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Tonosaki K, Fujimoto R, Dennis ES, Raboy V, Osabe K. Corrigendum: Will epigenetics be a key player in crop breeding? Front Plant Sci 2023; 14:1157933. [PMID: 36938034 PMCID: PMC10020614 DOI: 10.3389/fpls.2023.1157933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 02/22/2023] [Indexed: 06/18/2023]
Abstract
[This corrects the article DOI: 10.3389/fpls.2022.958350.].
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Affiliation(s)
- Kaoru Tonosaki
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Ryo Fujimoto
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Elizabeth S. Dennis
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture and Food, Canberra, ACT, Australia
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia
| | - Victor Raboy
- Independent Researcher Portland, Portland, OR, United States
| | - Kenji Osabe
- Institute of Scientific and Industrial Research (SANKEN), Osaka University, Osaka, Japan
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2
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Tran Q, Osabe K, Entani T, Wazawa T, Hattori M, Nagai T. Application of Green-enhanced Nano-lantern as a bioluminescent ratiometric indicator for measurement of Arabidopsis thaliana root apoplastic fluid pH. Plant Cell Environ 2022; 45:3157-3170. [PMID: 35864560 PMCID: PMC9542637 DOI: 10.1111/pce.14404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/11/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Plant root absorbs water and nutrients from the soil, and the root apoplastic fluid (AF) is an important intermediate between cells and the surrounding environment. The acid growth theory suggests that an acidic AF is needed for cell wall expansion during root growth. However, technical limitations have precluded the quantification of root apoplastic fluid pH (AF-pH). Here, we used Green-enhanced Nano-lantern (GeNL), a chimeric protein of the luciferase NanoLuc (Nluc) and the green fluorescent protein mNeonGreen (mNG), as a ratiometric pH indicator based on the pH dependency of bioluminescence resonance energy transfer efficiency from Nluc to mNG. Luminescence spectrum of GeNL changed reciprocally from pH 4.5 to 7.5, with a pKa of 5.5. By fusing GeNL to a novel signal peptide from Arabidopsis thaliana Cellulase 1, we localised GeNL in A. thaliana AF. We visualised AF dynamics at subcellular resolution over 30 min and determined flow velocity in the maturation zone to be 0.97± 0.06 μm/s. We confirmed that the developing root AF is acidic in the pH range of 5.1-5.7, suggesting that the AF-pH is tightly regulated during root elongation. These results support the acid growth theory and provide evidence for AF-pH maintenance despite changes in ambient pH.
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Affiliation(s)
- Quang Tran
- SANKEN (The Institute of Scientific and Industrial Research)Osaka UniversityIbarakiJapan
- Department of Biotechnology, Graduate School of EngineeringOsaka UniversitySuitaJapan
| | - Kenji Osabe
- SANKEN (The Institute of Scientific and Industrial Research)Osaka UniversityIbarakiJapan
- Department of Biotechnology, Graduate School of EngineeringOsaka UniversitySuitaJapan
| | - Tetsuyuki Entani
- SANKEN (The Institute of Scientific and Industrial Research)Osaka UniversityIbarakiJapan
| | - Tetsuichi Wazawa
- SANKEN (The Institute of Scientific and Industrial Research)Osaka UniversityIbarakiJapan
| | - Mitsuru Hattori
- SANKEN (The Institute of Scientific and Industrial Research)Osaka UniversityIbarakiJapan
- Department of Biotechnology, Graduate School of EngineeringOsaka UniversitySuitaJapan
| | - Takeharu Nagai
- SANKEN (The Institute of Scientific and Industrial Research)Osaka UniversityIbarakiJapan
- Department of Biotechnology, Graduate School of EngineeringOsaka UniversitySuitaJapan
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3
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Tonosaki K, Fujimoto R, Dennis ES, Raboy V, Osabe K. Will epigenetics be a key player in crop breeding? Front Plant Sci 2022; 13:958350. [PMID: 36247549 PMCID: PMC9562705 DOI: 10.3389/fpls.2022.958350] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 09/12/2022] [Indexed: 06/16/2023]
Abstract
If food and feed production are to keep up with world demand in the face of climate change, continued progress in understanding and utilizing both genetic and epigenetic sources of crop variation is necessary. Progress in plant breeding has traditionally been thought to be due to selection for spontaneous DNA sequence mutations that impart desirable phenotypes. These spontaneous mutations can expand phenotypic diversity, from which breeders can select agronomically useful traits. However, it has become clear that phenotypic diversity can be generated even when the genome sequence is unaltered. Epigenetic gene regulation is a mechanism by which genome expression is regulated without altering the DNA sequence. With the development of high throughput DNA sequencers, it has become possible to analyze the epigenetic state of the whole genome, which is termed the epigenome. These techniques enable us to identify spontaneous epigenetic mutations (epimutations) with high throughput and identify the epimutations that lead to increased phenotypic diversity. These epimutations can create new phenotypes and the causative epimutations can be inherited over generations. There is evidence of selected agronomic traits being conditioned by heritable epimutations, and breeders may have historically selected for epiallele-conditioned agronomic traits. These results imply that not only DNA sequence diversity, but the diversity of epigenetic states can contribute to increased phenotypic diversity. However, since the modes of induction and transmission of epialleles and their stability differ from that of genetic alleles, the importance of inheritance as classically defined also differs. For example, there may be a difference between the types of epigenetic inheritance important to crop breeding and crop production. The former may depend more on longer-term inheritance whereas the latter may simply take advantage of shorter-term phenomena. With the advances in our understanding of epigenetics, epigenetics may bring new perspectives for crop improvement, such as the use of epigenetic variation or epigenome editing in breeding. In this review, we will introduce the role of epigenetic variation in plant breeding, largely focusing on DNA methylation, and conclude by asking to what extent new knowledge of epigenetics in crop breeding has led to documented cases of its successful use.
