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Hsieh JWA, Chang P, Kuang LY, Hsing YIC, Chen PY. Rice transformation treatments leave specific epigenome changes beyond tissue culture. PLANT PHYSIOLOGY 2023; 193:1297-1312. [PMID: 37394940 PMCID: PMC10517251 DOI: 10.1093/plphys/kiad382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 05/16/2023] [Accepted: 05/16/2023] [Indexed: 07/04/2023]
Abstract
During transgenic plant production, tissue culture often carries epigenetic, and genetic changes that underlie somaclonal variations, leading to unpredictable phenotypes. Additionally, specific treatments for rice (Oryza sativa) transformation processes may individually or jointly contribute to somaclonal variations, but their specific impacts on rice epigenomes toward transcriptional variations remain unknown. Here, the impact of individual transformation treatments on genome-wide DNA methylation and the transcriptome were examined. In addition to activating stress-responsive genes, individual transformation components targeted different gene expression modules that were enriched in specific functional categories. The transformation treatments strongly impacted DNA methylation and expression; 75% were independent of tissue culture. Furthermore, our genome-wide analysis showed that the transformation treatments consistently resulted in global hypo-CHH methylation enriched at promoters highly associated with downregulation, particularly when the promoters were colocalized with miniature inverted-repeat transposable elements. Our results clearly highlight the specificity of impacts triggered by individual transformation treatments during rice transformation with the potential association between DNA methylation and gene expression. These changes in gene expression and DNA methylation resulting from rice transformation treatments explain a significant portion of somaclonal variations, that is, way beyond the tissue culture effect.
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Affiliation(s)
- Jo-Wei Allison Hsieh
- Institute of Plant and Microbial Biology, Academia Sinica,
Taipei 115201, Taiwan
- Genome and Systems Biology Degree Program, Academia Sinica and National
Taiwan University, Taipei 10617, Taiwan
| | - Pearl Chang
- Institute of Plant and Microbial Biology, Academia Sinica,
Taipei 115201, Taiwan
- Department of Tropical Agriculture and International Cooperation/Department
of Biological Science and Technology, National Pingtung University of Science and
Technology, Pingtung 91201, Taiwan
| | - Lin-Yun Kuang
- The Transgenic Plant Core Facility, Agricultural Biotechnology Research
Center, Academia Sinica, Taipei 115201, Taiwan
| | - Yue-Ie C Hsing
- Institute of Plant and Microbial Biology, Academia Sinica,
Taipei 115201, Taiwan
| | - Pao-Yang Chen
- Institute of Plant and Microbial Biology, Academia Sinica,
Taipei 115201, Taiwan
- Genome and Systems Biology Degree Program, Academia Sinica and National
Taiwan University, Taipei 10617, Taiwan
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2
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Ichikawa M, Kato N, Toda E, Kashihara M, Ishida Y, Hiei Y, Isobe SN, Shirasawa K, Hirakawa H, Okamoto T, Komari T. Whole-genome sequence analysis of mutations in rice plants regenerated from zygotes, mature embryos, and immature embryos. BREEDING SCIENCE 2023; 73:349-353. [PMID: 37840979 PMCID: PMC10570880 DOI: 10.1270/jsbbs.22100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/25/2023] [Indexed: 10/17/2023]
Abstract
Somaclonal variation was studied by whole-genome sequencing in rice plants (Oryza sativa L., 'Nipponbare') regenerated from the zygotes, mature embryos, and immature embryos of a single mother plant. The mother plant and its seed-propagated progeny were also sequenced. A total of 338 variants of the mother plant sequence were detected in the progeny, and mean values ranged from 9.0 of the seed-propagated plants to 37.4 of regenerants from mature embryos. The natural mutation rate of 1.2 × 10-8 calculated using the variants in the seed-propagated plants was consistent with the values reported previously. The ratio of single nucleotide variants (SNVs) among the variants in the seed-propagated plants was 91.1%, which is higher than 56.1% previously reported, and not significantly different from those in the regenerants. Overall, the ratio of transitions to transversions of SNVs was lower in the regenerants as shown previously. Plants regenerated from mature embryos had significantly more variants than different progeny types. Therefore, using zygotes and immature embryos can reduce somaclonal variation during the genetic manipulation of rice.
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Affiliation(s)
- Masako Ichikawa
- Plant Innovation Center, Japan Tobacco Inc., 700 Higashibara, Iwata, Shizuoka 438-0802, Japan
- Agri-Bio Research Center, KANEKA CORPORATION, 700 Higashibara, Iwata, Shizuoka 438-0802, Japan
| | - Norio Kato
- Plant Innovation Center, Japan Tobacco Inc., 700 Higashibara, Iwata, Shizuoka 438-0802, Japan
- RIKEN Cluster for Science, Technology and Innovation Hub, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
| | - Erika Toda
- RIKEN Cluster for Science, Technology and Innovation Hub, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
- Department of Biological Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masakazu Kashihara
- Plant Innovation Center, Japan Tobacco Inc., 700 Higashibara, Iwata, Shizuoka 438-0802, Japan
- Agri-Bio Research Center, KANEKA CORPORATION, 700 Higashibara, Iwata, Shizuoka 438-0802, Japan
| | - Yuji Ishida
- Plant Innovation Center, Japan Tobacco Inc., 700 Higashibara, Iwata, Shizuoka 438-0802, Japan
- Agri-Bio Research Center, KANEKA CORPORATION, 700 Higashibara, Iwata, Shizuoka 438-0802, Japan
| | - Yukoh Hiei
- Plant Innovation Center, Japan Tobacco Inc., 700 Higashibara, Iwata, Shizuoka 438-0802, Japan
| | - Sachiko N. Isobe
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Kenta Shirasawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Hideki Hirakawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Takashi Okamoto
- RIKEN Cluster for Science, Technology and Innovation Hub, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
| | - Toshihiko Komari
- Plant Innovation Center, Japan Tobacco Inc., 700 Higashibara, Iwata, Shizuoka 438-0802, Japan
- Agri-Bio Research Center, KANEKA CORPORATION, 700 Higashibara, Iwata, Shizuoka 438-0802, Japan
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3
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Karavolias NG, Patel-Tupper D, Seong K, Tjahjadi M, Gueorguieva GA, Tanaka J, Gallegos Cruz A, Lieberman S, Litvak L, Dahlbeck D, Cho MJ, Niyogi KK, Staskawicz BJ. Paralog editing tunes rice stomatal density to maintain photosynthesis and improve drought tolerance. PLANT PHYSIOLOGY 2023; 192:1168-1182. [PMID: 36960567 PMCID: PMC10231365 DOI: 10.1093/plphys/kiad183] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 03/03/2023] [Accepted: 03/03/2023] [Indexed: 06/01/2023]
Abstract
Rice (Oryza sativa) is of paramount importance for global nutrition, supplying at least 20% of global calories. However, water scarcity and increased drought severity are anticipated to reduce rice yields globally. We explored stomatal developmental genetics as a mechanism for improving drought resilience in rice while maintaining yield under climate stress. CRISPR/Cas9-mediated knockouts of the positive regulator of stomatal development STOMAGEN and its paralog EPIDERMAL PATTERNING FACTOR-LIKE10 (EPFL10) yielded lines with ∼25% and 80% of wild-type stomatal density, respectively. epfl10 lines with moderate reductions in stomatal density were able to conserve water to similar extents as stomagen lines but did not suffer from the concomitant reductions in stomatal conductance, carbon assimilation, or thermoregulation observed in stomagen knockouts. Moderate reductions in stomatal density achieved by editing EPFL10 present a climate-adaptive approach for safeguarding yield in rice. Editing the paralog of STOMAGEN in other species may provide a means for tuning stomatal density in agriculturally important crops beyond rice.
