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Tetrahymena as a Unicellular Model Eukaryote: Genetic and Genomic Tools. Genetics 2017; 203:649-65. [PMID: 27270699 DOI: 10.1534/genetics.114.169748] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 04/08/2016] [Indexed: 12/12/2022] Open
Abstract
Tetrahymena thermophila is a ciliate model organism whose study has led to important discoveries and insights into both conserved and divergent biological processes. In this review, we describe the tools for the use of Tetrahymena as a model eukaryote, including an overview of its life cycle, orientation to its evolutionary roots, and methodological approaches to forward and reverse genetics. Recent genomic tools have expanded Tetrahymena's utility as a genetic model system. With the unique advantages that Tetrahymena provide, we argue that it will continue to be a model organism of choice.
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Zhang K, Raboanatahiry N, Zhu B, Li M. Progress in Genome Editing Technology and Its Application in Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:177. [PMID: 28261237 PMCID: PMC5306361 DOI: 10.3389/fpls.2017.00177] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 01/27/2017] [Indexed: 05/19/2023]
Abstract
Genome editing technology (GET) is a versatile approach that has progressed rapidly as a mechanism to alter the genotype and phenotype of organisms. However, conventional genome modification using GET cannot satisfy current demand for high-efficiency and site-directed mutagenesis, retrofitting of artificial nucleases has developed into a new avenue within this field. Based on mechanisms to recognize target genes, newly-developed GETs can generally be subdivided into three cleavage systems, protein-dependent DNA cleavage systems (i.e., zinc-finger nucleases, ZFN, and transcription activator-like effector nucleases, TALEN), RNA-dependent DNA cleavage systems (i.e., clustered regularly interspaced short palindromic repeats-CRISPR associated proteins, CRISPR-Cas9, CRISPR-Cpf1, and CRISPR-C2c1), and RNA-dependent RNA cleavage systems (i.e., RNA interference, RNAi, and CRISPR-C2c2). All these techniques can lead to double-stranded (DSB) or single-stranded breaks (SSB), and result in either random mutations via non-homologous end-joining (NHEJ) or targeted mutation via homologous recombination (HR). Thus, site-directed mutagenesis can be induced via targeted gene knock-out, knock-in, or replacement to modify specific characteristics including morphology-modification, resistance-enhancement, and physiological mechanism-improvement along with plant growth and development. In this paper, an non-comprehensive review on the development of different GETs as applied to plants is presented.
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Affiliation(s)
- Kai Zhang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal UniversityHuanggang, China
| | - Nadia Raboanatahiry
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Bin Zhu
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal UniversityHuanggang, China
- *Correspondence: Maoteng Li
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Huang S, Balgi A, Pan Y, Li M, Zhang X, Du L, Zhou M, Roberge M, Li X. Identification of Methylosome Components as Negative Regulators of Plant Immunity Using Chemical Genetics. MOLECULAR PLANT 2016; 9:1620-1633. [PMID: 27756575 DOI: 10.1016/j.molp.2016.10.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 09/01/2016] [Accepted: 10/01/2016] [Indexed: 06/06/2023]
Abstract
Nucleotide-binding leucine-rich repeat (NLR) proteins serve as immune receptors in both plants and animals. To identify components required for NLR-mediated immunity, we designed and carried out a chemical genetics screen to search for small molecules that can alter immune responses in Arabidopsis thaliana. From 13 600 compounds, we identified Ro 8-4304 that was able to specifically suppress the severe autoimmune phenotypes of chs3-2D (chilling sensitive 3, 2D), including the arrested growth morphology and heightened PR (Pathogenesis Related) gene expression. Further, six Ro 8-4304 insensitive mutants were uncovered from the Ro 8-4304-insensitive mutant (rim) screen using a mutagenized chs3-2D population. Positional cloning revealed that rim1 encodes an allele of AtICln (I, currents; Cl, chloride; n, nucleotide). Genetic and biochemical analysis demonstrated that AtICln is in the same protein complex with the methylosome components small nuclear ribonucleoprotein D3b (SmD3b) and protein arginine methyltransferase 5 (PRMT5), which are required for the biogenesis of small nuclear ribonucleoproteins (snRNPs) involved in mRNA splicing. Double mutant analysis revealed that SmD3b is also involved in the sensitivity to Ro 8-4304, and the prmt5-1 chs3-2D double mutant is lethal. Loss of AtICln, SmD3b, or PRMT5 function results in enhanced disease resistance against the virulent oomycete pathogen Hyaloperonospora arabidopsidis Noco2, suggesting that mRNA splicing plays a previously unknown negative role in plant immunity. The successful implementation of a high-throughput chemical genetic screen and the identification of a small-molecule compound affecting plant immunity indicate that chemical genetics is a powerful tool to study whole-organism plant defense pathways.
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Affiliation(s)
- Shuai Huang
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Aruna Balgi
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Yaping Pan
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Meng Li
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Xiaoran Zhang
- National Institute of Biological Sciences, Beijing 102206, China
| | - Lilin Du
- National Institute of Biological Sciences, Beijing 102206, China
| | - Ming Zhou
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Michel Roberge
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Xin Li
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
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Zhu L, Zhang YH, Su F, Chen L, Huang T, Cai YD. A Shortest-Path-Based Method for the Analysis and Prediction of Fruit-Related Genes in Arabidopsis thaliana. PLoS One 2016; 11:e0159519. [PMID: 27434024 PMCID: PMC4951011 DOI: 10.1371/journal.pone.0159519] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 07/05/2016] [Indexed: 12/11/2022] Open
Abstract
Biologically, fruits are defined as seed-bearing reproductive structures in angiosperms that develop from the ovary. The fertilization, development and maturation of fruits are crucial for plant reproduction and are precisely regulated by intrinsic genetic regulatory factors. In this study, we used Arabidopsis thaliana as a model organism and attempted to identify novel genes related to fruit-associated biological processes. Specifically, using validated genes, we applied a shortest-path-based method to identify several novel genes in a large network constructed using the protein-protein interactions observed in Arabidopsis thaliana. The described analyses indicate that several of the discovered genes are associated with fruit fertilization, development and maturation in Arabidopsis thaliana.
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Affiliation(s)
- Liucun Zhu
- School of Life Sciences, Shanghai University, Shanghai, People’s Republic of China
| | - Yu-Hang Zhang
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People’s Republic of China
| | - Fangchu Su
- School of Life Sciences, Shanghai University, Shanghai, People’s Republic of China
| | - Lei Chen
- College of Information Engineering, Shanghai Maritime University, Shanghai, People’s Republic of China
| | - Tao Huang
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People’s Republic of China
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, People’s Republic of China
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Arabidopsis thaliana plants expressing Rift Valley fever virus antigens: Mice exhibit systemic immune responses as the result of oral administration of the transgenic plants. Protein Expr Purif 2016; 127:61-67. [PMID: 27402440 DOI: 10.1016/j.pep.2016.07.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 07/01/2016] [Accepted: 07/05/2016] [Indexed: 11/17/2022]
Abstract
The zoonotic Rift Valley fever virus affects livestock and humans in Africa and on the Arabian Peninsula. The economic impact of this pathogen due to livestock losses, as well as its relevance to public health, underscores the importance of developing effective and easily distributed vaccines. Vaccines that can be delivered orally are of particular interest. Here, we report the expression in transformed plants (Arabidopsis thaliana) of Rift Valley fever virus antigens. The antigens used in this study were the N protein and a deletion mutant of the Gn glycoprotein. Transformed lines were analysed for specific mRNA and protein content by RT-PCR and Western blotting, respectively. Furthermore, the plant-expressed antigens were evaluated for their immunogenicity in mice fed the transgenic plants. After oral intake of fresh transgenic plant material, a proportion of the mice elicited specific IgG antibody responses, as compared to the control animals that were fed wild-type plants and of which none sero-converted. Thus, we show that transgenic plants can be readily used to express and produce Rift Valley Fever virus proteins, and that the plants are immunogenic when given orally to mice. These are promising findings and provide a basis for further studies on edible plant vaccines against the Rift Valley fever virus.
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Kilgore MB, Kutchan TM. The Amaryllidaceae alkaloids: biosynthesis and methods for enzyme discovery. PHYTOCHEMISTRY REVIEWS : PROCEEDINGS OF THE PHYTOCHEMICAL SOCIETY OF EUROPE 2016; 15:317-337. [PMID: 27340382 PMCID: PMC4914137 DOI: 10.1007/s11101-015-9451-z] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 12/08/2015] [Indexed: 05/21/2023]
Abstract
Amaryllidaceae alkaloids are an example of the vast diversity of secondary metabolites with great therapeutic promise. The identification of novel compounds in this group with over 300 known structures continues to be an area of active study. The recent identification of norbelladine 4'-O-methyltransferase (N4OMT), an Amaryllidaceae alkaloid biosynthetic enzyme, and the assembly of transcriptomes for Narcissus sp. aff. pseudonarcissus and Lycoris aurea highlight the potential for discovery of Amaryllidaceae alkaloid biosynthetic genes with new technologies. Recent technical advances of interest include those in enzymology, next generation sequencing, genetic modification, nuclear magnetic resonance spectroscopy (NMR), and mass spectrometry (MS).
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Affiliation(s)
- Matthew B. Kilgore
- Donald Danforth Plant Science Center, 63132 St. Louis, Missouri, 975 N. Warson Rd., St. Louis, MO
| | - Toni M. Kutchan
- Donald Danforth Plant Science Center, 63132 St. Louis, Missouri, 975 N. Warson Rd., St. Louis, MO
- To whom correspondence should be addressed: Toni M. Kutchan, , Tel.: (314) 587-1473, Fax: (314) 587-1573
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Muraro D, Larrieu A, Lucas M, Chopard J, Byrne H, Godin C, King J. A multi-scale model of the interplay between cell signalling and hormone transport in specifying the root meristem of Arabidopsis thaliana. J Theor Biol 2016; 404:182-205. [PMID: 27157127 DOI: 10.1016/j.jtbi.2016.04.036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Revised: 10/25/2015] [Accepted: 04/29/2016] [Indexed: 10/21/2022]
Abstract
The growth of the root of Arabidopsis thaliana is sustained by the meristem, a region of cell proliferation and differentiation which is located in the root apex and generates cells which move shootwards, expanding rapidly to cause root growth. The balance between cell division and differentiation is maintained via a signalling network, primarily coordinated by the hormones auxin, cytokinin and gibberellin. Since these hormones interact at different levels of spatial organisation, we develop a multi-scale computational model which enables us to study the interplay between these signalling networks and cell-cell communication during the specification of the root meristem. We investigate the responses of our model to hormonal perturbations, validating the results of our simulations against experimental data. Our simulations suggest that one or more additional components are needed to explain the observed expression patterns of a regulator of cytokinin signalling, ARR1, in roots not producing gibberellin. By searching for novel network components, we identify two mutant lines that affect significantly both root length and meristem size, one of which also differentially expresses a central component of the interaction network (SHY2). More generally, our study demonstrates how a multi-scale investigation can provide valuable insight into the spatio-temporal dynamics of signalling networks in biological tissues.
