1
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Birchler JA, Kelly J, Singh J, Liu H, Zhang Z, Char SN, Sharma M, Yang H, Albert PS, Yang B. Synthetic minichromosomes in plants: past, present, and promise. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 120:2356-2366. [PMID: 39546384 DOI: 10.1111/tpj.17142] [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: 09/28/2024] [Revised: 11/01/2024] [Accepted: 11/04/2024] [Indexed: 11/17/2024]
Abstract
The status of engineered mini-chromosomes/artificial chromosomes/synthetic chromosomes in plants is summarized. Their promise is that they provide a means to accumulate foreign genes on an independent entity other than the normal chromosomes, which would facilitate stacking of novel traits in a way that would not be linked to endogenous genes and that would facilitate transfer between lines. Centromeres in plants are epigenetic, and therefore the isolation of DNA underlying centromeres and reintroduction into plant cells will not establish a functional kinetochore, which obviates this approach for in vitro assembly of plant artificial chromosomes. This issue was bypassed by using telomere-mediated chromosomal truncation to produce mini-chromosomes with little more than an endogenous centromere that could in turn be used as a foundation to build synthetic chromosomes. Site-specific recombinases and various iterations of CRISPR-Cas9 editing provide many tools for the development and re-engineering of synthetic chromosomes.
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Affiliation(s)
- James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, 65211, USA
| | - Jacob Kelly
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, 65211, USA
| | - Jasnoor Singh
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, 65211, USA
| | - Hua Liu
- Division of Plant Science and Technology, University of Missouri, Columbia, Missouri, 65211, USA
| | - Zhengzhi Zhang
- Division of Plant Science and Technology, University of Missouri, Columbia, Missouri, 65211, USA
| | - Si Nian Char
- Division of Plant Science and Technology, University of Missouri, Columbia, Missouri, 65211, USA
| | - Malika Sharma
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, 65211, USA
| | - Hua Yang
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, 65211, USA
| | - Patrice S Albert
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, 65211, USA
| | - Bing Yang
- Division of Plant Science and Technology, University of Missouri, Columbia, Missouri, 65211, USA
- Donald Danforth Plant Sciences Center, St. Louis, Missouri, 63132, USA
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2
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Liu Y, Liu Q, Yi C, Liu C, Shi Q, Wang M, Han F. Past innovations and future possibilities in plant chromosome engineering. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 39612312 DOI: 10.1111/pbi.14530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2024] [Revised: 10/24/2024] [Accepted: 11/14/2024] [Indexed: 12/01/2024]
Abstract
Plant chromosome engineering has emerged as a pivotal tool in modern plant breeding, facilitating the transfer of desirable traits through the incorporation of alien chromosome fragments into plants. Here, we provide a comprehensive overview of the past achievements, current methodologies and future prospects of plant chromosome engineering. We begin by examining the successful integration of specific examples such as the incorporation of rye chromosome segments (e.g. the 1BL/1RS translocation), Dasypyrum villosum segments (e.g. the 6VS segment for powdery mildew resistance), Thinopyrum intermedium segments (e.g. rust resistance genes) and Thinopyrum elongatum segments (e.g. Fusarium head blight resistance genes). In addition to trait transfer, advancements in plant centromere engineering have opened new possibilities for chromosomal manipulation. This includes the development of plant minichromosomes via centromere-mediated techniques, the generation of haploids through CENH3 gene editing, and the induction of aneuploidy using KaryoCreate. The advent of CRISPR/Cas technology has further revolutionized chromosome engineering, enabling large-scale chromosomal rearrangements, such as inversions and translocations, as well as enabling targeted insertion of large DNA fragments and increasing genetic recombination frequency. These advancements have significantly expanded the toolkit for genetic improvement in plants, opening new horizons for the future of plant breeding.
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Affiliation(s)
- Yang Liu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Qian Liu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Congyang Yi
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Chang Liu
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Qinghua Shi
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Mian Wang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Fangpu Han
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
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3
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Wang ML, Lin XJ, Mo BX, Kong WW. Plant Artificial Chromosomes: Construction and Transformation. ACS Synth Biol 2024; 13:15-24. [PMID: 38163256 DOI: 10.1021/acssynbio.3c00555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
With the decline of cultivated land and increase of the population in recent years, an agricultural revolution is urgently needed to produce more food to improve the living standards of humans. As one of the foundations of synthetic biology, artificial chromosomes hold great potential for advancing crop improvement. They offer opportunities to increase crop yield and quality, while enhancing crop resistance to disease. The progress made in plant artificial chromosome technology enables selective modification of existing chromosomes or the synthesis of new ones to improve crops and study gene function. However, current artificial chromosome technologies still face limitations, particularly in the synthesis of repeat sequences and the transformation of large DNA fragments. In this review, we will introduce the structure of plant centromeres, the construction of plant artificial chromosomes, and possible methods for transforming large fragments into plant cells.
