1
|
Singh VK, Ahmed S, Saini DK, Gahlaut V, Chauhan S, Khandare K, Kumar A, Sharma PK, Kumar J. Manipulating epigenetic diversity in crop plants: Techniques, challenges and opportunities. Biochim Biophys Acta Gen Subj 2024; 1868:130544. [PMID: 38104668 DOI: 10.1016/j.bbagen.2023.130544] [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] [Received: 09/18/2023] [Revised: 12/04/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
Epigenetic modifications act as conductors of inheritable alterations in gene expression, all while keeping the DNA sequence intact, thereby playing a pivotal role in shaping plant growth and development. This review article presents an overview of techniques employed to investigate and manipulate epigenetic diversity in crop plants, focusing on both naturally occurring and artificially induced epialleles. The significance of epigenetic modifications in facilitating adaptive responses is explored through the examination of how various biotic and abiotic stresses impact them. Further, environmental chemicals are explored for their role in inducing epigenetic changes, particularly focusing on inhibitors of DNA methylation like 5-AzaC and zebularine, as well as inhibitors of histone deacetylation including trichostatin A and sodium butyrate. The review delves into various approaches for generating epialleles, including tissue culture techniques, mutagenesis, and grafting, elucidating their potential to induce heritable epigenetic modifications in plants. In addition, the ground breaking CRISPR/Cas is emphasized for its accuracy in targeting specific epigenetic changes. This presents a potent tools for deciphering the intricacies of epigenetic mechanisms. Furthermore, the intricate relationship between epigenetic modifications and non-coding RNA expression, including siRNAs and miRNAs, is investigated. The emerging role of exo-RNAi in epigenetic regulation is also introduced, unveiling its promising potential for future applications. The article concludes by addressing the opportunities and challenges presented by these techniques, emphasizing their implications for crop improvement. Conclusively, this extensive review provides valuable insights into the intricate realm of epigenetic changes, illuminating their significance in phenotypic plasticity and their potential in advancing crop improvement.
Collapse
Affiliation(s)
| | - Shoeb Ahmed
- Ch. Charan Singh University, Meerut 250004, India
| | - Dinesh Kumar Saini
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, United States
| | - Vijay Gahlaut
- University Centre for Research and Development, Chandigarh University, Mohali 140413, Punjab, India
| | | | - Kiran Khandare
- Center of Innovative and Applied Bioprocessing, Mohali 140308, Punjab, India
| | - Ashutosh Kumar
- Center of Innovative and Applied Bioprocessing, Mohali 140308, Punjab, India
| | - Pradeep Kumar Sharma
- Ch. Charan Singh University, Meerut 250004, India; Maharaja Suhel Dev State University, Azamgarh 276404, U.P., India
| | - Jitendra Kumar
- National Agri-Food Biotechnology Institute, Sector-81, Mohali 140306, Punjab, India.
| |
Collapse
|
2
|
Ramakrishnan M, Zhou M, Ceasar SA, Ali DJ, Maharajan T, Vinod KK, Sharma A, Ahmad Z, Wei Q. Epigenetic modifications and miRNAs determine the transition of somatic cells into somatic embryos. PLANT CELL REPORTS 2023; 42:1845-1873. [PMID: 37792027 DOI: 10.1007/s00299-023-03071-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 09/13/2023] [Indexed: 10/05/2023]
Abstract
KEY MESSAGE This review discusses the epigenetic changes during somatic embryo (SE) development, highlights the genes and miRNAs involved in the transition of somatic cells into SEs as a result of epigenetic changes, and draws insights on biotechnological opportunities to study SE development. Somatic embryogenesis from somatic cells occurs in a series of steps. The transition of somatic cells into somatic embryos (SEs) is the most critical step under genetic and epigenetic regulations. Major regulatory genes such as SERK, WUS, BBM, FUS3/FUSA3, AGL15, and PKL, control SE steps and development by turning on and off other regulatory genes. Gene transcription profiles of somatic cells during SE development is the result of epigenetic changes, such as DNA and histone protein modifications, that control and decide the fate of SE formation. Depending on the type of somatic cells and the treatment with plant growth regulators, epigenetic changes take place dynamically. Either hypermethylation or hypomethylation of SE-related genes promotes the transition of somatic cells. For example, the reduced levels of DNA methylation of SERK and WUS promotes SE initiation. Histone modifications also promote SE induction by regulating SE-related genes in somatic cells. In addition, miRNAs contribute to the various stages of SE by regulating the expression of auxin signaling pathway genes (TIR1, AFB2, ARF6, and ARF8), transcription factors (CUC1 and CUC2), and growth-regulating factors (GRFs) involved in SE formation. These epigenetic and miRNA functions are unique and have the potential to regenerate bipolar structures from somatic cells when a pluripotent state is induced. However, an integrated overview of the key regulators involved in SE development and downstream processes is lacking. Therefore, this review discusses epigenetic modifications involved in SE development, SE-related genes and miRNAs associated with epigenetics, and common cis-regulatory elements in the promoters of SE-related genes. Finally, we highlight future biotechnological opportunities to alter epigenetic pathways using the genome editing tool and to study the transition mechanism of somatic cells.
Collapse
Affiliation(s)
- Muthusamy Ramakrishnan
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration On Subtropical Forest Biodiversity Conservation, School of Life Sciences, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Mingbing Zhou
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
- Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-Efficiency Utilization, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
| | - Stanislaus Antony Ceasar
- Department of Biosciences, Rajagiri College of Social Sciences (Autonomous), Kalamassery, Kochi, 683104, Kerala, India
| | - Doulathunnisa Jaffar Ali
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, Jiangsu, China
| | - Theivanayagam Maharajan
- Department of Biosciences, Rajagiri College of Social Sciences (Autonomous), Kalamassery, Kochi, 683104, Kerala, India
| | | | - Anket Sharma
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
| | - Zishan Ahmad
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration On Subtropical Forest Biodiversity Conservation, School of Life Sciences, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Qiang Wei
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration On Subtropical Forest Biodiversity Conservation, School of Life Sciences, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China.
| |
Collapse
|
3
|
Nuzzo F, Gambino G, Perrone I. Unlocking grapevine in vitro regeneration: Issues and perspectives for genetic improvement and functional genomic studies. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 193:99-109. [PMID: 36343465 DOI: 10.1016/j.plaphy.2022.10.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 10/24/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Abstract
In vitro plant regeneration is a pivotal process in genetic engineering to obtain large numbers of transgenic, cisgenic and gene edited plants in the frame of functional gene or genetic improvement studies. However, several issues emerge as regeneration is not universally possible across the plant kingdom and many variables must be considered. In grapevine (Vitis spp.), as in other woody and fruit tree species, the regeneration process is impaired by a recalcitrance that depends on numerous factors such as genotype and explant-dependent responses. This is one of the major obstacles in developing gene editing approaches and functional genome studies in grapevine and it is therefore crucial to understand how to achieve efficient regeneration across different genotypes. Further issues that emerge in regeneration need to be addressed, such as somaclonal mutations which do not allow the regeneration of individuals identical to the original mother plant, an essential factor for commercial use of the improved grapevines obtained through the New Breeding Techniques. Over the years, the evolution of protocols to achieve plant regeneration has relied mainly on optimizing protocols for genotypes of interest whilst nowadays with new genomic data available there is an emerging opportunity to have a clearer picture of its molecular regulation. The goal of this review is to discuss the latest information available about different aspects of grapevine in vitro regeneration, to address the main factors that can impair the efficiency of the plant regeneration process and cause post-regeneration problems and to propose strategies for investigating and solving them.
Collapse
Affiliation(s)
- Floriana Nuzzo
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Strada Delle Cacce 73, 10135, Torino, Italy
| | - Giorgio Gambino
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Strada Delle Cacce 73, 10135, Torino, Italy.
| | - Irene Perrone
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Strada Delle Cacce 73, 10135, Torino, Italy
| |
Collapse
|
4
|
Breen J, Mur LAJ, Sivakumaran A, Akinyemi A, Wilkinson MJ, Rodriguez Lopez CM. Botrytis cinerea Loss and Restoration of Virulence during In Vitro Culture Follows Flux in Global DNA Methylation. Int J Mol Sci 2022; 23:ijms23063034. [PMID: 35328468 PMCID: PMC8948621 DOI: 10.3390/ijms23063034] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/21/2022] [Accepted: 03/03/2022] [Indexed: 12/23/2022] Open
Abstract
Pathogenic fungi can lose virulence after protracted periods of culture, but little is known of the underlying mechanisms. Here, we present the first analysis of DNA methylation flux at a single-base resolution for the plant pathogen B. cinerea and identify differentially methylated genes/genomic regions associated with virulence erosion during in vitro culture. Cultures were maintained for eight months, with subcultures and virulence testing every month. Methylation-sensitive amplified polymorphisms were performed at monthly intervals to characterise global changes to the pathogen’s genome during culture and also on DNA from mycelium inoculated onto Arabidopsis thaliana after eight months in culture. Characterisation of culture-induced epialleles was assessed by whole-genome re-sequencing and whole-genome bisulfite sequencing. Virulence declined with time in culture and recovered after inoculation on A. thaliana. Variation detected by methylation-sensitive amplified polymorphisms followed virulence changes during culture. Whole-genome (bisulfite) sequencing showed marked changes in global and local methylation during culture but no significant genetic changes. We imply that virulence is a non-essential plastic character that is at least partly modified by the changing levels of DNA methylation during culture. We hypothesise that changing DNA methylation during culture may be responsible for the high virulence/low virulence transition in B. cinerea and speculate that this may offer fresh opportunities to control pathogen virulence.
Collapse
Affiliation(s)
- James Breen
- Indigenous Genomics, Telethon Kids Institute, Adelaide, SA 5000, Australia;
| | - Luis Alejandro Jose Mur
- Institute of Biological, Environmental and Rural Sciences, Edward Llywd Building, Penglais Campus, Aberystwyth SY23 3FG, UK; (L.A.J.M.); (A.S.); (A.A.); (M.J.W.)
| | - Anushen Sivakumaran
- Institute of Biological, Environmental and Rural Sciences, Edward Llywd Building, Penglais Campus, Aberystwyth SY23 3FG, UK; (L.A.J.M.); (A.S.); (A.A.); (M.J.W.)
| | - Aderemi Akinyemi
- Institute of Biological, Environmental and Rural Sciences, Edward Llywd Building, Penglais Campus, Aberystwyth SY23 3FG, UK; (L.A.J.M.); (A.S.); (A.A.); (M.J.W.)
| | - Michael James Wilkinson
- Institute of Biological, Environmental and Rural Sciences, Edward Llywd Building, Penglais Campus, Aberystwyth SY23 3FG, UK; (L.A.J.M.); (A.S.); (A.A.); (M.J.W.)
| | - Carlos Marcelino Rodriguez Lopez
- Environmental Epigenetics and Genetics Group, School of Agriculture, Food and Wine, Waite Research Precinct, University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia
- Correspondence:
| |
Collapse
|
5
|
Wang X, Ke L, Wang S, Fu J, Xu J, Hao Y, Kang C, Guo W, Deng X, Xu Q. Variation burst during dedifferentiation and increased CHH-type DNA methylation after 30 years of in vitro culture of sweet orange. HORTICULTURE RESEARCH 2022; 9:uhab036. [PMID: 35039837 PMCID: PMC8824543 DOI: 10.1093/hr/uhab036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 01/18/2022] [Accepted: 10/15/2021] [Indexed: 06/14/2023]
Abstract
Somaclonal variation arising from tissue culture may provide a valuable resource for the selection of new germplasm, but may not preserve true-to-type characteristics, which is a major concern for germplasm conservation or genome editing. The genomic changes associated with dedifferentiation and somaclonal variation during long-term in vitro culture are largely unknown. Sweet orange was one of the earliest plant species to be cultured in vitro and induced via somatic embryogenesis. We compared four sweet orange callus lines after 30 years of constant tissue culture with newly induced calli by comprehensively determining the single-nucleotide polymorphisms, copy number variations, transposable element insertions, methylomic and transcriptomic changes. We identified a burst of variation during early dedifferentiation, including a retrotransposon outbreak, followed by a variation purge during long-term in vitro culture. Notably, CHH methylation showed a dynamic pattern, initially disappearing during dedifferentiation and then more than recovering after 30 years of in vitro culture. We also analyzed the effects of somaclonal variation on transcriptional reprogramming, and indicated subgenome dominance was evident in the tetraploid callus. We identified a retrotransposon insertion and DNA modification alternations in the potential regeneration-related gene CLAVATA3/EMBRYO SURROUNDING REGION-RELATED 16. This study provides the foundation to harness in vitro variation and offers a deeper understanding of the variation introduced by tissue culture during germplasm conservation, somatic embryogenesis, gene editing, and breeding programs.