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Affiliation(s)
- Kaoru Tonosaki
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Ryo Fujimoto
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Elizabeth S. Dennis
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture and Food, Canberra, ACT, Australia
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia
| | - Victor Raboy
- Independent Researcher Portland, Portland, OR, United States
| | - Kenji Osabe
- Institute of Scientific and Industrial Research (SANKEN), Osaka University, Osaka, Japan
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Kaku T, Sugiura K, Entani T, Osabe K, Nagai T. Enhanced brightness of bacterial luciferase by bioluminescence resonance energy transfer. Sci Rep 2021; 11:14994. [PMID: 34294849 PMCID: PMC8298465 DOI: 10.1038/s41598-021-94551-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 07/06/2021] [Indexed: 02/01/2023] Open
Abstract
Using the lux operon (luxCDABE) of bacterial bioluminescence system as an autonomous luminous reporter has been demonstrated in bacteria, plant and mammalian cells. However, applications of bacterial bioluminescence-based imaging have been limited because of its low brightness. Here, we engineered the bacterial luciferase (heterodimer of luxA and luxB) by fusion with Venus, a bright variant of yellow fluorescent protein, to induce bioluminescence resonance energy transfer (BRET). By using decanal as an externally added substrate, color change and ten-times enhancement of brightness was achieved in Escherichia coli when circularly permuted Venus was fused to the C-terminus of luxB. Expression of the Venus-fused luciferase in human embryonic kidney cell lines (HEK293T) or in Nicotiana benthamiana leaves together with the substrate biosynthesis-related genes (luxC, luxD and luxE) enhanced the autonomous bioluminescence. We believe the improved luciferase will forge the way towards the potential development of autobioluminescent reporter system allowing spatiotemporal imaging in live cells.
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Affiliation(s)
- Tomomi Kaku
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Ibaraki, Osaka, 567-0047, Japan
| | - Kazunori Sugiura
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Ibaraki, Osaka, 567-0047, Japan
| | - Tetsuyuki Entani
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Ibaraki, Osaka, 567-0047, Japan
| | - Kenji Osabe
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Ibaraki, Osaka, 567-0047, Japan
| | - Takeharu Nagai
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Ibaraki, Osaka, 567-0047, Japan.
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Tran Q, Osabe K, Entani T, Nagai T. A novel petal up-regulated PhXTH7 promoter analysis in Petunia hybrida by using bioluminescence reporter gene. Plant Biotechnol (Tokyo) 2021; 38:197-204. [PMID: 34393598 PMCID: PMC8329265 DOI: 10.5511/plantbiotechnology.21.0130a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/30/2021] [Indexed: 06/13/2023]
Abstract
Flower opening is an important phenomenon in plant that indicates the readiness of the flower for pollination leading to petal expansion and pigmentation. This phenomenon has great impact on crop yield, which makes researches of its mechanism attractive for both plant physiology study and agriculture. Gene promoters directing the expression in petal during the petal cell wall modification and expansion when flower opens could be a convenient tool to analyze or monitor gene expression targeting this event. However, there are no reports of isolated gene promoters that can direct gene expression in petal or petal limb during the rapid cell wall dynamics when the flower opens. Xyloglucan endotransglucosylase/hydrolase 7 (XTH7), a cell wall modifying enzyme, was reported having up-regulated gene expression in the petal of Arabidopsis thaliana and Petunia hybrida. In this study, we fused a 1,904 bp length P. hybrida XTH7 promoter with a gene encoding a bright bioluminescent protein (Green enhanced Nano-lantern) to report gene expression and observed petal up-regulated bioluminescence activity by means of a consumer-grade camera. More importantly, this novel promoter demonstrated up-regulated activity in the petal limb of P. hybrida matured flower during flower opening. P. hybrida XTH7 promoter would be a useful tool for flowering study, especially for petal expansion research during flower opening.
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Affiliation(s)
- Quang Tran
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kenji Osabe
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Tetsuyuki Entani
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Takeharu Nagai
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
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6
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Akter A, Takahashi S, Deng W, Shea DJ, Itabashi E, Shimizu M, Miyaji N, Osabe K, Nishida N, Suzuki Y, Helliwell CA, Seki M, Peacock WJ, Dennis ES, Fujimoto R. The histone modification H3 lysine 27 tri-methylation has conserved gene regulatory roles in the triplicated genome of Brassica rapa L. DNA Res 2020; 26:433-443. [PMID: 31622476 PMCID: PMC6796510 DOI: 10.1093/dnares/dsz021] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 08/30/2019] [Indexed: 01/08/2023] Open
Abstract
Brassica rapa L. is an important vegetable and oilseed crop. We investigated the distribution of the histone mark tri-methylation of H3K27 (H3K27me3) in B. rapa and its role in the control of gene expression at two stages of development (2-day cotyledons and 14-day leaves) and among paralogs in the triplicated genome. H3K27me3 has a similar distribution in two inbred lines, while there was variation of H3K27me3 sites between tissues. Sites that are specific to 2-day cotyledons have increased transcriptional activity, and low levels of H3K27me3 in the gene body region. In 14-day leaves, levels of H3K27me3 were associated with decreased gene expression. In the triplicated genome, H3K27me3 is associated with paralogs that have tissue-specific expression. Even though B. rapa and Arabidopsis thaliana are not closely related within the Brassicaceae, there is conservation of H3K27me3-marked sites in the two species. Both B. rapa and A. thaliana require vernalization for floral initiation with FLC being the major controlling locus. In all four BrFLC paralogs, low-temperature treatment increases H3K27me3 at the proximal nucleation site reducing BrFLC expression. Following return to normal temperature growth conditions, H3K27me3 spreads along all four BrFLC paralogs providing stable repression of the gene.
