the copy number. MSAP analysis revealed the differences in the DNA methylation pattern of the regenerants derived from novel chromosome bearing mother plants. Some regenerated plants were associated with increase and decrease in DNA methylation of both internal and external cytosine of the CCGG sequence.
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Affiliation(s)
- Gurmeet Kour
- Plant Genomics Laboratory, School of Biotechnology, University of Jammu, Jammu 180006, India
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Wu R, Guo WL, Wang XR, Wang XL, Zhuang TT, Clarke JL, Liu B. Unintended consequence of plant transformation: biolistic transformation caused transpositional activation of an endogenous retrotransposon Tos17 in rice ssp. japonica cv. Matsumae. PLANT CELL REPORTS 2009; 28:1043-1051. [PMID: 19415284 DOI: 10.1007/s00299-009-0704-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2009] [Revised: 04/03/2009] [Accepted: 04/15/2009] [Indexed: 05/27/2023]
Abstract
Genetic instability could be provoked as an unintended consequence of genetic engineering in plants. Here, we report that the rice endogenous long terminal repeat (LTR) retrotransposon Tos17 was transpositionally activated only in transgenic calli and their regenerated plants produced by biolistic transformation in rice (Oryza sativa L.) ssp. japonica cv. Matsumae. Moreover, the transpositional activity of Tos17 was sustained after plant regeneration in the T0 generation, and produced new germinal insertions. In contrast, the element remained totally quiescent in calli and regenerated plants from tissue culture of this genotype. Nonetheless, transcriptional induction and cytosine demethylation of Tos17 were found to have occurred with no significant difference in both kinds of calli, tissue culture alone and transgenic. This suggests that callus culture is likely to have played an important role in destabilizing Tos17 in the direction towards transpositional activation, but that biolistic transformation is the direct causal factor.
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Affiliation(s)
- R Wu
- Key Laboratory of Molecular Epigenetics of MOE, Institute of Genetics and Cytology, Northeast Normal University, 130024, Changchun, China
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Schellenbaum P, Mohler V, Wenzel G, Walter B. Variation in DNA methylation patterns of grapevine somaclones (Vitis vinifera L.). BMC PLANT BIOLOGY 2008; 8:78. [PMID: 18627604 PMCID: PMC2491626 DOI: 10.1186/1471-2229-8-78] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2007] [Accepted: 07/15/2008] [Indexed: 05/04/2023]
Abstract
BACKGROUND In traditional vine areas, the production should present a typicity that partly depends on the grapevine variety. Therefore, vine improvement is considered difficult because of the limited choice in the natural variability of the cultivars within the limits of their characteristics. A possibility to circumvent this problem is the use of somatic variability. In vitro somatic embryogenesis and organogenesis can lead to genotypic and phenotypic variations, described as somaclonal variation, that could be useful for the selection of improved grapevine genotypes. RESULTS In order to study tissue culture-induced variation of grapevine, we have analysed 78 somaclones obtained from somatic embryos of two distinct cultivars using molecular marker techniques. SSRs were only useful to verify the conservation of the microsatellite genotype between the somaclones and the respective mother clones. AFLP polymorphism between mother clones and somaclones was 1.3-2.8 times higher to that found between clones. However, a majority of the somaclones (45/78) exhibited only few changes. Seven and five somaclones of 'Chardonnay 96' and 'Syrah 174', respectively, which covered at least all polymorphic loci found in AFLP analysis were used for MSAP study. All of the 120 polymorphic fragments were found only in the somaclones. The percentage of full methylation at CCGG recognition sites was slightly higher in somaclones due to more polymorphic bands generated after cleavage by EcoRI/HpaII. Different digestion patterns revealed different methylation status, especially different levels of de-methylation, that are the consequence of the in vitro culture. CONCLUSION MSAP highlights DNA methylation variation in somaclones compared to mother clones and, therefore, is a powerful tool for genotypic characterisation of somatic embryo-derived grapevines. The detection of the same polymorphic bands in numerous somaclones of different cultivars suggests the possibility of hot spots of DNA methylation variation. SSR profiles of the 'Chardonnay' and 'Syrah' somaclones were the same as of the respective mother clones. The somaclones exhibited a higher AFLP variation than clones obtained via traditional clonal selection in the field. Therefore, somatic embryogenesis through in vitro culture technique could be useful for the selection of improved cultivars with subtle changes but conserving their main characteristics.
