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Weßling R, Epple P, Altmann S, He Y, Yang L, Henz SR, McDonald N, Wiley K, Bader KC, Gläßer C, Mukhtar MS, Haigis S, Ghamsari L, Stephens AE, Ecker JR, Vidal M, Jones JDG, Mayer KFX, Ver Loren van Themaat E, Weigel D, Schulze-Lefert P, Dangl JL, Panstruga R, Braun P. Convergent targeting of a common host protein-network by pathogen effectors from three kingdoms of life. Cell Host Microbe 2015; 16:364-75. [PMID: 25211078 DOI: 10.1016/j.chom.2014.08.004] [Citation(s) in RCA: 269] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Revised: 06/27/2014] [Accepted: 08/14/2014] [Indexed: 01/31/2023]
Abstract
While conceptual principles governing plant immunity are becoming clear, its systems-level organization and the evolutionary dynamic of the host-pathogen interface are still obscure. We generated a systematic protein-protein interaction network of virulence effectors from the ascomycete pathogen Golovinomyces orontii and Arabidopsis thaliana host proteins. We combined this data set with corresponding data for the eubacterial pathogen Pseudomonas syringae and the oomycete pathogen Hyaloperonospora arabidopsidis. The resulting network identifies host proteins onto which intraspecies and interspecies pathogen effectors converge. Phenotyping of 124 Arabidopsis effector-interactor mutants revealed a correlation between intraspecies and interspecies convergence and several altered immune response phenotypes. Several effectors and the most heavily targeted host protein colocalized in subnuclear foci. Products of adaptively selected Arabidopsis genes are enriched for interactions with effector targets. Our data suggest the existence of a molecular host-pathogen interface that is conserved across Arabidopsis accessions, while evolutionary adaptation occurs in the immediate network neighborhood of effector targets.
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Affiliation(s)
- Ralf Weßling
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, D-50829, Germany
| | - Petra Epple
- Howard Hughes Medical Institute and Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Stefan Altmann
- Technische Universität München (TUM), Center for Life and Food Sciences Weihenstephan, Department for Plant Systems Biology, D-85354 Freising, Germany
| | - Yijian He
- Howard Hughes Medical Institute and Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Li Yang
- Howard Hughes Medical Institute and Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Stefan R Henz
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany
| | - Nathan McDonald
- Howard Hughes Medical Institute and Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kristin Wiley
- Howard Hughes Medical Institute and Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kai Christian Bader
- Plant Genome and Systems Biology, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
| | - Christine Gläßer
- Plant Genome and Systems Biology, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
| | - M Shahid Mukhtar
- Howard Hughes Medical Institute and Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Biology, University of Alabama Birmingham, Birmingham, AL 35294, USA
| | - Sabine Haigis
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, D-50829, Germany
| | - Lila Ghamsari
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana Farber Cancer Institute, and Harvard Medical School, Department of Genetics, Boston, MA 02215, USA
| | - Amber E Stephens
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, D-50829, Germany
| | - Joseph R Ecker
- Howard Hughes Medical Institute and Salk Institute for Biological Studies, Plant Biology Lab, La Jolla, CA 92037, USA
| | - Marc Vidal
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana Farber Cancer Institute, and Harvard Medical School, Department of Genetics, Boston, MA 02215, USA
| | - Jonathan D G Jones
- The Sainsbury Laboratory, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
| | - Klaus F X Mayer
- Plant Genome and Systems Biology, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
| | - Emiel Ver Loren van Themaat
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, D-50829, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany
| | - Paul Schulze-Lefert
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, D-50829, Germany
| | - Jeffery L Dangl
- Howard Hughes Medical Institute and Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Carolina Center for Genome Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Ralph Panstruga
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, D-50829, Germany; Rheinisch Westfälische Technische Hochschule (RWTH) Aachen University, Institute for Biology I, Unit of Plant Molecular Cell Biology, D-52074 Aachen, Germany.
| | - Pascal Braun
- Technische Universität München (TUM), Center for Life and Food Sciences Weihenstephan, Department for Plant Systems Biology, D-85354 Freising, Germany.