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Affiliation(s)
- Ayasha Akter
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Satoshi Takahashi
- Center for Sustainable Resource Science, RIKEN, Yokohama, Kanagawa, Japan
| | - Weiwei Deng
- Centre for Crop and Disease Management (CCDM), School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
| | - Daniel J Shea
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Etsuko Itabashi
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Motoki Shimizu
- Department of Genomics and Breeding, Iwate Biotechnology Research Center, Narita, Kitakami, Iwate, Japan
| | - Naomi Miyaji
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Kenji Osabe
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, Japan
| | - Namiko Nishida
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Yutaka Suzuki
- Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | | | - Motoaki Seki
- Center for Sustainable Resource Science, RIKEN, Yokohama, Kanagawa, Japan.,Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, Japan.,Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, Japan
| | - William James Peacock
- Agriculture and Food, CSIRO, Canberra, ACT, Australia.,Department of Life Sciences, University of Technology, Sydney, Broadway, NSW, Australia
| | - Elizabeth S Dennis
- Agriculture and Food, CSIRO, Canberra, ACT, Australia.,Department of Life Sciences, University of Technology, Sydney, Broadway, NSW, Australia
| | - Ryo Fujimoto
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
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7
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Takahashi S, Osabe K, Fukushima N, Takuno S, Miyaji N, Shimizu M, Takasaki-Yasuda T, Suzuki Y, Dennis ES, Seki M, Fujimoto R. Genome-wide characterization of DNA methylation, small RNA expression, and histone H3 lysine nine di-methylation in Brassica rapa L. DNA Res 2019; 25:511-520. [PMID: 29982343 PMCID: PMC6191303 DOI: 10.1093/dnares/dsy021] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 05/30/2018] [Indexed: 12/23/2022] Open
Abstract
Epigenetic gene regulation is crucial to plant life and can involve dynamic interactions between various histone modifications, DNA methylation, and small RNAs. Detailed analysis of epigenome information is anticipated to reveal how the DNA sequence of the genome is translated into the plant’s phenotype. The aim of this study was to map the DNA methylation state at the whole genome level and to clarify the relationship between DNA methylation and transcription, small RNA expression, and histone H3 lysine 9 di-methylation (H3K9me2) in Brassica rapa. We performed whole genome bisulfite sequencing, small RNA sequencing, and chromatin immunoprecipitation sequencing using H3K9me2 antibody in a Chinese cabbage inbred line, RJKB-T24, and examined the impact of epigenetic states on transcription. Cytosine methylation in DNA was analysed in different sequence contexts (CG, CHG, and CHH) (where H could be A, C, or T) and position (promoter, exon, intron, terminator, interspersed repeat regions), and the H3K9me2 and 24 nucleotide small interfering RNAs (24 nt-siRNA) were overlaid onto the B. rapa reference genome. The epigenome was compared with that of Arabidopsis thaliana and the relationship between the position of DNA methylation and gene expression, and the involvement of 24 nt siRNAs and H3K9me2 are discussed.
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Affiliation(s)
- Satoshi Takahashi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
| | - Kenji Osabe
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, Japan
| | - Naoki Fukushima
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe, Japan
| | - Shohei Takuno
- Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Kanagawa, Japan
| | - Naomi Miyaji
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe, Japan
| | - Motoki Shimizu
- Iwate Biotechnology Research Center, Narita Kitakami, Iwate, Japan
| | | | - Yutaka Suzuki
- Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Elizabeth S Dennis
- CSIRO Agriculture and Food, Canberra, ACT, Australia.,University of Technology, Sydney, Broadway, NSW, Australia
| | - Motoaki Seki
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan.,Core Research for Evolutional Science and Technology, Japan Science and Technology, Kawaguchi, Saitama, Japan.,RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
| | - Ryo Fujimoto
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe, Japan
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8
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Shea DJ, Shimizu M, Itabashi E, Miyaji N, Miyazaki J, Osabe K, Kaji M, Okazaki K, Fujimoto R. Genome re-sequencing, SNP analysis, and genetic mapping of the parental lines of a commercial F 1 hybrid cultivar of Chinese cabbage. Breed Sci 2018; 68:375-380. [PMID: 30100805 PMCID: PMC6081294 DOI: 10.1270/jsbbs.17124] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 02/04/2018] [Indexed: 06/08/2023]
Abstract
The genome-wide characterization of single nucleotide polymorphism (SNP) between cultivars or between inbred lines contributes to the creation of genetic markers that are important for plant breeding. Functional markers derived from polymorphisms within genes that affect phenotypic variation are especially valuable in plant breeding. Here, we report on the genome re-sequencing and analysis of the two parental inbred lines of the commercial F1 hybrid Chinese cabbage cultivar "W77". Through the genome-wide identification and classification of the SNPs and indels present in each parental line, we identified about 1,500 putative non-functional genes in each parent. We designed cleaved amplified polymorphic sequence (CAPS) markers using specific mutations found at Eco RI restriction sites in the parental lines and confirmed their Mendelian segregation by constructing a linkage map using 96 F2 plants derived from the F1 hybrid cultivar, "W77". Our results and data will be a useful genomic resource for future studies of gene function and metagenomic studies in Chinese cabbage.
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Affiliation(s)
- Daniel J. Shea
- Graduate School of Science and Technology, Niigata University,
Ikarashi-ninocho, Niigata 950-2181,
Japan
| | - Motoki Shimizu
- Iwate Biotechnology Research Center,
Narita, Kitakami, Iwate 024-0003,
Japan
| | - Etsuko Itabashi
- Institute of Vegetable and Floriculture Science, NARO,
Kusawa, Ano, Tsu, Mie 514-2392,
Japan
| | - Naomi Miyaji
- Graduate School of Agricultural Science, Kobe University,
Rokkodai, Nada-ku, Kobe, Hyogo 657-8501,
Japan
| | - Junji Miyazaki
- Centre for AgriBioscience, Department of Animal, Plant and Soil Sciences, La Trobe University,
Melbourne VICAustralia
| | - Kenji Osabe
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University,
Onna-son, Okinawa 904-0495,
Japan
| | - Makoto Kaji
- Watanabe Seed Co., Ltd.,
Machiyashiki, Misato-cho, Miyagi 987-0003,
Japan
| | - Keiichi Okazaki
- Graduate School of Science and Technology, Niigata University,
Ikarashi-ninocho, Niigata 950-2181,
Japan
| | - Ryo Fujimoto
- Graduate School of Agricultural Science, Kobe University,
Rokkodai, Nada-ku, Kobe, Hyogo 657-8501,
Japan
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9
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Fujimoto R, Uezono K, Ishikura S, Osabe K, Peacock WJ, Dennis ES. Recent research on the mechanism of heterosis is important for crop and vegetable breeding systems. Breed Sci 2018; 68:145-158. [PMID: 29875598 PMCID: PMC5982191 DOI: 10.1270/jsbbs.17155] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Accepted: 01/29/2018] [Indexed: 05/18/2023]
Abstract
Heterosis or hybrid vigor is a phenomenon where hybrid progeny have superior performance compared to their parental inbred lines. This is important in the use of F1 hybrid cultivars in many crops and vegetables. However, the molecular mechanism of heterosis is not clearly understood. Gene interactions between the two genomes such as dominance, overdominance, and epistasis have been suggested to explain the increased biomass and yield. Genetic analyses of F1 hybrids in maize, rice, and canola have defined a large number of quantitative trait loci, which may contribute to heterosis. Recent molecular analyses of transcriptomes together with reference to the epigenome of the parents and hybrids have begun to uncover new facts about the generation of heterosis. These include the identification of gene expression changes in hybrids, which may be important for heterosis, the role of epigenetic processes in heterosis, and the development of stable high yielding lines.