Collapse
Affiliation(s)
- Xia Wang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University,
No. 1, Shizishan Street, Wuhan 430070, China
| | - Lili Ke
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University,
No. 1, Shizishan Street, Wuhan 430070, China
| | - Shuting Wang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University,
No. 1, Shizishan Street, Wuhan 430070, China
| | - Jialing Fu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University,
No. 1, Shizishan Street, Wuhan 430070, China
| | - Jidi Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University,
No. 1, Shizishan Street, Wuhan 430070, China
| | - Yujin Hao
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University,
No. 1, Shizishan Street, Wuhan 430070, China
| | - Chunying Kang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University,
No. 1, Shizishan Street, Wuhan 430070, China
| | - Wenwu Guo
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University,
No. 1, Shizishan Street, Wuhan 430070, China
| | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University,
No. 1, Shizishan Street, Wuhan 430070, China
| | - Qiang Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University,
No. 1, Shizishan Street, Wuhan 430070, China
| |
Collapse
|
6
|
Yang A, Qi X, Wang QM, Wang H, Wang Y, Li L, Liu W, Qiao Y. The branch-thorn occurrence of Lycium ruthenicum is associated with leaf DNA hypermethylation in response to soil water content. Mol Biol Rep 2021; 49:1925-1934. [PMID: 34860320 DOI: 10.1007/s11033-021-07004-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 11/22/2021] [Indexed: 11/26/2022]
Abstract
BACKGROUND Lycium ruthenicum is an eco-economic shrub which can exist in two forms, thorny and thornless under varying soil moisture conditions. The aim of this study was to determine if the two forms of L. ruthenicum were influenced by soil water content (SWC) and to test the three-way link among SWC, occurrence of branch-thorn and DNA methylation modification. METHODS AND RESULTS Here, pot experiment was carried out to reveal the influence of SWC on the occurrence of branch-thorn and then paraffin sections, scanning electron microscope and methylation-sensitive amplification polymorphism(MSAP) analysis were used to determine the three-way link among SWC, branch-thorn occurrence and DNA methylation. The results showed that (a) soil drought promoted the development of thorn primordium into branch-thorn and (b) branch-thorn covered axillary bud to protect it against drought and other stresses; (c) the branch-thorn occurrence response to drought was correlated with hypermethylation of CCGG sites and (d) thorny and thornless plants of a clone were distinguished successfully based on the MSAP profiles of their leaves. CONCLUSIONS Branch-thorns of the L. ruthenicum clone, which occurred in response to drought, covered axillary buds to protect them against drought and other stresses; thorn primordium of the clone did not develop into branch-thorn under the adequate soil moisture condition. The occurrence and absence of the branch-thorns were correlated with the hyper- and hypo-methylation, respectively. We proposed that the branch-thorn plasticity might be an adjustment strategy for the environment, which seems to support the theory of "Use in, waste out".
Collapse
Affiliation(s)
- Ailin Yang
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Xinyu Qi
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Qin-Mei Wang
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China.
| | - Hao Wang
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Yucheng Wang
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Lujia Li
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Wen Liu
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Yang Qiao
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| |
Collapse
|
7
|
Singh D, Chaudhary P, Taunk J, Kumar Singh C, Sharma S, Singh VJ, Singh D, Chinnusamy V, Yadav R, Pal M. Plant epigenomics for extenuation of abiotic stresses: challenges and future perspectives. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6836-6855. [PMID: 34302734 DOI: 10.1093/jxb/erab337] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 07/23/2021] [Indexed: 06/13/2023]
Abstract
Climate change has escalated abiotic stresses, leading to adverse effects on plant growth and development, eventually having deleterious consequences on crop productivity. Environmental stresses induce epigenetic changes, namely cytosine DNA methylation and histone post-translational modifications, thus altering chromatin structure and gene expression. Stable epigenetic changes are inheritable across generations and this enables plants to adapt to environmental changes (epipriming). Hence, epigenomes serve as a good source of additional tier of variability for development of climate-smart crops. Epigenetic resources such as epialleles, epigenetic recombinant inbred lines (epiRILs), epigenetic quantitative trait loci (epiQTLs), and epigenetic hybrids (epihybrids) can be utilized in epibreeding for improving stress tolerance of crops. Epigenome engineering is also gaining momentum for developing sustainable epimarks associated with important agronomic traits. Different epigenome editing tools are available for creating, erasing, and reading such epigenetic codes in plant genomes. However, epigenome editing is still understudied in plants due to its complex nature. Epigenetic interventions such as epi-fingerprinting can be exploited in the near future for health and quality assessment of crops under stress conditions. Keeping in view the challenges and opportunities associated with this important technology, the present review intends to enhance understanding of stress-induced epigenetic changes in plants and its prospects for development of climate-ready crops.
Collapse
Affiliation(s)
- Dharmendra Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi,India
| | - Priya Chaudhary
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi,India
| | - Jyoti Taunk
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Chandan Kumar Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi,India
| | - Shristi Sharma
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi,India
| | - Vikram Jeet Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi,India
| | - Deepti Singh
- Department of Botany, Meerut College, Meerut, India
| | - Viswanathan Chinnusamy
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Rajbir Yadav
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi,India
| | - Madan Pal
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| |
Collapse
|
8
|
Dalakouras A, Vlachostergios D. Epigenetic approaches to crop breeding: current status and perspectives. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5356-5371. [PMID: 34017985 DOI: 10.1093/jxb/erab227] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 05/18/2021] [Indexed: 05/10/2023]
Abstract
In order to tackle the cumulative adverse effects of global climate change, reduced farmland, and heightened needs of an ever-increasing world population, modern agriculture is in urgent search of solutions that can ensure world food security and sustainable development. Classical crop breeding is still a powerful method to obtain crops with valued agronomical traits, but its potential is gradually being compromised by the menacing decline of genetic variation. Resorting to the epigenome as a source of variation could serve as a promising alternative. Here, we discuss current status of epigenetics-mediated crop breeding (epibreeding), highlight its advances and limitations, outline currently available methodologies, and propose novel RNA-based strategies to modify the epigenome in a gene-specific and transgene-free manner.
Collapse
Affiliation(s)
- Athanasios Dalakouras
- Institute of Industrial and Forage Crops, HAO-DEMETER, 41335 Larissa, Greece
- Institute of Plant Breeding and Genetic Resources, HAO-DEMETER, 57001 Thessaloniki, Greece
| | | |
Collapse
|
9
|
Zhang W, Wang Y, Diao S, Zhong S, Wu S, Wang L, Su X, Zhang B. Assessment of Epigenetic and Phenotypic Variation in Populus nigra Regenerated via Sequential Regeneration. FRONTIERS IN PLANT SCIENCE 2021; 12:632088. [PMID: 34295342 PMCID: PMC8290414 DOI: 10.3389/fpls.2021.632088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 06/14/2021] [Indexed: 06/13/2023]
Abstract
Somatic variation has been demonstrated in tissue culture regenerated plants of many species. In the genus Populus, phenotypic variation caused by changes in 5-methylcytosine within the plant genome have been reported. To date, the phenotypic and epigenetic stability of plants regenerated from sequential regeneration has not been tested in trees. In this study, we detected DNA methylation of CCGG sites in regenerated plants of five generations in Populus nigra using methylation-sensitive amplified polymorphisms, and evaluated their growth performance and physiological traits. About 10.86-26.80% of CCGG sites in the regenerated plant genome were demethylated and 5.50-8.45% were methylated, resulting in significantly lower DNA methylation levels among all regenerated plants than among donor plants. We detected a significant difference in methylation levels between first regeneration regenerated plants (G1) and those of the other four generations (G2-G5); there were no significant differences among the four later generations. Therefore, the dramatic decrease in DNA methylation levels occurred only in the first and second poplar regenerations; levels then stabilized later in the regeneration process, indicating that two regeneration events were sufficient to change the methylation statuses of almost all CCGG sites sensitive to regeneration. Differences in growth and physiological traits were observed between regenerated plants and donor plants, but were significant only among plants of certain generations. Significant correlations were detected between methylation level and transpiration rate, net photosynthetic rate, peroxidase activity, and instant water utilization efficiency, indicating the involvement of epigenetic regulation in this unpredictable phenotypic variation.
Collapse
Affiliation(s)
- Weixi Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Yanbo Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Nanchang Institute of Technology, Nanchang, China
| | - Shu Diao
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Shanchen Zhong
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Shu Wu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Li Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Xiaohua Su
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Bingyu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| |
Collapse
|
10
|
Orłowska R, Pachota KA, Dynkowska WM, Niedziela A, Bednarek PT. Androgenic-Induced Transposable Elements Dependent Sequence Variation in Barley. Int J Mol Sci 2021; 22:ijms22136783. [PMID: 34202586 PMCID: PMC8268840 DOI: 10.3390/ijms22136783] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/14/2021] [Accepted: 06/22/2021] [Indexed: 01/10/2023] Open
Abstract
A plant genome usually encompasses different families of transposable elements (TEs) that may constitute up to 85% of nuclear DNA. Under stressful conditions, some of them may activate, leading to sequence variation. In vitro plant regeneration may induce either phenotypic or genetic and epigenetic changes. While DNA methylation alternations might be related, i.e., to the Yang cycle problems, DNA pattern changes, especially DNA demethylation, may activate TEs that could result in point mutations in DNA sequence changes. Thus, TEs have the highest input into sequence variation (SV). A set of barley regenerants were derived via in vitro anther culture. High Performance Liquid Chromatography (RP-HPLC), used to study the global DNA methylation of donor plants and their regenerants, showed that the level of DNA methylation increased in regenerants by 1.45% compared to the donors. The Methyl-Sensitive Transposon Display (MSTD) based on methylation-sensitive Amplified Fragment Length Polymorphism (metAFLP) approach demonstrated that, depending on the selected elements belonging to the TEs family analyzed, varying levels of sequence variation were evaluated. DNA sequence contexts may have a different impact on SV generated by distinct mobile elements belonged to various TE families. Based on the presented study, some of the selected mobile elements contribute differently to TE-related SV. The surrounding context of the TEs DNA sequence is possibly important here, and the study explained some part of SV related to those contexts.
Collapse
|
11
|
Comparative Study of the Genetic and Biochemical Variability of Polyscias filicifolia (Araliaceae) Regenerants Obtained by Indirect and Direct Somatic Embryogenesis as a Source of Triterpenes. Int J Mol Sci 2021; 22:ijms22115752. [PMID: 34072251 PMCID: PMC8198449 DOI: 10.3390/ijms22115752] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/18/2021] [Accepted: 05/26/2021] [Indexed: 12/15/2022] Open
Abstract
Polyscias filicifolia (Araliaceae) is broadly used in traditional medicine in Southeast Asia due to its antimicrobial, immunomodulating and cytotoxic activities. The main groups of compounds responsible for pharmacological effects are believed to be oleanolic triterpene saponins. However, Polyscias plants demonstrate relatively slow growth in natural conditions, which led to applying a developing sustainable source of plant material via primary (PSE), secondary (DSE) and direct somatic embryogenesis from DSE (TSE). The AFLP and metAFLP genotyping resulted in 1277 markers, amplified by a total of 24 pairs of selective primers. Only 3.13% of the markers were polymorphic. The analysis of variance showed that the PSE and TSE regenerants differed only in terms of root number, while the DSE plantlets differed for all studied morphological characteristics. Further, the chemical analysis revealed that oleanolic acid (439.72 µg/g DW), ursolic acid (111.85 µg/g DW) and hederagenin (19.07 µg/g DW) were determined in TSE regenerants. Our results indicate that direct somatic embryogenesis ensures the production of homogeneous plant material, which can serve as a potential source of triterpene compounds. Plants obtained via somatic embryogenesis could also be reintroduced into the natural environment to protect and preserve its biodiversity.
Collapse
|
12
|
Orłowska R. Barley somatic embryogenesis-an attempt to modify variation induced in tissue culture. ACTA ACUST UNITED AC 2021; 28:9. [PMID: 33726856 PMCID: PMC7962293 DOI: 10.1186/s40709-021-00138-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 02/19/2021] [Indexed: 11/25/2022]
Abstract
Background Somatic embryogenesis is a phenomenon carried out in an environment that generates abiotic stress. Thus, regenerants may differ from the source of explants at the morphological, genetic, and epigenetic levels. The DNA changes may be the outcome of induction media ingredients (i.e., copper and silver ions) and their concentrations and time of in vitro cultures. Results This study optimised the level of copper and silver ion concentration in culture media parallel with the induction medium longevity step towards obtaining barley regenerants via somatic embryogenesis with a minimum or maximum level of tissue culture-induced differences between the donor plant and its regenerants. The optimisation process is based on tissue culture-induced variation evaluated via the metAFLP approach for regenerants derived under varying in vitro tissue culture conditions and exploited by the Taguchi method. In the optimisation and verification experiments, various copper and silver ion concentrations and the different number of days differentiated the tested trials concerning the tissue culture-induced variation level, DNA demethylation, and de novo methylation, including symmetric (CG, CHG) and asymmetric (CHH) DNA sequence contexts. Verification of optimised conditions towards obtaining regenerants with minimum and maximum variability compared to donor plants proved useful. The main changes that discriminate optimised conditions belonged to DNA demethylation events with particular stress on CHG context. Conclusions The combination of tissue culture-induced variation evaluated for eight experimental trials and implementation of the Taguchi method allowed the optimisation of the in vitro tissue culture conditions towards the minimum and maximum differences between a source of tissue explants (donor plant) and its regenerants from somatic embryos. The tissue culture-induced variation characteristic is mostly affected by demethylation with preferences towards CHG sequence context.