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Affiliation(s)
- D Muraro
- Centre for Plant Integrative Biology, University of Nottingham, Loughborough LE12 5RD, UK; The Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Mathematical Institute, University of Oxford, Oxford OX2 6GG, UK.
| | - A Larrieu
- Centre for Plant Integrative Biology, University of Nottingham, Loughborough LE12 5RD, UK
| | - M Lucas
- Centre for Plant Integrative Biology, University of Nottingham, Loughborough LE12 5RD, UK; Equipe CERES, UMR DIADE, IRD, 34394 Montpellier, France
| | - J Chopard
- Virtual Plants Project-Team, UMR AGAP, INRIA/CIRAD, Montpellier, France
| | - H Byrne
- Centre for Plant Integrative Biology, University of Nottingham, Loughborough LE12 5RD, UK; Mathematical Institute, University of Oxford, Oxford OX2 6GG, UK; School of Mathematical Sciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - C Godin
- Virtual Plants Project-Team, UMR AGAP, INRIA/CIRAD, Montpellier, France
| | - J King
- Centre for Plant Integrative Biology, University of Nottingham, Loughborough LE12 5RD, UK; School of Mathematical Sciences, University of Nottingham, Nottingham NG7 2RD, UK
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Manzanares C, Yates S, Ruckle M, Nay M, Studer B. TILLING in forage grasses for gene discovery and breeding improvement. N Biotechnol 2016; 33:594-603. [PMID: 26924175 DOI: 10.1016/j.nbt.2016.02.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 02/09/2016] [Accepted: 02/12/2016] [Indexed: 01/04/2023]
Abstract
Mutation breeding has a long-standing history and in some major crop species, many of the most important cultivars have their origin in germplasm generated by mutation induction. For almost two decades, methods for TILLING (Targeting Induced Local Lesions IN Genomes) have been established in model plant species such as Arabidopsis (Arabidopsis thaliana L.), enabling the functional analysis of genes. Recent advances in mutation detection by second generation sequencing technology have brought its utility to major crop species. However, it has remained difficult to apply similar approaches in forage and turf grasses, mainly due to their outbreeding nature maintained by an efficient self-incompatibility system. Starting with a description of the extent to which traditional mutagenesis methods have contributed to crop yield increase in the past, this review focuses on technological approaches to implement TILLING-based strategies for the improvement of forage grass breeding through forward and reverse genetics. We present first results from TILLING in allogamous forage grasses for traits such as stress tolerance and evaluate prospects for rapid implementation of beneficial alleles to forage grass breeding. In conclusion, large-scale induced mutation resources, used for forward genetic screens, constitute a valuable tool to increase the genetic diversity for breeding and can be generated with relatively small investments in forage grasses. Furthermore, large libraries of sequenced mutations can be readily established, providing enhanced opportunities to discover mutations in genes controlling traits of agricultural importance and to study gene functions by reverse genetics.
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Affiliation(s)
- Chloe Manzanares
- Forage Crop Genetics, Institute of Agricultural Sciences, ETH Zurich, 8092 Zurich, Switzerland
| | - Steven Yates
- Forage Crop Genetics, Institute of Agricultural Sciences, ETH Zurich, 8092 Zurich, Switzerland
| | - Michael Ruckle
- Forage Crop Genetics, Institute of Agricultural Sciences, ETH Zurich, 8092 Zurich, Switzerland
| | - Michelle Nay
- Forage Crop Genetics, Institute of Agricultural Sciences, ETH Zurich, 8092 Zurich, Switzerland
| | - Bruno Studer
- Forage Crop Genetics, Institute of Agricultural Sciences, ETH Zurich, 8092 Zurich, Switzerland.
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Ecovoiu AA, Ghionoiu IC, Ciuca AM, Ratiu AC. Genome ARTIST: a robust, high-accuracy aligner tool for mapping transposon insertions and self-insertions. Mob DNA 2016; 7:3. [PMID: 26855675 PMCID: PMC4744444 DOI: 10.1186/s13100-016-0061-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 01/19/2016] [Indexed: 01/16/2023] Open
Abstract
Background A critical topic of insertional mutagenesis experiments performed on model organisms is mapping the hits of artificial transposons (ATs) at nucleotide level accuracy. Mapping errors may occur when sequencing artifacts or mutations as single nucleotide polymorphisms (SNPs) and small indels are present very close to the junction between a genomic sequence and a transposon inverted repeat (TIR). Another particular item of insertional mutagenesis is mapping of the transposon self-insertions and, to our best knowledge, there is no publicly available mapping tool designed to analyze such molecular events. Results We developed Genome ARTIST, a pairwise gapped aligner tool which works out both issues by means of an original, robust mapping strategy. Genome ARTIST is not designed to use next-generation sequencing (NGS) data but to analyze ATs insertions obtained in small to medium-scale mutagenesis experiments. Genome ARTIST employs a heuristic approach to find DNA sequence similarities and harnesses a multi-step implementation of a Smith-Waterman adapted algorithm to compute the mapping alignments. The experience is enhanced by easily customizable parameters and a user-friendly interface that describes the genomic landscape surrounding the insertion. Genome ARTIST is functional with many genomes of bacteria and eukaryotes available in Ensembl and GenBank repositories. Our tool specifically harnesses the sequence annotation data provided by FlyBase for Drosophila melanogaster (the fruit fly), which enables mapping of insertions relative to various genomic features such as natural transposons. Genome ARTIST was tested against other alignment tools using relevant query sequences derived from the D. melanogaster and Mus musculus (mouse) genomes. Real and simulated query sequences were also comparatively inquired, revealing that Genome ARTIST is a very robust solution for mapping transposon insertions. Conclusions Genome ARTIST is a stand-alone user-friendly application, designed for high-accuracy mapping of transposon insertions and self-insertions. The tool is also useful for routine aligning assessments like detection of SNPs or checking the specificity of primers and probes. Genome ARTIST is an open source software and is available for download at www.genomeartist.ro and at GitHub (https://github.com/genomeartist/genomeartist ). Electronic supplementary material The online version of this article (doi:10.1186/s13100-016-0061-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexandru Al Ecovoiu
- Department of Genetics, Faculty of Biology, University of Bucharest, Bucharest, Romania
| | | | | | - Attila Cristian Ratiu
- Department of Genetics, Faculty of Biology, University of Bucharest, Bucharest, Romania
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60
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Dekkers BJW, He H, Hanson J, Willems LAJ, Jamar DCL, Cueff G, Rajjou L, Hilhorst HWM, Bentsink L. The Arabidopsis DELAY OF GERMINATION 1 gene affects ABSCISIC ACID INSENSITIVE 5 (ABI5) expression and genetically interacts with ABI3 during Arabidopsis seed development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 85:451-65. [PMID: 26729600 DOI: 10.1111/tpj.13118] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 12/22/2015] [Accepted: 12/23/2015] [Indexed: 05/18/2023]
Abstract
The seed expressed gene DELAY OF GERMINATION (DOG) 1 is absolutely required for the induction of dormancy. Next to a non-dormant phenotype, the dog1-1 mutant is also characterized by a reduced seed longevity suggesting that DOG1 may affect additional seed processes as well. This aspect however, has been hardly studied and is poorly understood. To uncover additional roles of DOG1 in seeds we performed a detailed analysis of the dog1 mutant using both transcriptomics and metabolomics to investigate the molecular consequences of a dysfunctional DOG1 gene. Further, we used a genetic approach taking advantage of the weak aba insensitive (abi) 3-1 allele as a sensitized genetic background in a cross with dog1-1. DOG1 affects the expression of hundreds of genes including LATE EMBRYOGENESIS ABUNDANT and HEAT SHOCK PROTEIN genes which are affected by DOG1 partly via control of ABI5 expression. Furthermore, the content of a subset of primary metabolites, which normally accumulate during seed maturation, was found to be affected in the dog1-1 mutant. Surprisingly, the abi3-1 dog1-1 double mutant produced green seeds which are highly ABA insensitive, phenocopying severe abi3 mutants, indicating that dog1-1 acts as an enhancer of the weak abi3-1 allele and thus revealing a genetic interaction between both genes. Analysis of the dog1 and dog1 abi3 mutants revealed additional seed phenotypes and therefore we hypothesize that DOG1 function is not limited to dormancy but that it is required for multiple aspects of seed maturation, in part by interfering with ABA signalling components.
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Affiliation(s)
- Bas J W Dekkers
- Wageningen Seed Laboratory, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB, Wageningen, The Netherlands
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, NL-6708, PB Wageningen, The Netherlands
- Department of Molecular Plant Physiology, Utrecht University, NL-3584 CH, Utrecht, The Netherlands
| | - Hanzi He
- Wageningen Seed Laboratory, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB, Wageningen, The Netherlands
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, NL-6708, PB Wageningen, The Netherlands
| | - Johannes Hanson
- Department of Molecular Plant Physiology, Utrecht University, NL-3584 CH, Utrecht, The Netherlands
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-90187, Umeå, Sweden
| | - Leo A J Willems
- Wageningen Seed Laboratory, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB, Wageningen, The Netherlands
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, NL-6708, PB Wageningen, The Netherlands
| | - Diaan C L Jamar
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, NL-6708, PB Wageningen, The Netherlands
| | - Gwendal Cueff
- INRA, Institut Jean-Pierre Bourgin (IJPB), UMR 1318 INRA/AgroParisTech, ERL CNRS 3559, Université Paris-Saclay, 'Saclay Plant Sciences' - RD10, F-78026, Versailles, France
- Chair of Plant Physiology, AgroParisTech, 16 rue Claude Bernard, F-75231, Paris Cedex 05, France
| | - Loïc Rajjou
- INRA, Institut Jean-Pierre Bourgin (IJPB), UMR 1318 INRA/AgroParisTech, ERL CNRS 3559, Université Paris-Saclay, 'Saclay Plant Sciences' - RD10, F-78026, Versailles, France
- Chair of Plant Physiology, AgroParisTech, 16 rue Claude Bernard, F-75231, Paris Cedex 05, France
| | - Henk W M Hilhorst
- Wageningen Seed Laboratory, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB, Wageningen, The Netherlands
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, NL-6708, PB Wageningen, The Netherlands
| | - Leónie Bentsink
- Wageningen Seed Laboratory, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB, Wageningen, The Netherlands
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, NL-6708, PB Wageningen, The Netherlands
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Mao Y, Zhang Z, Feng Z, Wei P, Zhang H, Botella JR, Zhu JK. Development of germ-line-specific CRISPR-Cas9 systems to improve the production of heritable gene modifications in Arabidopsis. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:519-32. [PMID: 26360626 PMCID: PMC5515382 DOI: 10.1111/pbi.12468] [Citation(s) in RCA: 154] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 07/30/2015] [Accepted: 08/05/2015] [Indexed: 05/18/2023]
Abstract
The Streptococcus-derived CRISPR/Cas9 system is being widely used to perform targeted gene modifications in plants. This customized endonuclease system has two components, the single-guide RNA (sgRNA) for target DNA recognition and the CRISPR-associated protein 9 (Cas9) for DNA cleavage. Ubiquitously expressed CRISPR/Cas9 systems (UC) generate targeted gene modifications with high efficiency but only those produced in reproductive cells are transmitted to the next generation. We report the design and characterization of a germ-line-specific Cas9 system (GSC) for Arabidopsis gene modification in male gametocytes, constructed using a SPOROCYTELESS (SPL) genomic expression cassette. Four loci in two endogenous genes were targeted by both systems for comparative analysis. Mutations generated by the GSC system were rare in T1 plants but were abundant (30%) in the T2 generation. The vast majority (70%) of the T2 mutant population generated using the UC system were chimeras while the newly developed GSC system produced only 29% chimeras, with 70% of the T2 mutants being heterozygous. Analysis of two loci in the T2 population showed that the abundance of heritable gene mutations was 37% higher in the GSC system compared to the UC system and the level of polymorphism of the mutations was also dramatically increased with the GSC system. Two additional systems based on germ-line-specific promoters (pDD45-GT and pLAT52-GT) were also tested, and one of them was capable of generating heritable homozygous T1 mutant plants. Our results suggest that future application of the described GSC system will facilitate the screening for targeted gene modifications, especially lethal mutations in the T2 population.