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Affiliation(s)
- Ryo Fujimoto
- Graduate School of Agricultural Science, Kobe University,
Rokkodai, Nada-ku, Kobe, Hyogo 657-8501,
Japan
- Corresponding author (e-mail: )
| | - Kosuke Uezono
- Graduate School of Agricultural Science, Kobe University,
Rokkodai, Nada-ku, Kobe, Hyogo 657-8501,
Japan
| | - Sonoko Ishikura
- Graduate School of Agricultural Science, Kobe University,
Rokkodai, Nada-ku, Kobe, Hyogo 657-8501,
Japan
| | - Kenji Osabe
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University,
Onna-son, Okinawa 904-0495,
Japan
| | - W. James Peacock
- CSIRO Agriculture and Food,
Canberra, ACT 2601,
Australia
- University of Technology, Sydney,
PO Box 123, Broadway, NSW 2007,
Australia
| | - Elizabeth S. Dennis
- CSIRO Agriculture and Food,
Canberra, ACT 2601,
Australia
- University of Technology, Sydney,
PO Box 123, Broadway, NSW 2007,
Australia
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10
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Itabashi E, Osabe K, Fujimoto R, Kakizaki T. Epigenetic regulation of agronomical traits in Brassicaceae. Plant Cell Rep 2018; 37:87-101. [PMID: 29058037 DOI: 10.1007/s00299-017-2223-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 10/05/2017] [Indexed: 05/08/2023]
Abstract
Epigenetic regulation, covalent modification of DNA and changes in histone proteins are closely linked to plant development and stress response through flexibly altering the chromatin structure to regulate gene expression. In this review, we will illustrate the importance of epigenetic influences by discussing three agriculturally important traits of Brassicaceae. (1) Vernalization, an acceleration of flowering by prolonged cold exposure regulated through epigenetic silencing of a central floral repressor, FLOWERING LOCUS C. This is associated with cold-dependent repressive histone mark accumulation, which confers competency of consequence vegetative-to-reproductive phase transition. (2) Hybrid vigor, in which an F1 hybrid shows superior performance to the parental lines. Combination of distinct epigenomes with different DNA methylation states between parental lines is important for increase in growth rate in a hybrid progeny. This is independent of siRNA-directed DNA methylation but dependent on the chromatin remodeler DDM1. (3) Self-incompatibility, a reproductive mating system to prevent self-fertilization. This is controlled by the S-locus consisting of SP11 and SRK which are responsible for self/non-self recognition. Because self-incompatibility in Brassicaceae is sporophytically controlled, there are dominance relationships between S haplotypes in the stigma and pollen. The dominance relationships in the pollen rely on de novo DNA methylation at the promoter region of a recessive allele, which is triggered by siRNA production from a flanking region of a dominant allele.
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Affiliation(s)
- Etsuko Itabashi
- Institute of Vegetable and Floriculture Science, NARO, Kusawa, Ano, Tsu, Mie, 514-2392, Japan.
| | - Kenji Osabe
- Okinawa Institute of Science and Technology Graduate University, Onna-son, Kunigami, Okinawa, 904-0495, Japan
| | - Ryo Fujimoto
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe, 657-8501, Japan
| | - Tomohiro Kakizaki
- Institute of Vegetable and Floriculture Science, NARO, Kusawa, Ano, Tsu, Mie, 514-2392, Japan
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11
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Miyaji N, Shimizu M, Miyazaki J, Osabe K, Sato M, Ebe Y, Takada S, Kaji M, Dennis ES, Fujimoto R, Okazaki K. Comparison of transcriptome profiles by Fusarium oxysporum inoculation between Fusarium yellows resistant and susceptible lines in Brassica rapa L. Plant Cell Rep 2017; 36:1841-1854. [PMID: 28819684 DOI: 10.1007/s00299-017-2198-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 08/07/2017] [Indexed: 05/25/2023]
Abstract
Resistant and susceptible lines in Brassica rapa have different immune responses against Fusarium oxysporum inoculation. Fusarium yellows caused by Fusarium oxysporum f. sp. conglutinans (Foc) is an important disease of Brassicaceae; however, the mechanism of how host plants respond to Foc is still unknown. By comparing with and without Foc inoculation in both resistant and susceptible lines of Chinese cabbage (Brassica rapa var. pekinensis), we identified differentially expressed genes (DEGs) between the bulked inoculated (6, 12, 24, and 72 h after inoculation (HAI)) and non-inoculated samples. Most of the DEGs were up-regulated by Foc inoculation. Quantitative real-time RT-PCR showed that most up-regulated genes increased their expression levels from 24 HAI. An independent transcriptome analysis at 24 and 72 HAI was performed in resistant and susceptible lines. GO analysis using up-regulated genes at 24 HAI indicated that Foc inoculation activated systemic acquired resistance (SAR) in resistant lines and tryptophan biosynthetic process and responses to chitin and ethylene in susceptible lines. By contrast, GO analysis using up-regulated genes at 72 HAI showed the overrepresentation of some categories for the defense response in susceptible lines but not in the resistant lines. We also compared DEGs between B. rapa and Arabidopsis thaliana after F. oxysporum inoculation at the same time point, and identified genes related to defense response that were up-regulated in the resistant lines of Chinese cabbage and A. thaliana. Particular genes that changed expression levels overlapped between the two species, suggesting that they are candidates for genes involved in the resistance mechanisms against F. oxysporum.
