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Wolella EK, Cheng Z, Li M, Xia D, Zhang J, Duan L, Liu L, Li Z, Zhang J. Large-Scale Rice Mutant Establishment and High-Throughput Mutant Manipulation Help Advance Rice Functional Genomics. PLANTS (BASEL, SWITZERLAND) 2025; 14:1492. [PMID: 40431057 PMCID: PMC12114927 DOI: 10.3390/plants14101492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2025] [Revised: 05/08/2025] [Accepted: 05/13/2025] [Indexed: 05/29/2025]
Abstract
Rice (Oryza sativa L.) is a stable food for over half of the world population, contributing 50-80% of the daily calorie intake. The completion of rice genome sequencing marks a significant milestone in understanding functional genomics, yet the systematic identification of gene functions remains a bottleneck for rice improvement. Large-scale mutant libraries in which the functions of genes are lost or gained (e.g., through chemical/physical treatments, T-DNA, transposons, RNAi, CRISPR/Cas9) have proven to be powerful tools for the systematic linking of genotypes to phenotypes. So far, using different mutagenesis approaches, a million mutant lines have been established and about 5-10% of the predicted rice gene functions have been identified due to the high demands of labor and low-throughput utilization. DNA-barcoding-based large-scale mutagenesis offers unprecedented precision and scalability in functional genomics. This review summarizes large-scale loss-of-function and gain-of-function mutant library development approaches and emphasizes the integration of DNA barcoding for pooled analysis. Unique DNA barcodes can be tagged to transposons/retrotransposons, DNA constructs, miRNA/siRNA, gRNA, and cDNA, allowing for pooling analysis and the assignment of functions to genes that cause phenotype alterations. In addition, the integration of high-throughput phenotyping and OMICS technologies can accelerate the identification of gene functions.
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Affiliation(s)
- Eyob Kassaye Wolella
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China; (E.K.W.); (Z.C.)
- Department of Biology, College of Natural and Computational Sciences, Debre Tabor University, Debre Tabor P.O. Box 272, Ethiopia
| | - Zhen Cheng
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China; (E.K.W.); (Z.C.)
- School of Life Sciences, Hubei University, Wuhan 430062, China; (L.D.); (L.L.)
| | - Mengyuan Li
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (M.L.); (D.X.); (J.Z.)
| | - Dandan Xia
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (M.L.); (D.X.); (J.Z.)
| | - Jianwei Zhang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (M.L.); (D.X.); (J.Z.)
| | - Liu Duan
- School of Life Sciences, Hubei University, Wuhan 430062, China; (L.D.); (L.L.)
| | - Li Liu
- School of Life Sciences, Hubei University, Wuhan 430062, China; (L.D.); (L.L.)
| | - Zhiyong Li
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China; (E.K.W.); (Z.C.)
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China
| | - Jian Zhang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China; (E.K.W.); (Z.C.)
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China
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Smirnov A, Makarenko M, Yunusova A. Transgene Mapping in Animals: What to Choose? Int J Mol Sci 2025; 26:4705. [PMID: 40429848 PMCID: PMC12111812 DOI: 10.3390/ijms26104705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2025] [Revised: 05/09/2025] [Accepted: 05/12/2025] [Indexed: 05/29/2025] Open
Abstract
The phenomenal progress in biotechnology and genomics is both inspiring and overwhelming-a classic curse of choice, particularly when it comes to selecting methods for mapping transgene DNA integration sites. Transgene localization remains a crucial task for the validation of transgenic mouse or other animal models generated by pronuclear microinjection. Due to the inherently random nature of DNA integration, reliable characterization of the insertion site is essential. Over the years, a vast number of mapping methods have been developed, and new approaches continue to emerge, making the choice of the most suitable technique increasingly complex. Factors such as cost, required reagents, and the nature of the generated data require careful consideration. In this review, we provide a structured overview of current transgene mapping techniques, which we have broadly classified into three categories: classic PCR-based methods (such as inverse PCR and TAIL-PCR), next-generation sequencing with target enrichment, and long-read sequencing platforms (PacBio and Oxford Nanopore). To aid in decision-making, we include a comparative table summarizing approximate costs for the methods. While each approach has its own advantages and limitations, we highlight our top four recommended methods, which we believe offer the best balance of cost-effectiveness, reliability, and simplicity for identifying transgene integration sites.