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Affiliation(s)
- Yanfei Mao
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, China
| | - Zhengjing Zhang
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences (CAS), Shanghai, China
| | - Zhengyan Feng
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences (CAS), Shanghai, China
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Pengliang Wei
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences (CAS), Shanghai, China
| | - Hui Zhang
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, China
| | - José Ramón Botella
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, Qld, Australia
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, China
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, USA
- Correspondence: (Tel 1-765-496-7601; fax 1-765-494-0391,
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62
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Kianian PMA, Liberatore KL, Miller ME, Hegstad JB, Kianian SF. Dissecting Plant Chromosomes by the Use of Ionizing Radiation. Methods Mol Biol 2016; 1429:91-101. [PMID: 27511169 DOI: 10.1007/978-1-4939-3622-9_8] [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: 06/06/2023]
Abstract
Radiation treatment of genomes is used to generate chromosome breaks for numerous applications. This protocol describes the preparation of seeds and the determination of the optimal level of irradiation dosage for the creation of a radiation hybrid (RH) population. These RH lines can be used to generate high-resolution physical maps for the assembly of sequenced genomes as well as the fine mapping of genes. This procedure can also be used for mutation breeding and forward/reverse genetics.
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Affiliation(s)
- Penny M A Kianian
- Department of Horticultural Science, University of Minnesota, 1970 Folwell Ave., St. Paul, MN, 55108, USA.
| | - Katie L Liberatore
- USDA-ARS, Cereal Disease Laboratory, Department of Plant Pathology, University of Minnesota, 1551 Lindig Ave., St. Paul, MN, 55108, USA
| | - Marisa E Miller
- Department of Horticultural Science, University of Minnesota, 1970 Folwell Ave., St. Paul, MN, 55108, USA
| | - Justin B Hegstad
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA
| | - Shahryar F Kianian
- USDA-ARS, Cereal Disease Laboratory, Department of Plant Pathology, University of Minnesota, 1551 Lindig Ave., St. Paul, MN, 55108, USA.
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Baute J, Herman D, Coppens F, De Block J, Slabbinck B, Dell'Acqua M, Pè ME, Maere S, Nelissen H, Inzé D. Correlation analysis of the transcriptome of growing leaves with mature leaf parameters in a maize RIL population. Genome Biol 2015; 16:168. [PMID: 26357925 PMCID: PMC4566308 DOI: 10.1186/s13059-015-0735-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 07/30/2015] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND To sustain the global requirements for food and renewable resources, unraveling the molecular networks underlying plant growth is becoming pivotal. Although several approaches to identify genes and networks involved in final organ size have been proven successful, our understanding remains fragmentary. RESULTS Here, we assessed variation in 103 lines of the Zea mays B73xH99 RIL population for a set of final leaf size and whole shoot traits at the seedling stage, complemented with measurements capturing growth dynamics, and cellular measurements. Most traits correlated well with the size of the division zone, implying that the molecular basis of final leaf size is already defined in dividing cells of growing leaves. Therefore, we searched for association between the transcriptional variation in dividing cells of the growing leaf and final leaf size and seedling biomass, allowing us to identify genes and processes correlated with the specific traits. A number of these genes have a known function in leaf development. Additionally, we illustrated that two independent mechanisms contribute to final leaf size, maximal growth rate and the duration of growth. CONCLUSIONS Untangling complex traits such as leaf size by applying in-depth phenotyping allows us to define the relative contributions of the components and their mutual associations, facilitating dissection of the biological processes and regulatory networks underneath.
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Affiliation(s)
- Joke Baute
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, Technologiepark 927, 9052, Ghent, Belgium. .,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium.
| | - Dorota Herman
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, Technologiepark 927, 9052, Ghent, Belgium. .,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium.
| | - Frederik Coppens
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, Technologiepark 927, 9052, Ghent, Belgium. .,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium.
| | - Jolien De Block
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, Technologiepark 927, 9052, Ghent, Belgium. .,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium.
| | - Bram Slabbinck
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, Technologiepark 927, 9052, Ghent, Belgium. .,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium.
| | - Matteo Dell'Acqua
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy.
| | - Mario Enrico Pè
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy.
| | - Steven Maere
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, Technologiepark 927, 9052, Ghent, Belgium. .,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium.
| | - Hilde Nelissen
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, Technologiepark 927, 9052, Ghent, Belgium. .,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium.
| | - Dirk Inzé
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, Technologiepark 927, 9052, Ghent, Belgium. .,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium.
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64
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Zhao Q, Gao C, Lee P, Liu L, Li S, Hu T, Shen J, Pan S, Ye H, Chen Y, Cao W, Cui Y, Zeng P, Yu S, Gao Y, Chen L, Mo B, Liu X, Xiao S, Zhao Y, Zhong S, Chen X, Jiang L. Fast-suppressor screening for new components in protein trafficking, organelle biogenesis and silencing pathway in Arabidopsis thaliana using DEX-inducible FREE1-RNAi plants. J Genet Genomics 2015; 42:319-30. [PMID: 26165498 DOI: 10.1016/j.jgg.2015.03.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 03/21/2015] [Accepted: 03/27/2015] [Indexed: 12/20/2022]
Abstract
Membrane trafficking is essential for plant growth and responses to external signals. The plant unique FYVE domain-containing protein FREE1 is a component of the ESCRT complex (endosomal sorting complex required for transport). FREE1 plays multiple roles in regulating protein trafficking and organelle biogenesis including the formation of intraluminal vesicles of multivesicular body (MVB), vacuolar protein transport and vacuole biogenesis, and autophagic degradation. FREE1 knockout plants show defective MVB formation, abnormal vacuolar transport, fragmented vacuoles, accumulated autophagosomes, and seedling lethality. To further uncover the underlying mechanisms of FREE1 function in plants, we performed a forward genetic screen for mutants that suppressed the seedling lethal phenotype of FREE1-RNAi transgenic plants. The obtained mutants are termed as suppressors of free1 (sof). To date, 229 putative sof mutants have been identified. Barely detecting of FREE1 protein with M3 plants further identified 84 FREE1-related suppressors. Also 145 mutants showing no reduction of FREE1 protein were termed as RNAi-related mutants. Through next-generation sequencing (NGS) of bulked DNA from F2 mapping population of two RNAi-related sof mutants, FREE1-RNAi T-DNA inserted on chromosome 1 was identified and the causal mutation of putative sof mutant is being identified similarly. These FREE1- and RNAi-related sof mutants will be useful tools and resources for illustrating the underlying mechanisms of FREE1 function in intracellular trafficking and organelle biogenesis, as well as for uncovering the new components involved in the regulation of silencing pathways in plants.
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Affiliation(s)
- Qiong Zhao
- Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Caiji Gao
- Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - PoShing Lee
- Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Lin Liu
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Shaofang Li
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Tangjin Hu
- CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518057, China
| | - Jinbo Shen
- Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Shuying Pan
- CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518057, China
| | - Hao Ye
- CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518057, China
| | - Yunru Chen
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Wenhan Cao
- Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Yong Cui
- Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Peng Zeng
- Beijing Genomics Institute at Shenzhen, Shenzhen 518083, China
| | - Sheng Yu
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Yangbin Gao
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Liang Chen
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Beixin Mo
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences, Shenzhen University, Shenzhen 518060, China
| | - Xin Liu
- Beijing Genomics Institute at Shenzhen, Shenzhen 518083, China
| | - Shi Xiao
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yunde Zhao
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Silin Zhong
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Liwen Jiang
- Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China; CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518057, China.
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65
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Abstract
Forward genetic screens are powerful tools for the discovery and functional annotation of genetic elements. Recently, the RNA-guided CRISPR (clustered regularly interspaced short palindromic repeat)-associated Cas9 nuclease has been combined with genome-scale guide RNA libraries for unbiased, phenotypic screening. In this Review, we describe recent advances using Cas9 for genome-scale screens, including knockout approaches that inactivate genomic loci and strategies that modulate transcriptional activity. We discuss practical aspects of screen design, provide comparisons with RNA interference (RNAi) screening, and outline future applications and challenges.
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Affiliation(s)
- Ophir Shalem
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA; McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, and Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Neville E Sanjana
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA; McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, and Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Feng Zhang
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA; McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, and Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
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66
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Chen LY, Shi DQ, Zhang WJ, Tang ZS, Liu J, Yang WC. The Arabidopsis alkaline ceramidase TOD1 is a key turgor pressure regulator in plant cells. Nat Commun 2015; 6:6030. [PMID: 25591940 PMCID: PMC4309442 DOI: 10.1038/ncomms7030] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 12/04/2014] [Indexed: 11/09/2022] Open
Abstract
Turgor pressure plays pivotal roles in the growth and movement of walled cells that make up plants and fungi. However, the molecular mechanisms regulating turgor pressure and the coordination between turgor pressure and cell wall remodelling for cell growth remain poorly understood. Here, we report the characterization of Arabidopsis TurgOr regulation Defect 1 (TOD1), which is preferentially expressed in pollen tubes and silique guard cells. We demonstrate that TOD1 is a Golgi-localized alkaline ceramidase. tod1 mutant pollen tubes have higher turgor than wild type and show growth retardation both in pistils and in agarose medium. In addition, tod1 guard cells are insensitive to abscisic acid (ABA)-induced stomatal closure, whereas sphingosine-1-phosphate, a putative downstream component of ABA signalling and product of alkaline ceramidases, promotes closure in both wild type and tod1. Our data suggest that TOD1 acts in turgor pressure regulation in both guard cells and pollen tubes.