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Affiliation(s)
- Ming L Wang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Xiao J Lin
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Bei X Mo
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Wen W Kong
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
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4
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Puchta H, Houben A. Plant chromosome engineering - past, present and future. THE NEW PHYTOLOGIST 2024; 241:541-552. [PMID: 37984056 DOI: 10.1111/nph.19414] [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: 09/06/2023] [Accepted: 10/24/2023] [Indexed: 11/22/2023]
Abstract
Spontaneous chromosomal rearrangements (CRs) play an essential role in speciation, genome evolution and crop domestication. To be able to use the potential of CRs for breeding, plant chromosome engineering was initiated by fragmenting chromosomes by X-ray irradiation. With the rise of the CRISPR/Cas system, it became possible to induce double-strand breaks (DSBs) in a highly efficient manner at will at any chromosomal position. This has enabled a completely new level of predesigned chromosome engineering. The genetic linkage between specific genes can be broken by inducing chromosomal translocations. Natural inversions, which suppress genetic exchange, can be reverted for breeding. In addition, various approaches for constructing minichromosomes by downsizing regular standard A or supernumerary B chromosomes, which could serve as future vectors in plant biotechnology, have been developed. Recently, a functional synthetic centromere could be constructed. Also, different ways of genome haploidization have been set up, some based on centromere manipulations. In the future, we expect to see even more complex rearrangements, which can be combined with previously developed engineering technologies such as recombinases. Chromosome engineering might help to redefine genetic linkage groups, change the number of chromosomes, stack beneficial genes on mini cargo chromosomes, or set up genetic isolation to avoid outcrossing.
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Affiliation(s)
- Holger Puchta
- Joseph Gottlieb Kölreuter Institute for Plant Sciences (JKIP) - Molecular Biology, Karlsruhe Institute of Technology (KIT), 76131, Karlsruhe, Germany
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
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Nowicka A, Ferková Ľ, Said M, Kovacik M, Zwyrtková J, Baroux C, Pecinka A. Non-Rabl chromosome organization in endoreduplicated nuclei of barley embryo and endosperm tissues. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:2527-2541. [PMID: 36705553 DOI: 10.1093/jxb/erad036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 01/25/2023] [Indexed: 06/06/2023]
Abstract
Rabl organization is a type of interphase chromosome arrangement with centromeres and telomeres clustering at opposite nuclear poles. Here, we analyzed nuclear morphology and chromosome organization in cycling and endoreduplicated nuclei isolated from embryo and endosperm tissues of developing barley seeds. We show that endoreduplicated nuclei have an irregular shape, less sister chromatid cohesion at 5S rDNA loci, and a reduced amount of centromeric histone CENH3. While the chromosomes of the embryo and endosperm nuclei are initially organized in Rabl configuration, the centromeres and telomeres are intermingled within the nuclear space in the endoreduplicated nuclei with an increasing endoreduplication level. Such a loss of chromosome organization suggests that Rabl configuration is introduced and further reinforced by mitotic divisions in barley cell nuclei in a tissue- and seed age-dependent manner.
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Affiliation(s)
- Anna Nowicka
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
- The Polish Academy of Sciences, The Franciszek Górski Institute of Plant Physiology, Niezapominajek 21, 30-239 Krakow, Poland
| | - Ľuboslava Ferková
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Mahmoud Said
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
- Field Crops Research Institute, Agricultural Research Centre, 9 Gamma Street, Giza, Cairo, 12619, Egypt
| | - Martin Kovacik
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Jana Zwyrtková
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Célia Baroux
- Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zollikerstrasse 107, 8008 Zürich, Switzerland
| | - Ales Pecinka
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
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Gomide MDS, Leitão MDC, Coelho CM. Biocircuits in plants and eukaryotic algae. FRONTIERS IN PLANT SCIENCE 2022; 13:982959. [PMID: 36212277 PMCID: PMC9545776 DOI: 10.3389/fpls.2022.982959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/22/2022] [Indexed: 06/16/2023]
Abstract
As one of synthetic biology's foundations, biocircuits are a strategy of genetic parts assembling to recognize a signal and to produce a desirable output to interfere with a biological function. In this review, we revisited the progress in the biocircuits technology basis and its mandatory elements, such as the characterization and assembly of functional parts. Furthermore, for a successful implementation, the transcriptional control systems are a relevant point, and the computational tools help to predict the best combinations among the biological parts planned to be used to achieve the desirable phenotype. However, many challenges are involved in delivering and stabilizing the synthetic structures. Some research experiences, such as the golden crops, biosensors, and artificial photosynthetic structures, can indicate the positive and limiting aspects of the practice. Finally, we envision that the modulatory structural feature and the possibility of finer gene regulation through biocircuits can contribute to the complex design of synthetic chromosomes aiming to develop plants and algae with new or improved functions.