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Affiliation(s)
- Nicholas G Karavolias
- Plant and Microbial Biology Department, UC Berkeley, Berkeley, CA 94720, USA
- Innovative Genomics Institute, Berkeley, CA 94704, USA
| | - Dhruv Patel-Tupper
- Plant and Microbial Biology Department, UC Berkeley, Berkeley, CA 94720, USA
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kyungyong Seong
- Plant and Microbial Biology Department, UC Berkeley, Berkeley, CA 94720, USA
| | | | - Gloria-Alexandra Gueorguieva
- Plant and Microbial Biology Department, UC Berkeley, Berkeley, CA 94720, USA
- Innovative Genomics Institute, Berkeley, CA 94704, USA
| | - Jaclyn Tanaka
- Innovative Genomics Institute, Berkeley, CA 94704, USA
| | | | | | | | - Douglas Dahlbeck
- Plant and Microbial Biology Department, UC Berkeley, Berkeley, CA 94720, USA
- Innovative Genomics Institute, Berkeley, CA 94704, USA
| | - Myeong-Je Cho
- Innovative Genomics Institute, Berkeley, CA 94704, USA
| | - Krishna K Niyogi
- Plant and Microbial Biology Department, UC Berkeley, Berkeley, CA 94720, USA
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Brian J Staskawicz
- Plant and Microbial Biology Department, UC Berkeley, Berkeley, CA 94720, USA
- Innovative Genomics Institute, Berkeley, CA 94704, USA
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4
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Zhang X, Hooykaas MJG, van Heusden GP, Hooykaas PJJ. The translocated virulence protein VirD5 causes DNA damage and mutation during Agrobacterium-mediated transformation of yeast. SCIENCE ADVANCES 2022; 8:eadd3912. [PMID: 36383666 PMCID: PMC9668295 DOI: 10.1126/sciadv.add3912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 09/27/2022] [Indexed: 06/16/2023]
Abstract
The soil bacterium Agrobacterium tumefaciens is a preferred gene vector not only for plants but also for fungi. Agrobacterium delivers a small set of virulence proteins into host cells concomitantly with transferred DNA (T-DNA) to support the transformation process. Here, we find that expression of one of these proteins, called VirD5, in yeast host cells causes replication stress and DNA damage. This can result in both genomic rearrangements and local mutations, especially small deletions. Delivery of VirD5 during cocultivation with Agrobacterium led to mutations in the yeast genome that were unlinked to the integration of T-DNA. This load of mutations can be prevented by using a virD5 mutant for genome engineering, but this leads to a lower transformation frequency.
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5
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Danila F, Schreiber T, Ermakova M, Hua L, Vlad D, Lo S, Chen Y, Lambret‐Frotte J, Hermanns AS, Athmer B, von Caemmerer S, Yu S, Hibberd JM, Tissier A, Furbank RT, Kelly S, Langdale JA. A single promoter-TALE system for tissue-specific and tuneable expression of multiple genes in rice. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1786-1806. [PMID: 35639605 PMCID: PMC9398400 DOI: 10.1111/pbi.13864] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 05/06/2022] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
Abstract
In biological discovery and engineering research, there is a need to spatially and/or temporally regulate transgene expression. However, the limited availability of promoter sequences that are uniquely active in specific tissue-types and/or at specific times often precludes co-expression of multiple transgenes in precisely controlled developmental contexts. Here, we developed a system for use in rice that comprises synthetic designer transcription activator-like effectors (dTALEs) and cognate synthetic TALE-activated promoters (STAPs). The system allows multiple transgenes to be expressed from different STAPs, with the spatial and temporal context determined by a single promoter that drives expression of the dTALE. We show that two different systems-dTALE1-STAP1 and dTALE2-STAP2-can activate STAP-driven reporter gene expression in stable transgenic rice lines, with transgene transcript levels dependent on both dTALE and STAP sequence identities. The relative strength of individual STAP sequences is consistent between dTALE1 and dTALE2 systems but differs between cell-types, requiring empirical evaluation in each case. dTALE expression leads to off-target activation of endogenous genes but the number of genes affected is substantially less than the number impacted by the somaclonal variation that occurs during the regeneration of transformed plants. With the potential to design fully orthogonal dTALEs for any genome of interest, the dTALE-STAP system thus provides a powerful approach to fine-tune the expression of multiple transgenes, and to simultaneously introduce different synthetic circuits into distinct developmental contexts.
