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Zhang Z, Huang Y, Dong Y, Ren Y, Du K, Wang J, Yang M. Effect of T-DNA Integration on Growth of Transgenic Populus × euramericana cv. Neva Underlying Field Stands. Int J Mol Sci 2023; 24:12952. [PMID: 37629133 PMCID: PMC10454723 DOI: 10.3390/ijms241612952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/05/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
Multigene cotransformation has been widely used in the study of genetic improvement in crops and trees. However, little is known about the unintended effects and causes of multigene cotransformation in poplars. To gain insight into the unintended effects of T-DNA integration during multigene cotransformation in field stands, here, three lines (A1-A3) of Populus × euramericana cv. Neva (PEN) carrying Cry1Ac-Cry3A-BADH genes and three lines (B1-B3) of PEN carrying Cry1Ac-Cry3A-NTHK1 genes were used as research objects, with non-transgenic PEN as the control. Experimental stands were established at three common gardens in three locations and next generation sequencing (NGS) was used to identify the insertion sites of exogenous genes in six transgenic lines. We compared the growth data of the transgenic and control lines for four consecutive years. The results demonstrated that the tree height and diameter at breast height (DBH) of transgenic lines were significantly lower than those of the control, and the adaptability of transgenic lines in different locations varied significantly. The genotype and the experimental environment showed an interaction effect. A total of seven insertion sites were detected in the six transgenic lines, with B3 having a double-site insertion and the other lines having single copies. There are four insertion sites in the gene region and three insertion sites in the intergenic region. Analysis of the bases near the insertion sites showed that AT content was higher than the average chromosome content in four of the seven insertion sites within 1000 bp. Transcriptome analysis suggested that the differential expression of genes related to plant hormone transduction and lignin synthesis might be responsible for the slow development of plant height and DBH in transgenic lines. This study provides an integrated analysis of the unintended effects of transgenic poplar, which will benefit the safety assessment and reasonable application of genetically modified trees.
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Affiliation(s)
- Zijie Zhang
- Institute of Forest Biotechnology, Forestry College, Hebei Agricultural University, Baoding 071000, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding 071000, China
| | - Yali Huang
- Institute of Forest Biotechnology, Forestry College, Hebei Agricultural University, Baoding 071000, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding 071000, China
| | - Yan Dong
- Institute of Forest Biotechnology, Forestry College, Hebei Agricultural University, Baoding 071000, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding 071000, China
| | - Yachao Ren
- Institute of Forest Biotechnology, Forestry College, Hebei Agricultural University, Baoding 071000, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding 071000, China
| | - Kejiu Du
- Institute of Forest Biotechnology, Forestry College, Hebei Agricultural University, Baoding 071000, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding 071000, China
| | - Jinmao Wang
- Institute of Forest Biotechnology, Forestry College, Hebei Agricultural University, Baoding 071000, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding 071000, China
| | - Minsheng Yang
- Institute of Forest Biotechnology, Forestry College, Hebei Agricultural University, Baoding 071000, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding 071000, China
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2
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Huang Z, 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 2023; 2686:131-162. [PMID: 37540357 DOI: 10.1007/978-1-0716-3299-4_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
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, modified high-efficiency thermal asymmetric interlaced PCR (mhiTAIL-PCR), and deep sequencing in the plant model Arabidopsis thaliana.
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Affiliation(s)
- Zhigang Huang
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha, China
| | - Thanh Theresa Dinh
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Elizabeth Luscher
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Shaofang Li
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Xigang Liu
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - So Youn Won
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Xuemei Chen
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA.
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Edwards B, Hornstein ED, Wilson NJ, Sederoff H. High-throughput detection of T-DNA insertion sites for multiple transgenes in complex genomes. BMC Genomics 2022; 23:685. [PMID: 36195834 PMCID: PMC9533571 DOI: 10.1186/s12864-022-08918-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 09/28/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genetic engineering of crop plants has been successful in transferring traits into elite lines beyond what can be achieved with breeding techniques. Introduction of transgenes originating from other species has conferred resistance to biotic and abiotic stresses, increased efficiency, and modified developmental programs. The next challenge is now to combine multiple transgenes into elite varieties via gene stacking to combine traits. Generating stable homozygous lines with multiple transgenes requires selection of segregating generations which is time consuming and labor intensive, especially if the crop is polyploid. Insertion site effects and transgene copy number are important metrics for commercialization and trait efficiency. RESULTS We have developed a simple method to identify the sites of transgene insertions using T-DNA-specific primers and high-throughput sequencing that enables identification of multiple insertion sites in the T1 generation of any crop transformed via Agrobacterium. We present an example using the allohexaploid oil-seed plant Camelina sativa to determine insertion site location of two transgenes. CONCLUSION This new methodology enables the early selection of desirable transgene location and copy number to generate homozygous lines within two generations.
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Affiliation(s)
- Brianne Edwards
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Eli D Hornstein
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Nathan J Wilson
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Heike Sederoff
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA.