Collapse
Affiliation(s)
- Renata Orłowska
- Plant Breeding & Acclimatization Institute-National Research Institute, 05-870 Błonie, Radzików, Poland.
| |
Collapse
|
13
|
Gao Y, Wang QM, An Q, Cui J, Zhou Y, Qi X, Zhang L, Li L. A novel micropropagation of Lycium ruthenicum and epigenetic fidelity assessment of three types of micropropagated plants in vitro and ex vitro. PLoS One 2021; 16:e0247666. [PMID: 33621255 PMCID: PMC7901770 DOI: 10.1371/journal.pone.0247666] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 02/10/2021] [Indexed: 11/18/2022] Open
Abstract
Lycium ruthenicum is an excellent eco-economic shrub. Numerous researches have been conducted for the function of its fruits but scarcely focused on the somaclonal variation and DNA methylation. An efficient micropropagation protocol from leaves and stems of L. ruthenicum was developed in this study, in which not only the leaf explants but also the stem explants of L. ruthenicum were dedifferentiated and produced adventitious buds/multiple shoots on one type of medium. Notably, the efficient indirect organogenesis of stem explants was independent of exogenous auxin, which is contrary to the common conclusion that induction and proliferation of calli is dependent on exogenous auxin. We proposed that sucrose supply might be the crucial regulator of stem callus induction and proliferation of L. ruthenicum. Furthermore, results of methylation-sensitive amplified polymorphism (MSAP) showed that DNA methylation somaclonal variation (MSV) of CNG decreased but that of CG increased after acclimatization. Three types of micropropagated plants (from leaf calli, stem calli and axillary buds) were epigenetically diverged more from each other after acclimatization and the ex vitro micropropagated plants should be selected to determine the fidelity. In summary, plants micropropagated from axillary buds and leaves of L. ruthenicum was more fidelity and might be suitable for preservation and propagation of elite germplasm. Also, leaf explants should be used in transformation. Meanwhile, plants from stem calli showed the highest MSV and might be used in somaclonal variation breeding. Moreover, one MSV hotspot was found based on biological replicates. The study not only provided foundations for molecular breeding, somaclonal variation breeding, preservation and propagation of elite germplasm, but also offered clues for further revealing novel mechanisms of both stem-explant dedifferentiation and MSV of L. ruthenicum.
Collapse
Affiliation(s)
- Yue Gao
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Qin-Mei Wang
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Qinxia An
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Jianguo Cui
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Yongbin Zhou
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Xinyu Qi
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Lijie Zhang
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Lujia Li
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, Liaoning, China
| |
Collapse
|
14
|
Chelomina GN, Rozhkovan KV, Burundukova OL, Gorpenchenko TY, Khrolenko YA, Zhuravlev YN. Age-Dependent and Tissue-Specific Alterations in the rDNA Clusters of the Panax ginseng C. A. Meyer Cultivated Cell Lines. Biomolecules 2020; 10:biom10101410. [PMID: 33036123 PMCID: PMC7599642 DOI: 10.3390/biom10101410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 09/30/2020] [Accepted: 10/01/2020] [Indexed: 01/25/2023] Open
Abstract
Long-term cultivation of Panax ginseng cell lines leads to a decreasing synthesis of the biologically active substances used in traditional medicine. To gain insight into the cellular mechanisms which may influence this process, we analyzed variations within the rDNA cluster of the Oriental ginseng cell lines. The cell lines were cultivated for 6 and 24 years; the number of nucleoli and chromosomes was analyzed. The complete 18S rDNA sequences were cloned and sequenced. The nucleotide polymorphism and phylogenetic relations of the sequences were analyzed, and the secondary structures for separate 18S rRNA regions were modeled. The 18S rDNA accumulated mutations during cell cultivation that correlate well with an increase in the number of chromosomes and nucleoli. The patterns of nucleotide diversity are culture-specific and the increasing polymorphism associates with cytosine methylation sites. The secondary structures of some 18S rRNA regions and their interaction can alter during cultivation. The phylogenetic tree topologies are particular for each cell line.The observed alterations in rDNA clusters are associated with a somaclonal variation, leading to changes in the pattern of intracellular synthesis during cell cultivation. The identified divergent rRNAs could provide additional gene expression regulation in P. ginseng cells by forming heterogeneous ribosomes.
Collapse
Affiliation(s)
- Galina N. Chelomina
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far-Eastern Branch of Russian Academy of Science, Vladivostok 690022, Russia; (K.V.R.); (O.L.B.); (T.Y.G.); (Y.A.K.); (Y.N.Z.)
- Correspondence: ; Tel.: +7-(423)-231-0410
| | - Konstantin V. Rozhkovan
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far-Eastern Branch of Russian Academy of Science, Vladivostok 690022, Russia; (K.V.R.); (O.L.B.); (T.Y.G.); (Y.A.K.); (Y.N.Z.)
- Saint-Petersburg State University Clinic, St. Petersburg 190103, Russia
| | - Olga L. Burundukova
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far-Eastern Branch of Russian Academy of Science, Vladivostok 690022, Russia; (K.V.R.); (O.L.B.); (T.Y.G.); (Y.A.K.); (Y.N.Z.)
| | - Tatiana Y. Gorpenchenko
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far-Eastern Branch of Russian Academy of Science, Vladivostok 690022, Russia; (K.V.R.); (O.L.B.); (T.Y.G.); (Y.A.K.); (Y.N.Z.)
| | - Yulia A. Khrolenko
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far-Eastern Branch of Russian Academy of Science, Vladivostok 690022, Russia; (K.V.R.); (O.L.B.); (T.Y.G.); (Y.A.K.); (Y.N.Z.)
| | - Yuri N. Zhuravlev
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far-Eastern Branch of Russian Academy of Science, Vladivostok 690022, Russia; (K.V.R.); (O.L.B.); (T.Y.G.); (Y.A.K.); (Y.N.Z.)
| |
Collapse
|
15
|
Time of In Vitro Anther Culture May Moderate Action of Copper and Silver Ions that Affect the Relationship between DNA Methylation Change and the Yield of Barley Green Regenerants. PLANTS 2020; 9:plants9091064. [PMID: 32825181 PMCID: PMC7570150 DOI: 10.3390/plants9091064] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/10/2020] [Accepted: 08/17/2020] [Indexed: 12/18/2022]
Abstract
Plant anther culture allows for the regeneration of uniform and homozygous double haploids. However, off-type regenerants may appear as a result of so-called tissue culture-induced variation (TCIV). In addition, the presence of Cu2+ and Ag+ ions in the culture medium might influence the number of green plants. The regenerants were obtained via anther cultures of barley under varying Cu2+ and Ag+ ion concentrations in the induction medium during distinct time conditions. DArTseqMet markers were evaluated based on regenerants and donor plants and delivering data on DNA demethylation (DM) and de novo methylation (DNM) and changes in methylation (Delta). The number of green regenerated plants per 100 anthers (GPs) was evaluated. The Cu2+ and Ag+ ion concentrations moderated relationships between Delta and the number of green plants conditional on time of tissue cultures. Depending on the ions, moderated moderation is valid within the different time of anther culture. When the highest concentration of copper is analyzed, plant regeneration is possible under short ‘Time’ (21 days) of anther culture wherein Delta is negative or under elongated Time when Delta is positive. Under 21 days of culture, the highest concentration of silver ions and when Delta is negative, some regenerants could be evaluated. However, under high Ag+ concentration when Time of culture is long and Delta positive, the highest number of green plants could be obtained.
Collapse
|
16
|
Azizi P, Hanafi MM, Sahebi M, Harikrishna JA, Taheri S, Yassoralipour A, Nasehi A. Epigenetic changes and their relationship to somaclonal variation: a need to monitor the micropropagation of plantation crops. FUNCTIONAL PLANT BIOLOGY : FPB 2020; 47:508-523. [PMID: 32349860 DOI: 10.1071/fp19077] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 02/23/2020] [Indexed: 06/11/2023]
Abstract
Chromatin modulation plays important roles in gene expression regulation and genome activities. In plants, epigenetic changes, including variations in histone modification and DNA methylation, are linked to alterations in gene expression. Despite the significance and potential of in vitro cell and tissue culture systems in fundamental research and marketable applications, these systems threaten the genetic and epigenetic networks of intact plant organs and tissues. Cell and tissue culture applications can lead to DNA variations, methylation alterations, transposon activation, and finally, somaclonal variations. In this review, we discuss the status of the current understanding of epigenomic changes that occur under in vitro conditions in plantation crops, including coconut, oil palm, rubber, cotton, coffee and tea. It is hoped that comprehensive knowledge of the molecular basis of these epigenomic variations will help researchers develop strategies to enhance the totipotent and embryogenic capabilities of tissue culture systems for plantation crops.
Collapse
Affiliation(s)
- Parisa Azizi
- Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; and Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Mohamed M Hanafi
- Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; and Department of Land Management, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; and Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; and Corresponding author.
| | - Mahbod Sahebi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Jennifer A Harikrishna
- Centre of Research in Biotechnology for Agriculture (CEBAR), University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Sima Taheri
- Centre of Research in Biotechnology for Agriculture (CEBAR), University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Ali Yassoralipour
- Department of Agricultural and Food Science, Faculty of Science (Kampar Campus), Universiti Tunku Abdul Rahman (UTAR), Jalan Universiti, Bandar Barat, 31900 Kampar, Perak, Malaysia
| | - Abbas Nasehi
- Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| |
Collapse
|
17
|
Bulut B, Aydinli Z, Türktaş-Erken M. MSAP analysis reveals diverse epigenetic statuses in opium poppy varieties with different benzyisoquinoline alkaloid content. ACTA ACUST UNITED AC 2020; 44:103-109. [PMID: 32256146 PMCID: PMC7129067 DOI: 10.3906/biy-1911-69] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
DNA methylation is one of the major epigenetic modifications influencing the regulation of gene expression. The opium poppy is an important medicinal plant. Its latex contains opium, which is a rich source of pharmaceutical benzyisoquinoline alkaloids (BIA). Here, the methylation-sensitive amplification polymorphism (MSAP) profiling technique using 21 MSAP molecular markers was applied in order to compare levels of DNA methylation between 6 opium poppy varieties. MSAP profiling reflected the different methylation statuses among opium poppy varieties having divergent BIA content. Moreover, different organ-specific epigenetic profiles were observed between the samples. Differential epigenetic profiles of capsules and shoots from the leaves pointed to the impact of methylation on BIA biosynthesis. The data implied that the different DNA methylation status may have important biological significance, in the case of alkaloid content in opium poppy in particular.
Collapse
Affiliation(s)
- Betül Bulut
- Department of Biology, Faculty of Science, Çankırı Karatekin University, Çankırı Turkey
| | - Zehra Aydinli
- Department of Biology, Faculty of Science, Çankırı Karatekin University, Çankırı Turkey
| | - Mine Türktaş-Erken
- Department of Biology, Faculty of Science, Çankırı Karatekin University, Çankırı Turkey
| |
Collapse
|
18
|
Sangra A, Shahin L, Dhir SK. Long-Term Maintainable Somatic Embryogenesis System in Alfalfa ( Medicago sativa) Using Leaf Explants: Embryogenic Sustainability Approach. PLANTS (BASEL, SWITZERLAND) 2019; 8:E278. [PMID: 31405007 PMCID: PMC6724077 DOI: 10.3390/plants8080278] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 08/04/2019] [Accepted: 08/07/2019] [Indexed: 11/17/2022]
Abstract
Alfalfa (Medicago sativa) is one of the most important forage legume crops because of its mass production and high feeding value. It originated in Asia and is one of the most ancient plants cultivated throughout the world as a fodder. Despite the well-studied somatic embryogenesis of alfalfa, there is a lack of a long-term maintainable somatic embryogenic system. Every time an embryogenic callus culture must be started from new explants, which is laborious, costly and time consuming. In addition to this, endogenous microorganisms present in ex vitro explants of alfalfa can often cause contamination, reducing the efficiency of callus culture. An attempt was made to establish long-term continuous somatic embryogenesis system in alfalfa using cultivar Regen-SY. Nine somatic embryogenesis pathways were studied and evaluated for embryo yield, plant conversion rate and embryogenic sustainability. Somatic embryos passed through the same stages (globular, heart-shaped, torpedo and cotyledonary) as characteristic of the zygotic embryo and secondary somatic embryogenesis was also observed. B5H-B5 system showed the highest embryo yield and plant conversion rate whereas SH4K-BOi2Y system demonstrated the highest embryogenic sustainability and maintained the embryogenic potential even after six subculture cycles. Scanning electron microscopy was applied to study the morphology of the somatic embryos and secondary somatic embryogenesis. Therefore, long-term maintainable somatic embryogenesis system protocol was developed through this study, which will help to enhance and accelerate the alfalfa biotechnology research.