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Affiliation(s)
- Florence Danila
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Plant Sciences Division, Research School of BiologyAustralian National UniversityCanberraAustralian Capital TerritoryAustralia
| | - Tom Schreiber
- Department of Cell and Metabolic BiologyLeibniz Institute of Plant BiochemistryHalleGermany
| | - Maria Ermakova
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Plant Sciences Division, Research School of BiologyAustralian National UniversityCanberraAustralian Capital TerritoryAustralia
| | - Lei Hua
- Department of Plant SciencesUniversity of CambridgeCambridgeUK
| | - Daniela Vlad
- Department of Plant SciencesUniversity of OxfordOxfordUK
| | - Shuen‐Fang Lo
- Biotechnology CenterNational Chung Hsing UniversityTaichungTaiwan
| | - Yi‐Shih Chen
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan
| | | | - Anna S. Hermanns
- Department of Plant SciencesUniversity of OxfordOxfordUK
- Present address:
Plant Breeding and Genetics Section, School of Integrative Plant ScienceCornell UniversityIthacaNew YorkUSA
| | - Benedikt Athmer
- Department of Cell and Metabolic BiologyLeibniz Institute of Plant BiochemistryHalleGermany
| | - Susanne von Caemmerer
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Plant Sciences Division, Research School of BiologyAustralian National UniversityCanberraAustralian Capital TerritoryAustralia
| | - Su‐May Yu
- Biotechnology CenterNational Chung Hsing UniversityTaichungTaiwan
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan
| | | | - Alain Tissier
- Department of Cell and Metabolic BiologyLeibniz Institute of Plant BiochemistryHalleGermany
| | - Robert T. Furbank
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Plant Sciences Division, Research School of BiologyAustralian National UniversityCanberraAustralian Capital TerritoryAustralia
| | - Steven Kelly
- Department of Plant SciencesUniversity of OxfordOxfordUK
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6
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Hou BH, Tsai YH, Chiang MH, Tsao SM, Huang SH, Chao CP, Chen HM. Cultivar-specific markers, mutations, and chimerisim of Cavendish banana somaclonal variants resistant to Fusarium oxysporum f. sp. cubense tropical race 4. BMC Genomics 2022; 23:470. [PMID: 35752751 PMCID: PMC9233791 DOI: 10.1186/s12864-022-08692-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 06/13/2022] [Indexed: 11/13/2022] Open
Abstract
Background The selection of tissue culture–derived somaclonal variants of Giant Cavendish banana (Musa spp., Cavendish sub-group AAA) by the Taiwan Banana Research Institute (TBRI) has resulted in several cultivars resistant to Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4), a destructive fungus threatening global banana production. However, the mutations in these somaclonal variants have not yet been determined. We performed an RNA-sequencing (RNA-seq) analysis of three TBRI Foc TR4–resistant cultivars: ‘Tai-Chiao No. 5’ (TC5), ‘Tai-Chiao No. 7’ (TC7), and ‘Formosana’ (FM), as well as their susceptible progenitor ‘Pei-Chiao’ (PC), to investigate the sequence variations among them and develop cultivar-specific markers. Results A group of single-nucleotide variants (SNVs) specific to one cultivar were identified from the analysis of RNA-seq data and validated using Sanger sequencing from genomic DNA. Several SNVs were further converted into cleaved amplified polymorphic sequence (CAPS) markers or derived CAPS markers that could identify the three Foc TR4–resistant cultivars among 6 local and 5 international Cavendish cultivars. Compared with PC, the three resistant cultivars showed a loss or alteration of heterozygosity in some chromosomal regions, which appears to be a consequence of single-copy chromosomal deletions. Notably, TC7 and FM shared a common deletion region on chromosome 5; however, different TC7 tissues displayed varying degrees of allele ratios in this region, suggesting the presence of chimerism in TC7. Conclusions This work demonstrates that reliable SNV markers of tissue culture–derived and propagated banana cultivars with a triploid genome can be developed through RNA-seq data analysis. Moreover, the analysis of sequence heterozygosity can uncover chromosomal deletions and chimerism in banana somaclonal variants. The markers obtained from this study will assist with the identification of TBRI Cavendish somaclonal variants for the quality control of tissue culture propagation, and the protection of breeders’ rights. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08692-5.
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Affiliation(s)
- Bo-Han Hou
- Agricultural Biotechnology Research Center, Academia Sinica, 11529, Taipei, Taiwan
| | - Yi-Heng Tsai
- Agricultural Biotechnology Research Center, Academia Sinica, 11529, Taipei, Taiwan
| | - Ming-Hau Chiang
- Agricultural Biotechnology Research Center, Academia Sinica, 11529, Taipei, Taiwan
| | - Shu-Ming Tsao
- Agricultural Biotechnology Research Center, Academia Sinica, 11529, Taipei, Taiwan
| | | | - Chih-Ping Chao
- Taiwan Banana Research Institute, 90442, Pingtung, Taiwan
| | - Ho-Ming Chen
- Agricultural Biotechnology Research Center, Academia Sinica, 11529, Taipei, Taiwan.
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7
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Barchenger DW, Hsu YM, Ou JY, Lin YP, Lin YC, Balendres MAO, Hsu YC, Schafleitner R, Hanson P. Whole genome resequencing and complementation tests reveal candidate loci contributing to bacterial wilt (Ralstonia sp.) resistance in tomato. Sci Rep 2022; 12:8374. [PMID: 35589778 PMCID: PMC9120091 DOI: 10.1038/s41598-022-12326-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 04/07/2022] [Indexed: 01/19/2023] Open
Abstract
Tomato (Solanum lycopersicum) is one of the most economically important vegetable crops worldwide. Bacterial wilt (BW), caused by the Ralstonia solanacearum species complex, has been reported as the second most important plant pathogenic bacteria worldwide, and likely the most destructive. Extensive research has identified two major loci, Bwr-6 and Bwr-12, that contribute to resistance to BW in tomato; however, these loci do not completely explain resistance. Segregation of resistance in two populations that were homozygous dominant or heterozygous for all Bwr-6 and Bwr-12 associated molecular markers suggested the action of one or two resistance loci in addition to these two major QTLs. We utilized whole genome sequence data analysis and pairwise comparison of six BW resistant and nine BW susceptible tomato lines to identify candidate genes that, in addition to Bwr-6 and Bwr-12, contributed to resistance. Through this approach we found 27,046 SNPs and 5975 indels specific to the six resistant lines, affecting 385 genes. One sequence variant on chromosome 3 captured by marker Bwr3.2dCAPS located in the Asc (Solyc03g114600.4.1) gene had significant association with resistance, but it did not completely explain the resistance phenotype. The SNP associated with Bwr3.2dCAPS was located within the resistance gene Asc which was inside the previously identified Bwr-3 locus. This study provides a foundation for further investigations into new loci distributed throughout the tomato genome that could contribute to BW resistance and into the role of resistance genes that may act against multiple pathogens.
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Affiliation(s)
| | - Yu-Ming Hsu
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Univ Evry, Université Paris-Saclay, 91405, Orsay, France
| | - Jheng-Yang Ou
- Biotechnology Center in Southern Taiwan, Agricultural Biotechnology Research Center, Academia Sinica, Tainan, Taiwan
| | | | - Yao-Cheng Lin
- Biotechnology Center in Southern Taiwan, Agricultural Biotechnology Research Center, Academia Sinica, Tainan, Taiwan
| | - Mark Angelo O Balendres
- Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, Los Baños, Laguna, Philippines
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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.