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Cheng J, Salentijn EMJ, Huang B, Denneboom C, Qi W, Dechesne AC, Krens FA, Visser RGF, van Loo EN. Detection of induced mutations in CaFAD2 genes by next-generation sequencing leading to the production of improved oil composition in Crambe abyssinica. PLANT BIOTECHNOLOGY JOURNAL 2015; 13:471-81. [PMID: 25393152 DOI: 10.1111/pbi.12269] [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: 04/11/2014] [Revised: 08/10/2014] [Accepted: 08/20/2014] [Indexed: 05/09/2023]
Abstract
Crambe abyssinica is a hexaploid oil crop for industrial applications. An increase of erucic acid (C22:1) and reduction of polyunsaturated fatty acid (PUFA) contents in crambe oil is a valuable improvement. An increase in oleic acid (C18:1), a reduction in PUFA and possibly an increase in C22:1 can be obtained by down-regulating the expression of fatty acid desaturase2 genes (CaFAD2), which code for the enzyme that converts C18:1 into C18:2. We conducted EMS-mutagenesis in crambe, followed by Illumina sequencing, to screen mutations in three expressed CaFAD2 genes. Two novel analysis strategies were used to detect mutation sites. In the first strategy, mutation detection targeted specific sequence motifs. In the second strategy, every nucleotide position in a CaFAD2 fragment was tested for the presence of mutations. Seventeen novel mutations were detected in 1100 one-dimensional pools (11 000 individuals) in three expressed CaFAD2 genes, including non-sense mutations and mis-sense mutations in CaFAD2-C1, -C2 and -C3. The homozygous non-sense mutants for CaFAD2-C3 resulted in a 25% higher content of C18:1 and 25% lower content of PUFA compared to the wild type. The mis-sense mutations only led to small changes in oil composition. Concluding, targeted mutation detection using NGS in a polyploid was successfully applied and it was found that a non-sense mutation in even a single CaFAD2 gene can lead to changes in crambe oil composition. Stacking the mutations in different CaFAD2 may gain additional changes in C18:1 and PUFA contents.
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Affiliation(s)
- Jihua Cheng
- Wageningen UR Plant Breeding, Wageningen, The Netherlands; College of Life Science, Hubei University, Hubei, China
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Galindo-González L, Pinzón-Latorre D, Bergen EA, Jensen DC, Deyholos MK. Ion Torrent sequencing as a tool for mutation discovery in the flax (Linum usitatissimum L.) genome. PLANT METHODS 2015; 11:19. [PMID: 25788971 PMCID: PMC4363359 DOI: 10.1186/s13007-015-0062-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Accepted: 03/02/2015] [Indexed: 05/29/2023]
Abstract
BACKGROUND Detection of induced mutations is valuable for inferring gene function and for developing novel germplasm for crop improvement. Many reverse genetics approaches have been developed to identify mutations in genes of interest within a mutagenized population, including some approaches that rely on next-generation sequencing (e.g. exome capture, whole genome resequencing). As an alternative to these genome or exome-scale methods, we sought to develop a scalable and efficient method for detection of induced mutations that could be applied to a small number of target genes, using Ion Torrent technology. We developed this method in flax (Linum usitatissimum), to demonstrate its utility in a crop species. RESULTS We used an amplicon-based approach in which DNA samples from an ethyl methanesulfonate (EMS)-mutagenized population were pooled and used as template in PCR reactions to amplify a region of each gene of interest. Barcodes were incorporated during PCR, and the pooled amplicons were sequenced using an Ion Torrent PGM. A pilot experiment with known SNPs showed that they could be detected at a frequency > 0.3% within the pools. We then selected eight genes for which we wanted to discover novel mutations, and applied our approach to screen 768 individuals from the EMS population, using either the Ion 314 or Ion 316 chips. Out of 29 potential mutations identified after processing the NGS reads, 16 mutations were confirmed using Sanger sequencing. CONCLUSIONS The methodology presented here demonstrates the utility of Ion Torrent technology in detecting mutation variants in specific genome regions for large populations of a species such as flax. The methodology could be scaled-up to test >100 genes using the higher capacity chips now available from Ion Torrent.