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Affiliation(s)
- Mayna da Silveira Gomide
- Laboratory of Synthetic Biology, Department of Genetics and Morphology, Institute of Biological Science, University of Brasília (UnB), Brasília, Distrito Federal, Brazil
- School of Medicine, Federal University of Juiz de Fora (UFJF), Juiz de Fora, Minas Gerais, Brazil
| | - Matheus de Castro Leitão
- Laboratory of Synthetic Biology, Department of Genetics and Morphology, Institute of Biological Science, University of Brasília (UnB), Brasília, Distrito Federal, Brazil
| | - Cíntia Marques Coelho
- Laboratory of Synthetic Biology, Department of Genetics and Morphology, Institute of Biological Science, University of Brasília (UnB), Brasília, Distrito Federal, Brazil
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7
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Telomeres and Their Neighbors. Genes (Basel) 2022; 13:genes13091663. [PMID: 36140830 PMCID: PMC9498494 DOI: 10.3390/genes13091663] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 11/21/2022] Open
Abstract
Telomeres are essential structures formed from satellite DNA repeats at the ends of chromosomes in most eukaryotes. Satellite DNA repeat sequences are useful markers for karyotyping, but have a more enigmatic role in the eukaryotic cell. Much work has been done to investigate the structure and arrangement of repetitive DNA elements in classical models with implications for species evolution. Still more is needed until there is a complete picture of the biological function of DNA satellite sequences, particularly when considering non-model organisms. Celebrating Gregor Mendel’s anniversary by going to the roots, this review is designed to inspire and aid new research into telomeres and satellites with a particular focus on non-model organisms and accessible experimental and in silico methods that do not require specialized equipment or expensive materials. We describe how to identify telomere (and satellite) repeats giving many examples of published (and some unpublished) data from these techniques to illustrate the principles behind the experiments. We also present advice on how to perform and analyse such experiments, including details of common pitfalls. Our examples are a selection of recent developments and underexplored areas of research from the past. As a nod to Mendel’s early work, we use many examples from plants and insects, especially as much recent work has expanded beyond the human and yeast models traditional in telomere research. We give a general introduction to the accepted knowledge of telomere and satellite systems and include references to specialized reviews for the interested reader.
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8
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Kan M, Huang T, Zhao P. Artificial chromosome technology and its potential application in plants. FRONTIERS IN PLANT SCIENCE 2022; 13:970943. [PMID: 36186059 PMCID: PMC9519882 DOI: 10.3389/fpls.2022.970943] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/26/2022] [Indexed: 06/16/2023]
Abstract
Plant genetic engineering and transgenic technology are powerful ways to study the function of genes and improve crop yield and quality in the past few years. However, only a few genes could be transformed by most available genetic engineering and transgenic technologies, so changes still need to be made to meet the demands for high throughput studies, such as investigating the whole genetic pathway of crop traits and avoiding undesirable genes simultaneously in the next generation. Plant artificial chromosome (PAC) technology provides a carrier which allows us to assemble multiple and specific genes to produce a variety of products by minichromosome. However, PAC technology also have limitations that may hinder its further development and application. In this review, we will introduce the current state of PACs technology from PACs formation, factors on PACs formation, problems and potential solutions of PACs and exogenous gene(s) integration.
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Affiliation(s)
- Manman Kan
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Tengbo Huang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, China
| | - Panpan Zhao
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, China
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Navrátilová P, Toegelová H, Tulpová Z, Kuo Y, Stein N, Doležel J, Houben A, Šimková H, Mascher M. Prospects of telomere-to-telomere assembly in barley: Analysis of sequence gaps in the MorexV3 reference genome. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1373-1386. [PMID: 35338551 PMCID: PMC9241371 DOI: 10.1111/pbi.13816] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 02/11/2022] [Accepted: 03/20/2022] [Indexed: 05/06/2023]
Abstract
The first gapless, telomere-to-telomere (T2T) sequence assemblies of plant chromosomes were reported recently. However, sequence assemblies of most plant genomes remain fragmented. Only recent breakthroughs in accurate long-read sequencing have made it possible to achieve highly contiguous sequence assemblies with a few tens of contigs per chromosome, that is a number small enough to allow for a systematic inquiry into the causes of the remaining sequence gaps and the approaches and resources needed to close them. Here, we analyse sequence gaps in the current reference genome sequence of barley cv. Morex (MorexV3). Optical map and sequence raw data, complemented by ChIP-seq data for centromeric histone variant CENH3, were used to estimate the abundance of centromeric, ribosomal DNA, and subtelomeric repeats in the barley genome. These estimates were compared with copy numbers in the MorexV3 pseudomolecule sequence. We found that almost all centromeric sequences and 45S ribosomal DNA repeat arrays were absent from the MorexV3 pseudomolecules and that the majority of sequence gaps can be attributed to assembly breakdown in long stretches of satellite repeats. However, missing sequences cannot fully account for the difference between assembly size and flow cytometric genome size estimates. We discuss the prospects of gap closure with ultra-long sequence reads.