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Affiliation(s)
- Li-Yu Chen
- 1] State Key Laboratory of Molecular Developmental Biology and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China [2] University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong-Qiao Shi
- State Key Laboratory of Molecular Developmental Biology and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wen-Juan Zhang
- 1] State Key Laboratory of Molecular Developmental Biology and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China [2] University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zuo-Shun Tang
- State Key Laboratory of Molecular Developmental Biology and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jie Liu
- State Key Laboratory of Molecular Developmental Biology and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wei-Cai Yang
- 1] State Key Laboratory of Molecular Developmental Biology and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China [2] Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai 200433, China
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67
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Arisha MH, Shah SNM, Gong ZH, Jing H, Li C, Zhang HX. Ethyl methane sulfonate induced mutations in M2 generation and physiological variations in M1 generation of peppers (Capsicum annuum L.). FRONTIERS IN PLANT SCIENCE 2015; 6:399. [PMID: 26089827 PMCID: PMC4454883 DOI: 10.3389/fpls.2015.00399] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Accepted: 05/18/2015] [Indexed: 05/10/2023]
Abstract
This study was conducted to enhance genetic variability in peppers (Capsicum annuum, cv B12) using ethyl methanesulphonate (EMS). Exposure to an EMS concentration of 0.6%, v/v for 12 h was used to mutagenize 2000 seeds for the first generation (M1). It was observed that the growth behaviors including plant height, flowering date, and number of seeds per first fruit were different in the M1 generation than in wild type (WT) plants. In addition one phenotypic mutation (leaf shape and plant architecture) was observed during the M1 generation. During the seedling stage in the M2 generation, the observed changes were in the form of slow growth or chlorophyll defect (e.g., albino, pale green, and yellow seedlings). At maturity, there were three kinds of phenotypic mutations observed in three different families of the mutant population. The first observed change was a plant with yellow leaf color, and the leaves of this mutant plant contained 62.19% less chlorophyll a and 64.06% less chlorophyll b as compared to the wild-type. The second mutation resulted in one dwarf plant with a very short stature (6 cm), compact internodes and the leaves and stem were rough and thick. The third type of mutation occurred in four plants and resulted in the leaves of these plants being very thick and longer than those of WT plants. Furthermore, anatomical observations of the leaf blade section of this mutant plant type contained more xylem and collenchyma tissue in the leaf midrib of the mutant plant than WT. In addition, its leaf blade contained thicker palisade and spongy tissue than the WT.
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Affiliation(s)
- Mohamed H. Arisha
- College of Horticulture, Northwest A&F University, YanglingChina
- State Key Laboratories for Stress Biology of Arid Region Crop, Northwest A&F University, YanglingChina
- Department of Horticulture, Faculty of Agriculture, Zagazig University, ZagazigEgypt
| | - Syed N. M. Shah
- College of Horticulture, Northwest A&F University, YanglingChina
- State Key Laboratories for Stress Biology of Arid Region Crop, Northwest A&F University, YanglingChina
- Department of Horticulture, Faculty of Agriculture, Gomal University, Dera Ismail KhanPakistan
| | - Zhen-Hui Gong
- College of Horticulture, Northwest A&F University, YanglingChina
- State Key Laboratories for Stress Biology of Arid Region Crop, Northwest A&F University, YanglingChina
- *Correspondence: Zhen-Hui Gong, College of Horticulture, Northwest A&F University, No.3 Taicheng Road, Yangling, Shaanxi Province 712100, China
| | - Hua Jing
- College of Horticulture, Northwest A&F University, YanglingChina
| | - Chao Li
- College of Horticulture, Northwest A&F University, YanglingChina
| | - Huai-Xia Zhang
- College of Horticulture, Northwest A&F University, YanglingChina
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68
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Chemical and Radiation Mutagenesis: Induction and Detection by Whole Genome Sequencing. GENETICS AND GENOMICS OF BRACHYPODIUM 2015. [DOI: 10.1007/7397_2015_20] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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69
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70
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Wilson-Sánchez D, Rubio-Díaz S, Muñoz-Viana R, Pérez-Pérez JM, Jover-Gil S, Ponce MR, Micol JL. Leaf phenomics: a systematic reverse genetic screen for Arabidopsis leaf mutants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 79:878-91. [PMID: 24946828 DOI: 10.1111/tpj.12595] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 06/07/2014] [Accepted: 06/09/2014] [Indexed: 05/10/2023]
Abstract
The study and eventual manipulation of leaf development in plants requires a thorough understanding of the genetic basis of leaf organogenesis. Forward genetic screens have identified hundreds of Arabidopsis mutants with altered leaf development, but the genome has not yet been saturated. To identify genes required for leaf development we are screening the Arabidopsis Salk Unimutant collection. We have identified 608 lines that exhibit a leaf phenotype with full penetrance and almost constant expressivity and 98 additional lines with segregating mutant phenotypes. To allow indexing and integration with other mutants, the mutant phenotypes were described using a custom leaf phenotype ontology. We found that the indexed mutation is present in the annotated locus for 78% of the 553 mutants genotyped, and that in half of these the annotated T-DNA is responsible for the phenotype. To quickly map non-annotated T-DNA insertions, we developed a reliable, cost-effective and easy method based on whole-genome sequencing. To enable comprehensive access to our data, we implemented a public web application named PhenoLeaf (http://genetics.umh.es/phenoleaf) that allows researchers to query the results of our screen, including text and visual phenotype information. We demonstrated how this new resource can facilitate gene function discovery by identifying and characterizing At1g77600, which we found to be required for proximal-distal cell cycle-driven leaf growth, and At3g62870, which encodes a ribosomal protein needed for cell proliferation and chloroplast function. This collection provides a valuable tool for the study of leaf development, characterization of biomass feedstocks and examination of other traits in this fundamental photosynthetic organ.
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Affiliation(s)
- David Wilson-Sánchez
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202, Elche, Spain
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71
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Yuan F, Yang H, Xue Y, Kong D, Ye R, Li C, Zhang J, Theprungsirikul L, Shrift T, Krichilsky B, Johnson DM, Swift GB, He Y, Siedow JN, Pei ZM. OSCA1 mediates osmotic-stress-evoked Ca2+ increases vital for osmosensing in Arabidopsis. Nature 2014; 514:367-71. [DOI: 10.1038/nature13593] [Citation(s) in RCA: 417] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 06/18/2014] [Indexed: 01/05/2023]
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72
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Schneeberger K. Using next-generation sequencing to isolate mutant genes from forward genetic screens. Nat Rev Genet 2014; 15:662-76. [PMID: 25139187 DOI: 10.1038/nrg3745] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The long-lasting success of forward genetic screens relies on the simple molecular basis of the characterized phenotypes, which are typically caused by mutations in single genes. Mapping the location of causal mutations using genetic crosses has traditionally been a complex, multistep procedure, but next-generation sequencing now allows the rapid identification of causal mutations at single-nucleotide resolution even in complex genetic backgrounds. Recent advances of this mapping-by-sequencing approach include methods that are independent of reference genome sequences, genetic crosses and any kind of linkage information, which make forward genetics amenable for species that have not been considered for forward genetic screens so far.
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Affiliation(s)
- Korbinian Schneeberger
- Genome Plasticity and Computational Genetics, Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
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73
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Wunderlich M, Groß-Hardt R, Schöffl F. Heat shock factor HSFB2a involved in gametophyte development of Arabidopsis thaliana and its expression is controlled by a heat-inducible long non-coding antisense RNA. PLANT MOLECULAR BIOLOGY 2014; 85:541-50. [PMID: 24874772 PMCID: PMC4099531 DOI: 10.1007/s11103-014-0202-0] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 05/15/2014] [Indexed: 05/04/2023]
Abstract
Heat stress transcription factors (HSFs) are central regulators of the heat stress response. Plant HSFs of subgroup B lack a conserved sequence motif present in the transcriptional activation domain of class A-HSFs. Arabidopsis members were found to be involved in non-heat shock functions. In the present analysis we investigated the expression, regulation and function of HSFB2a. HSFB2a expression was counteracted by a natural long non-coding antisense RNA, asHSFB2a. In leaves, the antisense RNA gene is only expressed after heat stress and dependent on the activity of HSFA1a/HSFA1b. HSFB2a and asHSFB2a RNAs were also present in the absence of heat stress in the female gametophyte. Transgenic overexpression of HSFB2a resulted in a complete knock down of the asHSFB2a expression. Conversely, asHSFB2a overexpression leads to the absence of HSFB2a RNA. The knockdown of HSFB2a by asHSFB2a correlated with an improved, knockdown of asHSFB2a by HSFB2a overexpression with an impaired biomass production early in vegetative development. In both cases the development of female gametophytes was impaired. A T-DNA knock-out line did not segregate homozygous mutant plants, only heterozygots hsfB2a-tt1/+ were viable. Approximately 50% of the female gametophytes were arrested in early development, before mitosis 3, resulting in 45% of sterile ovules. Our analysis indicates that the "Yin-Yang" regulation of gene expression at the HSFB2a locus influences vegetative and gametophytic development in Arabidopsis.
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Affiliation(s)
- Markus Wunderlich
- ZMBP General Genetics, University of Tübingen, 72076 Tübingen, Germany
| | - Rita Groß-Hardt
- ZMBP Developmental Genetics, University of Tübingen, 72076 Tübingen, Germany
| | - Friedrich Schöffl
- ZMBP General Genetics, University of Tübingen, 72076 Tübingen, Germany
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Xing A, Williams ME, Bourett TM, Hu W, Hou Z, Meeley RB, Jaqueth J, Dam T, Li B. A pair of homoeolog ClpP5 genes underlies a virescent yellow-like mutant and its modifier in maize. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 79:192-205. [PMID: 24888539 DOI: 10.1111/tpj.12568] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 04/28/2014] [Accepted: 05/13/2014] [Indexed: 05/24/2023]
Abstract
Gene-background interaction is a commonly observed phenomenon in many species, but the molecular mechanisms of such an interaction is less well understood. Here we report the cloning of a maize mutant gene and its modifier. A recessive mutant with a virescent yellow-like (vyl) phenotype was identified in an ethyl methanesulfonate-mutagenized population derived from the maize inbred line B73. Homozygous mutant maize plants exhibited a yellow leaf phenotype after emergence but gradually recovered and became indistinguishable from wild-type plants after approximately 2 weeks. Taking the positional cloning approach, the Chr.9_ClpP5 gene, one of the proteolytic subunits of the chloroplast Clp protease complex, was identified and validated as the candidate gene for vyl. When introgressed by backcross into the maize inbred line PH09B, the mutant phenotype of vyl lasted much longer in the greenhouse and was lethal in the field, implying the presence of a modifier(s) for vyl. A major modifier locus was identified on chromosome 1, and a paralogous ClpP5 gene was isolated and confirmed as the candidate for the vyl-modifier. Expression of Chr.1_ClpP5 is induced significantly in B73 by the vyl mutation, while the expression of Chr.1_ClpP5 in PH09B is not responsive to the vyl mutation. Moreover, expression and sequence analysis suggests that the PH09B Chr.1_ClpP5 allele is functionally weaker than the B73 allele. We propose that functional redundancy between duplicated paralogous genes is the molecular mechanism for the interaction between vyl and its modifier.