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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
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9
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Pucker B, Kleinbölting N, Weisshaar B. Large scale genomic rearrangements in selected Arabidopsis thaliana T-DNA lines are caused by T-DNA insertion mutagenesis. BMC Genomics 2021; 22:599. [PMID: 34362298 PMCID: PMC8348815 DOI: 10.1186/s12864-021-07877-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 07/06/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Experimental proof of gene function assignments in plants is based on mutant analyses. T-DNA insertion lines provided an invaluable resource of mutants and enabled systematic reverse genetics-based investigation of the functions of Arabidopsis thaliana genes during the last decades. RESULTS We sequenced the genomes of 14 A. thaliana GABI-Kat T-DNA insertion lines, which eluded flanking sequence tag-based attempts to characterize their insertion loci, with Oxford Nanopore Technologies (ONT) long reads. Complex T-DNA insertions were resolved and 11 previously unknown T-DNA loci identified, resulting in about 2 T-DNA insertions per line and suggesting that this number was previously underestimated. T-DNA mutagenesis caused fusions of chromosomes along with compensating translocations to keep the gene set complete throughout meiosis. Also, an inverted duplication of 800 kbp was detected. About 10 % of GABI-Kat lines might be affected by chromosomal rearrangements, some of which do not involve T-DNA. Local assembly of selected reads was shown to be a computationally effective method to resolve the structure of T-DNA insertion loci. We developed an automated workflow to support investigation of long read data from T-DNA insertion lines. All steps from DNA extraction to assembly of T-DNA loci can be completed within days. CONCLUSIONS Long read sequencing was demonstrated to be an effective way to resolve complex T-DNA insertions and chromosome fusions. Many T-DNA insertions comprise not just a single T-DNA, but complex arrays of multiple T-DNAs. It is becoming obvious that T-DNA insertion alleles must be characterized by exact identification of both T-DNA::genome junctions to generate clear genotype-to-phenotype relations.
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Affiliation(s)
- Boas Pucker
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec), Bielefeld University, Sequenz 1, 33615 Bielefeld, Germany
- Evolution and Diversity, Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Nils Kleinbölting
- Bioinformatics Resource Facility, Center for Biotechnology (CeBiTec, Bielefeld University, Sequenz 1, 33615 Bielefeld, Germany
| | - Bernd Weisshaar
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec), Bielefeld University, Sequenz 1, 33615 Bielefeld, Germany
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10
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An unbiased method for evaluating the genome-wide specificity of base editors in rice. Nat Protoc 2020; 16:431-457. [PMID: 33349703 DOI: 10.1038/s41596-020-00423-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 09/24/2020] [Indexed: 12/21/2022]
Abstract
Base editors can achieve targeted genomic base conversion. However, the off-target issue is one of the major concerns in their application. Whole-genome sequencing (WGS) at the individual level can provide direct information on genome-wide specificity, but it is difficult to distinguish true off-target single-nucleotide variants (SNVs) induced by base editors from background variation. Here we describe an unbiased WGS method for evaluating the specificity of base editors in rice. In this protocol, we describe the experimental design and provide details of vector construction, rice transformation and tissue culture, as well as a comprehensive WGS data analysis pipeline for overcoming two related core problems in various plant species: high background mutation rates and the heterogeneity of examined populations. Using this protocol, researchers can straightforwardly and accurately assess the genome-wide specificity of base editors and other genome editing tools in 12-15 weeks.
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11
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Loss Sperandio MV, Santos LA, Huertas Tavares OC, Fernandes MS, de Freitas Lima M, de Souza SR. Silencing the Oryza sativa plasma membrane H +-ATPase isoform OsA2 affects grain yield and shoot growth and decreases nitrogen concentration. JOURNAL OF PLANT PHYSIOLOGY 2020; 251:153220. [PMID: 32622271 DOI: 10.1016/j.jplph.2020.153220] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 06/09/2020] [Accepted: 06/09/2020] [Indexed: 06/11/2023]
Abstract
The plasma membrane (PM) H+-ATPase (EC 3.6.1.3.) is a key component involved in nutrient uptake. There are 10 PM H+-ATPase isoforms in the rice genome (OsA1-OsA10), and OsA2 is highly responsive to nitrate (NO3-). We investigated the role that the OsA2 isoform plays in the total N and growth of rice (Oryza sativa). By the use of artificial microRNA, mutant osa2 rice lines presented ∼70 % downregulated levels of OsA2. Three osa2 lines and control plants (transformed with an empty IRS154 vector and named IRS) were cultivated in the greenhouse to evaluate grain and shoot production. For hydroponic experiments, the same lines were grown in Hoagland solution under two different NO3- levels for 30 days - 0.2 mM NO3--N (low N) or 2.0 mM NO3--N (sufficient N) - or were grown for three days without NO3- (starvation) after 27 days under 2.0 mM NO3--N. In the greenhouse experiments, compared with the IRS plants, the osa2 lines had lower shoot fresh weights, grain yields and SPAD values. Moreover, compared with the IRS plants, the three osa2 lines grown hydroponically under low NO3- levels had lower N concentration and net flux of NO3-. PM H+-ATPase activity was lower in the osa2 mutants than in the IRS plants. The relatively low N concentration in the osa2 lines was not due to lower expression of OsNRT2.1, OsNRT2.2, or OsNAR2.1. These results indicate that the specific PM H+-ATPase isoform OsA2 affects the net flux of NO3-, N concentration, and grain yield.
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Affiliation(s)
- Marcus Vinícius Loss Sperandio
- Federal Rural University of Pernambuco, Department of Biology, R. Dom Manuel de Medeiros, Dois Irmãos, CEP 52171-900, Recife, Pernambuco, Brazil.