Collapse
Affiliation(s)
- Ankush Sangra
- College of Agriculture, Family Sciences and Technology, Fort Valley State University, Fort Valley, GA 31030, USA
| | - Lubana Shahin
- College of Agriculture, Family Sciences and Technology, Fort Valley State University, Fort Valley, GA 31030, USA
| | - Sarwan K Dhir
- Center for Biotechnology, Department of Plant Sciences, Fort Valley State University, Fort Valley, GA 31030, USA.
| |
Collapse
|
19
|
Gulyás A, Dobránszki J, Kiss E, da Silva JAT, Posta K, Hidvégi N. Changes in DNA methylation pattern of apple long-term in vitro shoot culture and acclimatized plants. JOURNAL OF PLANT PHYSIOLOGY 2019; 239:18-27. [PMID: 31177027 DOI: 10.1016/j.jplph.2019.05.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 04/17/2019] [Accepted: 05/13/2019] [Indexed: 06/09/2023]
Abstract
DNA methylation is a process of epigenetic modification that can alter the functionality of a genome. Using whole-genome bisulfite sequencing, this study quantify the level of DNA methylation in the epigenomes of two diploid apple (Malus x domestica) scion cultivars ('McIntosh' and 'Húsvéti rozmaring') derived from three environmental conditions: in vivo mother plants in an orchard, in vitro culture, and acclimatized in vitro plants. The global DNA methylation levels were not dependent on the source of plant material, and the average level of DNA methylation was 49.77%, 34.65% and 8.77% in CpG, CHG and CHH contexts, respectively. Significant differences in DNA methylation were identified in 586 (specifically 334, 201 and 131 in CpG, CHG and CHH contexts, respectively) out of 45,116 genes, including promoter and coding sequences. These were classified as differentially methylated genes (DMGs). This is a 1.3% difference in the level of DNA methylation of genes in response to a change in the environment. Differential methylation was visualised by MA plots and functional genomic maps were established for biological processes, molecular functions and cellular components. When the DMGs were considered, in vitro tissue culture resulted in the highest level of methylation, but it was lower in acclimatized in vitro plants which was similar to that in the mother tree. Methylation patterns of the two scions differed, indicating cultivar-specific epigenetic regulation of gene expression during adaptation to various environments. After selecting genes that displayed differences larger than ±10% in CpG and CHG contexts, or larger than ±1.35% in the CHH context from among the DMGs, they were annotated in Blast2 GO v5.1.12 for Gene Ontology. DMGs identified as MD07G1113000 (protein transport), MD08G1041600 (extracellular space), MD09G1054800 (phosphatidic acid binding), and MD10G1265800 (not annotated) were methylated in all three contexts in in vitro shoots. These DNA methylation results suggest that epigenetic changes may contribute to the adaptation of apple to environmental changes by modifying the epigenome and thereby gene expression.
Collapse
Affiliation(s)
- Andrea Gulyás
- Research Institute of Nyíregyháza, IAREF, University of Debrecen, Nyíregyháza, P.O. Box 12, H-4400, Hungary.
| | - Judit Dobránszki
- Research Institute of Nyíregyháza, IAREF, University of Debrecen, Nyíregyháza, P.O. Box 12, H-4400, Hungary.
| | - Erzsébet Kiss
- Institute of Genetics, Microbiology and Biotechnology, Faculty of Agricultural and Environmental Sciences, Szent István University, Gödöllő, Páter Károly u.1., H-2100, Hungary.
| | - Jaime A Teixeira da Silva
- Research Institute of Nyíregyháza, IAREF, University of Debrecen, Nyíregyháza, P.O. Box 12, H-4400, Hungary.
| | - Katalin Posta
- Institute of Genetics, Microbiology and Biotechnology, Faculty of Agricultural and Environmental Sciences, Szent István University, Gödöllő, Páter Károly u.1., H-2100, Hungary.
| | - Norbert Hidvégi
- Research Institute of Nyíregyháza, IAREF, University of Debrecen, Nyíregyháza, P.O. Box 12, H-4400, Hungary.
| |
Collapse
|
20
|
Akomeah B, Quain MD, Ramesh SA, Anand L, Rodríguez López CM. Common garden experiment reveals altered nutritional values and DNA methylation profiles in micropropagated three elite Ghanaian sweet potato genotypes. PLoS One 2019; 14:e0208214. [PMID: 31026262 PMCID: PMC6485893 DOI: 10.1371/journal.pone.0208214] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 04/07/2019] [Indexed: 11/18/2022] Open
Abstract
Micronutrient deficiency is the cause of multiple diseases in developing countries. Staple crop biofortification is an efficient means to combat such deficiencies in the diets of local consumers. Biofortified lines of sweet potato (Ipomoea batata L. Lam) with enhanced beta-carotene content have been developed in Ghana to alleviate Vitamin A Deficiency. These genotypes are propagated using meristem micropropagation to ensure the generation of virus-free propagules. In vitro culture exposes micropropagated plants to conditions that can lead to the accumulation of somaclonal variation with the potential to generate unwanted aberrant phenotypes. However, the effect of micropropagation induced somaclonal variation on the production of key nutrients by field-grown plants has not been previously studied. Here we assessed the extent of in vitro culture induced somaclonal variation, at a phenotypic, compositional and genetic/epigenetic level, by comparing field-maintained and micropropagated lines of three elite Ghanaian sweet potato genotypes grown in a common garden. Although micropropagated plants presented no observable morphological abnormalities compared to field maintained lines, they presented significantly lower levels of iron, total protein, zinc, and glucose. Methylation Sensitive Amplification Polymorphism analysis showed a high level of in vitro culture induced molecular variation in micropropagated plants. Epigenetic, rather than genetic variation, accounts for most of the observed molecular variability. Taken collectively, our results highlight the importance of ensuring the clonal fidelity of the micropropagated biofortified lines in order to reduce potential losses in the nutritional value prior to their commercial release.
Collapse
Affiliation(s)
- Belinda Akomeah
- ARC Centre of Excellence in Plant Energy Biology, University of Adelaide, Waite Campus, PMB1 Glen Osmond, South Africa, Australia
- The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, PMB1 Glen Osmond, South Africa, Australia
- CSIR-Crops Research Institute, Kumasi, Ghana
| | | | - Sunita A Ramesh
- ARC Centre of Excellence in Plant Energy Biology, University of Adelaide, Waite Campus, PMB1 Glen Osmond, South Africa, Australia
- The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, PMB1 Glen Osmond, South Africa, Australia
| | - Lakshay Anand
- Environmental Epigenetics and Genetics Group, Department of Horticulture, College of Agriculture, Food and Environment, University of Kentucky, Lexington, Kentucky, United States America
| | - Carlos M. Rodríguez López
- The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, PMB1 Glen Osmond, South Africa, Australia
- Environmental Epigenetics and Genetics Group, Department of Horticulture, College of Agriculture, Food and Environment, University of Kentucky, Lexington, Kentucky, United States America
- * E-mail:
| |
Collapse
|
21
|
Osorio-Montalvo P, Sáenz-Carbonell L, De-la-Peña C. 5-Azacytidine: A Promoter of Epigenetic Changes in the Quest to Improve Plant Somatic Embryogenesis. Int J Mol Sci 2018; 19:E3182. [PMID: 30332727 PMCID: PMC6214027 DOI: 10.3390/ijms19103182] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 10/09/2018] [Accepted: 10/10/2018] [Indexed: 02/06/2023] Open
Abstract
Somatic embryogenesis (SE) is a widely studied process due to its biotechnological potential to generate large quantities of plants in short time frames and from different sources of explants. The success of SE depends on many factors, such as the nature of the explant, the microenvironment generated by in vitro culture conditions, and the regulation of gene expression, among others. Epigenetics has recently been identified as an important factor influencing SE outcome. DNA methylation is one of the most studied epigenetic mechanisms due to its essential role in gene expression, and its participation in SE is crucial. DNA methylation levels can be modified through the use of drugs such as 5-Azacytidine (5-AzaC), an inhibitor of DNA methylation, which has been used during SE protocols. The balance between hypomethylation and hypermethylation seems to be the key to SE success. Here, we discuss the most prominent recent research on the role of 5-AzaC in the regulation of DNA methylation, highlighting its importance during the SE process. Also, the molecular implications that this inhibitor might have for the increase or decrease in the embryogenic potential of various explants are reviewed.
Collapse
Affiliation(s)
- Pedro Osorio-Montalvo
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34, Col. Chuburná de Hidalgo, 97205 Mérida, Yucatán, Mexico.
| | - Luis Sáenz-Carbonell
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34, Col. Chuburná de Hidalgo, 97205 Mérida, Yucatán, Mexico.
| | - Clelia De-la-Peña
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34, Col. Chuburná de Hidalgo, 97205 Mérida, Yucatán, Mexico.
| |
Collapse
|
22
|
Wickramasuriya AM, Dunwell JM. Cacao biotechnology: current status and future prospects. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:4-17. [PMID: 28985014 PMCID: PMC5785363 DOI: 10.1111/pbi.12848] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 09/25/2017] [Accepted: 09/28/2017] [Indexed: 05/03/2023]
Abstract
Theobroma cacao-The Food of the Gods, provides the raw material for the multibillion dollar chocolate industry and is also the main source of income for about 6 million smallholders around the world. Additionally, cocoa beans have a number of other nonfood uses in the pharmaceutical and cosmetic industries. Specifically, the potential health benefits of cocoa have received increasing attention as it is rich in polyphenols, particularly flavonoids. At present, the demand for cocoa and cocoa-based products in Asia is growing particularly rapidly and chocolate manufacturers are increasing investment in this region. However, in many Asian countries, cocoa production is hampered due to many reasons including technological, political and socio-economic issues. This review provides an overview of the present status of global cocoa production and recent advances in biotechnological applications for cacao improvement, with special emphasis on genetics/genomics, in vitro embryogenesis and genetic transformation. In addition, in order to obtain an insight into the latest innovations in the commercial sector, a survey was conducted on granted patents relating to T. cacao biotechnology.
Collapse
Affiliation(s)
| | - Jim M. Dunwell
- School of Agriculture, Policy and DevelopmentUniversity of ReadingReadingUK
| |
Collapse
|
23
|
Guillou C, Fillodeau A, Brulard E, Breton D, De Faria Maraschin S, Verdier D, Simon M, Ducos JP. Indirect somatic embryogenesis of Theobroma cacao L . in liquid medium and improvement of embryo-to-plantlet conversion rate. IN VITRO CELLULAR & DEVELOPMENTAL BIOLOGY. PLANT : JOURNAL OF THE TISSUE CULTURE ASSOCIATION 2018; 54:377-391. [PMID: 30147286 PMCID: PMC6096749 DOI: 10.1007/s11627-018-9909-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 05/15/2018] [Indexed: 05/08/2023]
Abstract
The establishment of cocoa embryogenic cell lines in liquid medium starting from high frequency somatic embryogenesis (HFSE) callus is described. The growth kinetics of the cultures during the multiplication and the expression steps conducted in 250 mL Erlenmeyer flasks were described for three genotypes selected for their agronomical traits (EET95, EET96, and EET103). The glucose and dissolved oxygen concentrations and the absorption of Murashige and Skoog medium macronutrients (nitrate, ammonium, potassium, sulfate, calcium, phosphorus, and magnesium) were monitored. The multiplication of the embryogenic calluses in a medium containing 2,4,5-trichlorophenoxyacetic acid (2,4,5-T) at 1 mg L-1, initiated with an inoculation density of 20 g L-1 of callus, was achieved. The growth rate was characterized by two phases, with the second being concomitant with a depletion of phosphorus and magnesium, and a decrease in the embryogenic potential of the callus. The expression of the callus embryogenic capacity was conducted in an auxin-free medium. The embryo production starting from 1 and 5 g L-1 inoculation densities was compared. When placed in the optimal expression conditions in flasks, 1 g of callus produced 1000 to 1500 embryos within 5 to 7 wk. Finally, two paths for improving the plantlet regenerative capacities of cocoa SE produced in liquid medium were identified. Supplementing the expression medium with myo-inositol used as an osmotic agent at a concentration of 50 g L-1 increased the embryo-to-plantlet conversion rate from 13-16% to 40-48%. A 6-wk culture of the embryos on a maturation medium in Petri dishes optimized their subsequent development into plantlets.