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Affiliation(s)
- Alexander Smirnov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Maksim Makarenko
- Department of Genetics and Life Sciences, Sirius University of Science and Technology, Sirius Federal Territory, Sochi 354340, Russia
| | - Anastasia Yunusova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
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Vollen K, Alonso JM, Stepanova AN. Beyond a few bases: methods for large DNA insertion and gene targeting in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2025; 121:e70099. [PMID: 40121601 PMCID: PMC11930290 DOI: 10.1111/tpj.70099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2025] [Revised: 02/25/2025] [Accepted: 03/03/2025] [Indexed: 03/25/2025]
Abstract
Genome editing technologies like CRISPR/Cas have greatly accelerated the pace of both fundamental research and translational applications in agriculture. However, many plant biologists are functionally limited to creating small, targeted DNA changes or large, random DNA insertions. The ability to efficiently generate large, yet precise, DNA changes will massively accelerate crop breeding cycles, enabling researchers to more efficiently engineer crops amidst a rapidly changing agricultural landscape. This review provides an overview of existing technologies that allow plant biologists to integrate large DNA sequences within a plant host and some associated technical bottlenecks. Additionally, this review explores a selection of emerging techniques in other host systems to inspire tool development in plants.
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Affiliation(s)
- Katie Vollen
- Department of Plant BiologyNorth Carolina State UniversityRaleighNorth Carolina27695USA
| | - Jose M. Alonso
- Department of Plant BiologyNorth Carolina State UniversityRaleighNorth Carolina27695USA
| | - Anna N. Stepanova
- Department of Plant BiologyNorth Carolina State UniversityRaleighNorth Carolina27695USA
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Zhu Z, Lu S, Wang H, Wang F, Xu W, Zhu Y, Xue J, Yang L. Innovations in Transgene Integration Analysis: A Comprehensive Review of Enrichment and Sequencing Strategies in Biotechnology. ACS APPLIED MATERIALS & INTERFACES 2025; 17:2716-2735. [PMID: 39760503 DOI: 10.1021/acsami.4c14208] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2025]
Abstract
Understanding the integration of transgene DNA (T-DNA) in transgenic crops, animals, and clinical applications is paramount for ensuring the stability and expression of inserted genes, which directly influence desired traits and therapeutic outcomes. Analyzing T-DNA integration patterns is essential for identifying potential unintended effects and evaluating the safety and environmental implications of genetically modified organisms (GMOs). This knowledge is crucial for regulatory compliance and fostering public trust in biotechnology by demonstrating transparency in genetic modifications. This review highlights recent advancements in T-DNA integration analysis, specifically focusing on targeted DNA enrichment and sequencing strategies. We examine key technologies, such as polymerase chain reaction (PCR)-based methods, hybridization capture, RNA/DNA-guided endonuclease-mediated enrichment, and high-throughput resequencing, emphasizing their contributions to enhancing precision and efficiency in transgene integration analysis. We discuss the principles, applications, and recent developments in these techniques, underscoring their critical role in advancing biotechnological products. Additionally, we address the existing challenges and future directions in the field, offering a comprehensive overview of how innovative DNA-targeted enrichment and sequencing strategies are reshaping biotechnology and genomics.