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Affiliation(s)
- Anqi Xing
- National Maize Improvement Center, China Agricultural University, 2 West Yuanmingyuan Rd., Beijing, 100094, China; DuPont Pioneer, 200 Powder Mill Road, Wilmington, DE, 19880, USA
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Abstract
In aphids, clonal individuals can show distinct morphologic traits in response to environmental cues. Such phenotypic plasticity cannot be studied with classical genetic model organisms such as Caenorhabditis elegans or Drosophila melanogaster. The genetic basis of this biological process remain unknown, as mutations affecting this process are not available in aphids. Here, we describe a protocol to treat third-stage larvae with an alkylating mutagen, ethyl methanesulfonate (EMS), to generate random mutations within the Acyrthosiphon pisum genome. We found that even low concentrations of EMS were toxic for two genotypes of A. pisum. Mutagenesis efficiency was nevertheless assessed by estimating the occurrence of mutational events on the X chromosome. Indeed, any lethal mutation on the X-chromosome would kill males that are haploid on the X so that we used the proportion of males as an estimation of mutagenesis efficacy. We could assess a putative mutation rate of 0.4 per X-chromosome at 10 mM of EMS. We then applied this protocol to perform a small-scale mutagenesis on parthenogenetic individuals, which were screened for defects in their ability to produce sexual individuals in response to photoperiod shortening. We found one mutant line showing a reproducible altered photoperiodic response with a reduced production of males and the appearance of aberrant winged males (wing atrophy, alteration of legs morphology). This mutation appeared to be stable because it could be transmitted over several generations of parthenogenetic individuals. To our knowledge, this study represents the first example of an EMS-generated aphid mutant.
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76
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Li XR, Li HJ, Yuan L, Liu M, Shi DQ, Liu J, Yang WC. Arabidopsis DAYU/ABERRANT PEROXISOME MORPHOLOGY9 is a key regulator of peroxisome biogenesis and plays critical roles during pollen maturation and germination in planta. THE PLANT CELL 2014; 26:619-35. [PMID: 24510720 PMCID: PMC3967029 DOI: 10.1105/tpc.113.121087] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2013] [Revised: 01/13/2014] [Accepted: 01/20/2014] [Indexed: 05/20/2023]
Abstract
Pollen undergo a maturation process to sustain pollen viability and prepare them for germination. Molecular mechanisms controlling these processes remain largely unknown. Here, we report an Arabidopsis thaliana mutant, dayu (dau), which impairs pollen maturation and in vivo germination. Molecular analysis indicated that DAU encodes the peroxisomal membrane protein ABERRANT PEROXISOME MORPHOLOGY9 (APEM9). DAU is transiently expressed from bicellular pollen to mature pollen during male gametogenesis. DAU interacts with peroxisomal membrane proteins PEROXIN13 (PEX13) and PEX16 in planta. Consistently, both peroxisome biogenesis and peroxisome protein import are impaired in dau pollen. In addition, the jasmonic acid (JA) level is significantly decreased in dau pollen, and the dau mutant phenotype is partially rescued by exogenous application of JA, indicating that the male sterility is mainly due to JA deficiency. In addition, the phenotypic survey of peroxin mutants indicates that the PEXs most likely play different roles in pollen germination. Taken together, these data indicate that DAU/APEM9 plays critical roles in peroxisome biogenesis and function, which is essential for JA production and pollen maturation and germination.
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Affiliation(s)
- Xin-Ran Li
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hong-Ju Li
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Li Yuan
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Man Liu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Dong-Qiao Shi
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jie Liu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wei-Cai Yang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- Address correspondence to
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77
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Etherington GJ, Monaghan J, Zipfel C, MacLean D. Mapping mutations in plant genomes with the user-friendly web application CandiSNP. PLANT METHODS 2014; 10:41. [PMID: 25610492 PMCID: PMC4301057 DOI: 10.1186/s13007-014-0041-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 12/05/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND Analysis of mutants isolated from forward-genetic screens has revealed key components of several plant signalling pathways. Mapping mutations by position, either using classical methods or whole genome high-throughput sequencing (HTS), largely relies on the analysis of genome-wide polymorphisms in F2 recombinant populations. Combining bulk segregant analysis with HTS has accelerated the identification of causative mutations and has been widely adopted in many research programmes. A major advantage of HTS is the ability to perform bulk segregant analysis after back-crossing to the parental line rather than out-crossing to a polymorphic ecotype, which reduces genetic complexity and avoids issues with phenotype penetrance in different ecotypes. Plotting the positions of homozygous polymorphisms in a mutant genome identifies areas of low recombination and is an effective way to detect molecular linkage to a phenotype of interest. RESULTS We describe the use of single nucleotide polymorphism (SNP) density plots as a mapping strategy to identify and refine chromosomal positions of causative mutations from screened plant populations. We developed a web application called CandiSNP that generates density plots from user-provided SNP data obtained from HTS. Candidate causative mutations, defined as SNPs causing non-synonymous changes in annotated coding regions are highlighted on the plots and listed in a table. We use data generated from a recent mutant screen in the model plant Arabidopsis thaliana as proof-of-concept for the validity of our tool. CONCLUSIONS CandiSNP is a user-friendly application that will aid in novel discoveries from forward-genetic mutant screens. It is particularly useful for analysing HTS data from bulked back-crossed mutants, which contain fewer polymorphisms than data generated from out-crosses. The web-application is freely available online at http://candisnp.tsl.ac.uk.
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Affiliation(s)
- Graham J Etherington
- />The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH UK
- />The Genome Analysis Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | | | - Cyril Zipfel
- />The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH UK
| | - Dan MacLean
- />The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH UK
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78
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Dinh TT, Luscher E, Li S, Liu X, Won SY, Chen X. Genetic screens for floral mutants in Arabidopsis thaliana: enhancers and suppressors. Methods Mol Biol 2014; 1110:127-56. [PMID: 24395255 DOI: 10.1007/978-1-4614-9408-9_6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The flower is a hallmark feature that has contributed to the evolutionary success of land plants. Diverse mutagenic agents have been employed as a tool to genetically perturb flower development and identify genes involved in floral patterning and morphogenesis. Since the initial studies to identify genes governing processes such as floral organ specification, mutagenesis in sensitized backgrounds has been used to isolate enhancers and suppressors to further probe the molecular basis of floral development. Here, we first describe two commonly employed methods for mutagenesis (using ethyl methanesulfonate (EMS) or T-DNAs as mutagens), and then describe three methods for identifying a mutation that leads to phenotypic alterations--traditional map-based cloning, TAIL-PCR, and deep sequencing in the plant model Arabidopsis thaliana.
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Affiliation(s)
- Thanh Theresa Dinh
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, USA
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79
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Callot C, Gallois JL. Pyramiding resistances based on translation initiation factors in Arabidopsis is impaired by male gametophyte lethality. PLANT SIGNALING & BEHAVIOR 2014; 9:e27940. [PMID: 24492391 PMCID: PMC4091535 DOI: 10.4161/psb.27940] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Accepted: 01/21/2014] [Indexed: 05/20/2023]
Abstract
In eukaryotes, eIF4E translation initiation factors are essential proteins encoded by a small multigene family. In plants, they are a major source of host plant resistance to potyviruses that require specific 4E factors to infect cells. Combining mutations in different eIF4E genes could be a way of broadening the spectrum of plant resistance to viruses. We attempted to combine null mutations affecting the two main Arabidopsis thaliana 4E factors eIF4E1 and eIFiso4E but discovered that this combination is lethal. Transmission through the male gametophyte is completely abolished in the eif4e1 eifiso4e double mutant. This shows that eIF4E1 and eIFiso4E are essential for male gametophyte development and act redundantly. These results may have implications for eIF4E-based pyramiding strategies to improve crop resistance.
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80
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Abstract
EMS mutant analysis is a routine experiment to identify new players in a specific biological process or signaling pathway using forward genetics. It begins with the generation of mutants by treating Arabidopsis seeds with EMS. A mutant with a phenotype of interest (mpi) is obtained by screening plants of the M2 generation under a specific condition. Once the phenotype of the mpi is confirmed in the next generation, map-based cloning is performed to locate the mpi mutation. During the map-based cloning, mpi plants (Arabidopsis Columbia-0 (Col-0) ecotype background) are first crossed with Arabidopsis Landsberg erecta (Ler) ecotype, and the presence or absence of the phenotype in the F1 hybrids indicates whether the mpi is recessive or dominant. F2 plants with phenotypes similar to the mpi, if the mpi is recessive, or those without the phenotype, if the mpi is dominant, are used as the mapping population. As few as 24 such plants are selected for rough mapping. After finding one marker (MA) linked to the mpi locus or mutant phenotype, more markers near MA are tested to identify recombinants. The recombinants indicate the interval in which the mpi is located. Additional recombinants and molecular markers are then required to narrow down the interval. This is an iterative process of narrowing down the mapping interval until no further recombinants or molecular markers are available. The genes in the mapping interval are then sequenced to look for the mutation. In the last step, the wild-type or mutated gene is cloned to generate binary constructs. Complementation or recapitulation provides the most convincing evidence in determining the mutation that causes the phenotype of the mpi. Here, we describe the procedures for generating mutants with EMS and analyzing EMS mutations by map-based cloning.