Collapse
Affiliation(s)
- Caroline Guillou
- Nestlé Research & Development Centre Tours–Plant Science Research Unit, 101 avenue Gustave Eiffel BP49716, 37097 Tours CEDEX 2, France
| | - Audrey Fillodeau
- Nestlé Research & Development Centre Tours–Plant Science Research Unit, 101 avenue Gustave Eiffel BP49716, 37097 Tours CEDEX 2, France
| | - Eric Brulard
- Nestlé Research & Development Centre Tours–Plant Science Research Unit, 101 avenue Gustave Eiffel BP49716, 37097 Tours CEDEX 2, France
| | - David Breton
- Nestlé Research & Development Centre Tours–Plant Science Research Unit, 101 avenue Gustave Eiffel BP49716, 37097 Tours CEDEX 2, France
| | - Simone De Faria Maraschin
- Nestlé Research & Development Centre Tours–Plant Science Research Unit, 101 avenue Gustave Eiffel BP49716, 37097 Tours CEDEX 2, France
| | - Dorothée Verdier
- Nestlé Research & Development Centre Tours–Plant Science Research Unit, 101 avenue Gustave Eiffel BP49716, 37097 Tours CEDEX 2, France
| | - Mathieu Simon
- Nestlé Research & Development Centre Tours–Plant Science Research Unit, 101 avenue Gustave Eiffel BP49716, 37097 Tours CEDEX 2, France
| | - Jean-Paul Ducos
- Nestlé Research & Development Centre Tours–Plant Science Research Unit, 101 avenue Gustave Eiffel BP49716, 37097 Tours CEDEX 2, France
| |
Collapse
|
24
|
He S, Xu W, Li F, Wang Y, Liu A. Intraspecific DNA methylation polymorphism in the non-edible oilseed plant castor bean. PLANT DIVERSITY 2017; 39:300-307. [PMID: 30159523 PMCID: PMC6112301 DOI: 10.1016/j.pld.2017.05.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Revised: 05/25/2017] [Accepted: 05/27/2017] [Indexed: 05/05/2023]
Abstract
Investigation of the relationships of phenotypic and epigenetic variations might be a good way to dissect the genetic or molecular basis of phenotypic variation and plasticity in plants. Castor bean (Ricinus communis L.), an important non-edible oilseed crop, is a mono-species genus plant in the family Euphorbiaceae. Since it displays rich phenotypic variations with low genetic diversity, castor bean is a good model to investigate the molecular basis of phenotypic and epigenetic variations. Cytosine DNA methylation represents a major molecular mechanism of epigenetic occurrence. In this study, epigenetic diversity of sixty landrace accessions collected worldwide was investigated using the methylation-sensitive amplification polymorphism (MSAP) technique. Results showed that the epigenetic diversity (based on the polymorphism of DNA methylated loci) exhibited a medium variation (Ne = 1.395, He = 0.242, I = 0.366) at the population level though the variation was great, ranging from 3.80% to 34.31% among accessions. Both population structure analysis and the phylogenetic construction (using the neighbor-joining criteria) revealed that the two main clades were identified, but they did not display a distinct geographic structure. After inspecting the location of polymorphic methylated loci on genome we identified that the polymorphic methylated loci occur widely in nuclear and organelle genomes. This study provides new data to understand phenotypic and epigenetic variations in castor bean.
Collapse
Affiliation(s)
- Shan He
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Xu
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Fei Li
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Yue Wang
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Aizhong Liu
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| |
Collapse
|
25
|
Origin of Secondary Somatic Embryos and Genetic Stability of the Regenerated Plants in Hevea brasiliensis. J RUBBER RES 2017. [DOI: 10.1007/bf03449145] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
|
26
|
Xie H, Konate M, Sai N, Tesfamicael KG, Cavagnaro T, Gilliham M, Breen J, Metcalfe A, Stephen JR, De Bei R, Collins C, Lopez CMR. Global DNA Methylation Patterns Can Play a Role in Defining Terroir in Grapevine ( Vitis vinifera cv. Shiraz). FRONTIERS IN PLANT SCIENCE 2017; 8:1860. [PMID: 29163587 PMCID: PMC5670326 DOI: 10.3389/fpls.2017.01860] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 10/11/2017] [Indexed: 05/21/2023]
Abstract
Understanding how grapevines perceive and adapt to different environments will provide us with an insight into how to better manage crop quality. Mounting evidence suggests that epigenetic mechanisms are a key interface between the environment and the genotype that ultimately affect the plant's phenotype. Moreover, it is now widely accepted that epigenetic mechanisms are a source of useful variability during crop varietal selection that could affect crop performance. While the contribution of DNA methylation to plant performance has been extensively studied in other major crops, very little work has been done in grapevine. To study the genetic and epigenetic diversity across 22 vineyards planted with the cultivar Shiraz in six wine sub-regions of the Barossa, South Australia. Methylation sensitive amplified polymorphisms (MSAPs) were used to obtain global patterns of DNA methylation. The observed epigenetic profiles showed a high level of differentiation that grouped vineyards by their area of provenance despite the low genetic differentiation between vineyards and sub-regions. Pairwise epigenetic distances between vineyards indicate that the main contributor (23-24%) to the detected variability is associated to the distribution of the vineyards on the N-S axis. Analysis of the methylation profiles of vineyards pruned with the same system increased the positive correlation observed between geographic distance and epigenetic distance suggesting that pruning system affects inter-vineyard epigenetic differentiation. Finally, methylation sensitive genotyping by sequencing identified 3,598 differentially methylated genes in grapevine leaves that were assigned to 1,144 unique gene ontology terms of which 8.6% were associated with response to environmental stimulus. Our results suggest that DNA methylation differences between vineyards and sub-regions within The Barossa are influenced both by the geographic location and, to a lesser extent, by pruning system. Finally, we discuss how epigenetic variability can be used as a tool to understand and potentially modulate terroir in grapevine.
Collapse
Affiliation(s)
- Huahan Xie
- Environmental Epigenetics and Genetics Group, University of Adelaide, Adelaide, SA, Australia
- The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
| | - Moumouni Konate
- Environmental Epigenetics and Genetics Group, University of Adelaide, Adelaide, SA, Australia
- The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
| | - Na Sai
- Environmental Epigenetics and Genetics Group, University of Adelaide, Adelaide, SA, Australia
- The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
- The ARC Centre of Excellence in Plant Energy Biology, University of Adelaide, Adelaide, SA, Australia
| | - Kiflu G. Tesfamicael
- Environmental Epigenetics and Genetics Group, University of Adelaide, Adelaide, SA, Australia
- The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
| | - Timothy Cavagnaro
- The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
| | - Matthew Gilliham
- The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
- The ARC Centre of Excellence in Plant Energy Biology, University of Adelaide, Adelaide, SA, Australia
| | - James Breen
- Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
- Bioinformatics Hub, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Andrew Metcalfe
- School of Mathematical Sciences, University of Adelaide, Adelaide, SA, Australia
| | - John R. Stephen
- Plant Genomics Centre, Australian Genome Research Facility Ltd., Adelaide, SA, Australia
| | - Roberta De Bei
- The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
| | - Cassandra Collins
- The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
| | - Carlos M. R. Lopez
- Environmental Epigenetics and Genetics Group, University of Adelaide, Adelaide, SA, Australia
- The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
- *Correspondence: Carlos M. R. Lopez,
| |
Collapse
|
27
|
Adu-Gyamfi R, Wetten A, Marcelino Rodríguez López C. Effect of Cryopreservation and Post-Cryopreservation Somatic Embryogenesis on the Epigenetic Fidelity of Cocoa (Theobroma cacao L.). PLoS One 2016; 11:e0158857. [PMID: 27403857 PMCID: PMC4942035 DOI: 10.1371/journal.pone.0158857] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 06/22/2016] [Indexed: 11/24/2022] Open
Abstract
UNLABELLED While cocoa plants regenerated from cryopreserved somatic embryos can demonstrate high levels of phenotypic variability, little is known about the sources of the observed variability. Previous studies have shown that the encapsulation-dehydration cryopreservation methodology imposes no significant extra mutational load since embryos carrying high levels of genetic variability are selected against during protracted culture. Also, the use of secondary rather than primary somatic embryos has been shown to further reduce the incidence of genetic somaclonal variation. Here, the effect of in vitro conservation, cryopreservation and post-cryopreservation generation of somatic embryos on the appearance of epigenetic somaclonal variation were comparatively assessed. To achieve this we compared the epigenetic profiles, generated using Methylation Sensitive Amplified Polymorphisms, of leaves collected from the ortet tree and from cocoa somatic embryos derived from three in vitro conditions: somatic embryos, somatic embryos cryopreserved in liquid nitrogen and somatic embryos generated from cryoproserved somatic embryos. Somatic embryos accumulated epigenetic changes but these were less extensive than in those regenerated after storage in LN. Furthermore, the passage of cryopreserved embryos through another embryogenic stage led to further increase in variation. Interestingly, this detected variability appears to be in some measure reversible. The outcome of this study indicates that the cryopreservation induced phenotypic variability could be, at least partially, due to DNA methylation changes. KEY MESSAGE Phenotypic variability observed in cryostored cocoa somatic-embryos is epigenetic in nature. This variability is partially reversible, not stochastic in nature but a directed response to the in-vitro culture and cryopreservation.
Collapse
Affiliation(s)
- Raphael Adu-Gyamfi
- Faculty of Agriculture, University for Development Studies, P.O. Box TL 1882, Tamale, Ghana
| | - Andy Wetten
- School of Agriculture, Policy and Development, University of Reading, Whiteknights, Reading, Berks, RG6 6AS, United Kingdom
| | - Carlos Marcelino Rodríguez López
- Environmental Epigenetics and Genetics Group, Plant Research Centre, School of Agriculture, Food and Wine, Faculty of Sciences, University of Adelaide, Waite Campus, PMB1, Glen Osmond, SA, 5064, Australia
| |
Collapse
|
28
|
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.
Collapse
|
29
|
Gimenez MD, Yañez-Santos AM, Paz RC, Quiroga MP, Marfil CF, Conci VC, García-Lampasona SC. Assessment of genetic and epigenetic changes in virus-free garlic (Allium sativum L.) plants obtained by meristem culture followed by in vitro propagation. PLANT CELL REPORTS 2016; 35:129-41. [PMID: 26466594 DOI: 10.1007/s00299-015-1874-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 08/14/2015] [Accepted: 09/25/2015] [Indexed: 05/05/2023]
Abstract
This is the first report assessing epigenetic variation in garlic. High genetic and epigenetic polymorphism during in vitro culture was detected.Sequencing of MSAP fragments revealed homology with ESTs. Garlic (Allium sativum) is a worldwide crop of economic importance susceptible to viral infections that can cause significant yield losses. Meristem tissue culture is the most employed method to sanitize elite cultivars.Often the virus-free garlic plants obtained are multiplied in vitro (micro propagation). However, it was reported that micro-propagation frequently produces somaclonal variation at the phenotypic level, which is an undesirable trait when breeders are seeking to maintain varietal stability. We employed amplification fragment length polymorphism and methylation sensitive amplified polymorphism (MSAP) methodologies to assess genetic and epigenetic modifications in two culture systems: virus-free plants obtained by meristem culture followed by in vitro multiplication and field culture. Our results suggest that garlic exhibits genetic and epigenetic polymorphism under field growing conditions. However, during in vitro culture system both kinds of polymorphisms intensify indicating that this system induces somaclonal variation. Furthermore, while genetic changes accumulated along the time of in vitro culture, epigenetic polymorphism reached the major variation at 6 months and then stabilize, being demethylation and CG methylation the principal conversions.Cloning and sequencing differentially methylated MSAP fragments allowed us to identify coding and unknown sequences of A. sativum, including sequences belonging to LTR Gypsy retrotransposons. Together, our results highlight that main changes occur in the initial 6 months of micro propagation. For the best of our knowledge, this is the first report on epigenetic assessment in garlic.
Collapse
|
30
|
Leljak-Levanić D, Mrvková M, Turečková V, Pěnčík A, Rolčík J, Strnad M, Mihaljević S. Hormonal and epigenetic regulation during embryogenic tissue habituation in Cucurbita pepo L. PLANT CELL REPORTS 2016; 35:77-89. [PMID: 26403461 DOI: 10.1007/s00299-015-1869-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 08/30/2015] [Accepted: 09/14/2015] [Indexed: 05/08/2023]
Abstract
Habituated embryogenic line of pumpkin contained more CKs and IAA, but less ABA than the non-habituated line. Pronounced hypomethylation correlated with the absence of 2,4-D, addition of 5-azaC, and the process of habituation. A comparative analysis between habituated and non-habituated embryogenic cultures of pumpkin (Cucurbita pepo L.) in relation to endogenous phytohormones, global DNA methylation, and developmental and regeneration capacities of the cultures was conducted. The analysis revealed more cytokinins (CKs) and indole-3-acetic acid (IAA), but less abscisic acid (ABA) in the habituated HEC line than in the non-habituated DEC line. Ribosides and ribotides were the most abundant CK forms in both HEC and DEC lines (75.9 and 57.6 %, respectively). HEC contained more free-base CKs (5.8 vs. 3.2 %), whereas DEC contained considerably more O-glycosides (39.1 vs. 18.3 %). Although prevalence of IAA was common for both lines, relative ratio of CKs and ABA differed between DEC and HEC lines. ABA was prevailing over CKs in DEC, while CKs prevailed over ABA in HEC line. Taking into account the importance of ABA for embryo maturation, the reduced endogenous ABA content in HEC line might be the reason for a 5-fold reduction in regeneration capacity compared to DEC. Both habituated and non-habituated embryogenic lines were highly methylated in the presence of 2,4-dichlorophenoxyacetic acid (2,4-D). Pronounced hypomethylation correlated with the absence of 2,4-D, addition of 5-azacytidine (5-azaC), but also with the process of habituation. The habituated line was resistant to the effect of hypomethylation drug 5-azaC and remained highly methylated even after the addition of 5-azaC. Also, 5-azaC did not change the developmental pattern in the habituated line, indicating the existence of separate mechanisms by which 2,4-D influences global DNA methylation in comparison to habituation-related global DNA methylation.