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Affiliation(s)
- Naomi Miyaji
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe, 657-8501, Japan
| | - Motoki Shimizu
- Iwate Biotechnology Research Center, Narita, Kitakami, Iwate, 024-0003, Japan
| | - Junji Miyazaki
- Department of Animal, Plant and Soil Sciences, Centre for AgriBioscience, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Kenji Osabe
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-Son, Okinawa, 904-0495, Japan
| | - Maho Sato
- Graduate School of Science and Technology, Niigata University, Ikarashi-ninocho, Niigata, 950-2181, Japan
| | - Yusuke Ebe
- Graduate School of Science and Technology, Niigata University, Ikarashi-ninocho, Niigata, 950-2181, Japan
| | - Satoko Takada
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe, 657-8501, Japan
| | - Makoto Kaji
- Watanabe seed Co., Ltd, Machiyashiki, Misato-Cho, Miyagi, 987-8607, Japan
| | | | - Ryo Fujimoto
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe, 657-8501, Japan.
| | - Keiichi Okazaki
- Graduate School of Science and Technology, Niigata University, Ikarashi-ninocho, Niigata, 950-2181, Japan
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Kawanabe T, Ishikura S, Miyaji N, Sasaki T, Wu LM, Itabashi E, Takada S, Shimizu M, Takasaki-Yasuda T, Osabe K, Peacock WJ, Dennis ES, Fujimoto R. Role of DNA methylation in hybrid vigor in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2016; 113:E6704-E6711. [PMID: 27791039 PMCID: PMC5087013 DOI: 10.1073/pnas.1613372113] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Hybrid vigor or heterosis refers to the superior performance of F1 hybrid plants over their parents. Heterosis is particularly important in the production systems of major crops. Recent studies have suggested that epigenetic regulation such as DNA methylation is involved in heterosis, but the molecular mechanism of heterosis is still unclear. To address the epigenetic contribution to heterosis in Arabidopsis thaliana, we used mutant genes that have roles in DNA methylation. Hybrids between C24 and Columbia-0 (Col) without RNA polymerase IV (Pol IV) or methyltransferase I (MET1) function did not reduce the level of biomass heterosis (as evaluated by rosette diameter). Hybrids with a mutation in decrease in dna methylation 1 (ddm1) showed a decreased heterosis level. Vegetative heterosis in the ddm1 mutant hybrid was reduced but not eliminated; a complete reduction could result if there was a change in methylation at all loci critical for generating the level of heterosis, whereas if only a proportion of the loci have methylation changes there may only be a partial reduction in heterosis.
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Affiliation(s)
- Takahiro Kawanabe
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe 657-8501, Japan
| | - Sonoko Ishikura
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe 657-8501, Japan
| | - Naomi Miyaji
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe 657-8501, Japan
| | - Taku Sasaki
- Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Li Min Wu
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Canberra, ACT 2601, Australia
| | - Etsuko Itabashi
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe 657-8501, Japan
| | - Satoko Takada
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe 657-8501, Japan
| | - Motoki Shimizu
- Iwate Biotechnology Research Center, 22-174-4, Narita, Kitakami, Iwate, 024-0003, Japan
| | - Takeshi Takasaki-Yasuda
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe 657-8501, Japan
| | - Kenji Osabe
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa 904-0495, Japan
| | - W James Peacock
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Canberra, ACT 2601, Australia; University of Technology, Sydney, Broadway, NSW 2007, Australia;
| | - Elizabeth S Dennis
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Canberra, ACT 2601, Australia; University of Technology, Sydney, Broadway, NSW 2007, Australia
| | - Ryo Fujimoto
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe 657-8501, Japan; Japan Science and Technology Agency, Precursory Research for Embryonic Science and Technology, Saitama, 332-0012 Japan
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Tonosaki K, Osabe K, Kawanabe T, Fujimoto R. The importance of reproductive barriers and the effect of allopolyploidization on crop breeding. Breed Sci 2016; 66:333-49. [PMID: 27436943 PMCID: PMC4902455 DOI: 10.1270/jsbbs.15114] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 01/25/2016] [Indexed: 05/04/2023]
Abstract
Inter-specific hybrids are a useful source for increasing genetic diversity. Some reproductive barriers before and/or after fertilization prevent production of hybrid plants by inter-specific crossing. Therefore, techniques to overcome the reproductive barrier have been developed, and have contributed to hybridization breeding. In recent studies, identification of molecules involved in plant reproduction has been studied to understand the mechanisms of reproductive barriers. Revealing the molecular mechanisms of reproductive barriers may allow us to overcome reproductive barriers in inter-specific crossing, and to efficiently produce inter-specific hybrids in cross-combinations that cannot be produced through artificial techniques. Inter-specific hybrid plants can potentially serve as an elite material for plant breeding, produced through the merging of genomes of parental species by allopolyploidization. Allopolyploidization provides some benefits, such as heterosis, increased genetic diversity and phenotypic variability, which are caused by dynamic changes of the genome and epigenome. Understanding of allopolyploidization mechanisms is important for practical utilization of inter-specific hybrids as a breeding material. This review discusses the importance of reproductive barriers and the effect of allopolyploidization in crop breeding programs.