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Affiliation(s)
- Pavla Navrátilová
- Institute of Experimental Botany of the Czech Academy of SciencesOlomoucCzech Republic
| | - Helena Toegelová
- Institute of Experimental Botany of the Czech Academy of SciencesOlomoucCzech Republic
| | - Zuzana Tulpová
- Institute of Experimental Botany of the Czech Academy of SciencesOlomoucCzech Republic
| | - Yi‐Tzu Kuo
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeelandGermany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeelandGermany
- Center for Integrated Breeding Research (CiBreed)Georg‐August‐University GöttingenGöttingenGermany
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of SciencesOlomoucCzech Republic
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeelandGermany
| | - Hana Šimková
- Institute of Experimental Botany of the Czech Academy of SciencesOlomoucCzech Republic
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeelandGermany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
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10
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Yin X, Zhang Y, Chen Y, Wang J, Wang RRC, Fan C, Hu Z. Precise Characterization and Tracking of Stably Inherited Artificial Minichromosomes Made by Telomere-Mediated Chromosome Truncation in Brassica napus. FRONTIERS IN PLANT SCIENCE 2021; 12:743792. [PMID: 34671377 PMCID: PMC8521072 DOI: 10.3389/fpls.2021.743792] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 09/08/2021] [Indexed: 06/13/2023]
Abstract
Plant artificial minichromosomes are the next-generation technology for plant genetic engineering and represent an independent platform for expressing foreign genes and the tools for studying the structure and function of chromosomes. Minichromosomes have been successfully produced by telomere-mediated chromosome truncation in several plants. However, previous studies have primarily focused on the construction and rough characterization of minichromosomes, while the development of stably inherited minichromosomes and their precise characterization and tracking over different generations have rarely been demonstrated. In this study, a 0.35-kb direct repeat of the Arabidopsis telomeric sequence was transformed into Brassica napus to produce artificial minichromosomes, which were analyzed by multifluorescence in situ hybridization (multi-FISH), Southern hybridization, and primer extension telomere rapid amplification (PETRA). The stably inherited minichromosomes C2 and C4 were developed by crossing transgenic plants with wild-type plants and then selfing the hybrids. Notably, two truncation sites on chromosomes C2 and C4, respectively, were identified by resequencing; thus, the artificial minichromosomes were tracked over different generations with insertion site-specific PCR. This study provided two stably inherited minichromosomes in oilseed rape and describes approaches to precisely characterize the truncation position and track the minichromosomes in offspring through multi-FISH, genome resequencing, and insertion site-specific PCR.
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Affiliation(s)
- Xiangzhen Yin
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Yingxin Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Agriculture, Yangtze University, Jingzhou, China
| | - Yuhong Chen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Jingqiao Wang
- Institute of Economical Crops, Yunnan Agricultural Academy, Kunming, China
| | - Richard R.-C. Wang
- Forage and Range Research Laboratory, United States Department of Agriculture, Agricultural Research Service, Utah State University, Logan, UT, United States
| | - Chengming Fan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Zanmin Hu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Agriculture, University of Chinese Academy of Sciences, Beijing, China
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11
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Birchler JA, Swyers NC. Engineered minichromosomes in plants. Exp Cell Res 2020; 388:111852. [PMID: 31972219 DOI: 10.1016/j.yexcr.2020.111852] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 01/14/2020] [Indexed: 11/17/2022]
Abstract
Artificial chromosome platforms are described in plants. Because the function of centromeres is largely epigenetic, attempts to produce artificial chromosomes with plant centromere DNA have failed. The removal of the centromeric sequences from the cell strips off the centromeric histone that is the apparent biochemical marker of centromere activity. Thus, engineered minichromosomes have been produced by telomere mediated chromosomal truncation. The introduction of telomere repeats will cleave the chromosome at the site of insertion and attach the accompanying transgenes in the process. Such truncation events have been documented in maize, Arabidopsis, barley, rice, Brassica and wheat. Truncation of the nonvital supernumerary B chromosome of maize is a favorite target but engineered minichromosomes derived from the normal A chromosomes have also been recovered. Transmission through mitosis of small chromosomes is apparently normal but there is loss during meiosis. Potential solutions to address this issue are discussed. With procedures now well established to produce the foundation for artificial chromosomes in plants, current efforts are directed at building them up to specification using gene stacking methods and editing techniques.
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Affiliation(s)
- James A Birchler
- Division of Biological Sciences, University of Missouri, 311 Tucker Hall, Columbia, MO, 65211-7400, USA.
| | - Nathan C Swyers
- Division of Biological Sciences, University of Missouri, 311 Tucker Hall, Columbia, MO, 65211-7400, USA
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12
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Ling YH, Lin Z, Yuen KWY. Genetic and epigenetic effects on centromere establishment. Chromosoma 2019; 129:1-24. [PMID: 31781852 DOI: 10.1007/s00412-019-00727-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 09/24/2019] [Accepted: 10/10/2019] [Indexed: 01/19/2023]
Abstract
Endogenous chromosomes contain centromeres to direct equal chromosomal segregation in mitosis and meiosis. The location and function of existing centromeres is usually maintained through cell cycles and generations. Recent studies have investigated how the centromere-specific histone H3 variant CENP-A is assembled and replenished after DNA replication to epigenetically propagate the centromere identity. However, existing centromeres occasionally become inactivated, with or without change in underlying DNA sequences, or lost after chromosomal rearrangements, resulting in acentric chromosomes. New centromeres, known as neocentromeres, may form on ectopic, non-centromeric chromosomal regions to rescue acentric chromosomes from being lost, or form dicentric chromosomes if the original centromere is still active. In addition, de novo centromeres can form after chromatinization of purified DNA that is exogenously introduced into cells. Here, we review the phenomena of naturally occurring and experimentally induced new centromeres and summarize the genetic (DNA sequence) and epigenetic features of these new centromeres. We compare the characteristics of new and native centromeres to understand whether there are different requirements for centromere establishment and propagation. Based on our understanding of the mechanisms of new centromere formation, we discuss the perspectives of developing more stably segregating human artificial chromosomes to facilitate gene delivery in therapeutics and research.