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4
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Gong W, Zhou Y, Wang R, Wei X, Zhang L, Dai Y, Zhu Z. Analysis of T-DNA integration events in transgenic rice. JOURNAL OF PLANT PHYSIOLOGY 2021; 266:153527. [PMID: 34563791 DOI: 10.1016/j.jplph.2021.153527] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 09/13/2021] [Accepted: 09/13/2021] [Indexed: 06/13/2023]
Abstract
Agrobacterium-mediated plant transformation has been widely used for introducing transgene(s) into a plant genome and plant breeding. However, our understanding of T-DNA integration into rice genome remains limited relative to that in the model dicot Arabidopsis. To better elucidate the T-DNA integration into the rice genome, we investigated extensively the T-DNA ends and their flanking rice genomic sequences from two transgenic rice plants carrying Cowpea Trypsin Inhibitor (CpTI)-derived gene Signal-CpTI-KDEL (SCK) and Bacillus thuringiensis (BT) gene, respectively, by TAIL-PCR method. Analysis of the junction sequences between the T-DNA ends and rice genome DNA indicated that there were three joining patterns of microhomology, filler DNA sequences, and exact joining, and both the T-DNA ends tend to adopt identical manner to join the rice genome. After T-DNA integration, there were several variations of rice genomic sequences, including small deletions at the integration sites, superfluous DNA inserted between T-DNA and genome, and translocation of genomic DNA in the flanking regions. The translocation block could be from a noncontiguous region in the same chromosome or different chromosomes at the integration sites, and the originating position of the translocated block resulted in comparable deletion based on a cut/paste mechanism rather than a replication mechanism. Our study may lead to a better understand of T-DNA integration mechanism and facilitate functional genomic studies and further crop improvement.
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Affiliation(s)
- Wankui Gong
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, 455000, China.
| | - Yun Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Rui Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China; Public Health Emergency Center, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
| | - Xiaoli Wei
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Lei Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Yan Dai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Zhen Zhu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
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5
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The Mechanism of T-DNA Integration: Some Major Unresolved Questions. Curr Top Microbiol Immunol 2018; 418:287-317. [DOI: 10.1007/82_2018_98] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Kleinboelting N, Huep G, Weisshaar B. Enhancing the GABI-Kat Arabidopsis thaliana T-DNA Insertion Mutant Database by Incorporating Araport11 Annotation. PLANT & CELL PHYSIOLOGY 2017; 58:e7. [PMID: 28013277 PMCID: PMC5444572 DOI: 10.1093/pcp/pcw205] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 11/11/2016] [Indexed: 05/29/2023]
Abstract
SimpleSearch provides access to a database containing information about T-DNA insertion lines of the GABI-Kat collection of Arabidopsis thaliana mutants. These mutants are an important tool for reverse genetics, and GABI-Kat is the second largest collection of such T-DNA insertion mutants. Insertion sites were deduced from flanking sequence tags (FSTs), and the database contains information about mutant plant lines as well as insertion alleles. Here, we describe improvements within the interface (available at http://www.gabi-kat.de/db/genehits.php) and with regard to the database content that have been realized in the last five years. These improvements include the integration of the Araport11 genome sequence annotation data containing the recently updated A. thaliana structural gene descriptions, an updated visualization component that displays groups of insertions with very similar insertion positions, mapped confirmation sequences, and primers. The visualization component provides a quick way to identify insertions of interest, and access to improved data about the exact structure of confirmed insertion alleles. In addition, the database content has been extended by incorporating additional insertion alleles that were detected during the confirmation process, as well as by adding new FSTs that have been produced during continued efforts to complement gaps in FST availability. Finally, the current database content regarding predicted and confirmed insertion alleles as well as primer sequences has been made available as downloadable flat files.
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Affiliation(s)
- Nils Kleinboelting
- Center for Biotechnology and Department of Biology, Bielefeld University, Universitaetsstrasse 25, D-33615 Bielefeld, Germany
| | - Gunnar Huep
- Center for Biotechnology and Department of Biology, Bielefeld University, Universitaetsstrasse 25, D-33615 Bielefeld, Germany
| | - Bernd Weisshaar
- Center for Biotechnology and Department of Biology, Bielefeld University, Universitaetsstrasse 25, D-33615 Bielefeld, Germany
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Kleinboelting N, Huep G, Appelhagen I, Viehoever P, Li Y, Weisshaar B. The Structural Features of Thousands of T-DNA Insertion Sites Are Consistent with a Double-Strand Break Repair-Based Insertion Mechanism. MOLECULAR PLANT 2015; 8:1651-64. [PMID: 26343971 DOI: 10.1016/j.molp.2015.08.011] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 07/28/2015] [Accepted: 08/13/2015] [Indexed: 05/06/2023]
Abstract
Transformation by Agrobacterium tumefaciens, an important tool in modern plant research, involves the integration of T-DNA initially present on a plasmid in agrobacteria into the genome of plant cells. The process of attachment of the agrobacteria to plant cells and the transport of T-DNA into the cell and further to the nucleus has been well described. However, the exact mechanism of integration into the host's DNA is still unclear, although several models have been proposed. During confirmation of T-DNA insertion alleles from the GABI-Kat collection of Arabidopsis thaliana mutants, we have generated about 34,000 sequences from the junctions between inserted T-DNA and adjacent genome regions. Here, we describe the evaluation of this dataset with regard to existing models for T-DNA integration. The results suggest that integration into the plant genome is mainly mediated by the endogenous plant DNA repair machinery. The observed integration events showed characteristics highly similar to those of repair sites of double-strand breaks with respect to microhomology and deletion sizes. In addition, we describe unexpected integration events, such as large deletions and inversions at the integration site that are relevant for correct interpretation of results from T-DNA insertion mutants in reverse genetics experiments.
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Affiliation(s)
- Nils Kleinboelting
- Center for Biotechnology & Department of Biology, Bielefeld University, Universitaetsstrasse 25, 33615 Bielefeld, Germany
| | - Gunnar Huep
- Center for Biotechnology & Department of Biology, Bielefeld University, Universitaetsstrasse 25, 33615 Bielefeld, Germany
| | - Ingo Appelhagen
- Center for Biotechnology & Department of Biology, Bielefeld University, Universitaetsstrasse 25, 33615 Bielefeld, Germany
| | - Prisca Viehoever
- Center for Biotechnology & Department of Biology, Bielefeld University, Universitaetsstrasse 25, 33615 Bielefeld, Germany
| | - Yong Li
- Department of Medicine IV, University Hospital Freiburg, Berliner Allee 29, 79110 Freiburg, Germany
| | - Bernd Weisshaar
- Center for Biotechnology & Department of Biology, Bielefeld University, Universitaetsstrasse 25, 33615 Bielefeld, Germany.