| | - Leandro Azevedo Santos
- Federal Rural University of Rio de Janeiro, BR 465, Km 7.0, Seropédica, Rio de Janeiro, Brazil
| | | | | | - Marcelo de Freitas Lima
- Federal Rural University of Rio de Janeiro, BR 465, Km 7.0, Seropédica, Rio de Janeiro, Brazil
| | - Sonia Regina de Souza
- Federal Rural University of Rio de Janeiro, BR 465, Km 7.0, Seropédica, Rio de Janeiro, Brazil
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12
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Viana VE, Pegoraro C, Busanello C, Costa de Oliveira A. Mutagenesis in Rice: The Basis for Breeding a New Super Plant. FRONTIERS IN PLANT SCIENCE 2019; 10:1326. [PMID: 31781133 PMCID: PMC6857675 DOI: 10.3389/fpls.2019.01326] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 09/24/2019] [Indexed: 05/28/2023]
Abstract
The high selection pressure applied in rice breeding since its domestication thousands of years ago has caused a narrowing in its genetic variability. Obtaining new rice cultivars therefore becomes a major challenge for breeders and developing strategies to increase the genetic variability has demanded the attention of several research groups. Understanding mutations and their applications have paved the way for advances in the elucidation of a genetic, physiological, and biochemical basis of rice traits. Creating variability through mutations has therefore grown to be among the most important tools to improve rice. The small genome size of rice has enabled a faster release of higher quality sequence drafts as compared to other crops. The move from structural to functional genomics is possible due to an array of mutant databases, highlighting mutagenesis as an important player in this progress. Furthermore, due to the synteny among the Poaceae, other grasses can also benefit from these findings. Successful gene modifications have been obtained by random and targeted mutations. Furthermore, following mutation induction pathways, techniques have been applied to identify mutations and the molecular control of DNA damage repair mechanisms in the rice genome. This review highlights findings in generating rice genome resources showing strategies applied for variability increasing, detection and genetic mechanisms of DNA damage repair.
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Affiliation(s)
| | | | | | - Antonio Costa de Oliveira
- Centro de Genômica e Fitomelhoramento, Faculdade de Agronomia Eliseu Maciel, Departamento de Fitotecnia, Universidade Federal de Pelotas, Campus Capão do Leão, Rio Grande do Sul, Brazil
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13
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Chang CL, Serapion JC, Hung HH, Lin YC, Tsai YC, Jane WN, Chang MC, Lai MH, Hsing YIC. Studies of a rice sterile mutant sstl from the TRIM collection. BOTANICAL STUDIES 2019; 60:12. [PMID: 31292815 PMCID: PMC6620220 DOI: 10.1186/s40529-019-0260-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 06/30/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND Rice (Oryza sativa) is one of the main crops in the world, and more than 3.9 billion people will consume rice by 2025. Sterility significantly affects rice production and leads to yield defects. The undeveloped anthers or abnormal pollen represent serious defects in rice male sterility. Therefore, understanding the mechanism of male sterility is an important task. Here, we investigated a rice sterile mutant according to its developmental morphology and transcriptional profiles. RESULTS An untagged T-DNA insertional mutant showed defective pollen and abnormal anthers as compared with its semi-sterile mutant (sstl) progeny segregates. Transcriptomic analysis of sterile sstl-s revealed several biosynthesis pathways, such as downregulated cell wall, lipids, secondary metabolism, and starch synthesis. This downregulation is consistent with the morphological characterization of sstl-s anthers with irregular exine, absence of intine, no starch accumulation in pollen grains and no accumulated flavonoids in anthers. Moreover, defective microsporangia development led to abnormal anther locule and aborted microspores. The downregulated lipids, starch, and cell wall synthesis-related genes resulted in loss of fertility. CONCLUSIONS We illustrate the importance of microsporangia in the development of anthers and functional microspores. Abnormal development of pollen grains, pollen wall, anther locule, etc. result in severe yield reduction.
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Affiliation(s)
- Chia-Ling Chang
- Department of Agronomy, National Taiwan University, Taipei, 106 Taiwan
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei, 115 Taiwan
| | - Jerry C. Serapion
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei, 115 Taiwan
| | - Han-Hui Hung
- Crop Science Division, Taiwan Agricultural Research Institute, Taichung, 413 Taiwan
| | - Yan-Cheng Lin
- Department of Life Science, National Taiwan University, Taipei, 106 Taiwan
| | - Yuan-Ching Tsai
- Department of Agronomy, National Chiayi University, Chiayi, 600 Taiwan
| | - Wann-Neng Jane
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei, 115 Taiwan
| | - Men-Chi Chang
- Department of Agronomy, National Taiwan University, Taipei, 106 Taiwan
| | - Ming-Hsin Lai
- Crop Science Division, Taiwan Agricultural Research Institute, Taichung, 413 Taiwan
| | - Yue-ie C. Hsing
- Department of Agronomy, National Taiwan University, Taipei, 106 Taiwan
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei, 115 Taiwan
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14
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Young J, Zastrow-Hayes G, Deschamps S, Svitashev S, Zaremba M, Acharya A, Paulraj S, Peterson-Burch B, Schwartz C, Djukanovic V, Lenderts B, Feigenbutz L, Wang L, Alarcon C, Siksnys V, May G, Chilcoat ND, Kumar S. CRISPR-Cas9 Editing in Maize: Systematic Evaluation of Off-target Activity and Its Relevance in Crop Improvement. Sci Rep 2019; 9:6729. [PMID: 31040331 PMCID: PMC6491584 DOI: 10.1038/s41598-019-43141-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 04/15/2019] [Indexed: 12/18/2022] Open
Abstract
CRISPR-Cas9 enabled genome engineering has great potential for improving agriculture productivity, but the possibility of unintended off-target edits has evoked some concerns. Here we employ a three-step strategy to investigate Cas9 nuclease specificity in a complex plant genome. Our approach pairs computational prediction with genome-wide biochemical off-target detection followed by validation in maize plants. Our results reveal high frequency (up to 90%) on-target editing with no evidence of off-target cleavage activity when guide RNAs were bioinformatically predicted to be specific. Predictable off-target edits were observed but only with a promiscuous guide RNA intentionally designed to validate our approach. Off-target editing can be minimized by designing guide RNAs that are different from other genomic locations by at least three mismatches in combination with at least one mismatch occurring in the PAM proximal region. With well-designed guides, genetic variation from Cas9 off-target cleavage in plants is negligible, and much less than inherent variation.
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Affiliation(s)
- Joshua Young
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Johnston, IA, 50131, USA
| | - Gina Zastrow-Hayes
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Johnston, IA, 50131, USA
| | - Stéphane Deschamps
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Johnston, IA, 50131, USA
| | - Sergei Svitashev
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Johnston, IA, 50131, USA
| | - Mindaugas Zaremba
- Institute of Biotechnology, Vilnius University, Vilnius, LT, 10257, Lithuania
| | - Ananta Acharya
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Johnston, IA, 50131, USA
| | - Sushmitha Paulraj
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Johnston, IA, 50131, USA
| | | | - Chris Schwartz
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Johnston, IA, 50131, USA
| | - Vesna Djukanovic
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Johnston, IA, 50131, USA
| | - Brian Lenderts
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Johnston, IA, 50131, USA
| | - Lanie Feigenbutz
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Johnston, IA, 50131, USA
| | - Lijuan Wang
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Johnston, IA, 50131, USA
| | - Clara Alarcon
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Johnston, IA, 50131, USA
| | - Virginijus Siksnys
- Institute of Biotechnology, Vilnius University, Vilnius, LT, 10257, Lithuania
| | - Gregory May
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Johnston, IA, 50131, USA
| | - N Doane Chilcoat
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Johnston, IA, 50131, USA
| | - Sandeep Kumar
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Johnston, IA, 50131, USA.