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Affiliation(s)
- Kaoru Tonosaki
- Kihara Institute for Biological Research, Yokohama City University,
641-12 Maioka, Totsuka, Yokohama, Kanagawa 244-0813,
Japan
- Corresponding author (e-mail: )
| | - Kenji Osabe
- Okinawa Institute of Science and Technology,
1919-1 Tancha, Onna-son, Kunigami, Okinawa 904-0495,
Japan
| | - Takahiro Kawanabe
- Graduate School of Agricultural Science, Kobe University,
Rokkodai, Nada-ku, Kobe 657-8501,
Japan
| | - Ryo Fujimoto
- Graduate School of Agricultural Science, Kobe University,
Rokkodai, Nada-ku, Kobe 657-8501,
Japan
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14
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Kawanabe T, Osabe K, Itabashi E, Okazaki K, Dennis ES, Fujimoto R. Development of primer sets that can verify the enrichment of histone modifications, and their application to examining vernalization-mediated chromatin changes in Brassica rapa L. Genes Genet Syst 2016; 91:1-10. [PMID: 27074983 DOI: 10.1266/ggs.15-00058] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Epigenetic regulation is crucial for the development of plants and for adaptation to a changing environment. Recently, genome-wide profiles of histone modifications have been determined by a combination of chromatin immunoprecipitation (ChIP) and genomic tiling arrays (ChIP on chip) or ChIP and high-throughput sequencing (ChIP-seq) in species including Arabidopsis thaliana, rice and maize. Validation of ChIP analysis by PCR or qPCR using positive and negative regions of histone modification is necessary. In contrast, information about histone modifications is limited in Chinese cabbage, Brassica rapa. The aim of this study was to develop positive and negative control primer sets for H3K4me3 (trimethylation of the 4(th) lysine of H3), H3K9me2, H3K27me3 and H3K36me3 in B. rapa. The expression and histone modification of four FLC paralogs in B. rapa, before and after vernalization, were examined using the method developed here. After vernalization, expression of all four BrFLC genes was reduced, and accumulation of H3K27me3 was observed in three of them. As with A. thaliana, the vernalization response and stability of FLC repression correlated with the accumulation of H3K27me3. These results suggest that the epigenetic state during vernalization is important for high bolting resistance in B. rapa. The positive and negative control primer sets developed here revealed positive and negative histone modifications in B. rapa that can be used as a control for future studies.
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Kawamura K, Kawanabe T, Shimizu M, Nagano AJ, Saeki N, Okazaki K, Kaji M, Dennis ES, Osabe K, Fujimoto R. Genetic distance of inbred lines of Chinese cabbage and its relationship to heterosis. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.plgene.2015.10.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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16
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Kawamura K, Kawanabe T, Shimizu M, Okazaki K, Kaji M, Dennis ES, Osabe K, Fujimoto R. Genetic characterization of inbred lines of Chinese cabbage by DNA markers; towards the application of DNA markers to breeding of F1 hybrid cultivars. Data Brief 2015; 6:229-37. [PMID: 26862564 PMCID: PMC4707182 DOI: 10.1016/j.dib.2015.11.058] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 11/21/2015] [Accepted: 11/25/2015] [Indexed: 11/30/2022] Open
Abstract
Chinese cabbage (Brassica rapa L. var. pekinensis) is an important vegetable in Asia, and most Japanese commercial cultivars of Chinese cabbage use an F1 hybrid seed production system. Self-incompatibility is successfully used for the production of F1 hybrid seeds in B. rapa vegetables to avoid contamination by non-hybrid seeds, and the strength of self-incompatibility is important for harvesting a highly pure F1 seeds. Prediction of agronomically important traits such as disease resistance based on DNA markers is useful. In this dataset, we identified the S haplotypes by DNA markers and evaluated the strength of self-incompatibility in Chinese cabbage inbred lines. The data described the predicted disease resistance to Fusarium yellows or clubroot in 22 Chinese cabbage inbred lines using gene associated or gene linked DNA markers.
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Affiliation(s)
- Kazutaka Kawamura
- Graduate School of Science and Technology, Niigata University, Ikarashi-ninocho, Niigata 950-2181, Japan
| | - Takahiro Kawanabe
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe 657-8501, Japan
| | - Motoki Shimizu
- Graduate School of Science and Technology, Niigata University, Ikarashi-ninocho, Niigata 950-2181, Japan
| | - Keiichi Okazaki
- Graduate School of Science and Technology, Niigata University, Ikarashi-ninocho, Niigata 950-2181, Japan
| | - Makoto Kaji
- Watanabe seed Co., Ltd., Machiyashiki, Misato-cho, Miyagi 987-0003, Japan
| | | | - Kenji Osabe
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa 904-0495, Japan
| | - Ryo Fujimoto
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe 657-8501, Japan; JST PRESTO, Honcho 4-1-8, Kawaguchi, Saitama 332-0012, Japan
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17
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Osabe K, Clement JD, Bedon F, Pettolino FA, Ziolkowski L, Llewellyn DJ, Finnegan EJ, Wilson IW. Genetic and DNA methylation changes in cotton (Gossypium) genotypes and tissues. PLoS One 2014; 9:e86049. [PMID: 24465864 PMCID: PMC3896429 DOI: 10.1371/journal.pone.0086049] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 12/05/2013] [Indexed: 12/19/2022] Open
Abstract
In plants, epigenetic regulation is important in normal development and in modulating some agronomic traits. The potential contribution of DNA methylation mediated gene regulation to phenotypic diversity and development in cotton was investigated between cotton genotypes and various tissues. DNA methylation diversity, genetic diversity, and changes in methylation context were investigated using methylation-sensitive amplified polymorphism (MSAP) assays including a methylation insensitive enzyme (BsiSI), and the total DNA methylation level was measured by high-performance liquid chromatography (HPLC). DNA methylation diversity was greater than the genetic diversity in the selected cotton genotypes and significantly different levels of DNA methylation were identified between tissues, including fibre. The higher DNA methylation diversity (CHG methylation being more diverse than CG methylation) in cotton genotypes suggest epigenetic regulation may be important for cotton, and the change in DNA methylation between fibre and other tissues hints that some genes may be epigenetically regulated for fibre development. The novel approach using BsiSI allowed direct comparison between genetic and epigenetic diversity, and also measured CC methylation level that cannot be detected by conventional MSAP.