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8
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Park SY, Vaghchhipawala Z, Vasudevan B, Lee LY, Shen Y, Singer K, Waterworth WM, Zhang ZJ, West CE, Mysore KS, Gelvin SB. Agrobacterium T-DNA integration into the plant genome can occur without the activity of key non-homologous end-joining proteins. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 81:934-46. [PMID: 25641249 DOI: 10.1111/tpj.12779] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 01/19/2015] [Accepted: 01/20/2015] [Indexed: 05/29/2023]
Abstract
Non-homologous end joining (NHEJ) is the major model proposed for Agrobacterium T-DNA integration into the plant genome. In animal cells, several proteins, including KU70, KU80, ARTEMIS, DNA-PKcs, DNA ligase IV (LIG4), Ataxia telangiectasia mutated (ATM), and ATM- and Rad3-related (ATR), play an important role in 'classical' (c)NHEJ. Other proteins, including histone H1 (HON1), XRCC1, and PARP1, participate in a 'backup' (b)NHEJ process. We examined transient and stable transformation frequencies of Arabidopsis thaliana roots mutant for numerous NHEJ and other related genes. Mutants of KU70, KU80, and the plant-specific DNA Ligase VI (LIG6) showed increased stable transformation susceptibility. However, these mutants showed transient transformation susceptibility similar to that of wild-type plants, suggesting enhanced T-DNA integration in these mutants. These results were confirmed using a promoter-trap transformation vector that requires T-DNA integration into the plant genome to activate a promoterless gusA (uidA) gene, by virus-induced gene silencing (VIGS) of Nicotiana benthamiana NHEJ genes, and by biochemical assays for T-DNA integration. No alteration in transient or stable transformation frequencies was detected with atm, atr, lig4, xrcc1, or parp1 mutants. However, mutation of parp1 caused high levels of T-DNA integration and transgene methylation. A double mutant (ku80/parp1), knocking out components of both NHEJ pathways, did not show any decrease in stable transformation or T-DNA integration. Thus, T-DNA integration does not require known NHEJ proteins, suggesting an alternative route for integration.
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Affiliation(s)
- So-Yon Park
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA; Plant Transformation Core Facility, University of Missouri, Columbia, MO, 65211, USA; Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, 24061, USA
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Taheri A, Gao P, Yu M, Cui D, Regan S, Parkin I, Gruber M. A landscape of hairy and twisted: hunting for new trichome mutants in the Saskatoon Arabidopsis T-DNA population. PLANT BIOLOGY (STUTTGART, GERMANY) 2015; 17:384-94. [PMID: 25348773 DOI: 10.1111/plb.12230] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 06/10/2014] [Indexed: 05/13/2023]
Abstract
A total of 88 new Arabidopsis lines with trichome variation were recovered by screening 49,200 single-seed descent T3 lines from the SK activation-tagged population and from a new 20,000-line T-DNA insertion population (called pAG). Trichome variant lines were classified into 12 distinct phenotype categories. Single or multiple T-DNA insertion sites were identified for 89% of these mutant lines. Alleles of the well-known trichome genes TRY, GL2 and TTG1 were recovered with atypical phenotype variation not reported previously. Moreover, atypical gene expression profiles were documented for two additional mutants specifying TRY and GL2 disruptions. In remaining mutants, ten lines were disrupted in genes coding for proteins not implicated in trichome development, five were disrupted in hypothetical proteins and 11 were disrupted in proteins with unknown function. The collection represents new opportunities for the plant biology community to define trichome development more precisely and to refine the function of individual trichome genes.
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Affiliation(s)
- A Taheri
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon, SK, Canada; College of Agriculture, Human and Natural Sciences, Tennessee State University, 3500 John A. Merritt Blvd., Nashville, TN, 37209-1561
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10
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Cheng X, Wang M, Lee HK, Tadege M, Ratet P, Udvardi M, Mysore KS, Wen J. An efficient reverse genetics platform in the model legume Medicago truncatula. THE NEW PHYTOLOGIST 2014; 201:1065-1076. [PMID: 24206427 DOI: 10.1111/nph.12575] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 10/01/2013] [Indexed: 05/07/2023]
Abstract
Medicago truncatula is one of the model species for legume studies. In an effort to develop legume genetics resources, > 21 700 Tnt1 retrotransposon insertion lines have been generated. To facilitate fast-growing needs in functional genomics, two reverse genetics approaches have been established: web-based database searching and PCR-based reverse screening. More than 840 genes have been reverse screened using the PCR-based approach over the past 6 yr to identify mutants in these genes. Overall, c. 84% (705 genes) success rate was achieved in identifying mutants with at least one Tnt1 insertion, of which c. 50% (358 genes) had three or more alleles. To demonstrate the utility of the two reverse genetics platforms, two mutant alleles were isolated for each of the two floral homeotic MADS-box genes, MtPISTILATA and MtAGAMOUS. Molecular and genetic analyses indicate that Tnt1 insertions in exons of both genes are responsible for the defects in floral organ development. In summary, we have developed two efficient reverse genetics platforms to facilitate functional characterization of M. truncatula genes.