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15
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Park D, Park SH, Kim YS, Choi BS, Kim JK, Kim NS, Choi IY. NGS sequencing reveals that many of the genetic variations in transgenic rice plants match the variations found in natural rice population. Genes Genomics 2018; 41:213-222. [PMID: 30406575 DOI: 10.1007/s13258-018-0754-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 10/15/2018] [Indexed: 11/27/2022]
Abstract
BACKGROUND As the transformation process can induce mutations in host plants, molecular characterization of the associated genomic changes is important not only for practical food safety but also for understanding the fundamental theories of genome evolution. OBJECTIVES To investigate a population-scale comparative study of the genome-wide spectrum of sequence variants in the transgenic genome with the variations present in 3000 rice varieties. RESULTS On average, we identified 19,273 SNPs (including Indels) per transgenic line in which 10,729 SNPs were at the identical locations in the three transgenic rice plants. We found that these variations were predominantly present in specific regions in chromosomes 8 and 10. Majority (88%) of the identified variations were detected at the same genomic locations as those in natural rice population, implying that the transgenic induced mutations had a tendency to be common alleles. CONCLUSION Genomic variations in transgenic rice plants frequently occurred at the same sites as the major alleles found in the natural rice population, which implies that the sequence variations occur within the limits of a biological system to ensure survival.
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Affiliation(s)
- Doori Park
- Department of Molecular Bioscience, Kangwon National University, Chuncheon, South Korea
| | - Su-Hyun Park
- Graduate School of International Agricultural Technology and Crop Biotech Institute/GreenBio Science and Technology, Seoul National University, Pyeongchang, South Korea
- Laboratory of Plant Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Youn Shic Kim
- Graduate School of International Agricultural Technology and Crop Biotech Institute/GreenBio Science and Technology, Seoul National University, Pyeongchang, South Korea
| | | | - Ju-Kon Kim
- Graduate School of International Agricultural Technology and Crop Biotech Institute/GreenBio Science and Technology, Seoul National University, Pyeongchang, South Korea.
| | - Nam-Soo Kim
- Department of Molecular Bioscience, Kangwon National University, Chuncheon, South Korea.
- Institute of Bioscience and Biomedical Sciences, Kangwon National University, Chuncheon, South Korea.
| | - Ik-Young Choi
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon, South Korea.
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16
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Abstract
Oryza sativa indica (cv. IR64) and Oryza sativa japonica (cv. TNG67) vary in their regeneration efficiency. Such variation may occur in response to cultural environments that induce somaclonal variation. Somaclonal variations may arise from epigenetic factors, such as DNA methylation. We hypothesized that somaclonal variation may be associated with the differential regeneration efficiency between IR64 and TNG67 through changes in DNA methylation. We generated the stage-associated methylome and transcriptome profiles of the embryo, induced calli, sub-cultured calli, and regenerated calli (including both successful and failed regeneration) of IR64 and TNG67. We found that stage-associated changes are evident by the increase in the cytosine methylation of all contexts upon induction and decline upon regeneration. These changes in the methylome are largely random, but a few regions are consistently targeted at the later stages of culture. The expression profiles showed a dominant tissue-specific difference between the embryo and the calli. A prominent cultivar-associated divide in the global methylation pattern was observed, and a subset of cultivar-associated differentially methylated regions also showed stage-associated changes, implying a close association between differential methylation and the regeneration programs of these two rice cultivars. Based on these findings, we speculate that the differential epigenetic regulation of stress response and developmental pathways may be coupled with genetic differences, ultimately leading to differential regeneration efficiency. The present study elucidates the impact of tissue culture on callus formation and delineates the impact of stage and cultivar to determine the dynamics of the methylome and transcriptome in culture.
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17
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Tang X, Liu G, Zhou J, Ren Q, You Q, Tian L, Xin X, Zhong Z, Liu B, Zheng X, Zhang D, Malzahn A, Gong Z, Qi Y, Zhang T, Zhang Y. A large-scale whole-genome sequencing analysis reveals highly specific genome editing by both Cas9 and Cpf1 (Cas12a) nucleases in rice. Genome Biol 2018; 19:84. [PMID: 29973285 PMCID: PMC6031188 DOI: 10.1186/s13059-018-1458-5] [Citation(s) in RCA: 166] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 05/27/2018] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Targeting specificity has been a barrier to applying genome editing systems in functional genomics, precise medicine and plant breeding. In plants, only limited studies have used whole-genome sequencing (WGS) to test off-target effects of Cas9. The cause of numerous discovered mutations is still controversial. Furthermore, WGS-based off-target analysis of Cpf1 (Cas12a) has not been reported in any higher organism to date. RESULTS We conduct a WGS analysis of 34 plants edited by Cas9 and 15 plants edited by Cpf1 in T0 and T1 generations along with 20 diverse control plants in rice. The sequencing depths range from 45× to 105× with read mapping rates above 96%. Our results clearly show that most mutations in edited plants are created by the tissue culture process, which causes approximately 102 to 148 single nucleotide variations (SNVs) and approximately 32 to 83 insertions/deletions (indels) per plant. Among 12 Cas9 single guide RNAs (sgRNAs) and three Cpf1 CRISPR RNAs (crRNAs) assessed by WGS, only one Cas9 sgRNA resulted in off-target mutations in T0 lines at sites predicted by computer programs. Moreover, we cannot find evidence for bona fide off-target mutations due to continued expression of Cas9 or Cpf1 with guide RNAs in T1 generation. CONCLUSIONS Our comprehensive and rigorous analysis of WGS data across multiple sample types suggests both Cas9 and Cpf1 nucleases are very specific in generating targeted DNA modifications and off-targeting can be avoided by designing guide RNAs with high specificity.
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Affiliation(s)
- Xu Tang
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Guanqing Liu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Jianping Zhou
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Qiurong Ren
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Qi You
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Li Tian
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Xuhui Xin
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Zhaohui Zhong
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Binglin Liu
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Xuelian Zheng
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Dengwei Zhang
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Aimee Malzahn
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA
| | - Zhiyun Gong
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA.
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, 20850, USA.
| | - Tao Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China.