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Affiliation(s)
- Li-Jia Qu
- State Key Laboratory of Protein and Plant Gene Research, Center for Life Sciences, College of Life Sciences, Peking University, Beijing, People's Republic of China
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81
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Kast EJ, Nguyen MDT, Lawrence RE, Rabeler C, Kaplinsky NJ. The RootScope: a simple high-throughput screening system for quantitating gene expression dynamics in plant roots. BMC PLANT BIOLOGY 2013; 13:158. [PMID: 24119322 PMCID: PMC3852858 DOI: 10.1186/1471-2229-13-158] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 10/09/2013] [Indexed: 06/02/2023]
Abstract
BACKGROUND High temperature stress responses are vital for plant survival. The mechanisms that plants use to sense high temperatures are only partially understood and involve multiple sensing and signaling pathways. Here we describe the development of the RootScope, an automated microscopy system for quantitating heat shock responses in plant roots. RESULTS The promoter of Hsp17.6 was used to build a Hsp17.6p:GFP transcriptional reporter that is induced by heat shock in Arabidopsis. An automated fluorescence microscopy system which enables multiple roots to be imaged in rapid succession was used to quantitate Hsp17.6p:GFP response dynamics. Hsp17.6p:GFP signal increased with temperature increases from 28°C to 37°C. At 40°C the kinetics and localization of the response are markedly different from those at 37°C. This suggests that different mechanisms mediate heat shock responses above and below 37°C. Finally, we demonstrate that Hsp17.6p:GFP expression exhibits wave like dynamics in growing roots. CONCLUSIONS The RootScope system is a simple and powerful platform for investigating the heat shock response in plants.
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Affiliation(s)
- Erin J Kast
- Department of Biology, Swarthmore College, Swarthmore, PA, 19081, USA
| | | | | | - Christina Rabeler
- Department of Biology, Swarthmore College, Swarthmore, PA, 19081, USA
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82
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Dalmais M, Antelme S, Ho-Yue-Kuang S, Wang Y, Darracq O, d’Yvoire MB, Cézard L, Légée F, Blondet E, Oria N, Troadec C, Brunaud V, Jouanin L, Höfte H, Bendahmane A, Lapierre C, Sibout R. A TILLING Platform for Functional Genomics in Brachypodium distachyon. PLoS One 2013; 8:e65503. [PMID: 23840336 PMCID: PMC3686759 DOI: 10.1371/journal.pone.0065503] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Accepted: 04/25/2013] [Indexed: 11/18/2022] Open
Abstract
The new model plant for temperate grasses, Brachypodium distachyon offers great potential as a tool for functional genomics. We have established a sodium azide-induced mutant collection and a TILLING platform, called "BRACHYTIL", for the inbred line Bd21-3. The TILLING collection consists of DNA isolated from 5530 different families. Phenotypes were reported and organized in a phenotypic tree that is freely available online. The tilling platform was validated by the isolation of mutants for seven genes belonging to multigene families of the lignin biosynthesis pathway. In particular, a large allelic series for BdCOMT6, a caffeic acid O-methyl transferase was identified. Some mutants show lower lignin content when compared to wild-type plants as well as a typical decrease of syringyl units, a hallmark of COMT-deficient plants. The mutation rate was estimated at one mutation per 396 kb, or an average of 680 mutations per line. The collection was also used to assess the Genetically Effective Cell Number that was shown to be at least equal to 4 cells in Brachypodium distachyon. The mutant population and the TILLING platform should greatly facilitate functional genomics approaches in this model organism.
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Affiliation(s)
- Marion Dalmais
- URGV, Unité de Recherche en Génomique Végétale, Université d’Evry Val d’Essonne, INRA, Evry, France
| | - Sébastien Antelme
- Institut National de la Recherche Agronomique, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, Versailles, France
- AgroParisTech, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, Versailles, France
| | - Séverine Ho-Yue-Kuang
- Institut National de la Recherche Agronomique, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, Versailles, France
- AgroParisTech, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, Versailles, France
| | - Yin Wang
- Institut National de la Recherche Agronomique, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, Versailles, France
- AgroParisTech, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, Versailles, France
| | - Olivier Darracq
- Institut National de la Recherche Agronomique, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, Versailles, France
- AgroParisTech, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, Versailles, France
| | - Madeleine Bouvier d’Yvoire
- Institut National de la Recherche Agronomique, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, Versailles, France
- AgroParisTech, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, Versailles, France
| | - Laurent Cézard
- Institut National de la Recherche Agronomique, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, Versailles, France
- AgroParisTech, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, Versailles, France
| | - Frédéric Légée
- Institut National de la Recherche Agronomique, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, Versailles, France
- AgroParisTech, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, Versailles, France
| | - Eddy Blondet
- URGV, Unité de Recherche en Génomique Végétale, Université d’Evry Val d’Essonne, INRA, Evry, France
| | - Nicolas Oria
- Institut National de la Recherche Agronomique, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, Versailles, France
- AgroParisTech, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, Versailles, France
| | - Christelle Troadec
- URGV, Unité de Recherche en Génomique Végétale, Université d’Evry Val d’Essonne, INRA, Evry, France
| | - Véronique Brunaud
- URGV, Unité de Recherche en Génomique Végétale, Université d’Evry Val d’Essonne, INRA, Evry, France
| | - Lise Jouanin
- Institut National de la Recherche Agronomique, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, Versailles, France
- AgroParisTech, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, Versailles, France
| | - Herman Höfte
- Institut National de la Recherche Agronomique, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, Versailles, France
- AgroParisTech, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, Versailles, France
| | - Abdelafid Bendahmane
- URGV, Unité de Recherche en Génomique Végétale, Université d’Evry Val d’Essonne, INRA, Evry, France
| | - Catherine Lapierre
- Institut National de la Recherche Agronomique, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, Versailles, France
- AgroParisTech, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, Versailles, France
| | - Richard Sibout
- Institut National de la Recherche Agronomique, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, Versailles, France
- AgroParisTech, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, Versailles, France
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83
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James GV, Patel V, Nordström KJV, Klasen JR, Salomé PA, Weigel D, Schneeberger K. User guide for mapping-by-sequencing in Arabidopsis. Genome Biol 2013; 14:R61. [PMID: 23773572 PMCID: PMC3706810 DOI: 10.1186/gb-2013-14-6-r61] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 06/17/2013] [Indexed: 12/27/2022] Open
Abstract
Mapping-by-sequencing combines genetic mapping with whole-genome sequencing in order to accelerate mutant identification. However, application of mapping-by-sequencing requires decisions on various practical settings on the experimental design that are not intuitively answered. Following an experimentally determined recombination landscape of Arabidopsis and next generation sequencing-specific biases, we simulated more than 400,000 mapping-by-sequencing experiments. This allowed us to evaluate a broad range of different types of experiments and to develop general rules for mapping-by-sequencing in Arabidopsis. Most importantly, this informs about the properties of different crossing scenarios, the number of recombinants and sequencing depth needed for successful mapping experiments.
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84
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Nordström KJV, Albani MC, James GV, Gutjahr C, Hartwig B, Turck F, Paszkowski U, Coupland G, Schneeberger K. Mutation identification by direct comparison of whole-genome sequencing data from mutant and wild-type individuals using k-mers. Nat Biotechnol 2013; 31:325-30. [PMID: 23475072 DOI: 10.1038/nbt.2515] [Citation(s) in RCA: 124] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 01/22/2013] [Indexed: 12/31/2022]
Abstract
Genes underlying mutant phenotypes can be isolated by combining marker discovery, genetic mapping and resequencing, but a more straightforward strategy for mapping mutations would be the direct comparison of mutant and wild-type genomes. Applying such an approach, however, is hampered by the need for reference sequences and by mutational loads that confound the unambiguous identification of causal mutations. Here we introduce NIKS (needle in the k-stack), a reference-free algorithm based on comparing k-mers in whole-genome sequencing data for precise discovery of homozygous mutations. We applied NIKS to eight mutants induced in nonreference rice cultivars and to two mutants of the nonmodel species Arabis alpina. In both species, comparing pooled F2 individuals selected for mutant phenotypes revealed small sets of mutations including the causal changes. Moreover, comparing M3 seedlings of two allelic mutants unambiguously identified the causal gene. Thus, for any species amenable to mutagenesis, NIKS enables forward genetics without requiring segregating populations, genetic maps and reference sequences.
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85
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RNAi phenotypes are influenced by the genetic background of the injected strain. BMC Genomics 2013; 14:5. [PMID: 23324472 PMCID: PMC3574008 DOI: 10.1186/1471-2164-14-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Accepted: 12/19/2012] [Indexed: 12/22/2022] Open
Abstract
Background RNA interference (RNAi) is a powerful tool to study gene function in organisms that are not amenable to classical forward genetics. Hence, together with the ease of comprehensively identifying genes by new generation sequencing, RNAi is expanding the scope of animal species and questions that can be addressed in terms of gene function. In the case of genetic mutants, the genetic background of the strains used is known to influence the phenotype while this has not been described for RNAi experiments. Results Here we show in the red flour beetle Tribolium castaneum that RNAi against Tc-importin α1 leads to different phenotypes depending on the injected strain. We rule out off target effects and show that sequence divergence does not account for this difference. By quantitatively comparing phenotypes elicited by RNAi knockdown of four different genes we show that there is no general difference in RNAi sensitivity between these strains. Finally, we show that in case of Tc-importin α1 the difference depends on the maternal genotype. Conclusions These results show that in RNAi experiments strain specific differences have to be considered and that a proper documentation of the injected strain is required. This is especially important for the increasing number of emerging model organisms that are being functionally investigated using RNAi. In addition, our work shows that RNAi is suitable to systematically identify the differences in the gene regulatory networks present in populations of the same species, which will allow novel insights into the evolution of animal diversity.
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86
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Allen RS, Nakasugi K, Doran RL, Millar AA, Waterhouse PM. Facile mutant identification via a single parental backcross method and application of whole genome sequencing based mapping pipelines. FRONTIERS IN PLANT SCIENCE 2013; 4:362. [PMID: 24062760 PMCID: PMC3772335 DOI: 10.3389/fpls.2013.00362] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 08/26/2013] [Indexed: 05/22/2023]
Abstract
Forward genetic screens have identified numerous genes involved in development and metabolism, and remain a cornerstone of biological research. However, to locate a causal mutation, the practice of crossing to a polymorphic background to generate a mapping population can be problematic if the mutant phenotype is difficult to recognize in the hybrid F2 progeny, or dependent on parental specific traits. Here in a screen for leaf hyponasty mutants, we have performed a single backcross of an Ethane Methyl Sulphonate (EMS) generated hyponastic mutant to its parent. Whole genome deep sequencing of a bulked homozygous F2 population and analysis via the Next Generation EMS mutation mapping pipeline (NGM) unambiguously determined the causal mutation to be a single nucleotide polymorphisim (SNP) residing in HASTY, a previously characterized gene involved in microRNA biogenesis. We have evaluated the feasibility of this backcross approach using three additional SNP mapping pipelines; SHOREmap, the GATK pipeline, and the samtools pipeline. Although there was variance in the identification of EMS SNPs, all returned the same outcome in clearly identifying the causal mutation in HASTY. The simplicity of performing a single parental backcross and genome sequencing a small pool of segregating mutants has great promise for identifying mutations that may be difficult to map using conventional approaches.