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18
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Mudge SR, Basnayake SWV, Moyle RL, Osabe K, Graham MW, Morgan TE, Birch RG. Mature-stem expression of a silencing-resistant sucrose isomerase gene drives isomaltulose accumulation to high levels in sugarcane. Plant Biotechnol J 2013; 11:502-9. [PMID: 23297683 DOI: 10.1111/pbi.12038] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 11/22/2012] [Accepted: 11/26/2012] [Indexed: 05/25/2023]
Abstract
Isomaltulose (IM) is a natural isomer of sucrose. It is widely approved as a food with properties including slower digestion, lower glycaemic index and low cariogenicity, which can benefit consumers. Availability is currently limited by the cost of fermentative conversion from sucrose. Transgenic sugarcane plants with developmentally-controlled expression of a silencing-resistant gene encoding a vacuole-targeted IM synthase were tested under field conditions typical of commercial sugarcane cultivation. High yields of IM were obtained, up to 483 mm or 81% of total sugars in whole-cane juice from plants aged 13 months. Using promoters from sugarcane to drive expression preferentially in the sugarcane stem, IM levels were consistent between stalks and stools within a transgenic line and across consecutive vegetative field generations of tested high-isomer lines. Germination and early growth of plants from setts were unaffected by IM accumulation, up to the tested level around 500 mm in flanking stem internodes. These are the highest yields ever achieved of value-added materials through plant metabolic engineering. The sugarcane stem promoters are promising for strategies to achieve even higher IM levels and for other applications in sugarcane molecular improvement. Silencing-resistant transgenes are critical to deliver the potential of these promoters in practical sugarcane improvement. At the IM levels now achieved in field-grown sugarcane, direct production of IM in plants is feasible at a cost approaching that of sucrose, which should make the benefits of IM affordable on a much wider scale.
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Affiliation(s)
- Stephen R Mudge
- Hines Plant Science Building, The University of Queensland, Brisbane, Qld, Australia
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19
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Fujimoto R, Sasaki T, Ishikawa R, Osabe K, Kawanabe T, Dennis ES. Molecular mechanisms of epigenetic variation in plants. Int J Mol Sci 2012; 13:9900-9922. [PMID: 22949838 PMCID: PMC3431836 DOI: 10.3390/ijms13089900] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 07/27/2012] [Accepted: 07/30/2012] [Indexed: 12/11/2022] Open
Abstract
Natural variation is defined as the phenotypic variation caused by spontaneous mutations. In general, mutations are associated with changes of nucleotide sequence, and many mutations in genes that can cause changes in plant development have been identified. Epigenetic change, which does not involve alteration to the nucleotide sequence, can also cause changes in gene activity by changing the structure of chromatin through DNA methylation or histone modifications. Now there is evidence based on induced or spontaneous mutants that epigenetic changes can cause altering plant phenotypes. Epigenetic changes have occurred frequently in plants, and some are heritable or metastable causing variation in epigenetic status within or between species. Therefore, heritable epigenetic variation as well as genetic variation has the potential to drive natural variation.
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Affiliation(s)
- Ryo Fujimoto
- Graduate School of Science and Technology, Niigata University, Nishi-ku, Niigata 950-2181, Japan
| | - Taku Sasaki
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Dr. Bohrgasse 3, Vienna 1030, Austria; E-Mail:
| | - Ryo Ishikawa
- Laboratory of Plant Breeding, Graduate School of Agricultural Science, Kobe University, Nada, Kobe 657-8510, Japan; E-Mail:
- Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
| | - Kenji Osabe
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Plant Industry, Canberra ACT 2601, Australia; E-Mails: (K.O.); (E.S.D.)
| | - Takahiro Kawanabe
- Watanabe Seed Co., Ltd, Machiyashiki, Misato-cho, Miyagi 987-8607, Japan; E-Mail:
| | - Elizabeth S. Dennis
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Plant Industry, Canberra ACT 2601, Australia; E-Mails: (K.O.); (E.S.D.)
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Osabe K, Kawanabe T, Sasaki T, Ishikawa R, Okazaki K, Dennis ES, Kazama T, Fujimoto R. Multiple mechanisms and challenges for the application of allopolyploidy in plants. Int J Mol Sci 2012; 13:8696-8721. [PMID: 22942729 PMCID: PMC3430260 DOI: 10.3390/ijms13078696] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Revised: 07/04/2012] [Accepted: 07/04/2012] [Indexed: 11/16/2022] Open
Abstract
An allopolyploid is an individual having two or more complete sets of chromosomes derived from different species. Generation of allopolyploids might be rare because of the need to overcome limitations such as co-existing populations of parental lines, overcoming hybrid incompatibility, gametic non-reduction, and the requirement for chromosome doubling. However, allopolyploids are widely observed among plant species, so allopolyploids have succeeded in overcoming these limitations and may have a selective advantage. As techniques for making allopolyploids are developed, we can compare transcription, genome organization, and epigenetic modifications between synthesized allopolyploids and their direct parental lines or between several generations of allopolyploids. It has been suggested that divergence of transcription caused either genetically or epigenetically, which can contribute to plant phenotype, is important for the adaptation of allopolyploids.
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Affiliation(s)
- Kenji Osabe
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Plant Industry, Canberra, ACT 2601, Australia; E-Mails: (K.O.); (E.S.D.)
| | - Takahiro Kawanabe
- Watanabe Seed Co., Ltd, Machiyashiki, Misato-cho, Miyagi 987-8607, Japan; E-Mail:
| | - Taku Sasaki
- Watanabe Seed Co., Ltd, Machiyashiki, Misato-cho, Miyagi 987-8607, Japan; E-Mail:
| | - Ryo Ishikawa
- Laboratory of Plant Breeding, Graduate School of Agricultural Science, Kobe University, Nada, Kobe 657-8510, Japan; E-Mail:
- Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK; E-Mail:
| | - Keiichi Okazaki
- Graduate School of Science and Technology, Niigata University, Ikarashi-ninocho, Niigata 950-2181, Japan; E-Mail:
| | - Elizabeth S. Dennis
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Plant Industry, Canberra, ACT 2601, Australia; E-Mails: (K.O.); (E.S.D.)