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Affiliation(s)
| | - David Pinzón-Latorre
- />Department of Biological Sciences, University of Alberta, Edmonton, AB Canada T6G 2E9
| | - Erik A Bergen
- />Department of Biological Sciences, University of Alberta, Edmonton, AB Canada T6G 2E9
| | - Dustin C Jensen
- />Department of Computing Sciences, Kings University College, Edmonton, AB Canada T6B 2H3
| | - Michael K Deyholos
- />IK Barber School of Arts & Sciences, University of British Columbia, Okanagan campus, Kelowna, BC Canada V1V 1 V7
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54
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Gandhi SG, Mahajan V, Bedi YS. Changing trends in biotechnology of secondary metabolism in medicinal and aromatic plants. PLANTA 2015; 241:303-17. [PMID: 25549846 DOI: 10.1007/s00425-014-2232-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 12/16/2014] [Indexed: 05/02/2023]
Abstract
Medicinal and aromatic plants are known to produce secondary metabolites that find uses as flavoring agents, fragrances, insecticides, dyes and drugs. Biotechnology offers several choices through which secondary metabolism in medicinal plants can be altered in innovative ways, to overproduce phytochemicals of interest, to reduce the content of toxic compounds or even to produce novel chemicals. Detailed investigation of chromatin organization and microRNAs affecting biosynthesis of secondary metabolites as well as exploring cryptic biosynthetic clusters and synthetic biology options, may provide additional ways to harness this resource. Plant secondary metabolites are a fascinating class of phytochemicals exhibiting immense chemical diversity. Considerable enigma regarding their natural biological functions and the vast array of pharmacological activities, amongst other uses, make secondary metabolites interesting and important candidates for research. Here, we present an update on changing trends in the biotechnological approaches that are used to understand and exploit the secondary metabolism in medicinal and aromatic plants. Bioprocessing in the form of suspension culture, organ culture or transformed hairy roots has been successful in scaling up secondary metabolite production in many cases. Pathway elucidation and metabolic engineering have been useful to get enhanced yield of the metabolite of interest; or, for producing novel metabolites. Heterologous expression of putative plant secondary metabolite biosynthesis genes in a microbe is useful to validate their functions, and in some cases, also, to produce plant metabolites in microbes. Endophytes, the microbes that normally colonize plant tissues, may also produce the phytochemicals produced by the host plant. The review also provides perspectives on future research in the field.
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Affiliation(s)
- Sumit G Gandhi
- Plant Biotechnology Division, Indian Institute of Integrative Medicine (CSIR-IIIM), Council of Scientific and Industrial Research, Canal Road, Jammu Tawi, 180001, India,
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55
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Aliyu S, Massawe F, Mayes S. Beyond landraces: developing improved germplasm resources for underutilized species - a case for Bambara groundnut. Biotechnol Genet Eng Rev 2015; 30:127-41. [PMID: 25603880 DOI: 10.1080/02648725.2014.992625] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The potential for underutilized crops (also known as minor, neglected or orphan crops) to improve food and nutrition security has been gaining prominence within the research community in recent years. This is due to their significance for diversified agricultural systems which is a necessary component of future agriculture to address food and nutritional security concerns posed by changing climate and a growing world population. Developing workable value chain systems for underutilized crop species, coupled with comparative trait studies with major crops, potentially allows us to identify suitable agricultural modalities for such species. Bambara groundnut (Vigna subterranea L. Verdc.), an underutilized leguminous species, is of interest for its reported high levels of drought tolerance in particular, which contributes to environmental resilience in semi-arid environments. Here, we present a synopsis of suitable strategies for the genetic improvement of Bambara groundnut as a guide to other underutilized crop species. Underutilized crops have often been adapted over thousands of years in particular regions by farmers and largely still exist as landraces with little or no genetic knowledge of key phenotypic traits. Breeding in these species is fundamentally different to breeding in major crops, where significant pedigree structures and history allow highly directed improvement. In this regard, deploying new integrated germplasm development approaches for variety development and genetic analysis, such as multi-parent advance generation inter-crosses (MAGIC), within breeding programmes of underutilized species will be important to be able to fully utilize such crops.