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Affiliation(s)
- Zaobing Zhu
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Yazhou Bay Institute of Deepsea Sci-Tech, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, People's Republic of China
- Zhejiang Yuzhi Biotechnology Company, Limited, Ningbo 315032, People's Republic of China
| | - Shengtao Lu
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Yazhou Bay Institute of Deepsea Sci-Tech, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
- Zhejiang Yuzhi Biotechnology Company, Limited, Ningbo 315032, People's Republic of China
| | - Hongchun Wang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, People's Republic of China
| | - Fan Wang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Yazhou Bay Institute of Deepsea Sci-Tech, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Wenting Xu
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Yazhou Bay Institute of Deepsea Sci-Tech, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Yulei Zhu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, People's Republic of China
| | - Jing Xue
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, People's Republic of China
| | - Litao Yang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Yazhou Bay Institute of Deepsea Sci-Tech, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
- Zhejiang Yuzhi Biotechnology Company, Limited, Ningbo 315032, People's Republic of China
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Lu H, Jawdy S, Chen JG, Yang X, Kalluri UC. Poplar transformation with variable explant sources to maximize transformation efficiency. Sci Rep 2025; 15:1320. [PMID: 39779752 PMCID: PMC11711765 DOI: 10.1038/s41598-024-81235-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2024] [Accepted: 11/25/2024] [Indexed: 01/11/2025] Open
Abstract
For decades, Agrobacterium tumefaciens-mediated plant transformation has played an integral role in advancing fundamental and applied plant biology. The recent omnipresent emergence of synthetic biology, which relies on plant transformation to manipulate plant DNA and gene expression for novel product biosynthesis, has further propelled basic as well as applied interests in plant transformation technologies. The strong demand for a faster design-build-test-learn cycle, the essence of synthetic biology, is, however, still ill-matched with the long-standing issues of high tissue culture recalcitrance and low transformation efficiency of a wide range of plant species especially food, fiber and energy crops. To maximize the utility of plant material and improve the transformation productivity per unit plant form, we studied the regeneration and transformation efficiency of different types of explants, including leaf, stem, petiole, and root from Populus, a woody perennial bioenergy crop. Our results show that root explants, in addition to the above-ground tissues, have considerable regeneration capacity and amenability to A. tumefaciens and, the resulting transformants have largely comparable morphology, reporter gene expression, and transcriptome profile, independent of the explant source tissue. Transcriptome analyses mapped to regeneration stages and transformation efficiencies further revealed the expression of the auxin and cytokinin signaling and various developmental pathway genes in leaf and root explants undergoing early organogenesis. We further report high-potential candidate genes that may potentially be associated with higher regeneration and transformation efficiency. Overall, our study shows that explants from above- and belowground organs of a Populus plant are suitable for genetic transformation and tissue culture regeneration, and together with the underlying transcriptome data open new routes to maximize plant explant utilization, stable transformation productivity, and plant transformation efficiency.
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Affiliation(s)
- Haiwei Lu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Department of Biology, University of NE - Kearney, Kearney, NE, USA
| | - Sara Jawdy
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Udaya C Kalluri
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
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Chen HJ, Sawasdee A, Lin YL, Chiang MY, Chang HY, Li WH, Wang CS. Reverse Mutations in Pigmentation Induced by Sodium Azide in the IR64 Rice Variety. Curr Issues Mol Biol 2024; 46:13328-13346. [PMID: 39727923 PMCID: PMC11727009 DOI: 10.3390/cimb46120795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2024] [Revised: 11/15/2024] [Accepted: 11/20/2024] [Indexed: 12/28/2024] Open
Abstract
Pigmentation in rice is due mainly to the accumulation of anthocyanins. Five color mutant lines, AZ1701, AZ1702, AZ1711, AZ1714, and AZ1715, derived from the sodium azide mutagenesis on the non-pigmented IR64 variety, were applied to study inheritance modes and genes for pigmentation. The mutant line AZ1711, when crossed with IR64, displays pigmentation in various tissues, exhibiting a 3:1 pigmented to non-pigmented ratio in the F2 progeny, indicating a single dominant locus controlling pigmentation. Eighty-four simple sequence repeat (SSR) markers were applied to map the pigment gene using 92 F2 individuals. RM6773, RM5754, RM253, and RM2615 markers are found to be linked to the color phenotype. RM253 explains 78% of the phenotypic variation, implying linkage to the pigmentation gene(s). Three candidate genes, OsC1 (MYB), bHLH, and 3GT, as anthocyanin biosynthesis-related genes, were identified within a 0.83 Mb region tightly linked to RM253. PCR cloning and sequencing revealed 10 bp and 72 bp insertions in the OsC1 and 3GT genes, respectively, restoring pigmentation as in wild rice. The 72 bp insertion is highly homologous to a sequence of Ty1-Copia retrotransposon and shows a particular secondary structure, suggesting that it was derived from the transposition of Ty1-Copia in the IR64 genome.