Collapse
Affiliation(s)
- Dunja Leljak-Levanić
- Faculty of Science, University of Zagreb, Horvatovac 102a, 10000, Zagreb, Croatia
| | - Mihaela Mrvková
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University and Institute of Experimental Botany ASCR, Šlechtitelů 11, 783 71, Olomouc, Czech Republic
| | - Veronika Turečková
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University and Institute of Experimental Botany ASCR, Šlechtitelů 11, 783 71, Olomouc, Czech Republic
| | - Aleš Pěnčík
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University and Institute of Experimental Botany ASCR, Šlechtitelů 11, 783 71, Olomouc, Czech Republic
| | - Jakub Rolčík
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University and Institute of Experimental Botany ASCR, Šlechtitelů 11, 783 71, Olomouc, Czech Republic
| | - Miroslav Strnad
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University and Institute of Experimental Botany ASCR, Šlechtitelů 11, 783 71, Olomouc, Czech Republic
| | | |
Collapse
|
31
|
Vogt G. Stochastic developmental variation, an epigenetic source of phenotypic diversity with far-reaching biological consequences. J Biosci 2015; 40:159-204. [PMID: 25740150 DOI: 10.1007/s12038-015-9506-8] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
This article reviews the production of different phenotypes from the same genotype in the same environment by stochastic cellular events, nonlinear mechanisms during patterning and morphogenesis, and probabilistic self-reinforcing circuitries in the adult life. These aspects of phenotypic variation are summarized under the term 'stochastic developmental variation' (SDV) in the following. In the past, SDV has been viewed primarily as a nuisance, impairing laboratory experiments, pharmaceutical testing, and true-to-type breeding. This article also emphasizes the positive biological effects of SDV and discusses implications for genotype-to-phenotype mapping, biological individuation, ecology, evolution, and applied biology. There is strong evidence from experiments with genetically identical organisms performed in narrowly standardized laboratory set-ups that SDV is a source of phenotypic variation in its own right aside from genetic variation and environmental variation. It is obviously mediated by molecular and higher-order epigenetic mechanisms. Comparison of SDV in animals, plants, fungi, protists, bacteria, archaeans, and viruses suggests that it is a ubiquitous and phylogenetically old phenomenon. In animals, it is usually smallest for morphometric traits and highest for life history traits and behaviour. SDV is thought to contribute to phenotypic diversity in all populations but is particularly relevant for asexually reproducing and genetically impoverished populations, where it generates individuality despite genetic uniformity. In each generation, SDV produces a range of phenotypes around a well-adapted target phenotype, which is interpreted as a bet-hedging strategy to cope with the unpredictability of dynamic environments. At least some manifestations of SDV are heritable, adaptable, selectable, and evolvable, and therefore, SDV may be seen as a hitherto overlooked evolution factor. SDV is also relevant for husbandry, agriculture, and medicine because most pathogens are asexuals that exploit this third source of phenotypic variation to modify infectivity and resistance to antibiotics. Since SDV affects all types of organisms and almost all aspects of life, it urgently requires more intense research and a better integration into biological thinking.
Collapse
Affiliation(s)
- Günter Vogt
- Faculty of Biosciences, University of Heidelberg, Im Neuenheimer Feld 230, D-69120, Heidelberg, Germany,
| |
Collapse
|
32
|
Soen Y, Knafo M, Elgart M. A principle of organization which facilitates broad Lamarckian-like adaptations by improvisation. Biol Direct 2015; 10:68. [PMID: 26631109 PMCID: PMC4668624 DOI: 10.1186/s13062-015-0097-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 11/18/2015] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND During the lifetime of an organism, every individual encounters many combinations of diverse changes in the somatic genome, epigenome and microbiome. This gives rise to many novel combinations of internal failures which are unique to each individual. How any individual can tolerate this high load of new, individual-specific scenarios of failure is not clear. While stress-induced plasticity and hidden variation have been proposed as potential mechanisms of tolerance, the main conceptual problem remains unaddressed, namely: how largely non-beneficial random variation can be rapidly and safely organized into net benefits to every individual. PRESENTATION OF THE HYPOTHESIS We propose an organizational principle which explains how every individual can alleviate a high load of novel stressful scenarios using many random variations in flexible and inherently less harmful traits. Random changes which happen to reduce stress, benefit the organism and decrease the drive for additional changes. This adaptation (termed 'Adaptive Improvisation') can be further enhanced, propagated, stabilized and memorized when beneficial changes reinforce themselves by auto-regulatory mechanisms. This principle implicates stress not only in driving diverse variations in cells tissues and organs, but also in organizing these variations into adaptive outcomes. Specific (but not exclusive) examples include stress reduction by rapid exchange of mobile genetic elements (or exosomes) in unicellular, and rapid changes in the symbiotic microorganisms of animals. In all cases, adaptive changes can be transmitted across generations, allowing rapid improvement and assimilation in a few generations. TESTING THE HYPOTHESIS We provide testable predictions derived from the hypothesis. IMPLICATIONS OF THE HYPOTHESIS The hypothesis raises a critical, but thus far overlooked adaptation problem and explains how random variation can self-organize to confer a wide range of individual-specific adaptations beyond the existing outcomes of natural selection. It portrays gene regulation as an inseparable synergy between natural selection and adaptation by improvisation. The latter provides a basis for Lamarckian adaptation that is not limited to a specific mechanism and readily accounts for the remarkable resistance of tumors to treatment.
Collapse
Affiliation(s)
- Yoav Soen
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, 76100, Israel.
| | - Maor Knafo
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, 76100, Israel.
| | - Michael Elgart
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, 76100, Israel.
| |
Collapse
|
33
|
Abstract
AbstractPlant tissue culture techniques have become an integral part of progress in plant science research due to the opportunity offered for close study of detailed plant development with applications in food production through crop improvement, secondary metabolites production and conservation of species. Because the techniques involve growing plants under controlled conditions different from their natural outdoor environment, the plants need adjustments in physiology, anatomy and metabolism for successfulin vitropropagation. Therefore, the protocol has to be optimized for a given species or genotype due to the variability in physiological and growth requirement. Developing the protocol is hampered by several physiological and developmental aberrations in the anatomy and physiology of the plantlets, attributed toin vitroculture conditions of high humidity, low light levels and hetero- or mixotrophic conditions. Some of the culture-induced anomalies become genetic, and the phenotype is inherited by clonal progenies while others are temporary and can be corrected at a later stage of protocol development through changes in anatomy, physiology and metabolism. The success of protocols relies on the transfer of plantlets to field conditions which has been achieved with many species through stages of acclimatization, while with others it remains a challenging task. This review discusses various adjustments in nutrition, physiology and anatomy of micro-propagated plants and field grown ones, as well as anomalies induced by thein vitroculture conditions.
Collapse
|
34
|
Kitimu SR, Taylor J, March TJ, Tairo F, Wilkinson MJ, Rodríguez López CM. Meristem micropropagation of cassava (Manihot esculenta) evokes genome-wide changes in DNA methylation. FRONTIERS IN PLANT SCIENCE 2015; 6:590. [PMID: 26322052 PMCID: PMC4534864 DOI: 10.3389/fpls.2015.00590] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 07/16/2015] [Indexed: 05/25/2023]
Abstract
There is great interest in the phenotypic, genetic and epigenetic changes associated with plant in vitro culture known as somaclonal variation. In vitro propagation systems that are based on the use of microcuttings or meristem cultures are considered analogous to clonal cuttings and so widely viewed to be largely free from such somaclonal effects. In this study, we surveyed for epigenetic changes during propagation by meristem culture and by field cuttings in five cassava (Manihot esculenta) cultivars. Principal Co-ordinate Analysis of profiles generated by methylation-sensitive amplified polymorphism revealed clear divergence between samples taken from field-grown cuttings and those recovered from meristem culture. There was also good separation between the tissues of field samples but this effect was less distinct among the meristem culture materials. Application of methylation-sensitive Genotype by sequencing identified 105 candidate epimarks that distinguish between field cutting and meristem culture samples. Cross referencing the sequences of these epimarks to the draft cassava genome revealed 102 sites associated with genes whose homologs have been implicated in a range of fundamental biological processes including cell differentiation, development, sugar metabolism, DNA methylation, stress response, photosynthesis, and transposon activation. We explore the relevance of these findings for the selection of micropropagation systems for use on this and other crops.
Collapse
Affiliation(s)
- Shedrack R. Kitimu
- Plant Research Centre, School of Agriculture Food and Wine, Faculty of Sciences, University of AdelaideAdelaide, SA, Australia
| | - Julian Taylor
- Biometry Hub, School of Agriculture Food and Wine, Faculty of Sciences, University of AdelaideAdelaide, SA, Australia
| | - Timothy J. March
- School of Agriculture Food and Wine, Faculty of Sciences, University of AdelaideAdelaide, SA, Australia
| | - Fred Tairo
- Mikocheni Agricultural Research InstituteDar es Salaam, Tanzania
| | - Mike J. Wilkinson
- Plant Research Centre, School of Agriculture Food and Wine, Faculty of Sciences, University of AdelaideAdelaide, SA, Australia
| | - Carlos M. Rodríguez López
- Plant Research Centre, School of Agriculture Food and Wine, Faculty of Sciences, University of AdelaideAdelaide, SA, Australia
| |
Collapse
|
35
|
Lin YT, Wei HM, Lu HY, Lee YI, Fu SF. Developmental- and Tissue-Specific Expression of NbCMT3-2 Encoding a Chromomethylase in Nicotiana benthamiana. PLANT & CELL PHYSIOLOGY 2015; 56:1124-43. [PMID: 25745030 DOI: 10.1093/pcp/pcv036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 02/23/2015] [Indexed: 05/11/2023]
Abstract
The chromomethylase (CMT) protein family is unique to plants and controls non-CpG methylation. Here, we investigated the developmental expression of CMT3-2 in Nicotiana benthamiana (NbCMT3-2) and its significance by analyzing plants with silenced NbCMT3-2 and leaf tissues transiently expressing the N-terminal polypeptide. Alignment of the NbCMT3-2 amino acid sequence with that of other plant CMT3s showed a specific N-terminal extension required for nuclear localization. Transient expression of the N-terminal polypeptide in N. benthamiana resulted in chlorotic lesions. NbCMT3-2 was expressed mainly in proliferating tissues such as the shoot apex and developing leaves. We generated transgenic N. benthamiana harboring a fusion reporter construct linking the NbCMT3-2 promoter region and the β-glucuronidase (GUS) reporter (pNbCMT3-2::GUS) to analyze the tissue-specific expression of NbCMT3-2. NbCMT3-2 was expressed in the shoot and root apical meristem and leaf primordia in young seedlings and highly expressed in developing leaves and ovary as well as lateral buds in mature plants. Virus-induced gene silencing used to knock down the expression of NbCMT3 or NbCMT3-2 or both led to partial loss of genomic DNA methylation. Plants with suppressed NbCMT3 expression grew and developed normally, whereas leaves with NbCMT3-2 knockdown showed mild curling as compared with controls. Silencing NbCMT3/3-2 severely interfered with leaf development and directly or indirectly affected the expression of genes involved in jasmonate homeostasis. The differential roles of NbCMT3 and NbCMT3-2 were investigated and compared. We reveal the expression patterns of NbCMT3-2 in proliferating tissues. NbCMT3-2 may play an essential role in leaf development by modulating jasmonate pathways.