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China.
| | - Yong Zhang
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China.
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18
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Tang X, Liu G, Zhou J, Ren Q, You Q, Tian L, Xin X, Zhong Z, Liu B, Zheng X, Zhang D, Malzahn A, Gong Z, Qi Y, Zhang T, Zhang Y. A large-scale whole-genome sequencing analysis reveals highly specific genome editing by both Cas9 and Cpf1 (Cas12a) nucleases in rice. Genome Biol 2018; 19:84. [PMID: 29973285 DOI: 10.1101/292086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 05/27/2018] [Indexed: 05/25/2023] Open
Abstract
BACKGROUND Targeting specificity has been a barrier to applying genome editing systems in functional genomics, precise medicine and plant breeding. In plants, only limited studies have used whole-genome sequencing (WGS) to test off-target effects of Cas9. The cause of numerous discovered mutations is still controversial. Furthermore, WGS-based off-target analysis of Cpf1 (Cas12a) has not been reported in any higher organism to date. RESULTS We conduct a WGS analysis of 34 plants edited by Cas9 and 15 plants edited by Cpf1 in T0 and T1 generations along with 20 diverse control plants in rice. The sequencing depths range from 45× to 105× with read mapping rates above 96%. Our results clearly show that most mutations in edited plants are created by the tissue culture process, which causes approximately 102 to 148 single nucleotide variations (SNVs) and approximately 32 to 83 insertions/deletions (indels) per plant. Among 12 Cas9 single guide RNAs (sgRNAs) and three Cpf1 CRISPR RNAs (crRNAs) assessed by WGS, only one Cas9 sgRNA resulted in off-target mutations in T0 lines at sites predicted by computer programs. Moreover, we cannot find evidence for bona fide off-target mutations due to continued expression of Cas9 or Cpf1 with guide RNAs in T1 generation. CONCLUSIONS Our comprehensive and rigorous analysis of WGS data across multiple sample types suggests both Cas9 and Cpf1 nucleases are very specific in generating targeted DNA modifications and off-targeting can be avoided by designing guide RNAs with high specificity.
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Affiliation(s)
- Xu Tang
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Guanqing Liu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Jianping Zhou
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Qiurong Ren
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Qi You
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Li Tian
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Xuhui Xin
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Zhaohui Zhong
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Binglin Liu
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Xuelian Zheng
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Dengwei Zhang
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Aimee Malzahn
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA
| | - Zhiyun Gong
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA.
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, 20850, USA.
| | - Tao Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China.
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China.
| | - Yong Zhang
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China.
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19
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Wu HP, Wei FJ, Wu CC, Lo SF, Chen LJ, Fan MJ, Chen S, Wen IC, Yu SM, Ho THD, Lai MH, Hsing YIC. Large-scale phenomics analysis of a T-DNA tagged mutant population. Gigascience 2018; 6:1-7. [PMID: 28854617 PMCID: PMC5570018 DOI: 10.1093/gigascience/gix055] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 07/04/2017] [Indexed: 01/26/2023] Open
Abstract
Rice, Oryza sativa L., is one of the most important crops in the world. With the rising world population, feeding people in a more sustainable and environmentally friendly way becomes increasingly important. Therefore, the rice research community needs to share resources to better understand the functions of rice genes that are the foundation for future agricultural biotechnology development, and one way to achieve this goal is via the extensive study of insertional mutants. We have constructed a large rice insertional mutant population in a japonica rice variety, Tainung 67. The collection contains about 93 000 mutant lines, among them 85% with phenomics data and 65% with flanking sequence data. We screened the phenotypes of 12 individual plants for each line grown under field conditions according to 68 subcategories and 3 quantitative traits. Both phenotypes and integration sites are searchable in the Taiwan Rice Insertional Mutants Database. Detailed analyses of phenomics data, T-DNA flanking sequences, and whole-genome sequencing data for rice insertional mutants can lead to the discovery of novel genes. In addition, studies of mutant phenotypes can reveal relationships among varieties, cultivation locations, and cropping seasons.
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Affiliation(s)
- Hshin-Ping Wu
- Institute of Plant and Microbial Biology, Academia Sinica, 128, Section 2, Yien-chu-yuan Road, Nankang, Taipei 115, Taiwan
| | - Fu-Jin Wei
- Institute of Plant and Microbial Biology, Academia Sinica, 128, Section 2, Yien-chu-yuan Road, Nankang, Taipei 115, Taiwan
| | - Cheng-Chieh Wu
- Institute of Plant and Microbial Biology, Academia Sinica, 128, Section 2, Yien-chu-yuan Road, Nankang, Taipei 115, Taiwan.,Institute of Plant Biology, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
| | - Shuen-Fang Lo
- Institute of Molecular Biology, Academia Sinica, 128, Section 2, Yien-chu-yuan Road, Nankang, Taipei 115, Taiwan.,Agricultural Biotechnology Center, National Chung Hsing University, 145, Xingda Road, Taichung 402, Taiwan
| | - Liang-Jwu Chen
- Institute of Molecular Biology, National Chung Hsing University, 145, Xingda Road, Taichung 402, Taiwan
| | - Ming-Jen Fan
- Department of Biotechnology, Asia University, 500, Lioufeng Road, Taichung 413, Taiwan
| | - Shu Chen
- Plant Germplasm Division, Taiwan Agricultural Research Institute, 189, Zhongzheng Road, Taichung 413, Taiwan
| | - Ien-Chie Wen
- Plant Germplasm Division, Taiwan Agricultural Research Institute, 189, Zhongzheng Road, Taichung 413, Taiwan
| | - Su-May Yu
- Institute of Molecular Biology, Academia Sinica, 128, Section 2, Yien-chu-yuan Road, Nankang, Taipei 115, Taiwan.,Agricultural Biotechnology Center, National Chung Hsing University, 145, Xingda Road, Taichung 402, Taiwan.,Department of Life Sciences, National Chung Hsing University, 145, Xingda Road, Taichung 402, Taiwan
| | - Tuan-Hua David Ho
- Institute of Plant and Microbial Biology, Academia Sinica, 128, Section 2, Yien-chu-yuan Road, Nankang, Taipei 115, Taiwan.,Agricultural Biotechnology Center, National Chung Hsing University, 145, Xingda Road, Taichung 402, Taiwan.,Department of Life Sciences, National Chung Hsing University, 145, Xingda Road, Taichung 402, Taiwan
| | - Ming-Hsin Lai
- Crop Science Division, Taiwan Agricultural Research Institute, 189, Zhongzheng Road, Taichung 413, Taiwan
| | - Yue-Ie C Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, 128, Section 2, Yien-chu-yuan Road, Nankang, Taipei 115, Taiwan.,Department of Agronomy, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
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20
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Advancing Agrobacterium-Based Crop Transformation and Genome Modification Technology for Agricultural Biotechnology. Curr Top Microbiol Immunol 2018; 418:489-507. [PMID: 29959543 DOI: 10.1007/82_2018_97] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The last decade has seen significant strides in Agrobacterium-mediated plant transformation technology. This has not only expanded the number of crop species that can be transformed by Agrobacterium, but has also made it possible to routinely transform several recalcitrant crop species including cereals (e.g., maize, sorghum, and wheat). However, the technology is limited by the random nature of DNA insertions, genotype dependency, low frequency of quality events, and variation in gene expression arising from genomic insertion sites. A majority of these deficiencies have now been addressed by improving the frequency of quality events, developing genotype-independent transformation capability in maize, developing an Agrobacterium-based site-specific integration technology for precise gene targeting, and adopting Agrobacterium-delivered CRISPR-Cas genes for gene editing. These improved transformation technologies are discussed in detail in this chapter.