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Affiliation(s)
- Xiaofei Cheng
- Division of Plant Biology, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Mingyi Wang
- Division of Plant Biology, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Hee-Kyung Lee
- Division of Plant Biology, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Million Tadege
- Division of Plant Biology, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Pascal Ratet
- Institut des Sciences du Végétal, CNRS, Avenue de la Terrasse, 91198, Gif sur Yvette Cedex, France
| | - Michael Udvardi
- Division of Plant Biology, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Kirankumar S Mysore
- Division of Plant Biology, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Jiangqi Wen
- Division of Plant Biology, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
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Huep G, Kleinboelting N, Weisshaar B. An easy-to-use primer design tool to address paralogous loci and T-DNA insertion sites in the genome of Arabidopsis thaliana. PLANT METHODS 2014; 10:28. [PMID: 25324895 PMCID: PMC4169229 DOI: 10.1186/1746-4811-10-28] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 09/09/2014] [Indexed: 05/22/2023]
Abstract
BACKGROUND More than 90% of the Arabidopsis thaliana genes are members of multigene families. DNA sequence similarities present in such related genes can cause trouble, e.g. when molecularly analysing mutant alleles of these genes. Also, flanking-sequence-tag (FST) based predictions of T-DNA insertion positions are often located within paralogous regions of the genome. In such cases, the prediction of the correct insertion site must include careful sequence analyses on the one hand and a paralog specific primer design for experimental confirmation of the prediction on the other hand. RESULTS GABI-Kat is a large A. thaliana insertion line resource, which uses in-house confirmation to provide highly reliable access to T-DNA insertion alleles. To offer trustworthy mutant alleles of paralogous loci, we considered multiple insertion site predictions for single FSTs and implemented this 1-to-N relation in our database. The resulting paralogous predictions were addressed experimentally and the correct insertion locus was identified in most cases, including cases in which there were multiple predictions with identical prediction scores. A newly developed primer design tool that takes paralogous regions into account was developed to streamline the confirmation process for paralogs. The tool is suitable for all parts of the genome and is freely available at the GABI-Kat website. Although the tool was initially designed for the analysis of T-DNA insertion mutants, it can be used for any experiment that requires locus-specific primers for the A. thaliana genome. It is easy to use and also able to design amplimers with two genome-specific primers as required for genotyping segregating families of insertion mutants when looking for homozygous offspring. CONCLUSIONS The paralog-aware confirmation process significantly improved the reliability of the insertion site assignment when paralogous regions of the genome were affected. An automatic online primer design tool that incorporates experience from the in-house confirmation of T-DNA insertion lines has been made available. It provides easy access to primers for the analysis of T-DNA insertion alleles, but it is also beneficial for other applications as well.
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Affiliation(s)
- Gunnar Huep
- Center for Biotechnology & Department of Biology, Bielefeld University, Universitaetsstrasse 25, D-33615 Bielefeld, Germany
| | - Nils Kleinboelting
- Center for Biotechnology & Department of Biology, Bielefeld University, Universitaetsstrasse 25, D-33615 Bielefeld, Germany
| | - Bernd Weisshaar
- Center for Biotechnology & Department of Biology, Bielefeld University, Universitaetsstrasse 25, D-33615 Bielefeld, Germany
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12
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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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13
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Matvienko M, Kozik A, Froenicke L, Lavelle D, Martineau B, Perroud B, Michelmore R. Consequences of normalizing transcriptomic and genomic libraries of plant genomes using a duplex-specific nuclease and tetramethylammonium chloride. PLoS One 2013; 8:e55913. [PMID: 23409088 PMCID: PMC3568094 DOI: 10.1371/journal.pone.0055913] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Accepted: 01/04/2013] [Indexed: 12/22/2022] Open
Abstract
Several applications of high throughput genome and transcriptome sequencing would benefit from a reduction of the high-copy-number sequences in the libraries being sequenced and analyzed, particularly when applied to species with large genomes. We adapted and analyzed the consequences of a method that utilizes a thermostable duplex-specific nuclease for reducing the high-copy components in transcriptomic and genomic libraries prior to sequencing. This reduces the time, cost, and computational effort of obtaining informative transcriptomic and genomic sequence data for both fully sequenced and non-sequenced genomes. It also reduces contamination from organellar DNA in preparations of nuclear DNA. Hybridization in the presence of 3 M tetramethylammonium chloride (TMAC), which equalizes the rates of hybridization of GC and AT nucleotide pairs, reduced the bias against sequences with high GC content. Consequences of this method on the reduction of high-copy and enrichment of low-copy sequences are reported for Arabidopsis and lettuce.
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Affiliation(s)
- Marta Matvienko
- Genome Center, University of California Davis, Davis, California, United States of America
| | - Alexander Kozik
- Genome Center, University of California Davis, Davis, California, United States of America
| | - Lutz Froenicke
- Genome Center, University of California Davis, Davis, California, United States of America
| | - Dean Lavelle
- Genome Center, University of California Davis, Davis, California, United States of America
| | - Belinda Martineau
- Genome Center, University of California Davis, Davis, California, United States of America
| | - Bertrand Perroud
- Genome Center, University of California Davis, Davis, California, United States of America
| | - Richard Michelmore
- Genome Center, University of California Davis, Davis, California, United States of America
- Departments of Plant Sciences, Molecular and Cellular Biology, and Medical Microbiology and Immunology, University of California Davis, Davis, California, United States of America
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14
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Monroe-Augustus M, Ramón NM, Ratzel SE, Lingard MJ, Christensen SE, Murali C, Bartel B. Matrix proteins are inefficiently imported into Arabidopsis peroxisomes lacking the receptor-docking peroxin PEX14. PLANT MOLECULAR BIOLOGY 2011; 77:1-15. [PMID: 21553312 PMCID: PMC3529590 DOI: 10.1007/s11103-011-9782-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Accepted: 04/24/2011] [Indexed: 05/24/2023]
Abstract
Mutations in peroxisome biogenesis proteins (peroxins) can lead to developmental deficiencies in various eukaryotes. PEX14 and PEX13 are peroxins involved in docking cargo-receptor complexes at the peroxisomal membrane, thus aiding in the transport of the cargo into the peroxisomal matrix. Genetic screens have revealed numerous Arabidopsis thaliana peroxins acting in peroxisomal matrix protein import; the viable alleles isolated through these screens are generally partial loss-of-function alleles, whereas null mutations that disrupt delivery of matrix proteins to peroxisomes can confer embryonic lethality. In this study, we used forward and reverse genetics in Arabidopsis to isolate four pex14 alleles. We found that all four alleles conferred reduced PEX14 mRNA levels and displayed physiological and molecular defects suggesting reduced but not abolished peroxisomal matrix protein import. The least severe pex14 allele, pex14-3, accumulated low levels of a C-terminally truncated PEX14 product that retained partial function. Surprisingly, even the severe pex14-2 allele, which lacked detectable PEX14 mRNA and PEX14 protein, was viable, fertile, and displayed residual peroxisome matrix protein import. As pex14 plants matured, import improved. Together, our data indicate that PEX14 facilitates, but is not essential for peroxisomal matrix protein import in plants.