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Affiliation(s)
- Siise Aliyu
- a School of Biosciences , The University of Nottingham , Sutton Bonington Campus, Loughborough , Leicestershire , UK
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56
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SNF2 chromatin remodeler-family proteins FRG1 and -2 are required for RNA-directed DNA methylation. Proc Natl Acad Sci U S A 2014; 111:17666-71. [PMID: 25425661 DOI: 10.1073/pnas.1420515111] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
DNA methylation in Arabidopsis thaliana is maintained by at least four different enzymes: DNA methyltransferase1 (MET1), chromomethylase3 (CMT3), domains rearranged methyltransferase2 (DRM2), and chromomethylase2 (CMT2). However, DNA methylation is established exclusively by the enzyme DRM2, which acts in the RNA-directed DNA methylation (RdDM) pathway. Some RdDM components belong to gene families and have partially redundant functions, such as the endoribonucleases dicer-like 2, 3, and 4, and involved in de novo2 (IDN2) interactors IDN2-like 1 and 2. Traditional mutagenesis screens usually fail to detect genes if they are redundant, as the loss of one gene can be compensated by a related gene. In an effort to circumvent this issue, we used coexpression data to identify closely related genes that are coregulated with genes in the RdDM pathway. Here we report the discovery of two redundant proteins, SNF2-ring-helicase-like1 and -2 (FRG1 and -2) that are putative chromatin modifiers belonging to the SNF2 family of helicase-like proteins. Analysis of genome-wide bisulfite sequencing shows that simultaneous mutations of FRG1 and -2 cause defects in methylation at specific RdDM targeted loci. We also show that FRG1 physically associates with Su(var)3-9-related SUVR2, a known RdDM component, in vivo. Combined, our results identify FRG1 and FRG2 as previously unidentified components of the RdDM machinery.
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57
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Alam G, Jones BC. Toxicogenetics: in search of host susceptibility to environmental toxicants. Front Genet 2014; 5:327. [PMID: 25295052 PMCID: PMC4170107 DOI: 10.3389/fgene.2014.00327] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 09/02/2014] [Indexed: 01/02/2023] Open
Abstract
Heavy metals, various pesticide and herbicides are implicated as risk factors for human health. Paraquat, maneb, and rotenone, carbamate, and organophosphorous insecticides are examples of toxicants for which acute and chronic exposure are associated with multiple neurological disorders including Parkinson’s disease. Nevertheless, the role of pesticide exposure in neurodegenerative diseases is not clear-cut, as there are inconsistencies in both the epidemiological and preclinical research. The aim of this short review is to show that at least, some of the inconsistencies are related to individual differences in susceptibility to the effects of neurotoxicants, individual differences that can be traced to the genetic constitution of the individuals and animals studies, i.e., host-based susceptibility.