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21
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Abstract
Agrobacterium strains transfer a single-strand form of T-DNA (T-strands) and Virulence (Vir) effector proteins to plant cells. Following transfer, T-strands likely form complexes with Vir and plant proteins that traffic through the cytoplasm and enter the nucleus. T-strands may subsequently randomly integrate into plant chromosomes and permanently express encoded transgenes, a process known as stable transformation. The molecular processes by which T-strands integrate into the host genome remain unknown. Although integration resembles DNA repair processes, the requirement of known DNA repair pathways for integration is controversial. The configuration and genomic position of integrated T-DNA molecules likely affect transgene expression, and control of integration is consequently important for basic research and agricultural biotechnology applications. This article reviews our current knowledge of the process of T-DNA integration and proposes ways in which this knowledge may be manipulated for genome editing and synthetic biology purposes.
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Affiliation(s)
- Stanton B Gelvin
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907-1392, USA;
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22
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Li WX, Wu SL, Liu YH, Jin GL, Zhao HJ, Fan LJ, Shu QY. Genome-wide profiling of genetic variation in Agrobacterium-transformed rice plants. J Zhejiang Univ Sci B 2017; 17:992-996. [PMID: 27921404 DOI: 10.1631/jzus.b1600301] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Agrobacterium-mediated transformation has been widely used in producing transgenic plants, and was recently used to generate "transgene-clean" targeted genomic modifications coupled with the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas9) system. Although tremendous variation in morphological and agronomic traits, such as plant height, seed fertility, and grain size, was observed in transgenic plants, the underlying mechanisms are not yet well understood, and the types and frequency of genetic variation in transformed plants have not been fully disclosed. To reveal the genome-wide variation in transformed plants, we sequenced the genomes of five independent T0 rice plants using next-generation sequencing (NGS) techniques. Bioinformatics analyses followed by experimental validation revealed the following: (1) in addition to transfer-DNA (T-DNA) insertions, three transformed plants carried heritable plasmid backbone DNA of variable sizes (855-5216 bp) and in different configurations with the T-DNA insertions (linked or apart); (2) each transgenic plant contained an estimated 338-1774 independent genetic variations (single nucleotide variations (SNVs) or small insertion/deletions); and (3) 2-6 new Tos17 insertions were detected in each transformed plant, but no other transposable elements or bacterial genomic DNA.
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Affiliation(s)
- Wen-Xu Li
- State Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou 310058, China.,Institute for Wheat Research, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - San-Ling Wu
- Analysis Center of Agrobiology and Environmental Sciences, Faculty of Agriculture, Life and Environment Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yan-Hua Liu
- State Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou 310058, China
| | - Gu-Lei Jin
- Hangzhou Guhe Information and Technology Co., Ltd., Hangzhou 310058, China
| | - Hai-Jun Zhao
- State Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou 310058, China
| | - Long-Jiang Fan
- IBM Biocomputational Laboratory, Institute of Crop Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qing-Yao Shu
- State Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou 310058, China
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23
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Wei FJ, Tsai YC, Hsu YM, Chen YA, Huang CT, Wu HP, Huang LT, Lai MH, Kuang LY, Lo SF, Yu SM, Lin YR, Hsing YIC. Lack of Genotype and Phenotype Correlation in a Rice T-DNA Tagged Line Is Likely Caused by Introgression in the Seed Source. PLoS One 2016; 11:e0155768. [PMID: 27186981 PMCID: PMC4871347 DOI: 10.1371/journal.pone.0155768] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 05/03/2016] [Indexed: 01/12/2023] Open
Abstract
Rice (Oryza sativa) is one of the most important crops in the world. Several rice insertional mutant libraries are publicly available for systematic analysis of gene functions. However, the tagging efficiency of these mutant resources-the relationship between genotype and phenotype-is very low. We used whole-genome sequencing to analyze a T-DNA-tagged transformant from the Taiwan Rice Insertional Mutants (TRIM) resource. The phenomics records for M0028590, one of the TRIM lines, revealed three phenotypes-wild type, large grains, and tillering dwarf-in the 12 T1 plants. Using the sequencing data for 7 plants from three generations of this specific line, we demonstrate that introgression from an indica rice variety might occur in one generation before the seed was used for callus generation and transformation of this line. In addition, the large-grain trait came from the GS3 gene of the introgressed region and the tillering dwarf phenotype came from a single nucleotide change in the D17 gene that occurred during the callus induction to regeneration of the transformant. As well, another regenerant showed completely heterozygous single-nucleotide polymorphisms across the whole genome. In addition to the known sequence changes such as T-DNA integration, single nucleotide polymorphism, insertion, deletion, chromosome rearrangement and doubling, spontaneous outcrossing occurred in the rice field may also explain some mutated traits in a tagged mutant population. Thus, the co-segregation of an integration event and the phenotype should be checked when using these mutant populations.
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Affiliation(s)
- Fu-Jin Wei
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Yuan-Ching Tsai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yu-Ming Hsu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yu-An Chen
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Ching-Ting Huang
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Hshin-Ping Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Lin-Tzu Huang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Ming-Hsin Lai
- Crop Science Division, Taiwan Agriculture Research Institute, Taichung, Taiwan
| | - Lin-Yun Kuang
- Transgenic Plant Core Facility, Academia Sinica, Taipei, Taiwan
| | - Shuen-Fang Lo
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Su-May Yu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Yann-Rong Lin
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Yue-Ie Caroline Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
- * E-mail:
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