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Affiliation(s)
- Yick Hin Ling
- School of Biological Sciences, The University of Hong Kong, Kadoorie Biological Sciences Building, Pokfulam Road, Hong Kong
| | - Zhongyang Lin
- School of Biological Sciences, The University of Hong Kong, Kadoorie Biological Sciences Building, Pokfulam Road, Hong Kong
| | - Karen Wing Yee Yuen
- School of Biological Sciences, The University of Hong Kong, Kadoorie Biological Sciences Building, Pokfulam Road, Hong Kong.
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13
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Baby V, Labroussaa F, Lartigue C, Rodrigue S. [Synthetic chromosomes: rewriting the code of life]. Med Sci (Paris) 2019; 35:753-760. [PMID: 31625897 DOI: 10.1051/medsci/2019153] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The past decade has seen vast improvements in DNA synthesis and assembly methods. The creation of synthetic DNA molecules is becoming easier and more affordable, such that entire chromosomes can now be synthesized. These advances mark the beginning of synthetic genomics, a new discipline interested in the construction of complete genomes tailored for the study and application of biological systems. From viral genome synthesis to the reconstruction of the yeast 16 chromosomes, we discuss the main discoveries, the regulations and ethical considerations along with the potential of this emerging discipline for the future.
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Affiliation(s)
- Vincent Baby
- INRA, UMR 1332 de biologie du fruit et pathologie, 71 avenue E. Bourlaux, 33140 Villenave d'Ornon, France - Univ. Bordeaux, UMR 1332 de biologie du fruit et pathologie, 71 avenue E. Bourlaux 33140 Villenave d'Ornon, France
| | - Fabien Labroussaa
- Institute of veterinary bacteriology of Bern, Vetsuisse Faculty, University of Bern, 3001 Berne, Suisse
| | - Carole Lartigue
- INRA, UMR 1332 de biologie du fruit et pathologie, 71 avenue E. Bourlaux, 33140 Villenave d'Ornon, France - Univ. Bordeaux, UMR 1332 de biologie du fruit et pathologie, 71 avenue E. Bourlaux 33140 Villenave d'Ornon, France
| | - Sébastien Rodrigue
- Département de biologie, Université de Sherbrooke, 2500 boulevard de l'Université, J1K 2R1 Sherbrooke, Québec, Canada
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14
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Site-specific transfer of chromosomal segments and genes in wheat engineered chromosomes. J Genet Genomics 2017; 44:531-539. [DOI: 10.1016/j.jgg.2017.08.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 07/30/2017] [Accepted: 08/07/2017] [Indexed: 11/18/2022]
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15
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Yan X, Li C, Yang J, Wang L, Jiang C, Wei W. Induction of telomere-mediated chromosomal truncation and behavior of truncated chromosomes in Brassica napus. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:700-713. [PMID: 28500683 DOI: 10.1111/tpj.13598] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 05/09/2017] [Indexed: 06/07/2023]
Abstract
Engineered minichromosomes could be stably inherited and serve as a platform for simultaneously transferring and stably expressing multiple genes. Chromosomal truncation mediated by repeats of telomeric sequences is a promising approach for the generation of minichromosomes. In the present work, direct repetitive sequences of Arabidopsis telomere were used to study telomere-mediated truncation of chromosomes in Brassica napus. Transgenes containing alien Arabidopsis telomere were successfully obtained, and Southern blotting and fluorescence in situ hybridization (FISH) results show that the transgenes resulted in successful chromosomal truncation in B. napus. In addition, truncated chromosomes were inherited at rates lower than that predicted by Mendelian rules. To determine the potential manipulations and applications of the engineered chromosomes, such as the stacking of multiple transgenes and the Cre/lox and FRT/FLP recombination systems, both amenable to genetic manipulations through site-specific recombination in somatic cells, were tested for their ability to undergo recombination in B. napus. These results demonstrate that alien Arabidopsis telomere is able to mediate chromosomal truncation in B. napus. This technology would be feasible for chromosomal engineering and for studies on chromosome structure and function in B. napus.