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Affiliation(s)
- Gelareh Alam
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, PA USA
| | - Byron C Jones
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, PA USA
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58
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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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Desta ZA, Ortiz R. Genomic selection: genome-wide prediction in plant improvement. TRENDS IN PLANT SCIENCE 2014; 19:592-601. [PMID: 24970707 DOI: 10.1016/j.tplants.2014.05.006] [Citation(s) in RCA: 282] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 05/08/2014] [Accepted: 05/23/2014] [Indexed: 05/18/2023]
Abstract
Association analysis is used to measure relations between markers and quantitative trait loci (QTL). Their estimation ignores genes with small effects that trigger underpinning quantitative traits. By contrast, genome-wide selection estimates marker effects across the whole genome on the target population based on a prediction model developed in the training population (TP). Whole-genome prediction models estimate all marker effects in all loci and capture small QTL effects. Here, we review several genomic selection (GS) models with respect to both the prediction accuracy and genetic gain from selection. Phenotypic selection or marker-assisted breeding protocols can be replaced by selection, based on whole-genome predictions in which phenotyping updates the model to build up the prediction accuracy.
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Affiliation(s)
- Zeratsion Abera Desta
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Sundsvagen 14, Box 101, Alnarp, SE 23053, Sweden
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Sundsvagen 14, Box 101, Alnarp, SE 23053, Sweden.
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60
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Alonso JM, Stepanova AN. Arabidopsis transformation with large bacterial artificial chromosomes. Methods Mol Biol 2014; 1062:271-83. [PMID: 24057372 DOI: 10.1007/978-1-62703-580-4_15] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The study of a gene's function requires, in many cases, the ability to reintroduce the gene of interest or its modified version back into the organism of choice. One potential caveat of this approach is that not only the coding region but also the regulatory sequences of a gene should be included in the corresponding transgenic construct. Even in species with well-annotated genomes, such as Arabidopsis, it is nearly impossible to predict which sequences are responsible for the proper expression of a gene. One way to circumvent this problem is to utilize a large fragment of genomic DNA that contains the coding region of the gene of interest and at least 5-10 kb of flanking genomic sequences. To facilitate these types of experiments, libraries harboring large genomic DNA fragments in binary vectors have been constructed for Arabidopsis and several other plant species. Working with these large clones, however, requires some special precautions. In this chapter, we describe the experimental procedures and extra cautionary measures involved in the identification of the clone containing the gene of interest, its transfer from E. coli to Agrobacterium, and the generation, verification, and analysis of the corresponding transgenic plants.
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Affiliation(s)
- Jose M Alonso
- Department of Genetics, North Caroline State University, Raleigh, NC, USA
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61
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Belfield EJ, Brown C, Gan X, Jiang C, Baban D, Mithani A, Mott R, Ragoussis J, Harberd NP. Microarray-based ultra-high resolution discovery of genomic deletion mutations. BMC Genomics 2014; 15:224. [PMID: 24655320 PMCID: PMC3998191 DOI: 10.1186/1471-2164-15-224] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 02/28/2014] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Oligonucleotide microarray-based comparative genomic hybridization (CGH) offers an attractive possible route for the rapid and cost-effective genome-wide discovery of deletion mutations. CGH typically involves comparison of the hybridization intensities of genomic DNA samples with microarray chip representations of entire genomes, and has widespread potential application in experimental research and medical diagnostics. However, the power to detect small deletions is low. RESULTS Here we use a graduated series of Arabidopsis thaliana genomic deletion mutations (of sizes ranging from 4 bp to ~5 kb) to optimize CGH-based genomic deletion detection. We show that the power to detect smaller deletions (4, 28 and 104 bp) depends upon oligonucleotide density (essentially the number of genome-representative oligonucleotides on the microarray chip), and determine the oligonucleotide spacings necessary to guarantee detection of deletions of specified size. CONCLUSIONS Our findings will enhance a wide range of research and clinical applications, and in particular will aid in the discovery of genomic deletions in the absence of a priori knowledge of their existence.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Nicholas P Harberd
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK.