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Affiliation(s)
- Robert S. Allen
- School of Molecular Bioscience, University of SydneySydney, NSW, Australia
- School of Biological Sciences, University of SydneySydney, NSW, Australia
- Plant Sciences Division, Research School of Biology, Australian National UniversityCanberra, ACT, Australia
- *Correspondence: Robert S. Allen, Plant Sciences Division, Research School of Biology, Australian National University, Building 134, Linnaeus Way, Canberra, 0200 ACT, Australia e-mail:
| | - Kenlee Nakasugi
- School of Molecular Bioscience, University of SydneySydney, NSW, Australia
| | - Rachel L. Doran
- School of Molecular Bioscience, University of SydneySydney, NSW, Australia
| | - Anthony A. Millar
- Plant Sciences Division, Research School of Biology, Australian National UniversityCanberra, ACT, Australia
| | - Peter M. Waterhouse
- School of Molecular Bioscience, University of SydneySydney, NSW, Australia
- School of Biological Sciences, University of SydneySydney, NSW, Australia
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87
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Abstract
The complexity of food organism interactions necessitates the use of model organisms to understand physiological and pathological processes. In nutrition research, model organisms were initially used to understand how macro and micronutrients are handled in the organism. Currently, in nutritional systems biology, models of increasing complexity are needed in order to determine the global organisation of a biological system and the interaction with food and food components. Originally driven by genetics, certain model organisms have become most prominent. Model organisms are more accessible systems than human beings and include bacteria, yeast, flies, worms, and mammals such as mice. Here, the origin and the reasons to become the most prominent models are presented. Moreover, their applicability in molecular nutrition research is illustrated with selected examples.
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Affiliation(s)
- Isabel Rubio-Aliaga
- Molecular Nutrition Unit, Department of Food and Nutrition, Technische Universität München, Freising, Germany.
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88
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Hartwig B, James GV, Konrad K, Schneeberger K, Turck F. Fast isogenic mapping-by-sequencing of ethyl methanesulfonate-induced mutant bulks. PLANT PHYSIOLOGY 2012; 160:591-600. [PMID: 22837357 PMCID: PMC3461541 DOI: 10.1104/pp.112.200311] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Accepted: 07/25/2012] [Indexed: 05/18/2023]
Abstract
Mapping-by-sequencing (or SHOREmapping) has revitalized the powerful concept of forward genetic screens in plants. However, as in conventional genetic mapping approaches, mapping-by-sequencing requires phenotyping of mapping populations established from crosses between two diverged accessions. In addition to the segregation of the focal phenotype, this introduces natural phenotypic variation, which can interfere with the recognition of quantitative phenotypes. Here, we demonstrate how mapping-by-sequencing and candidate gene identification can be performed within the same genetic background using only mutagen-induced changes as segregating markers. Using a previously unknown suppressor of mutants of like heterochromatin protein1 (lhp1), which in its functional form is involved in chromatin-mediated gene repression, we identified three closely linked ethyl methanesulfonate-induced changes as putative candidates. In order to assess allele frequency differences between such closely linked mutations, we introduced deep candidate resequencing using the new Ion Torrent Personal Genome Machine sequencing platform to our mutant identification pipeline and thereby reduced the number of causal candidate mutations to only one. Genetic analysis of two independent additional alleles confirmed that this mutation was causal for the suppression of lhp1.
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89
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Finke A, Kuhlmann M, Mette MF. IDN2 has a role downstream of siRNA formation in RNA-directed DNA methylation. Epigenetics 2012; 7:950-60. [PMID: 22810086 PMCID: PMC3427290 DOI: 10.4161/epi.21237] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In plants, a particular class of short interfering (si)RNAs can serve as a signal to induce cytosine methylation at homologous genomic regions. If the targeted DNA has promoter function, this RNA-directed DNA methylation (RdDM) can result in transcriptional gene silencing (TGS). RNA-directed transcriptional gene silencing (RdTGS) of transgenes provides a versatile system for the study of epigenetic gene regulation. We used transcription of a nopaline synthase promoter (ProNOS)-inverted repeat (IR) to provide a RNA signal that triggers de novo cytosine methylation and TGS of a homologous ProNOS copy in trans. Utilizing a ProNOS-NPTII reporter gene showing high sensitivity to silencing in this two component system, a forward genetic screen for EMS-induced no rna-directed transcriptional silencing (nrd) mutations was performed in Arabidopsis thaliana. Three nrd mutant lines were found to contain one novel loss-of-function allele of idn2/rdm12 and two of nrpd2a/nrpe2a. IDN2/RDM12 encodes a XH/XS domain protein that is able to bind double-stranded RNA with 5′ overhangs, while NRPD2a/NRPE2a encodes the common second-largest subunit of the plant specific DNA-dependent RNA polymerases IV and V involved in silencing processes. Both idn2/rdm12 and nrpd2a/nrpe2a release target transgene expression and reduce CHH context methylation at transgenic as well as endogenous RdDM target regions to similar extents. Nevertheless, accumulation of IR-derived siRNA is not affected, allowing us to present a refined model for the pathway of RdDM and RdTGS that positions function of IDN2 downstream of siRNA formation and points to an important role for its XH domain.
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Affiliation(s)
- Andreas Finke
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
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90
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SNP-Ratio Mapping (SRM): identifying lethal alleles and mutations in complex genetic backgrounds by next-generation sequencing. Genetics 2012; 191:1381-6. [PMID: 22649081 DOI: 10.1534/genetics.112.141341] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We present a generally applicable method allowing rapid identification of causal alleles in mutagenized genomes by next-generation sequencing. Currently used approaches rely on recovering homozygotes or extensive backcrossing. In contrast, SNP-ratio mapping allows rapid cloning of lethal and/or poorly transmitted mutations and second-site modifiers, which are often in complex genetic/transgenic backgrounds.
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91
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Zwiewka M, Friml J. Fluorescence imaging-based forward genetic screens to identify trafficking regulators in plants. FRONTIERS IN PLANT SCIENCE 2012; 3:97. [PMID: 22654887 PMCID: PMC3359526 DOI: 10.3389/fpls.2012.00097] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2012] [Accepted: 04/25/2012] [Indexed: 05/25/2023]
Abstract
Coordinated, subcellular trafficking of proteins is one of the fundamental properties of the multicellular eukaryotic organisms. Trafficking involves a large diversity of compartments, pathways, cargo molecules, and vesicle-sorting events. It is also crucial in regulating the localization and, thus, the activity of various proteins, but the process is still poorly genetically defined in plants. In the past, forward genetics screens had been used to determine the function of genes by searching for a specific morphological phenotype in the organism population in which mutations had been induced chemically or by irradiation. Unfortunately, these straightforward genetic screens turned out to be limited in identifying new regulators of intracellular protein transport, because mutations affecting essential trafficking pathways often lead to lethality. In addition, the use of these approaches has been restricted by functional redundancy among trafficking regulators. Screens for mutants that rely on the observation of changes in the cellular localization or dynamics of fluorescent subcellular markers enable, at least partially, to circumvent these issues. Hence, such image-based screens provide the possibility to identify either alleles with weak effects or components of the subcellular trafficking machinery that have no strong impact on the plant growth.
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Affiliation(s)
- Marta Zwiewka
- Department of Plant Systems Biology, VIB Life Sciences Research InstituteGent, Belgium
- Department of Plant Biotechnology and Genetics, Ghent UniversityGent, Belgium
| | - Jiří Friml
- Department of Plant Systems Biology, VIB Life Sciences Research InstituteGent, Belgium
- Department of Plant Biotechnology and Genetics, Ghent UniversityGent, Belgium
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92
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Rangani G, Khodakovskaya M, Alimohammadi M, Hoecker U, Srivastava V. Site-specific methylation in gene coding region underlies transcriptional silencing of the Phytochrome A epiallele in Arabidopsis thaliana. PLANT MOLECULAR BIOLOGY 2012; 79:191-202. [PMID: 22466452 DOI: 10.1007/s11103-012-9906-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Accepted: 03/17/2012] [Indexed: 05/31/2023]
Abstract
DNA methylation in cytosine residues plays an important role in regulating gene expression. Densely methylated transgenes are often silenced. In contrast, several eukaryotic genomes express moderately methylated genes. These methylations are found in the CG context within the coding region (gene body). The role of gene body methylation in gene expression, however, is not clear. The Arabidopsis Phytochrome A epiallele, phyA', carries hypermethylation in several CG sites resident to the coding region. As a result, phyA' is transcriptionally silenced and confers strong mutant phenotype. Mutations in chromatin modification factors and RNAi genes failed to revert the mutant phenotype, suggesting the involvement of a distinct epigenetic mechanism associated with phyA' silencing. Using the forward genetics approach, a suppressor line, termed as suppressor of p hyA' silencing 1 (sps1), was isolated. Genetic and molecular analysis revealed that sps1 mutation reactivates the phyA' locus without altering its methylation density. However, hypomethylation at a specific CG site in exon 1 was consistently associated with the release of phyA' silencing. While gene underlying sps1 mutation is yet to be identified, microarray analysis suggested that its targets are the expressed genes or euchromatic loci in Arabidopsis genome. By identifying the association of phyA' silencing with the methylation of a specific CG site in exon 1, the present work shows that site-specific methylation confers greater effect on transcription than the methylation density within gene-body. Further, as the identified site (exon 1) is not critical for the promoter activity, transcription elongation rather than transcription initiation is likely to be affected by this site-specific CG methylation.
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Affiliation(s)
- Gulab Rangani
- Department of Crop, Soil and Environmental Sciences, Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72701, USA.
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93
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Biedrzycki ML, Jilany TA, Dudley SA, Bais HP. Root exudates mediate kin recognition in plants. Commun Integr Biol 2011; 3:28-35. [PMID: 20539778 DOI: 10.4161/cib.3.1.10118] [Citation(s) in RCA: 135] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2009] [Revised: 09/16/2009] [Accepted: 09/17/2009] [Indexed: 11/19/2022] Open
Abstract
Though recent work has demonstrated that plants can recognize species, kin versus strangers, and self/non-self roots, no mechanism for identity recognition in plants has yet been found. Here we examined the role of soluble chemicals in signaling among roots. Utilizing Arabidopsis thaliana, we exposed young seedlings to liquid media containing exudates from siblings, strangers (non-siblings), or only their own exudates. In one experiment, root secretions were inhibited by sodium orthovanadate and root length and number of lateral roots were measured. In a second experiment, responses to siblings, strangers, and their own exudates were measured for several accessions (genotypes), and the traits of length of the longest lateral root and hypocotyl length were also measured. The exposure of plants to the root exudates of strangers induced greater lateral root formation than exposure of plants to sibling exudates. Stranger recognition was abolished upon treatment with the secretion inhibitor. In one experiment, plants exposed to sibling or stranger exudates have shorter roots than plants only exposed to their own exudates. This self/non-self recognition response was not affected by the secretion inhibitor. The results demonstrate that that kin recognition and self/non-self are two separate identity recognition systems involving soluble chemicals. Kin recognition requires active secretion by roots.