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Affiliation(s)
- Xiaohong Yan
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062, China
| | - Chen Li
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062, China
- College of Life Science and Technology, Henan Institute of Science and Technology/Collaborative Innovation Center of Modern Biological Breeding of Henan Province, Xinxiang, 453003, China
- College of Food Science and Technology, Agricultural University of Hebei, Baoding, 071001, China
| | - Jie Yang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062, China
| | - Lijun Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062, China
| | - Chenghong Jiang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062, China
| | - Wenhui Wei
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062, China
- College of Life Science and Technology, Henan Institute of Science and Technology/Collaborative Innovation Center of Modern Biological Breeding of Henan Province, Xinxiang, 453003, China
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16
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Swyers NC, Cody JP, McCaw ME, Graham ND, Zhao C, Gaeta RT, Birchler JA. Telomere-Mediated Chromosomal Truncation for Generating Engineered Minichromosomes in Maize. CURRENT PROTOCOLS IN PLANT BIOLOGY 2016; 1:488-500. [PMID: 31725959 DOI: 10.1002/cppb.20031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Minichromosomes have been generated in maize using telomere-mediated truncation. Telomere DNA, because of its repetitive nature, can be difficult to manipulate. The protocols in this unit describe two methods for generating the telomere DNA required for the initiation of telomere-mediated truncation. The resulting DNA can then be used with truncation cassettes for introduction into maize via transformation. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Nathan C Swyers
- Division of Biological Sciences, University of Missouri, Columbia, Missouri
| | - Jon P Cody
- Division of Biological Sciences, University of Missouri, Columbia, Missouri
| | - Morgan E McCaw
- Division of Biological Sciences, University of Missouri, Columbia, Missouri
| | - Nathaniel D Graham
- Division of Biological Sciences, University of Missouri, Columbia, Missouri
| | - Changzeng Zhao
- Division of Biological Sciences, University of Missouri, Columbia, Missouri
| | - Robert T Gaeta
- Division of Biological Sciences, University of Missouri, Columbia, Missouri
| | - James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, Missouri
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17
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Puchta H. Using CRISPR/Cas in three dimensions: towards synthetic plant genomes, transcriptomes and epigenomes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 87:5-15. [PMID: 26677816 DOI: 10.1111/tpj.13100] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 11/23/2015] [Accepted: 11/25/2015] [Indexed: 05/21/2023]
Abstract
It is possible to target individual sequence motives within genomes by using synthetic DNA-binding domains. This one-dimensional approach has been used successfully in plants to induce mutations or for the transcriptional regulation of single genes. When the CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 system was discovered, a tool became available allowing the extension of this approach from one to three dimensions and to construct at least partly synthetic entities on the genome, epigenome and transcriptome levels. The second dimension can be obtained by targeting the Cas9 protein to multiple unique genomic sites by applying multiple different single guiding (sg) RNAs, each defining a different DNA-binding site. Finally, the simultaneous use of phylogenetically different Cas9 proteins or sgRNAs that harbour different types of protein binding motives, allows for a third dimension of control. Thus, different types of enzyme activities - fused either to one type of Cas9 orthologue or to one type of RNA-binding domain specific to one type of sgRNA - can be targeted to multiple different genomic sites simultaneously. Thus, it should be possible to induce quantitatively different levels of expression of certain sets of genes and at the same time to repress other genes, redefining the nuclear transcriptome. Likewise, by the use of different types of histone-modifying and/or DNA (de)methylating activities, the epigenome of plants should be reprogrammable. On our way to synthetic plant genomes, the next steps will be to use complex genome engineering approaches within or between species borders to restructure and recombine natural or artificial chromosomes.
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Affiliation(s)
- Holger Puchta
- Botanical Institute II, Karlsruhe Institute of Technology, POB 6980, 76049, Karlsruhe, Germany
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18
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Xu C, Yu W. Artificial Chromosomes in Rice (Oryza sativa). CURRENT PROTOCOLS IN PLANT BIOLOGY 2016; 1:107-120. [PMID: 31725987 DOI: 10.1002/cppb.20008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Chromosomes are the carriers of genetic material in biological organisms. Each chromosome has three essential components: a centromere, telomeres, and origins of replication. The understanding of the essential structural and functional organization of chromosomes has made it possible to produce artificial chromosomes (ACs), which are human-engineered minichromosomes. There are two approaches to make ACs: de novo assembly (bottom-up) and truncation of existing chromosomes (top-down). Rice (Oryza sativa) ACs are produced by telomere-mediated chromosome truncation, and may have many applications, such as genetic engineering to stack and express multiple genes in rice to combat diseases caused by bacteria, fungi, and viruses, to enhance tolerance of rice to environmental stresses such as drought, heat, and salinity, and to improve yield and quality. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Chunhui Xu
- School of Life Sciences, Shandong University, Jinan, Shandong, China
| | - Weichang Yu
- Shenzhen Research Institute of The Chinese University of Hong Kong, Shenzhen, China
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19
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Murata M. Artificial Chromosome Preparation in Arabidopsis. CURRENT PROTOCOLS IN PLANT BIOLOGY 2016; 1:53-66. [PMID: 31725989 DOI: 10.1002/cppb.20010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In Arabidopsis thaliana, various attempts have been made to create artificial chromosomes as a new tool for cytological and genetic analyses. However, most of the efforts have been unsuccessful until recently. Most eukaryotic chromosomes are linear, and therefore the Arabidopsis artificial chromosomes have also been designed to be linear and to carry the telomere structure at both ends. In contrast, circular artificial chromosomes were successfully created by the Cre/LoxP system combined with Ac/Ds transposon system, on the basis of the discovery that ring minichromosomes are relatively stable and transmissible to the next generations in A. thaliana. Because ring minichromosomes ∼1 to 6 Mb in size have been generated, in this article, the protocol for inducing large chromosomal rearrangements resulting in ring chromosome formation is described. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Minoru Murata
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
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Yu W, Yau YY, Birchler JA. Plant artificial chromosome technology and its potential application in genetic engineering. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1175-82. [PMID: 26369910 PMCID: PMC11389009 DOI: 10.1111/pbi.12466] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 07/16/2015] [Accepted: 08/07/2015] [Indexed: 06/05/2023]
Abstract
Genetic engineering with just a few genes has changed agriculture in the last 20 years. The most frequently used transgenes are the herbicide resistance genes for efficient weed control and the Bt toxin genes for insect resistance. The adoption of the first-generation genetically engineered crops has been very successful in improving farming practices, reducing the application of pesticides that are harmful to both human health and the environment, and producing more profit for farmers. However, there is more potential for genetic engineering to be realized by technical advances. The recent development of plant artificial chromosome technology provides a super vector platform, which allows the management of a large number of genes for the next generation of genetic engineering. With the development of other tools such as gene assembly, genome editing, gene targeting and chromosome delivery systems, it should become possible to engineer crops with multiple genes to produce more agricultural products with less input of natural resources to meet future demands.