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Affiliation(s)
- Melanie Monroe-Augustus
- Department of Biochemistry and Cell Biology, Rice University, 6100 South Main Street, Houston, TX 77005, USA
| | - Naxhiely Martínez Ramón
- Department of Biochemistry and Cell Biology, Rice University, 6100 South Main Street, Houston, TX 77005, USA
| | - Sarah E. Ratzel
- Department of Biochemistry and Cell Biology, Rice University, 6100 South Main Street, Houston, TX 77005, USA
| | - Matthew J. Lingard
- Department of Biochemistry and Cell Biology, Rice University, 6100 South Main Street, Houston, TX 77005, USA. 700 Chesterfield Parkway, Chesterfield, MO 63017, USA
| | - Sarah E. Christensen
- Department of Biochemistry and Cell Biology, Rice University, 6100 South Main Street, Houston, TX 77005, USA
| | - Chaya Murali
- Department of Biochemistry and Cell Biology, Rice University, 6100 South Main Street, Houston, TX 77005, USA
| | - Bonnie Bartel
- Department of Biochemistry and Cell Biology, Rice University, 6100 South Main Street, Houston, TX 77005, USA
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15
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Ruiz-Rojas JJ, Sargent DJ, Shulaev V, Dickerman AW, Pattison J, Holt SH, Ciordia A, Veilleux RE. SNP discovery and genetic mapping of T-DNA insertional mutants in Fragaria vesca L. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 121:449-463. [PMID: 20349033 DOI: 10.1007/s00122-010-1322-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2009] [Accepted: 03/05/2010] [Indexed: 05/29/2023]
Abstract
As part of a program to develop forward and reverse genetics platforms in the diploid strawberry [Fragaria vesca L.; (2n = 2x = 14)] we have generated insertional mutant lines by T-DNA mutagenesis using pCAMBIA vectors. To characterize the T-DNA insertion sites of a population of 108 unique single copy mutants, we utilized thermal asymmetric interlaced PCR (hiTAIL-PCR) to amplify the flanking region surrounding either the left or right border of the T-DNA. Bioinformatics analysis of flanking sequences revealed little preference for insertion site with regard to G/C content; left borders tended to retain more of the plasmid backbone than right borders. Primers were developed from F. vesca flanking sequences to attempt to amplify products from both parents of the reference F. vesca 815 x F. bucharica 601 mapping population. Polymorphism occurred as: presence/absence of an amplification product for 16 primer pairs and different size products for 12 primer pairs, For 46 mutants, where polymorphism was not found by PCR, the amplification products were sequenced to reveal SNP polymorphism. A cleaved amplified polymorphic sequence/derived cleaved amplified polymorphism sequence (CAPS/dCAPS) strategy was then applied to find restriction endonuclease recognition sites in one of the parental lines to map the SNP position of 74 of the T-DNA insertion lines. BLAST search of flanking regions against GenBank revealed that 46 of 108 flanking sequences were close to presumed strawberry genes related to annotated genes from other plants.
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Affiliation(s)
- J J Ruiz-Rojas
- Department of Horticulture, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
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16
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O'Malley RC, Ecker JR. Linking genotype to phenotype using the Arabidopsis unimutant collection. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 61:928-40. [PMID: 20409268 DOI: 10.1111/j.1365-313x.2010.04119.x] [Citation(s) in RCA: 129] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The large collections of Arabidopsis thaliana sequence-indexed T-DNA insertion mutants are among the most important resources to emerge from the sequencing of the genome. Several laboratories around the world have used the Arabidopsis reference genome sequence to map T-DNA flanking sequence tags (FST) for over 325,000 T-DNA insertion lines. Over the past decade, phenotypes identified with T-DNA-induced mutants have played a critical role in advancing both basic and applied plant research. These widely used mutants are an invaluable tool for direct interrogation of gene function. However, most lines are hemizygous for the insertion, necessitating a genotyping step to identify homozygous plants for the quantification of phenotypes. This situation has limited the application of these collections for genome-wide screens. Isolating multiple homozygous insert lines for every gene in the genome would make it possible to systematically test the phenotypic consequence of gene loss under a wide variety of conditions. One major obstacle to achieving this goal is that 12% of genes have no insertion and 8% are only represented by a single allele. Generation of additional mutations to achieve full genome coverage has been slow and expensive since each insertion is sequenced one at a time. Recent advances in high-throughput sequencing technology open up a potentially faster and cost-effective means to create new, very large insertion mutant populations for plants or animals. With the combination of new tools for genome-wide studies and emerging phenotyping platforms, these sequence-indexed mutant collections are poised to have a larger impact on our understanding of gene function.