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62
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Yang Y, Li S, Zhang K, Dong Z, Li Y, An X, Chen J, Chen Q, Jiao Z, Liu X, Qin H, Wang D. Efficient isolation of ion beam-induced mutants for homoeologous loci in common wheat and comparison of the contributions of Glu-1 loci to gluten functionality. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:359-72. [PMID: 24212587 DOI: 10.1007/s00122-013-2224-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 10/18/2013] [Indexed: 05/15/2023]
Abstract
Ion beam mutations can be efficiently isolated and deployed for functional comparison of homoeologous loci in polyploid plants, and Glu - 1 loci differ substantially in their contribution to wheat gluten functionality. To efficiently conduct genetic analysis, it is beneficial to have multiple types of mutants for the genes under investigation. Here, we demonstrate that ion beam-induced deletion mutants can be efficiently isolated for comparing the function of homoeologous loci of common wheat (Triticum aestivum). Through fragment analysis of PCR products from M2 plants, ion beam mutants lacking homoeologous Glu-A1, Glu-B1 or Glu-D1 loci, which encode high molecular weight glutenin subunits (HMW-GSs) and affect gluten functionality and end-use quality of common wheat, could be isolated simultaneously. Three deletion lines missing Glu-A1, Glu-B1 or Glu-D1 were developed from the original mutants, with the Glu-1 genomic regions deleted in these lines estimated using newly developed DNA markers. Apart from lacking the target HMW-GSs, the three lines all showed decreased accumulation of low molecular weight glutenin subunits (LMW-GSs) and increased amounts of gliadins. Based on the test data of five gluten and glutenin macropolymer (GMP) parameters obtained with grain samples harvested from two environments, we conclude that the genetic effects of Glu-1 loci on gluten functionality can be ranked as Glu-D1 > Glu-B1 > Glu-A1. Furthermore, it is suggested that Glu-1 loci contribute to gluten functionality both directly (by promoting the formation of GMP) and indirectly (through keeping the balance among HMW-GSs, LMW-GSs and gliadins). Finally, the efficient isolation of ion beam mutations for functional comparison of homoeologous loci in polyploid plants and the usefulness of Glu-1 deletion lines for further studying the contribution of Glu-1 loci to gluten functionality are discussed.
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Affiliation(s)
- Yushuang Yang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
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63
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Juraniec M, Lequeux H, Hermans C, Willems G, Nordborg M, Schneeberger K, Salis P, Vromant M, Lutts S, Verbruggen N. Towards the discovery of novel genetic component involved in stress resistance in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2014; 201:810-824. [PMID: 24134393 DOI: 10.1111/nph.12554] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 09/16/2013] [Indexed: 05/23/2023]
Abstract
The exposure of plants to high concentrations of trace metallic elements such as copper involves a remodeling of the root system, characterized by a primary root growth inhibition and an increase in the lateral root density. These characteristics constitute easy and suitable markers for screening mutants altered in their response to copper excess. A forward genetic approach was undertaken in order to discover novel genetic factors involved in the response to copper excess. A Cu(2+) -sensitive mutant named copper modified resistance1 (cmr1) was isolated and a causative mutation in the CMR1 gene was identified by using positional cloning and next-generation sequencing. CMR1 encodes a plant-specific protein of unknown function. The analysis of the cmr1 mutant indicates that the CMR1 protein is required for optimal growth under normal conditions and has an essential role in the stress response. Impairment of the CMR1 activity alters root growth through aberrant activity of the root meristem, and modifies potassium concentration and hormonal balance (ethylene production and auxin accumulation). Our data support a putative role for CMR1 in cell division regulation and meristem maintenance. Research on the role of CMR1 will contribute to the understanding of the plasticity of plants in response to changing environments.