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Affiliation(s)
- Weichang Yu
- Shenzhen Research Institute, Chinese University of Hong Kong, Shenzhen, China
| | - Yuan-Yeu Yau
- Department of Natural Sciences, Northeastern State University, Broken Arrow, OK, USA
| | - James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA
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21
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Plant minichromosomes. Curr Opin Biotechnol 2016; 37:135-142. [DOI: 10.1016/j.copbio.2015.11.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 11/06/2015] [Accepted: 11/23/2015] [Indexed: 11/23/2022]
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Fujimoto S, Matsunaga S. Which Is a Reliable Approach in the Generation of Artificial Minichromosomes, Bottom-Up or Top-Down? CYTOLOGIA 2016. [DOI: 10.1508/cytologia.81.251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Satoru Fujimoto
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science
| | - Sachihiro Matsunaga
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science
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23
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24
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Promises and pitfalls of synthetic chromosomes in plants. Trends Biotechnol 2015; 33:189-94. [DOI: 10.1016/j.tibtech.2014.12.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 12/21/2014] [Accepted: 12/30/2014] [Indexed: 12/28/2022]
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Abstract
The centromere-the primary constriction of monocentric chromosomes-is essential for correct segregation of chromosomes during mitosis and meiosis. Centromeric DNA varies between different organisms in sequence composition and extension. The main components of centromeric and pericentromeric DNA of Brassicaceae species are centromeric satellite repeats. Centromeric DNA initiates assembly of the kinetochore, the large protein complex where the spindle fibers attach during nuclear division to pull sister chromatids apart. Kinetochore assembly is initiated by incorporation of the centromeric histone H3 cenH3 into centromeric nucleosomes. The spindle assembly checkpoint acts during mitosis and meiosis at centromeres and maintains genome stability by preventing chromosome segregation before all kinetochores are correctly attached to microtubules. The function of the spindle assembly checkpoint in plants is still poorly understood. Here, we review recent advances of studies on structure and functional importance of centromeric DNA of Brassicaceae, assembly and function of cenH3 in Arabidopsis thaliana and characterization of core SAC proteins of A. thaliana in comparison with non-plant homologues.
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Affiliation(s)
- Inna Lermontova
- Leibniz Institute of Plant Genetics and Crop Plant Research, 06466, Gatersleben, Germany,
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26
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Abstract
Engineered minimal chromosomes with sufficient mitotic and meiotic stability have an enormous potential as vectors for stacking multiple genes required for complex traits in plant biotechnology. Proof of principle for essential steps in chromosome engineering such as truncation of chromosomes by T-DNA-mediated telomere seeding and de novo formation of centromeres by cenH3 fusion protein tethering has been recently obtained. In order to generate robust protocols for application in plant biotechnology, these steps need to be combined and supplemented with additional methods such as site-specific recombination for the directed transfer of multiple genes of interest on the minichromosomes. At the same time, the development of these methods allows new insight into basic aspects of plant chromosome functions such as how centromeres assure proper distribution of chromosomes to daughter cells or how telomeres serve to cap the chromosome ends to prevent shortening of ends over DNA replication cycles and chromosome end fusion.
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Affiliation(s)
- Michael Florian Mette
- Research Group Chromosome Structure and Function, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466, Stadt Seeland OT Gatersleben, Germany,
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Birchler JA. Engineered minichromosomes in plants. CURRENT OPINION IN PLANT BIOLOGY 2014; 19:76-80. [PMID: 24906050 DOI: 10.1016/j.pbi.2014.05.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 04/23/2014] [Accepted: 05/06/2014] [Indexed: 06/03/2023]
Abstract
Platforms for the development of synthetic chromosomes in plants have been produced in several species using telomere mediated chromosomal truncation with the simultaneous inclusion of sites that facilitate further additions to the newly generated minichromosome. By utilizing truncated supernumerary or B chromosomes, the output of the genes on the minichromosome can be amplified. Proof of concept experiments have been successful illustrating that minichromosome platforms can be modified in vivo. Engineered minichromosomes can likely be combined with haploid breeding if they are incorporated into inducer lines given that the observations that basically inert chromosomes from haploid inducer lines can be recovered at workable frequencies in otherwise haploid plants. Future needs of synthetic chromosome development are discussed.
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Affiliation(s)
- James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, United States.