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Affiliation(s)
- Hsian-Jun Chen
- Department of Agronomy, National Chung Hsing University, Taichung 402, Taiwan; (H.-J.C.); (A.S.); (Y.-L.L.); (M.-Y.C.); (H.-Y.C.)
| | - Anuchart Sawasdee
- Department of Agronomy, National Chung Hsing University, Taichung 402, Taiwan; (H.-J.C.); (A.S.); (Y.-L.L.); (M.-Y.C.); (H.-Y.C.)
| | - Yu-Ling Lin
- Department of Agronomy, National Chung Hsing University, Taichung 402, Taiwan; (H.-J.C.); (A.S.); (Y.-L.L.); (M.-Y.C.); (H.-Y.C.)
| | - Min-Yu Chiang
- Department of Agronomy, National Chung Hsing University, Taichung 402, Taiwan; (H.-J.C.); (A.S.); (Y.-L.L.); (M.-Y.C.); (H.-Y.C.)
| | - Hsin-Yi Chang
- Department of Agronomy, National Chung Hsing University, Taichung 402, Taiwan; (H.-J.C.); (A.S.); (Y.-L.L.); (M.-Y.C.); (H.-Y.C.)
| | - Wen-Hsiung Li
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
| | - Chang-Sheng Wang
- Department of Agronomy, National Chung Hsing University, Taichung 402, Taiwan; (H.-J.C.); (A.S.); (Y.-L.L.); (M.-Y.C.); (H.-Y.C.)
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Wang P, Abbas M, He J, Zhou L, Cheng H, Guo H. Advances in genome sequencing and artificially induced mutation provides new avenues for cotton breeding. FRONTIERS IN PLANT SCIENCE 2024; 15:1400201. [PMID: 39015293 PMCID: PMC11250495 DOI: 10.3389/fpls.2024.1400201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 06/10/2024] [Indexed: 07/18/2024]
Abstract
Cotton production faces challenges in fluctuating environmental conditions due to limited genetic variation in cultivated cotton species. To enhance the genetic diversity crucial for this primary fiber crop, it is essential to augment current germplasm resources. High-throughput sequencing has significantly impacted cotton functional genomics, enabling the creation of diverse mutant libraries and the identification of mutant functional genes and new germplasm resources. Artificial mutation, established through physical or chemical methods, stands as a highly efficient strategy to enrich cotton germplasm resources, yielding stable and high-quality raw materials. In this paper, we discuss the good foundation laid by high-throughput sequencing of cotton genome for mutant identification and functional genome, and focus on the construction methods of mutant libraries and diverse sequencing strategies based on mutants. In addition, the important functional genes identified by the cotton mutant library have greatly enriched the germplasm resources and promoted the development of functional genomes. Finally, an innovative strategy for constructing a cotton CRISPR mutant library was proposed, and the possibility of high-throughput screening of cotton mutants based on a UAV phenotyping platform was discussed. The aim of this review was to expand cotton germplasm resources, mine functional genes, and develop adaptable materials in a variety of complex environments.
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Affiliation(s)
- Peilin Wang
- Nanfan Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Sanya, Hainan, China
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mubashir Abbas
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jianhan He
- Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Hebei Key Laboratory of Crop Genetics and Breeding, Shijiazhuang, Hebei, China
| | - Lili Zhou
- Yazhouwan National Laboratory, Sanya, Hainan, China
| | - Hongmei Cheng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huiming Guo
- Nanfan Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Sanya, Hainan, China
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
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Jiang YX, Li MY, Han Q, Tan JL, Wang ZY, Jing TZ. Transgenic poplar (Populus davidiana×P. bolleana Loucne) expressing dsRNA of insect chitinase gene: lines identification and resistance assay. JOURNAL OF INSECT SCIENCE (ONLINE) 2024; 24:21. [PMID: 39225032 PMCID: PMC11369501 DOI: 10.1093/jisesa/ieae087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 07/26/2024] [Accepted: 08/16/2024] [Indexed: 09/04/2024]
Abstract
Poplar is a valuable tree species that is distributed all over the world. However, many insect pests infest poplar trees and have caused significant damage. To control poplar pests, we transformed a poplar species, Populus davidiana × P. bolleana Loucne, with the dsRNA of the chitinase gene of a poplar defoliator, Clostera anastomosis (Linnaeus) (Lepidoptera: Notodontidae), employing an Agrobaterium-mediated approach. The transgenic plant has been identified by cloning the T-DNA flanking sequences using TAIL-PCR and quantifying the expression of the dsRNA using qPCR. The toxicity assay of the transgenic poplar lines was carried out by feeding the target insect species (C. anastomosis). The results showed that, in C. anastomosis, the activity of chitinase was significantly decreased, consistent with the expression on mRNA levels, and the larval mortality was significantly increased. These results suggested that the transgenic poplar of dsRNA could be used for pest control.