Collapse
Affiliation(s)
- Yu-Ting Lin
- Department of Biology, National Changhua University of Education, No. 1, Jin-De Road, Changhua, 500, Taiwan
| | - Huei-Mei Wei
- Department of Biology, National Changhua University of Education, No. 1, Jin-De Road, Changhua, 500, Taiwan
| | - Hsueh-Yu Lu
- Department of Biology, National Changhua University of Education, No. 1, Jin-De Road, Changhua, 500, Taiwan
| | - Yung-I Lee
- Botany Department, National Museum of Natural Science, No. 1, Guancian Road, Taichung 404, Taiwan
| | - Shih-Feng Fu
- Department of Biology, National Changhua University of Education, No. 1, Jin-De Road, Changhua, 500, Taiwan
| |
Collapse
|
36
|
Baránek M, Čechová J, Raddová J, Holleinová V, Ondrušíková E, Pidra M. Dynamics and Reversibility of the DNA Methylation Landscape of Grapevine Plants (Vitis vinifera) Stressed by In Vitro Cultivation and Thermotherapy. PLoS One 2015; 10:e0126638. [PMID: 25973746 PMCID: PMC4431845 DOI: 10.1371/journal.pone.0126638] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 04/05/2015] [Indexed: 11/19/2022] Open
Abstract
There is relatively little information concerning long-term alterations in DNA methylation following exposure of plants to environmental stress. As little is known about the ratio of non-heritable changes in DNA methylation and mitotically-inherited methylation changes, dynamics and reversibility of the DNA methylation states were investigated in grapevine plants (Vitis vinifera) stressed by in vitro cultivation. It was observed that significant part of induced epigenetic changes could be repeatedly established by exposure to particular planting and stress conditions. However, once stress conditions were discontinued, many methylation changes gradually reverted and plants returned to epigenetic states similar to those of maternal plants. In fact, in the period of one to three years after in vitro cultivation it was difficult to distinguish the epigenetic states of somaclones and maternal plants. Forty percent of the observed epigenetic changes disappeared within a year subsequent to termination of stress conditions ending and these probably reflect changes caused by transient and reversible stress-responsive acclimation mechanisms. However, sixty percent of DNA methylation diversity remained after 1 year and probably represents mitotically-inherited epimutations. Sequencing of regions remaining variable between maternal and regenerant plants revealed that 29.3% of sequences corresponded to non-coding regions of grapevine genome. Eight sequences (19.5%) corresponded to previously identified genes and the remaining ones (51.2%) were annotated as "hypothetical proteins" based on their similarity to genes described in other species, including genes likely to undergo methylation changes following exposure to stress (V. vinifera gypsy-type retrotransposon Gret1, auxin-responsive transcription factor 6-like, SAM-dependent carboxyl methyltransferase).
Collapse
Affiliation(s)
- Miroslav Baránek
- Mendeleum—Department of Genetics, Horticulture Faculty of Mendel University in Brno, Lednice, Czech Republic
| | - Jana Čechová
- Mendeleum—Department of Genetics, Horticulture Faculty of Mendel University in Brno, Lednice, Czech Republic
| | - Jana Raddová
- Mendeleum—Department of Genetics, Horticulture Faculty of Mendel University in Brno, Lednice, Czech Republic
| | - Věra Holleinová
- Mendeleum—Department of Genetics, Horticulture Faculty of Mendel University in Brno, Lednice, Czech Republic
| | - Eva Ondrušíková
- Mendeleum—Department of Genetics, Horticulture Faculty of Mendel University in Brno, Lednice, Czech Republic
| | - Miroslav Pidra
- Mendeleum—Department of Genetics, Horticulture Faculty of Mendel University in Brno, Lednice, Czech Republic
| |
Collapse
|
37
|
Rodríguez López CM, Wilkinson MJ. Epi-fingerprinting and epi-interventions for improved crop production and food quality. FRONTIERS IN PLANT SCIENCE 2015; 6:397. [PMID: 26097484 PMCID: PMC4456566 DOI: 10.3389/fpls.2015.00397] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Accepted: 05/18/2015] [Indexed: 05/05/2023]
Abstract
Increasing crop production at a time of rapid climate change represents the greatest challenge facing contemporary agricultural research. Our understanding of the genetic control of yield derives from controlled field experiments designed to minimize environmental variance. In spite of these efforts there is substantial residual variability among plants attributable to Genotype × Environment interactions. Recent advances in the field of epigenetics have revealed a plethora of gene control mechanisms that could account for much of this unassigned variation. These systems act as a regulatory interface between the perception of the environment and associated alterations in gene expression. Direct intervention of epigenetic control systems hold the enticing promise of creating new sources of variability that could enhance crop performance. Equally, understanding the relationship between various epigenetic states and responses of the crop to specific aspects of the growing environment (epigenetic fingerprinting) could allow for a more tailored approach to plant agronomy. In this review, we explore the many ways in which epigenetic interventions and epigenetic fingerprinting can be deployed for the improvement of crop production and quality.
Collapse
Affiliation(s)
- Carlos M. Rodríguez López
- *Correspondence: Carlos M. Rodríguez López, Plant Research Centre, School of Agriculture, Food and Wine, Faculty of Sciences, University of Adelaide, Waite Campus, PMB1, Glen Osmond, Adelaide, SA 5064, Australia
| | | |
Collapse
|
38
|
Gao Y, Ran L, Kong Y, Jiang J, Sokolov V, Wang Y. Assessment of DNA methylation changes in tissue culture of Brassica napus. RUSS J GENET+ 2014. [DOI: 10.1134/s1022795414100032] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
39
|
Maximova SN, Florez S, Shen X, Niemenak N, Zhang Y, Curtis W, Guiltinan MJ. Genome-wide analysis reveals divergent patterns of gene expression during zygotic and somatic embryo maturation of Theobroma cacao L., the chocolate tree. BMC PLANT BIOLOGY 2014; 14:185. [PMID: 25030026 PMCID: PMC4110631 DOI: 10.1186/1471-2229-14-185] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 07/03/2014] [Indexed: 05/03/2023]
Abstract
BACKGROUND Theobroma cacao L. is a tropical fruit tree, the seeds of which are used to create chocolate. In vitro somatic embryogenesis (SE) of cacao is a propagation system useful for rapid mass-multiplication to accelerate breeding programs and to provide plants directly to farmers. Two major limitations of cacao SE remain: the efficiency of embryo production is highly genotype dependent and the lack of full cotyledon development results in low embryo to plant conversion rates. With the goal to better understand SE development and to improve the efficiency of SE conversion we examined gene expression differences between zygotic and somatic embryos using a whole genome microarray. RESULTS The expression of 28,752 genes was determined at 4 developmental time points during zygotic embryogenesis (ZE) and 2 time points during cacao somatic embryogenesis (SE). Within the ZE time course, 10,288 differentially expressed genes were enriched for functions related to responses to abiotic and biotic stimulus, metabolic and cellular processes. A comparison ZE and SE expression profiles identified 10,175 differentially expressed genes. Many TF genes, putatively involved in ethylene metabolism and response, were more strongly expressed in SEs as compared to ZEs. Expression levels of genes involved in fatty acid metabolism, flavonoid biosynthesis and seed storage protein genes were also differentially expressed in the two types of embryos. CONCLUSIONS Large numbers of genes were differentially regulated during various stages of both ZE and SE development in cacao. The relatively higher expression of ethylene and flavonoid related genes during SE suggests that the developing tissues may be experiencing high levels of stress during SE maturation caused by the in vitro environment. The expression of genes involved in the synthesis of auxin, polyunsaturated fatty acids and secondary metabolites was higher in SEs relative to ZEs despite lack of lipid and metabolite accumulation. These differences in gene transcript levels associated with critical processes during seed development are consistent with the fact that somatic embryos do not fully develop the large storage cotyledons found in zygotic embryos. These results provide insight towards design of improved protocols for cacao somatic embryogenesis.
Collapse
Affiliation(s)
- Siela N Maximova
- Department of Plant Science and Huck Institute of Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Sergio Florez
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Xiangling Shen
- Department of Plant Science and Huck Institute of Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Nicolas Niemenak
- Laboratory of Plant Physiology, Department of Biological Science, Higher Teachers’ Training College, University of Yaounde, Yaounde, Cameroon
| | - Yufan Zhang
- Department of Plant Science and Huck Institute of Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Wayne Curtis
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Mark J Guiltinan
- Department of Plant Science and Huck Institute of Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| |
Collapse
|
40
|
Consistent and heritable alterations of DNA methylation are induced by tissue culture in maize. Genetics 2014; 198:209-18. [PMID: 25023398 DOI: 10.1534/genetics.114.165480] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Plants regenerated from tissue culture and their progenies are expected to be identical clones, but often display heritable molecular and phenotypic variation. We characterized DNA methylation patterns in callus, primary regenerants, and regenerant-derived progenies of maize using immunoprecipitation of methylated DNA (meDIP) to assess the genome-wide frequency, pattern, and heritability of DNA methylation changes. Although genome-wide DNA methylation levels remained similar following tissue culture, numerous regions exhibited altered DNA methylation levels. Hypomethylation events were observed more frequently than hypermethylation following tissue culture. Many of the hypomethylation events occur at the same genomic sites across independent regenerants and cell lines. The DNA methylation changes were often heritable in progenies produced from self-pollination of primary regenerants. Methylation changes were enriched in regions upstream of genes and loss of DNA methylation at promoters was associated with altered expression at a subset of loci. Differentially methylated regions (DMRs) found in tissue culture regenerants overlap with the position of naturally occurring DMRs more often than expected by chance with 8% of tissue culture hypomethylated DMRs overlapping with DMRs identified by profiling natural variation, consistent with the hypotheses that genomic stresses similar to those causing somaclonal variation may also occur in nature, and that certain loci are particularly susceptible to epigenetic change in response to these stresses. The consistency of methylation changes across regenerants from independent cultures suggests a mechanistic response to the culture environment as opposed to an overall loss of fidelity in the maintenance of epigenetic states.
Collapse
|
41
|
Hopkins MT, Khalid AM, Chang PC, Vanderhoek KC, Lai D, Doerr MD, Lolle SJ. De novo genetic variation revealed in somatic sectors of single Arabidopsis plants. F1000Res 2014; 2:5. [PMID: 24555023 PMCID: PMC3894806 DOI: 10.12688/f1000research.2-5.v2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/29/2013] [Indexed: 12/17/2022] Open
Abstract
Concern over the tremendous loss of genetic diversity among many of our most important crops has prompted major efforts to preserve seed stocks derived from cultivated species and their wild relatives.
Arabidopsis thaliana propagates mainly by self-fertilizing, and therefore, like many crop plants, theoretically has a limited potential for producing genetically diverse offspring. Despite this, inbreeding has persisted in Arabidopsis for over a million years suggesting that some underlying adaptive mechanism buffers the deleterious consequences of this reproductive strategy. Using presence-absence molecular markers we demonstrate that single Arabidopsis plants can have multiple genotypes. Sequence analyses reveal single nucleotide changes, loss of sequences and, surprisingly, acquisition of unique genomic insertions. Estimates based on quantitative analyses suggest that these genetically discordant sectors are very small but can have a complex genetic makeup. In ruling out more trivial explanations for these data, our findings raise the possibility that intrinsic drivers of genetic variation are responsible for the targeted sequence changes we detect. Given the evolutionary advantage afforded to populations with greater genetic diversity, we hypothesize that organisms that primarily self-fertilize or propagate clonally counteract the genetic cost of such reproductive strategies by leveraging a cryptic reserve of extra-genomic information.
Collapse
Affiliation(s)
- Marianne T Hopkins
- Department of Biology, University of Waterloo, Waterloo, N2L 3G1, Canada
| | - Aaron M Khalid
- Department of Biology, University of Waterloo, Waterloo, N2L 3G1, Canada
| | - Pei-Chun Chang
- Department of Biology, University of Waterloo, Waterloo, N2L 3G1, Canada
| | - Karen C Vanderhoek
- Department of Biology, University of Waterloo, Waterloo, N2L 3G1, Canada
| | - Dulcie Lai
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, K7L 3N6, Canada
| | - Meghan D Doerr
- Department of Biology, University of Waterloo, Waterloo, N2L 3G1, Canada
| | - Susan J Lolle
- Department of Biology, University of Waterloo, Waterloo, N2L 3G1, Canada
| |
Collapse
|
42
|
Teyssier C, Maury S, Beaufour M, Grondin C, Delaunay A, Le Metté C, Ader K, Cadene M, Label P, Lelu-Walter MA. In search of markers for somatic embryo maturation in hybrid larch (Larix × eurolepis): global DNA methylation and proteomic analyses. PHYSIOLOGIA PLANTARUM 2014; 150:271-91. [PMID: 23789891 DOI: 10.1111/ppl.12081] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 04/08/2013] [Accepted: 05/28/2013] [Indexed: 05/22/2023]
Abstract
A global DNA methylation and proteomics approach was used to investigate somatic embryo maturation in hybrid larch. Each developmental step during somatic embryogenesis was associated with a distinct and significantly different global DNA methylation level: from 45.8% mC for undifferentiated somatic embryos (1-week proliferation) to 61.5% mC for immature somatic embryos (1-week maturation), while maturation was associated with a decrease in DNA methylation to 53.4% for mature cotyledonary somatic embryos (8-weeks maturation). The presence of 5-azacytidine (hypo-methylating agent) or hydroxyurea (hyper-methylating agent) in the maturation medium altered the global DNA methylation status of the embryogenic cultures, and significantly reduced both their relative growth rate and embryogenic potential, suggesting an important role for DNA methylation in embryogenesis. Maturation was also assessed by examining changes in the total protein profile. Storage proteins, identified as legumin- and vicilin-like, appeared at the precotyledonary stage. In the proteomic study, total soluble proteins were extracted from embryos after 1 and 8 weeks of maturation, and separated by two-dimensional gel electrophoresis. There were 147 spots which showed significant differences between the stages of maturation; they were found to be involved mainly in primary metabolism and the stabilization of the resulting metabolites. This indicated that the somatic embryo was still metabolically active at 8 weeks of maturation. This is the first report of analyses of global DNA methylation (including the effects of hyper- and hypo-treatments) and proteome during somatic embryogenesis in hybrid larch, and thus provides novel insights into maturation of conifer somatic embryos.