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Affiliation(s)
- Ronan C O'Malley
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92307, USA
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17
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Gelvin SB. Plant proteins involved in Agrobacterium-mediated genetic transformation. ANNUAL REVIEW OF PHYTOPATHOLOGY 2010; 48:45-68. [PMID: 20337518 DOI: 10.1146/annurev-phyto-080508-081852] [Citation(s) in RCA: 134] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Agrobacterium species genetically transform plants by transferring a region of plasmid DNA, T-DNA, into host plant cells. The bacteria also transfer several virulence effector proteins. T-DNA and virulence proteins presumably form T-complexes within the plant cell. Super-T-complexes likely also form by interaction of plant-encoded proteins with T-complexes. These protein-nucleic acid complexes traffic through the plant cytoplasm, enter the nucleus, and eventually deliver T-DNA to plant chromatin. Integration of T-DNA into the plant genome establishes a permanent transformation event, permitting stable expression of T-DNA-encoded transgenes. The transformation process is complex and requires participation of numerous plant proteins. This review discusses our current knowledge of plant proteins that contribute to Agrobacterium-mediated transformation, the roles these proteins play in the transformation process, and the modern technologies that have been employed to elucidate the cell biology of transformation.
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Affiliation(s)
- Stanton B Gelvin
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907-1392, USA.
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18
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Papdi C, Leung J, Joseph MP, Salamó IP, Szabados L. Genetic screens to identify plant stress genes. Methods Mol Biol 2010; 639:121-139. [PMID: 20387043 DOI: 10.1007/978-1-60761-702-0_7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
A powerful means to learn about gene functions in a developmental or physiological context in an organism is to isolate the corresponding mutants with altered phenotypes. Diverse mutagenic agents, including chemical and biological, have been widely employed, and each comes with its own advantages and inconveniences. For Arabidopsis thaliana, whose genome sequence is publicly available, the reliance of reverse genetics to understand the relevant roles of genes particularly those coding for proteins in growth and development is now a common practice. Identifying multiple alleles at each locus is important because they can potentially reveal epistatic relationship in a signaling pathway or components belonging to a common signaling complex by their synergistic or even allele-specific enhancement of the phenotypic severity. In this article, we describe mutagenesis by using ethyl methanesulfonate (EMS) and transfer (T)-DNA-mediated insertion or activation tagging as applied to the most widely used genetic plant model A. thaliana. Also, we demonstrate the utility of several genetic screening approaches to dissect adaptive responses to various abiotic stresses.
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Affiliation(s)
- Csaba Papdi
- Institute of Plant Biology, Biological Research Center, Szeged, Hungary
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19
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Youseff BH, Dougherty JA, Rappleye CA. Reverse genetics through random mutagenesis in Histoplasma capsulatum. BMC Microbiol 2009; 9:236. [PMID: 19919692 PMCID: PMC2781022 DOI: 10.1186/1471-2180-9-236] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Accepted: 11/17/2009] [Indexed: 11/10/2022] Open
Abstract
Background The dimorphic fungal pathogen Histoplasma capsulatum causes respiratory and systemic disease in humans and other mammals. Progress in understanding the mechanisms underlying the biology and the pathogenesis of Histoplasma has been hindered by a shortage of methodologies for mutating a gene of interest. Results We describe a reverse genetics process that combines the random mutagenesis of Agrobacterium-mediated transformation with screening techniques to identify targeted gene disruptions in a collection of insertion mutants. Isolation of the desired mutant is accomplished by arraying individual clones from a pool and employing a PCR-addressing method. Application of this procedure facilitated the isolation of a cbp1 mutant in a North American type 2 strain, a Histoplasma strain recalcitrant to gene knock-outs through homologous recombination. Optimization of cryopreservation conditions allows pools of mutants to be banked for later analysis and recovery of targeted mutants. Conclusion This methodology improves our ability to isolate mutants in targeted genes, thereby facilitating the molecular genetic analysis of Histoplasma biology. The procedures described are widely applicable to many fungal systems and will be of particular interest to those for which homologous recombination techniques are inefficient or do not currently exist.
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Affiliation(s)
- Brian H Youseff
- Departments of Microbiology and Internal Medicine, The Center for Microbial Interface Biology, Ohio State University, Columbus, OH 43210, USA.
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20
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Papdi C, Joseph MP, Salamó IP, Vidal S, Szabados L. Genetic technologies for the identification of plant genes controlling environmental stress responses. FUNCTIONAL PLANT BIOLOGY : FPB 2009; 36:696-720. [PMID: 32688681 DOI: 10.1071/fp09047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2009] [Accepted: 06/11/2009] [Indexed: 06/11/2023]
Abstract
Abiotic conditions such as light, temperature, water availability and soil parameters determine plant growth and development. The adaptation of plants to extreme environments or to sudden changes in their growth conditions is controlled by a well balanced, genetically determined signalling system, which is still far from being understood. The identification and characterisation of plant genes which control responses to environmental stresses is an essential step to elucidate the complex regulatory network, which determines stress tolerance. Here, we review the genetic approaches, which have been used with success to identify plant genes which control responses to different abiotic stress factors. We describe strategies and concepts for forward and reverse genetic screens, conventional and insertion mutagenesis, TILLING, gene tagging, promoter trapping, activation mutagenesis and cDNA library transfer. The utility of the various genetic approaches in plant stress research we review is illustrated by several published examples.