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Hofinger BJ, Huynh OA, Jankowicz-Cieslak J, Müller A, Otto I, Kumlehn J, Till BJ. Validation of doubled haploid plants by enzymatic mismatch cleavage. PLANT METHODS 2013; 9:43. [PMID: 24220637 PMCID: PMC3831592 DOI: 10.1186/1746-4811-9-43] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 11/01/2013] [Indexed: 05/25/2023]
Abstract
BACKGROUND Doubled haploidy is a fundamental tool in plant breeding as it provides the fastest way to generate populations of meiotic recombinants in a genetically fixed state. A wide range of methods has been developed to produce doubled haploid (DH) plants and recent advances promise efficient DH production in otherwise recalcitrant species. Since the cellular origin of the plants produced is not always certain, rapid screening techniques are needed to validate that the produced individuals are indeed homozygous and genetically distinct from each other. Ideal methods are easily implemented across species and in crops where whole genome sequence and marker resources are limited. RESULTS We have adapted enzymatic mismatch cleavage techniques commonly used for TILLING (Targeting Induced Local Lesions IN Genomes) for the evaluation of heterozygosity in parental, F1 and putative DH plants. We used barley as a model crop and tested 26 amplicons previously developed for TILLING. Experiments were performed using self-extracted single-strand-specific nuclease and standard native agarose gels. Eleven of the twenty-six tested primers allowed unambiguous assignment of heterozygosity in material from F1 crosses and loss of heterozygosity in the DH plants. Through parallel testing of previously developed Simple Sequence Repeat (SSR) markers, we show that 3/32 SSR markers were suitable for screening. This suggests that enzymatic mismatch cleavage approaches can be more efficient than SSR based screening, even in species with well-developed markers. CONCLUSIONS Enzymatic mismatch cleavage has been applied for mutation discovery in many plant species, including those with little or no available genomic DNA sequence information. Here, we show that the same methods provide an efficient system to screen for the production of DH material without the need of specialized equipment. This gene target based approach further allows discovery of novel nucleotide polymorphisms in candidate genes in the parental lines.
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Affiliation(s)
- Bernhard J Hofinger
- Plant Breeding and Genetics Laboratory, Joint FAO/IAEA Division, International Atomic Energy Agency, Vienna International Centre, PO Box 100, A-1400, Vienna, Austria
| | - Owen A Huynh
- Plant Breeding and Genetics Laboratory, Joint FAO/IAEA Division, International Atomic Energy Agency, Vienna International Centre, PO Box 100, A-1400, Vienna, Austria
| | - Joanna Jankowicz-Cieslak
- Plant Breeding and Genetics Laboratory, Joint FAO/IAEA Division, International Atomic Energy Agency, Vienna International Centre, PO Box 100, A-1400, Vienna, Austria
| | - Andrea Müller
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Plant Reproductive Biology, Corrensstrasse 3, D-06466 Seeland, OT Gatersleben, Germany
| | - Ingrid Otto
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Plant Reproductive Biology, Corrensstrasse 3, D-06466 Seeland, OT Gatersleben, Germany
| | - Jochen Kumlehn
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Plant Reproductive Biology, Corrensstrasse 3, D-06466 Seeland, OT Gatersleben, Germany
| | - Bradley J Till
- Plant Breeding and Genetics Laboratory, Joint FAO/IAEA Division, International Atomic Energy Agency, Vienna International Centre, PO Box 100, A-1400, Vienna, Austria
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Abstract
Basic research has provided a much better understanding of the genetic networks and regulatory hierarchies in plants. To meet the challenges of agriculture, we must be able to rapidly translate this knowledge into generating improved plants. Therefore, in this Review, we discuss advanced tools that are currently available for use in plant biotechnology to produce new products in plants and to generate plants with new functions. These tools include synthetic promoters, 'tunable' transcription factors, genome-editing tools and site-specific recombinases. We also review some tools with the potential to enable crop improvement, such as methods for the assembly and synthesis of large DNA molecules, plant transformation with linked multigenes and plant artificial chromosomes. These genetic technologies should be integrated to realize their potential for applications to pressing agricultural and environmental problems.
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De novo generation of plant centromeres at tandem repeats. Chromosoma 2013; 122:233-41. [PMID: 23525657 DOI: 10.1007/s00412-013-0406-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 03/03/2013] [Accepted: 03/06/2013] [Indexed: 10/27/2022]
Abstract
Artificial minichromosomes are highly desirable tools for basic research, breeding, and biotechnology purposes. We present an option to generate plant artificial minichromosomes via de novo engineering of plant centromeres in Arabidopsis thaliana by targeting kinetochore proteins to tandem repeat arrays at non-centromeric positions. We employed the bacterial lactose repressor/lactose operator system to guide derivatives of the centromeric histone H3 variant cenH3 to LacO operator sequences. Tethering of cenH3 to non-centromeric loci led to de novo assembly of kinetochore proteins and to dicentric carrier chromosomes which potentially form anaphase bridges. This approach will be further developed and may contribute to generating minichromosomes from preselected genomic regions, potentially even in a diploid background.
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In vivo modification of a maize engineered minichromosome. Chromosoma 2013; 122:221-32. [DOI: 10.1007/s00412-013-0403-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Revised: 02/25/2013] [Accepted: 02/27/2013] [Indexed: 10/27/2022]
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