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Affiliation(s)
- Yun-Xiao Jiang
- College of Forestry, Northeast Forestry University, Harbin, China
| | - Man-Yu Li
- College of Forestry, Northeast Forestry University, Harbin, China
| | - Qing Han
- College of Forestry, Northeast Forestry University, Harbin, China
| | - Jia-Lin Tan
- College of Forestry, Northeast Forestry University, Harbin, China
| | - Zi-Yan Wang
- College of Forestry, Northeast Forestry University, Harbin, China
| | - Tian-Zhong Jing
- College of Forestry, Northeast Forestry University, Harbin, China
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Thomson G, Dickinson L, Jacob Y. Genomic consequences associated with Agrobacterium-mediated transformation of plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:342-363. [PMID: 37831618 PMCID: PMC10841553 DOI: 10.1111/tpj.16496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/22/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023]
Abstract
Attenuated strains of the naturally occurring plant pathogen Agrobacterium tumefaciens can transfer virtually any DNA sequence of interest to model plants and crops. This has made Agrobacterium-mediated transformation (AMT) one of the most commonly used tools in agricultural biotechnology. Understanding AMT, and its functional consequences, is of fundamental importance given that it sits at the intersection of many fundamental fields of study, including plant-microbe interactions, DNA repair/genome stability, and epigenetic regulation of gene expression. Despite extensive research and use of AMT over the last 40 years, the extent of genomic disruption associated with integrating exogenous DNA into plant genomes using this method remains underappreciated. However, new technologies like long-read sequencing make this disruption more apparent, complementing previous findings from multiple research groups that have tackled this question in the past. In this review, we cover progress on the molecular mechanisms involved in Agrobacterium-mediated DNA integration into plant genomes. We also discuss localized mutations at the site of insertion and describe the structure of these DNA insertions, which can range from single copy insertions to large concatemers, consisting of complex DNA originating from different sources. Finally, we discuss the prevalence of large-scale genomic rearrangements associated with the integration of DNA during AMT with examples. Understanding the intended and unintended effects of AMT on genome stability is critical to all plant researchers who use this methodology to generate new genetic variants.
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Affiliation(s)
- Geoffrey Thomson
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences; New Haven, Connecticut 06511, USA
| | - Lauren Dickinson
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences; New Haven, Connecticut 06511, USA
| | - Yannick Jacob
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences; New Haven, Connecticut 06511, USA
- Yale Cancer Center, Yale School of Medicine; New Haven, Connecticut 06511, USA
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Liu Y, Ma X, Long Y, Yao S, Wei C, Han X, Gan B, Yan J, Xie B. Effects of β-1,6-Glucan Synthase Gene ( FfGS6) Overexpression on Stress Response and Fruit Body Development in Flammulina filiformis. Genes (Basel) 2022; 13:1753. [PMID: 36292637 PMCID: PMC9601887 DOI: 10.3390/genes13101753] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/20/2022] [Accepted: 09/26/2022] [Indexed: 12/29/2023] Open
Abstract
β-1, 6-glucan synthase is a key enzyme of β-1, 6-glucan synthesis, which plays a vital role in the cell wall cross-linking of fungi. However, the role of the β-1, 6-glucan synthase gene in the development of the fruiting body and the stress response of macrofungi is largely unknown. In this study, four overexpression transformants of the β-1, 6-glucan synthase gene (FfGS6) were successfully obtained, and gene function was studied in Flammulina filiformis. The overexpression of FfGS6 can increase the width of mycelium cells and improve the tolerance ability under mechanical injury and oxidative stress. Moreover, FfGS6 gene expression fluctuated in up-regulation during the recovery process of mycelium injury but showed a negative correlation with H2O2 concentration. Fruiting body phenotype tests showed that mycelia's recovery ability after scratching improved when the FfGS6 gene was overexpressed. However, primordia formation and the stipe elongation ability were significantly inhibited. Our findings indicate that FfGS6 is involved in regulating mycelial cell morphology, the mycelial stress response, and fruit body development in F. filiformis.
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Affiliation(s)
- Yuanyuan Liu
- Mycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xinbin Ma
- Mycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ying Long
- Mycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Sen Yao
- Mycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chuanzheng Wei
- Mycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xing Han
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610213, China
| | - Bingcheng Gan
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610213, China
| | - Junjie Yan
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610213, China
| | - Baogui Xie
- Mycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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