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94
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Suwabe K, Suzuki G, Watanabe M. Achievement of genetics in plant reproduction research: the past decade for the coming decade. Genes Genet Syst 2011; 85:297-310. [PMID: 21317542 DOI: 10.1266/ggs.85.297] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
In the last decade, a variety of innovations of emerging technologies in science have been accomplished. Advanced research environment in plant science has made it possible to obtain whole genome sequence in plant species. But now we recognize this by itself is not sufficient to understand the overall biological significance. Since Gregor Mendel established a principle of genetics, known as Mendel's Laws of Inheritance, genetics plays a prominent role in life science, and this aspect is indispensable even in modern plant biology. In this review, we focus on achievements of genetics on plant sexual reproduction research in the last decade and discuss the role of genetics for the coming decade. It is our hope that this will shed light on the importance of genetics in plant biology and provide valuable information to plant biologists.
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Affiliation(s)
- Keita Suwabe
- Graduate School of Bioresources, Mie University, Tsu, Japan
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95
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Sharma PD, Singh N, Ahuja PS, Reddy TV. Abscisic acid response element binding factor 1 is required for establishment of Arabidopsis seedlings during winter. Mol Biol Rep 2010; 38:5147-59. [PMID: 21181499 DOI: 10.1007/s11033-010-0664-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2010] [Accepted: 12/07/2010] [Indexed: 01/02/2023]
Abstract
Abscisic acid (ABA) plays a crucial role in abiotic stress response apart from its influence on growth and development of a plant. Our studies on abscisic acid response element binding factor 1 (ABF1) gene in Arabidopsis demonstrate that it is required for seedling establishment during winter. ABF1 is also involved in regulating seed dormancy and seed germination to some extent. Analysis of transcriptional activity of ABF1 promoter reveals that ABF1 expresses specifically in trichomes of young leaves and constitutively in cotyledons, roots, older leaves and flowers. The expression is induced upon exposure to ABA, cold and heat. The alignment of cDNAs of ABF1 (At1g49720) and At1g49730 (encodes a protein kinase of unknown function), reveals an overlap of 88 bp at their 3' UTR region suggesting that they can potentially form natural cis-antisense mRNAs pair in a tail-to-tail manner. Analysis by Genevestigator microarray stress response viewer further supports the regulatory role of these genes. An inverse proportion is observed in the transcription the two loci in number of stress responses. The abf1 mutants do not show any seedling establishment defects when grown under standard growth conditions. The mutant seedlings exhibit growth defects during winter in the western Himalayan region. Our study also signifies the importance of functional analysis for mutant phenotypes in natural habitats by reverse genetic approaches, in order to identify specific function of particular gene/s whose expression level is altered upon exposure to changes in environmental cues such as temperature and light.
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Affiliation(s)
- Pitamber Dutt Sharma
- Biotechnology Division, Institute of Himalayan Bioresource Technology-CSIR, Palampur 176061, Himachal Pradesh, India
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96
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Fakheran S, Paul-Victor C, Heichinger C, Schmid B, Grossniklaus U, Turnbull LA. Adaptation and extinction in experimentally fragmented landscapes. Proc Natl Acad Sci U S A 2010; 107:19120-5. [PMID: 20956303 PMCID: PMC2973902 DOI: 10.1073/pnas.1010846107] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Competition and disturbance are potent ecological forces that shape evolutionary trajectories. These forces typically work in opposition: when disturbance is infrequent, densities are high and competition is intense. In contrast, frequent disturbance creates a low-density environment in which competition is weak and good dispersal essential. We exploited recent advances in genomic research to quantify the response to selection by these powerful ecological forces at the phenotypic and molecular genetic level in experimental landscapes. We grew the annual plant Arabidopsis thaliana in discrete patches embedded in a hostile matrix and varied the number and size of patches and the intensity of disturbance, by creating both static and dynamic landscapes. In static landscapes all patches were undisturbed, whereas in dynamic landscapes all patches were destroyed in each generation, forcing seeds to disperse to new locations. We measured the resulting changes in phenotypic, genetic, and genotypic diversity after five generations of selection. Simulations revealed that the observed loss of genetic diversity dwarfed that expected under drift, with dramatic diversity loss, particularly from dynamic landscapes. In line with ecological theory, static landscapes favored good competitors; however, competitive ability was linked to growth rate and not, as expected, to seed mass. In dynamic landscapes, there was strong selection for increased dispersal ability in the form of increased inflorescence height and reduced seed mass. The most competitive genotypes were almost eliminated from highly disturbed landscapes, raising concern over the impact of increased levels of human-induced disturbance in natural landscapes.
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Affiliation(s)
- Sima Fakheran
- Institute of Evolutionary Biology and Environmental Studies and Zürich-Basel Plant Science Center, University of Zürich, CH-8057 Zürich, Switzerland; and
| | - Cloé Paul-Victor
- Institute of Evolutionary Biology and Environmental Studies and Zürich-Basel Plant Science Center, University of Zürich, CH-8057 Zürich, Switzerland; and
| | - Christian Heichinger
- Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, CH-8008 Zürich, Switzerland
| | - Bernhard Schmid
- Institute of Evolutionary Biology and Environmental Studies and Zürich-Basel Plant Science Center, University of Zürich, CH-8057 Zürich, Switzerland; and
| | - Ueli Grossniklaus
- Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, CH-8008 Zürich, Switzerland
| | - Lindsay A. Turnbull
- Institute of Evolutionary Biology and Environmental Studies and Zürich-Basel Plant Science Center, University of Zürich, CH-8057 Zürich, Switzerland; and
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97
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Koornneef M, Meinke D. The development of Arabidopsis as a model plant. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 61:909-21. [PMID: 20409266 DOI: 10.1111/j.1365-313x.2009.04086.x] [Citation(s) in RCA: 220] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Twenty-five years ago, Arabidopsis thaliana emerged as the model organism of choice for research in plant biology. A consensus was reached about the need to focus on a single organism to integrate the classical disciplines of plant science with the expanding fields of genetics and molecular biology. Ten years after publication of its genome sequence, Arabidopsis remains the standard reference plant for all of biology. We reflect here on the major advances and shared resources that led to the extraordinary growth of the Arabidopsis research community. We also underscore the importance of continuing to expand and refine our detailed knowledge of Arabidopsis while seeking to appreciate the remarkable diversity that characterizes the plant kingdom.
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Affiliation(s)
- Maarten Koornneef
- Department of Plant Breeding and Genetics at the Max Planck Institute for Plant Breeding Research, Carl-von Linné Weg 10, Cologne, Germany.
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98
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Identification of a maize locus that modulates the hypersensitive defense response, using mutant-assisted gene identification and characterization. Genetics 2010; 184:813-25. [PMID: 20176981 DOI: 10.1534/genetics.109.111880] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Potentially useful naturally occurring genetic variation is often difficult to identify as the effects of individual genes are subtle and difficult to observe. In this study, a novel genetic technique called Mutant-Assisted Gene Identification and Characterization is used to identify naturally occurring loci modulating the hypersensitive defense response (HR) in maize. Mutant-Assisted Gene Identification and Characterization facilitates the identification of naturally occurring alleles underlying phenotypic variation from diverse germplasm, using a mutant phenotype as a "reporter." In this study the reporter phenotype was caused by a partially dominant autoactive disease resistance gene, Rp1-D21, which caused HR lesions to form spontaneously all over the plant. Here it is demonstrated that the Rp1-D21 phenotype is profoundly affected by genetic background. By crossing the Rp1-D21 gene into the IBM mapping population, it was possible to map and identify Hrml1 on chromosome 10, a locus responsible for modulating the HR phenotype conferred by Rp1-D21. Other loci with smaller effects were identified on chromosomes 1 and 9. These results demonstrate that Mutant-Assisted Gene Identification and Characterization is a viable approach for identifying naturally occurring useful genetic variation.
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99
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Ajjawi I, Lu Y, Savage LJ, Bell SM, Last RL. Large-scale reverse genetics in Arabidopsis: case studies from the Chloroplast 2010 Project. PLANT PHYSIOLOGY 2010; 152:529-40. [PMID: 19906890 PMCID: PMC2815874 DOI: 10.1104/pp.109.148494] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2009] [Accepted: 11/09/2009] [Indexed: 05/18/2023]
Abstract
Traditionally, phenotype-driven forward genetic plant mutant studies have been among the most successful approaches to revealing the roles of genes and their products and elucidating biochemical, developmental, and signaling pathways. A limitation is that it is time consuming, and sometimes technically challenging, to discover the gene responsible for a phenotype by map-based cloning or discovery of the insertion element. Reverse genetics is also an excellent way to associate genes with phenotypes, although an absence of detectable phenotypes often results when screening a small number of mutants with a limited range of phenotypic assays. The Arabidopsis Chloroplast 2010 Project (www.plastid.msu.edu) seeks synergy between forward and reverse genetics by screening thousands of sequence-indexed Arabidopsis (Arabidopsis thaliana) T-DNA insertion mutants for a diverse set of phenotypes. Results from this project are discussed that highlight the strengths and limitations of the approach. We describe the discovery of altered fatty acid desaturation phenotypes associated with mutants of At1g10310, previously described as a pterin aldehyde reductase in folate metabolism. Data are presented to show that growth, fatty acid, and chlorophyll fluorescence defects previously associated with antisense inhibition of synthesis of the family of acyl carrier proteins can be attributed to a single gene insertion in Acyl Carrier Protein4 (At4g25050). A variety of cautionary examples associated with the use of sequence-indexed T-DNA mutants are described, including the need to genotype all lines chosen for analysis (even when they number in the thousands) and the presence of tagged and untagged secondary mutations that can lead to the observed phenotypes.
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100
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Abstract
In plants, gametes are formed in multicellular haploid structures, termed gametophytes. The female gametophyte of most higher plants comprises seven cells, which develop from a single haploid spore through nuclear proliferation and subsequent cellularization. The female gametophytic cells differentiate into four distinct cell types, which play specific roles during fertilization and seed formation thereby ensuring reproductive success. In recent years many new techniques and cell type-specific marker lines have been established, making the female gametophyte an attractive system to study mechanisms of reproduction as well as cell specification. The following chapter describes a basic protocol for, first of all, recognizing a female gametophytic mutant and subsequently analyzing the phenotype on a morphological, molecular, and functional level.
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Affiliation(s)
- Ronny Völz
- Center for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
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