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Affiliation(s)
- Paul Schellenbaum
- Université de Haute Alsace, Laboratoire Vigne Biotechnologies & Environnement, 33 rue de Herrlisheim, BP 50568, F-68008 Colmar, France
| | - Volker Mohler
- Technische Universität München, Lehrstuhl für Pflanzenzüchtung, Am Hochanger 2, D-85350 Freising-Weihenstephan, Germany
- Bavarian State Research Centre for Agriculture, Institute for Crop Science and Plant Breeding, Am Gereuth 8, D-85354 Freising, Germany
| | - Gerhard Wenzel
- Technische Universität München, Lehrstuhl für Pflanzenzüchtung, Am Hochanger 2, D-85350 Freising-Weihenstephan, Germany
| | - Bernard Walter
- Université de Haute Alsace, Laboratoire Vigne Biotechnologies & Environnement, 33 rue de Herrlisheim, BP 50568, F-68008 Colmar, France
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Malik MR, Wang F, Dirpaul JM, Zhou N, Hammerlindl J, Keller W, Abrams SR, Ferrie AMR, Krochko JE. Isolation of an embryogenic line from non-embryogenic Brassica napus cv. Westar through microspore embryogenesis. JOURNAL OF EXPERIMENTAL BOTANY 2008; 59:2857-73. [PMID: 18552352 PMCID: PMC2486481 DOI: 10.1093/jxb/ern149] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2008] [Revised: 04/25/2008] [Accepted: 04/29/2008] [Indexed: 05/18/2023]
Abstract
Brassica napus cultivar Westar is non-embryogenic under all standard protocols for induction of microspore embryogenesis; however, the rare embryos produced in Westar microspore cultures, induced with added brassinosteroids, were found to develop into heritably stable embryogenic lines after chromosome doubling. One of the Westar-derived doubled haploid (DH) lines, DH-2, produced up to 30% the number of embryos as the highly embryogenic B. napus line, Topas DH4079. Expression analysis of marker genes for embryogenesis in Westar and the derived DH-2 line, using real-time reverse transcription-PCR, revealed that the timely expression of embryogenesis-related genes such as LEAFY COTYLEDON1 (LEC1), LEC2, ABSCISIC ACID INSENSITIVE3, and BABY BOOM1, and an accompanying down-regulation of pollen-related transcripts, were associated with commitment to embryo development in Brassica microspores. Microarray comparisons of 7 d cultures of Westar and Westar DH-2, using a B. napus seed-focused cDNA array (10 642 unigenes), identified highly expressed genes related to protein synthesis, translation, and response to stimulus (Gene Ontology) in the embryogenic DH-2 microspore-derived cell cultures. In contrast, transcripts for pollen-expressed genes were predominant in the recalcitrant Westar microspores. Besides being embryogenic, DH-2 plants showed alterations in morphology and architecture as compared with Westar, for example epinastic leaves, non-abscised petals, pale flower colour, and longer lateral branches. Auxin, cytokinin, and abscisic acid (ABA) profiles in young leaves, mature leaves, and inflorescences of Westar and DH-2 revealed no significant differences that could account for the alterations in embryogenic potential or phenotype. Various mechanisms accounting for the increased capacity for embryogenesis in Westar-derived DH lines are considered.
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Affiliation(s)
- Meghna R. Malik
- Plant Biotechnology Institute, National Research Council of Canada, 110 Gymnasium Place, Saskatoon, Saskatchewan, Canada S7N 0W9
| | - Feng Wang
- Plant Biotechnology Institute, National Research Council of Canada, 110 Gymnasium Place, Saskatoon, Saskatchewan, Canada S7N 0W9
| | - Joan M. Dirpaul
- Plant Biotechnology Institute, National Research Council of Canada, 110 Gymnasium Place, Saskatoon, Saskatchewan, Canada S7N 0W9
| | - Ning Zhou
- Plant Biotechnology Institute, National Research Council of Canada, 110 Gymnasium Place, Saskatoon, Saskatchewan, Canada S7N 0W9
| | - Joe Hammerlindl
- Plant Biotechnology Institute, National Research Council of Canada, 110 Gymnasium Place, Saskatoon, Saskatchewan, Canada S7N 0W9
| | - Wilf Keller
- Plant Biotechnology Institute, National Research Council of Canada, 110 Gymnasium Place, Saskatoon, Saskatchewan, Canada S7N 0W9
| | - Suzanne R. Abrams
- Plant Biotechnology Institute, National Research Council of Canada, 110 Gymnasium Place, Saskatoon, Saskatchewan, Canada S7N 0W9
| | - Alison M. R. Ferrie
- Plant Biotechnology Institute, National Research Council of Canada, 110 Gymnasium Place, Saskatoon, Saskatchewan, Canada S7N 0W9
| | - Joan E. Krochko
- Plant Biotechnology Institute, National Research Council of Canada, 110 Gymnasium Place, Saskatoon, Saskatchewan, Canada S7N 0W9
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