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Affiliation(s)
- Csaba Papdi
- Institute of Plant Biology, Biological Research Centre, 6726-Szeged, Temesvári krt. 62, Hungary
| | - Mary Prathiba Joseph
- Institute of Plant Biology, Biological Research Centre, 6726-Szeged, Temesvári krt. 62, Hungary
| | - Imma Pérez Salamó
- Institute of Plant Biology, Biological Research Centre, 6726-Szeged, Temesvári krt. 62, Hungary
| | - Sabina Vidal
- Facultad de Ciencias, Universidad de la República, Iguá 4225, CP 11400, Montevideo, Uruguay
| | - László Szabados
- Institute of Plant Biology, Biological Research Centre, 6726-Szeged, Temesvári krt. 62, Hungary
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21
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Robinson SJ, Tang LH, Mooney BAG, McKay SJ, Clarke WE, Links MG, Karcz S, Regan S, Wu YY, Gruber MY, Cui D, Yu M, Parkin IAP. An archived activation tagged population of Arabidopsis thaliana to facilitate forward genetics approaches. BMC PLANT BIOLOGY 2009; 9:101. [PMID: 19646253 PMCID: PMC3091532 DOI: 10.1186/1471-2229-9-101] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2009] [Accepted: 07/31/2009] [Indexed: 05/18/2023]
Abstract
BACKGROUND Functional genomics tools provide researchers with the ability to apply high-throughput techniques to determine the function and interaction of a diverse range of genes. Mutagenized plant populations are one such resource that facilitate gene characterisation. They allow complex physiological responses to be correlated with the expression of single genes in planta, through either reverse genetics where target genes are mutagenized to assay the affect, or through forward genetics where populations of mutant lines are screened to identify those whose phenotype diverges from wild type for a particular trait. One limitation of these types of populations is the prevalence of gene redundancy within plant genomes, which can mask the affect of individual genes. Activation or enhancer populations, which not only provide knock-out but also dominant activation mutations, can facilitate the study of such genes. RESULTS We have developed a population of almost 50,000 activation tagged A. thaliana lines that have been archived as individual lines to the T3 generation. The population is an excellent tool for both reverse and forward genetic screens and has been used successfully to identify a number of novel mutants. Insertion site sequences have been generated and mapped for 15,507 lines to enable further application of the population, while providing a clear distribution of T-DNA insertions across the genome. The population is being screened for a number of biochemical and developmental phenotypes, provisional data identifying novel alleles and genes controlling steps in proanthocyanidin biosynthesis and trichome development is presented. CONCLUSION This publicly available population provides an additional tool for plant researcher's to assist with determining gene function for the many as yet uncharacterised genes annotated within the Arabidopsis genome sequence http://aafc-aac.usask.ca/FST. The presence of enhancer elements on the inserted T-DNA molecule allows both knock-out and dominant activation phenotypes to be identified for traits of interest.
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Affiliation(s)
- Stephen J Robinson
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Place, Saskatoon, S7N 0X2, Canada
| | - Lily H Tang
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Place, Saskatoon, S7N 0X2, Canada
| | - Brent AG Mooney
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Place, Saskatoon, S7N 0X2, Canada
| | - Sheldon J McKay
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Place, Saskatoon, S7N 0X2, Canada
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Wayne E Clarke
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Place, Saskatoon, S7N 0X2, Canada
| | - Matthew G Links
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Place, Saskatoon, S7N 0X2, Canada
| | - Steven Karcz
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Place, Saskatoon, S7N 0X2, Canada
| | - Sharon Regan
- Department of Biology, Biosciences Complex, Queens University, Kingston, Ontario, K7L 3N6, Canada
| | - Yun-Yun Wu
- Department of Biology, Biosciences Complex, Queens University, Kingston, Ontario, K7L 3N6, Canada
| | - Margaret Y Gruber
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Place, Saskatoon, S7N 0X2, Canada
| | - Dejun Cui
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Place, Saskatoon, S7N 0X2, Canada
| | - Min Yu
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Place, Saskatoon, S7N 0X2, Canada
| | - Isobel AP Parkin
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Place, Saskatoon, S7N 0X2, Canada
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22
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Ulker B, Peiter E, Dixon DP, Moffat C, Capper R, Bouché N, Edwards R, Sanders D, Knight H, Knight MR. Getting the most out of publicly available T-DNA insertion lines. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2008; 56:665-77. [PMID: 18644000 DOI: 10.1111/j.1365-313x.2008.03608.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
In the course of several different projects, we came to realize that there is a significant amount of untapped potential in the publicly available T-DNA insertion lines. In addition to the GABI-Kat lines, which were designed specifically for activation tagging, lines from the SAIL and FLAGdb collections are also useful for this purpose. As well as the 35S promoter chosen for activation tagging in GABI-Kat lines, we found that the 1'2' bidirectional promoter is capable of activating expression of flanking genomic sequences in both GABI-Kat and SAIL lines. Thus these lines have added potential for activation tagging. We also show that these lines are capable of generating antisense transcripts and so have the potential to be used for suppression (loss/reduction of function) studies. By virtue of weak terminator sequences in some T-DNA constructs, transcript read-through from selectable markers is also possible, which again has the potential to be exploited in activation/suppression studies. Finally, we show that, by selecting and characterizing lines in which the T-DNA insertions are present specifically within introns of a target gene, an allelic series of mutants with varying levels of reduced expression can be generated, due to differences in efficiency of intron splicing. Taken together, our analyses demonstrate that there is a wealth of untapped potential within existing insertion lines for studies on gene function, and the effective exploitation of these resources is discussed.