| | - Tomohiko Kazama
- Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai 981-8555, Japan; E-Mail:
| | - Ryo Fujimoto
- Graduate School of Science and Technology, Niigata University, Ikarashi-ninocho, Niigata 950-2181, Japan; E-Mail:
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21
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Yang X, Yu Y, Jiang L, Lin X, Zhang C, Ou X, Osabe K, Liu B. Changes in DNA methylation and transgenerational mobilization of a transposable element (mPing) by the topoisomerase II inhibitor, etoposide, in rice. BMC Plant Biol 2012; 12:48. [PMID: 22482475 PMCID: PMC3480845 DOI: 10.1186/1471-2229-12-48] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2011] [Accepted: 03/24/2012] [Indexed: 05/31/2023]
Abstract
BACKGROUND Etoposide (epipodophyllotoxin) is a chemical commonly used as an anti-cancer drug which inhibits DNA synthesis by blocking topoisomerase II activity. Previous studies in animal cells have demonstrated that etoposide constitutes a genotoxic stress which may induce genomic instability including mobilization of normally quiescent transposable elements (TEs). However, it remained unknown whether similar genetically mutagenic effects could be imposed by etoposide in plant cells. Also, no information is available with regard to whether the drug may cause a perturbation of epigenetic stability in any organism. RESULTS To investigate whether etoposide could generate genetic and/or epigenetic instability in plant cells, we applied etoposide to germinating seeds of six cultivated rice (Oryza sativa L.) genotypes including both subspecies, japonica and indica. Based on the methylation-sensitive gel-blotting results, epigenetic changes in DNA methylation of three TEs (Tos17, Osr23 and Osr36) and two protein-encoding genes (Homeobox and CDPK-related genes) were detected in the etoposide-treated plants (S0 generation) in four of the six studied japonica cultivars, Nipponbare, RZ1, RZ2, and RZ35, but not in the rest japonica cultivar (Matsumae) and the indica cultivar (93-11). DNA methylation changes in the etoposide-treated S0 rice plants were validated by bisulfite sequencing at both of two analyzed loci (Tos17 and Osr36). Transpositional activity was tested for eight TEs endogenous to the rice genome in both the S0 plants and their selfed progenies (S1 and S2) of one of the cultivars, RZ1, which manifested heritable phenotypic variations. Results indicated that no transposition occurred in the etoposide-treated S0 plants for any of the TEs. Nonetheless, a MITE transposon, mPing, showed rampant mobilization in the S1 and S2 progenies descended from the drug-treated S0 plants. CONCLUSIONS Our results demonstrate that etoposide imposes a similar genotoxic stress on plant cells as it does on animal and human cells, which may induce transgenerational genomic instability by instigating transpositional activation of otherwise dormant TEs. In addition, we show for the first time that etoposide may induce epigenetic instability in the form of altered DNA methylation patterns in eukaryotes. However, penetrance of the genotoxic effects of etoposide on plant cells, as being reflected as genetic and epigenetic instability, appears to be in a strictly genotype- and/or generation-dependent manner.
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Affiliation(s)
- Xuejiao Yang
- Key Laboratory of Molecular Epigenetics of MOE, and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024, China
| | - Yingjie Yu
- Key Laboratory of Molecular Epigenetics of MOE, and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024, China
| | - Lily Jiang
- Key Laboratory of Molecular Epigenetics of MOE, and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024, China
| | - Xiuyun Lin
- Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Chunyu Zhang
- Key Laboratory of Molecular Epigenetics of MOE, and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024, China
| | - Xiufang Ou
- Key Laboratory of Molecular Epigenetics of MOE, and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024, China
| | - Kenji Osabe
- CSIRO Plant Industry, Canberra, ACT, 2601, Australia
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of MOE, and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024, China
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Mudge SR, Osabe K, Casu RE, Bonnett GD, Manners JM, Birch RG. Efficient silencing of reporter transgenes coupled to known functional promoters in sugarcane, a highly polyploid crop species. Planta 2009; 229:549-58. [PMID: 19011894 DOI: 10.1007/s00425-008-0852-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2008] [Accepted: 10/24/2008] [Indexed: 05/25/2023]
Abstract
Sugarcane is a crop of great interest for engineering of sustainable biomaterials and biofuel production. Isolated sugarcane promoters have generally not maintained the expected patterns of reporter transgene expression. This could arise from defective promoters on redundant alleles in the highly polyploid genome, or from efficient transgene silencing. To resolve this question we undertook detailed analysis of a sugarcane gene that combines a simple pattern in genomic Southern hybridization analysis with potentially useful, sink-specific, expression. Sequence analysis indicates that this gene encodes a member of the SHAQYF subfamily of MYB transcription factors. At least eight alleles were revealed by PCR analysis in sugarcane cultivar Q117 and a similar level of heterozygosity was seen in BAC clones from cultivar Q200. Eight distinct promoter sequences were isolated from Q117, of which at least three are associated with expressed alleles. All of the isolated promoter variants were tested for ability to drive reporter gene expression in sugarcane. Most were functional soon after transfer, but none drove reporter activity in mature stems of regenerated plants. These results show that the ineffectiveness of previously tested sugarcane promoters is not simply due to the isolation of non-functional promoter copies from the polyploid genome. If the unpredictable onset of silencing observed in most other plant species is associated with developmental polyploidy, approaches that avoid efficient transgene silencing in polyploid sugarcane are likely to have much wider utility in molecular improvement.
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Affiliation(s)
- Stephen R Mudge
- Botany Department, School of Integrative Biology, The University of Queensland, Brisbane, 4072, Australia.
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Kobayashi M, Kondo K, Osabe K, Mitsuhashi H. Marine terpenes and terpenoids. V. Oxidation of sarcophytol A, a potent anti-tumor-promoter from the soft coral Sarcophyton glaucum. Chem Pharm Bull (Tokyo) 1988; 36:2331-41. [PMID: 2907304 DOI: 10.1248/cpb.36.2331] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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