Collapse
Affiliation(s)
- Caroline Teyssier
- INRA, UR 0588, Research Unit for Breeding, Genetics and Physiology of Forest Trees, Orléans, F-45075, France
| | | | | | | | | | | | | | | | | | | |
Collapse
|
43
|
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.
Collapse
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
| |
Collapse
|
44
|
Vining K, Pomraning KR, Wilhelm LJ, Ma C, Pellegrini M, Di Y, Mockler TC, Freitag M, Strauss SH. Methylome reorganization during in vitro dedifferentiation and regeneration of Populus trichocarpa. BMC PLANT BIOLOGY 2013; 13:92. [PMID: 23799904 PMCID: PMC3728041 DOI: 10.1186/1471-2229-13-92] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 06/12/2013] [Indexed: 05/22/2023]
Abstract
BACKGROUND Cytosine DNA methylation (5mC) is an epigenetic modification that is important to genome stability and regulation of gene expression. Perturbations of 5mC have been implicated as a cause of phenotypic variation among plants regenerated through in vitro culture systems. However, the pattern of change in 5mC and its functional role with respect to gene expression, are poorly understood at the genome scale. A fuller understanding of how 5mC changes during in vitro manipulation may aid the development of methods for reducing or amplifying the mutagenic and epigenetic effects of in vitro culture and plant transformation. RESULTS We investigated the in vitro methylome of the model tree species Populus trichocarpa in a system that mimics routine methods for regeneration and plant transformation in the genus Populus (poplar). Using methylated DNA immunoprecipitation followed by high-throughput sequencing (MeDIP-seq), we compared the methylomes of internode stem segments from micropropagated explants, dedifferentiated calli, and internodes from regenerated plants. We found that more than half (56%) of the methylated portion of the genome appeared to be differentially methylated among the three tissue types. Surprisingly, gene promoter methylation varied little among tissues, however, the percentage of body-methylated genes increased from 9% to 14% between explants and callus tissue, then decreased to 8% in regenerated internodes. Forty-five percent of differentially-methylated genes underwent transient methylation, becoming methylated in calli, and demethylated in regenerants. These genes were more frequent in chromosomal regions with higher gene density. Comparisons with an expression microarray dataset showed that genes methylated at both promoters and gene bodies had lower expression than genes that were unmethylated or only promoter-methylated in all three tissues. Four types of abundant transposable elements showed their highest levels of 5mC in regenerated internodes. CONCLUSIONS DNA methylation varies in a highly gene- and chromosome-differential manner during in vitro differentiation and regeneration. 5mC in redifferentiated tissues was not reset to that in original explants during the study period. Hypermethylation of gene bodies in dedifferentiated cells did not interfere with transcription, and may serve a protective role against activation of abundant transposable elements.
Collapse
Affiliation(s)
- Kelly Vining
- Department of Forest Ecosystems and Society, 321 Richardson Hall, Corvallis, OR, USA
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA
| | - Kyle R Pomraning
- Molecular and Cellular Biology Program, Corvallis, OR 97331, USA
- Department of Biochemistry and Biophysics, Corvallis, OR 97331, USA
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA
| | | | - Cathleen Ma
- Department of Forest Ecosystems and Society, 321 Richardson Hall, Corvallis, OR, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA
| | - Yanming Di
- Statistics Department, Oregon State University, Corvallis, Oregon, USA
| | - Todd C Mockler
- The Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Michael Freitag
- Molecular and Cellular Biology Program, Corvallis, OR 97331, USA
- Department of Biochemistry and Biophysics, Corvallis, OR 97331, USA
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA
| | - Steven H Strauss
- Department of Forest Ecosystems and Society, 321 Richardson Hall, Corvallis, OR, USA
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA
| |
Collapse
|
45
|
Bräutigam K, Vining KJ, Lafon-Placette C, Fossdal CG, Mirouze M, Marcos JG, Fluch S, Fraga MF, Guevara MÁ, Abarca D, Johnsen Ø, Maury S, Strauss SH, Campbell MM, Rohde A, Díaz-Sala C, Cervera MT. Epigenetic regulation of adaptive responses of forest tree species to the environment. Ecol Evol 2013; 3:399-415. [PMID: 23467802 PMCID: PMC3586649 DOI: 10.1002/ece3.461] [Citation(s) in RCA: 222] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 11/19/2012] [Accepted: 11/27/2012] [Indexed: 12/25/2022] Open
Abstract
Epigenetic variation is likely to contribute to the phenotypic plasticity and adaptative capacity of plant species, and may be especially important for long-lived organisms with complex life cycles, including forest trees. Diverse environmental stresses and hybridization/polyploidization events can create reversible heritable epigenetic marks that can be transmitted to subsequent generations as a form of molecular "memory". Epigenetic changes might also contribute to the ability of plants to colonize or persist in variable environments. In this review, we provide an overview of recent data on epigenetic mechanisms involved in developmental processes and responses to environmental cues in plant, with a focus on forest tree species. We consider the possible role of forest tree epigenetics as a new source of adaptive traits in plant breeding, biotechnology, and ecosystem conservation under rapid climate change.
Collapse
Affiliation(s)
- Katharina Bräutigam
- Centre for the Analysis of Genome Evolution and Function, Department of Cell & Systems Biology, University of TorontoToronto, ON, M5S 3B2, Canada
| | - Kelly J Vining
- Department of Forest Ecosystems and Society, Oregon State UniversityCorvallis, OR, 97331-5752, USA
| | - Clément Lafon-Placette
- UFR-Faculté des Sciences, UPRES EA 1207 ‘Laboratoire de Biologie des Ligneux et des Grandes Cultures’ (LBLGC), INRA, USC1328 ‘Arbres et Réponses aux Contraintes Hydrique et Environnementales’ (ARCHE), University of OrléansRue de Chartres, BP 6759, F-45067, Orléans, France
| | - Carl G Fossdal
- Department of Biology and Environment, Norwegian Forest and Landscape InstitutePO Box 115, N-1431, Aas, Norway
| | - Marie Mirouze
- Epigenetic Regulations and Seed Development, Institut de Recherche pour le Développement, UMR232 ERL5300 CNRS-IRD911 Av. Agropolis, 34394, Montpellier, France
| | - José Gutiérrez Marcos
- School of Life Sciences, University of WarwickWellesbourne, Warkwick, CV35 9EF, United Kingdom
| | - Silvia Fluch
- Platform for Integrated Clone Management (PICME), Health & Environment Department, AIT Austrian Institute of Technology GmbHKonrad-Lorenz-Straße 24, 3430, Tulln, Austria
| | - Mario Fernández Fraga
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA–HUCA), University of OviedoSpain
| | - M Ángeles Guevara
- Dpt. of Forest Ecology and Genetics, Forest Genomics and Ecophysiology group, Forest Research Centre (CIFOR). INIACrta. La Coruña km 7,5, 28040, Madrid, Spain
- Mixed Unit of Forest Genomics and Ecophysiology, INIA/UPMMadrid, Spain
| | - Dolores Abarca
- Department of Life Sciences, University of AlcaláCtra. Madrid-Barcelona Km. 33,600, 28871, Alcalá de Henares, Madrid, Spain
| | - Øystein Johnsen
- Department of Plant and Environmental Sciences, Norwegian University of Life SciencesPO Box 5003, N-1432, Ås, Norway
| | - Stéphane Maury
- UFR-Faculté des Sciences, UPRES EA 1207 ‘Laboratoire de Biologie des Ligneux et des Grandes Cultures’ (LBLGC), INRA, USC1328 ‘Arbres et Réponses aux Contraintes Hydrique et Environnementales’ (ARCHE), University of OrléansRue de Chartres, BP 6759, F-45067, Orléans, France
| | - Steven H Strauss
- Department of Forest Ecosystems and Society, Oregon State UniversityCorvallis, OR, 97331-5752, USA
| | - Malcolm M Campbell
- Centre for the Analysis of Genome Evolution and Function, Department of Cell & Systems Biology, University of TorontoToronto, ON, M5S 3B2, Canada
- Department of Biological Sciences, University of Toronto Scarborough, University of Toronto1265 Military Trail, Toronto, ON, M1C 1A4, Canada
| | - Antje Rohde
- Department Plant Growth & Development, Institute of Agriculture and Fisheries ResearchCaritasstraat 21, 9090, Melle, Belgium
| | - Carmen Díaz-Sala
- Department of Life Sciences, University of AlcaláCtra. Madrid-Barcelona Km. 33,600, 28871, Alcalá de Henares, Madrid, Spain
| | - María-Teresa Cervera
- Dpt. of Forest Ecology and Genetics, Forest Genomics and Ecophysiology group, Forest Research Centre (CIFOR). INIACrta. La Coruña km 7,5, 28040, Madrid, Spain
- Mixed Unit of Forest Genomics and Ecophysiology, INIA/UPMMadrid, Spain
| |
Collapse
|
46
|
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).
Collapse
Affiliation(s)
- Qin-Mei Wang
- Institute of Genetics and Cytology, Northeast Normal University, Changchun, 130024, People's Republic of China.
| | | |
Collapse
|
47
|
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.
Collapse
Affiliation(s)
- Qin-Mei Wang
- Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, People's Republic of China
| | | | | | | | | | | | | | | |
Collapse
|
48
|
Fu C, Li L, Wu W, Li M, Yu X, Yu L. Assessment of genetic and epigenetic variation during long-term Taxus cell culture. PLANT CELL REPORTS 2012; 31:1321-1331. [PMID: 22562779 DOI: 10.1007/s00299-012-1251-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Revised: 03/15/2012] [Accepted: 03/17/2012] [Indexed: 05/31/2023]
Abstract
UNLABELLED Gradual loss of secondary metabolite production is a common obstacle in the development of a large-scale plant cell production system. In this study, cell morphology, paclitaxel (Taxol®) biosynthetic ability, and genetic and epigenetic variations in the long-term culture of Taxus media cv Hicksii cells were assessed over a 5-year period to evaluate the mechanisms of the loss of secondary metabolites biosynthesis capacity in Taxus cell. The results revealed that morphological variations, gradual loss of paclitaxel yield and decreased transcriptional level of paclitaxel biosynthesis key genes occurred during long-term subculture. Genetic and epigenetic variations in these cultures were also studied at different times during culture using amplified fragment-length polymorphism (AFLP), methylation-sensitive amplified polymorphism (MSAP), and high-performance liquid chromatography (HPLC) analyses. A total of 32 primer combinations were used in AFLP amplification, and none of the AFLP loci were found to be polymorphic, thus no major genetic rearrangements were detected in any of the tested samples. However, results from both MSAP and HPLC indicated that there was a higher level of DNA methylation in the low-paclitaxel yielding cell line after long-term culture. Based on these results, we proposed that accumulation of paclitaxel in Taxus cell cultures might be regulated by DNA methylation. To our knowledge, this is the first report of increased methylation with the prolongation of culture time in Taxus cell culture. It provides substantial clues for exploring the gradual loss of the taxol biosynthesis capacity of Taxus cell lines during long-term subculture. KEY MESSAGE DNA methylation maybe involved in the regulation of paclitaxel biosynthesis in Taxus cell culture.
Collapse
Affiliation(s)
- Chunhua Fu
- Department of Biotechnology, College of Life Science and Technology, Institute of Resource Biology and Biotechnology, Huazhong University of Science and Technology, 430074 Wuhan, China
| | | | | | | | | | | |
Collapse
|
49
|
Transcriptome Analysis of Age-Related Gain of Callus-Forming Capacity in Arabidopsis Hypocotyls. ACTA ACUST UNITED AC 2012; 53:1457-69. [DOI: 10.1093/pcp/pcs090] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
|
50
|
Rodríguez López CM, Morán P, Lago F, Espiñeira M, Beckmann M, Consuegra S. Detection and quantification of tissue of origin in salmon and veal products using methylation sensitive AFLPs. Food Chem 2012. [DOI: 10.1016/j.foodchem.2011.09.120] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
|