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MESH Headings
- Antisense Elements (Genetics)
- Arabidopsis/genetics
- DNA, Bacterial/genetics
- DNA, Plant/genetics
- Gene Expression Regulation, Plant
- Gene Silencing
- Genes, Plant
- Genetic Vectors
- Genome, Plant
- Mutagenesis, Insertional/methods
- Plants, Genetically Modified/genetics
- Promoter Regions, Genetic
- Sequence Analysis, DNA
- Transcription, Genetic
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Affiliation(s)
- Bekir Ulker
- School of Biological and Biomedical Sciences, Durham University, South Road, Durham DH1 3LE, UK
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23
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Meinke D, Muralla R, Sweeney C, Dickerman A. Identifying essential genes in Arabidopsis thaliana. TRENDS IN PLANT SCIENCE 2008; 13:483-91. [PMID: 18684657 DOI: 10.1016/j.tplants.2008.06.003] [Citation(s) in RCA: 163] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2008] [Revised: 06/06/2008] [Accepted: 06/10/2008] [Indexed: 05/20/2023]
Abstract
Eight years after publication of the Arabidopsis genome sequence and two years before completing the first phase of an international effort to characterize the function of every Arabidopsis gene, plant biologists remain unable to provide a definitive answer to the following basic question: what is the minimal gene set required for normal growth and development? The purpose of this review is to summarize different strategies employed to identify essential genes in Arabidopsis, an important component of the minimal gene set in plants, to present an overview of the datasets and specific genes identified to date, and to discuss the prospects for future saturation of this important class of genes. The long-term goal of this collaborative effort is to facilitate basic research in plant biology and complement ongoing research with other model organisms.
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Affiliation(s)
- David Meinke
- Department of Botany, Oklahoma State University, Stillwater, OK 74078, USA.
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24
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Gelvin SB, Kim SI. Effect of chromatin upon Agrobacterium T-DNA integration and transgene expression. ACTA ACUST UNITED AC 2007; 1769:410-21. [PMID: 17544520 DOI: 10.1016/j.bbaexp.2007.04.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2007] [Revised: 04/09/2007] [Accepted: 04/12/2007] [Indexed: 11/22/2022]
Abstract
Agrobacterium tumefaciens transfers DNA (T-DNA) to plant cells, where it integrates into the plant genome. Little is known about how T-DNA chooses sites within the plant chromosome for integration. Previous studies indicated that T-DNA preferentially integrates into transcriptionally active regions of the genome, especially in 5'-promoter regions. This would make sense, considering that chromatin structure surrounding active promoters may be more "open" and accessible to foreign DNA. However, recent results suggest that this seemingly non-random pattern of integration may be an artifact of selection bias, and that T-DNA may integrate more randomly than previously thought. In this chapter, I discuss the history of these observations and the role chromatin proteins may play in T-DNA integration and transgene expression. Understanding how chromatin conformation may influence T-DNA integration will be important in developing strategies for reproducible and stable transgene expression, and for gene targeting.
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Affiliation(s)
- Stanton B Gelvin
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907-1392, USA.
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25
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Zhang J, Guo D, Chang Y, You C, Li X, Dai X, Weng Q, Zhang J, Chen G, Li X, Liu H, Han B, Zhang Q, Wu C. Non-random distribution of T-DNA insertions at various levels of the genome hierarchy as revealed by analyzing 13 804 T-DNA flanking sequences from an enhancer-trap mutant library. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2007; 49:947-59. [PMID: 17253985 DOI: 10.1111/j.1365-313x.2006.03001.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
We isolated 13 804 T-DNA flanking sequence tags (FSTs) from a T-DNA insertion library of rice. A comprehensive analysis of the 13 804 FSTs revealed a number of features demonstrating a highly non-random distribution of the T-DNA insertions in the rice genome: T-DNA insertions were biased towards large chromosomes, not only in the absolute number of insertions but also in the relative density; within chromosomes the insertions occurred more densely in the distal ends, and less densely in the centromeric regions; the distribution of the T-DNA insertions was highly correlated with that of full-length cDNAs, but the correlations were highly heterogeneous among the chromosomes; T-DNA insertions strongly disfavored transposable element (TE)-related sequences, but favored genic sequences with a strong bias toward the 5' upstream and 3' downstream regions of the genes; T-DNA insertions preferentially occurred among the various classes of functional genes, such that the numbers of insertions were in excess in certain functional categories but were deficient in other categories. The analysis of DNA sequence compositions around the T-DNA insertion sites also revealed several prominent features, including an elevated bendability from -200 to 200 bp relative to the insertion sites, an inverse relationship between the GC and TA skews, and reversed GC and TA skews in sequences upstream and downstream of the insertion sites, with both GC and TA skews equal to zero at the insertion sites. It was estimated that 365 380 insertions are needed to saturate the genome with P = 0.95, and that the 45 441 FSTs that have been isolated so far by various groups tagged 14 287 of the 42 653 non-TE related genes.
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Affiliation(s)
- Jian Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
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26
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Galbraith DW. DNA Microarray Analyses in Higher Plants. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2006; 10:455-73. [PMID: 17233557 DOI: 10.1089/omi.2006.10.455] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
DNA microarrays were originally devised and described as a convenient technology for the global analysis of plant gene expression. Over the past decade, their use has expanded enormously to cover all kingdoms of living organisms. At the same time, the scope of applications of microarrays has increased beyond expression analyses, with plant genomics playing a leadership role in the on-going development of this technology. As the field has matured, the rate-limiting step has moved from that of the technical process of data generation to that of data analysis. We currently face major problems in dealing with the accumulating datasets, not simply with respect to how to archive, access, and process the huge amounts of data that have been and are being produced, but also in determining the relative quality of the different datasets. A major recognized concern is the appropriate use of statistical design in microarray experiments, without which the datasets are rendered useless. A vigorous area of current research involves the development of novel statistical tools specifically for microarray experiments. This article describes, in a necessarily selective manner, the types of platforms currently employed in microarray research and provides an overview of recent activities using these platforms in plant biology.
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Affiliation(s)
- David W Galbraith
- Department of Plant Sciences, Bio5 Institute, University of Arizona, Tucson, Arizona 85721, USA.
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