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Affiliation(s)
- Michal Juraniec
- Laboratory of Plant Physiology and Molecular Genetics, Université Libre de Bruxelles, 1050, Brussels, Belgium
| | - Hélène Lequeux
- Laboratory of Plant Physiology and Molecular Genetics, Université Libre de Bruxelles, 1050, Brussels, Belgium
- Groupe de Recherche en Physiologie Végétale, Earth and Life Institute, Université catholique de Louvain, 5 bte13, Croix du Sud, 1348, Louvain-La-Neuve, Belgium
| | - Christian Hermans
- Laboratory of Plant Physiology and Molecular Genetics, Université Libre de Bruxelles, 1050, Brussels, Belgium
| | - Glenda Willems
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Dr. Bohr-Gasse 3, 1030, Vienna, Austria
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Magnus Nordborg
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Korbinian Schneeberger
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Pietrino Salis
- Laboratory of Plant Physiology and Molecular Genetics, Université Libre de Bruxelles, 1050, Brussels, Belgium
| | - Maud Vromant
- Laboratory of Plant Physiology and Molecular Genetics, Université Libre de Bruxelles, 1050, Brussels, Belgium
| | - Stanley Lutts
- Groupe de Recherche en Physiologie Végétale, Earth and Life Institute, Université catholique de Louvain, 5 bte13, Croix du Sud, 1348, Louvain-La-Neuve, Belgium
| | - Nathalie Verbruggen
- Laboratory of Plant Physiology and Molecular Genetics, Université Libre de Bruxelles, 1050, Brussels, Belgium
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Berenschot AS, Quecini V. A reverse genetics approach identifies novel mutants in light responses and anthocyanin metabolism in petunia. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2014; 20:1-13. [PMID: 24554834 PMCID: PMC3925473 DOI: 10.1007/s12298-013-0212-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 09/22/2013] [Accepted: 10/18/2013] [Indexed: 05/03/2023]
Abstract
Flower color and plant architecture are important commercially valuable features for ornamental petunias (Petunia x hybrida Vilm.). Photoperception and light signaling are the major environmental factors controlling anthocyanin and chlorophyll biosynthesis and shade-avoidance responses in higher plants. The genetic regulators of these processes were investigated in petunia by in silico analyses and the sequence information was used to devise a reverse genetics approach to probe mutant populations. Petunia orthologs of photoreceptor, light-signaling components and anthocyanin metabolism genes were identified and investigated for functional conservation by phylogenetic and protein motif analyses. The expression profiles of photoreceptor gene families and of transcription factors regulating anthocyanin biosynthesis were obtained by bioinformatic tools. Two mutant populations, generated by an alkalyting agent and by gamma irradiation, were screened using a phenotype-independent, sequence-based method by high-throughput PCR-based assay. The strategy allowed the identification of novel mutant alleles for anthocyanin biosynthesis (CHALCONE SYNTHASE) and regulation (PH4), and for light signaling (CONSTANS) genes.
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Affiliation(s)
- Amanda S. Berenschot
- />Centro de Pesquisa e Desenvolvimento de Recursos Genéticos, Instituto Agronômico, Caixa Postal 28, 13001-970 Campinas, SP Brazil
| | - Vera Quecini
- />Embrapa Uva e Vinho, Rua Livramento, 515, 95700-000 Bento Gonçalves, RS Brazil
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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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66
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Rodríguez MC, Wawrzyńska A, Sirko A. Intronic T-DNA insertion in Arabidopsis NBR1 conditionally affects wild-type transcript level. PLANT SIGNALING & BEHAVIOR 2014; 9:e975659. [PMID: 25482782 PMCID: PMC4622546 DOI: 10.4161/15592324.2014.975659] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 08/05/2014] [Accepted: 08/07/2014] [Indexed: 05/25/2023]
Abstract
The SALK_135513 line of Arabidopsis thaliana is annotated by GenBank to have the T-DNA insertion in the fourth exon of NBR1 (At4g24690). Careful molecular analyses of the homozygous plants of SALK_135513 line indicated the place of T-DNA insertion in the fourth intron. Unexpectedly, 2 kinds of NBR1 transcripts, the wild-type and the mutated, resulting from alternative splicing events, were detected in those plants. Our findings explain the problems encountered by us with phenotypic evaluation of this line and emphasize the necessity for independent verification of the exact insertion site followed by careful expression studies when working with Arabidopsis T-DNA insertional mutants.
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Affiliation(s)
| | - Anna Wawrzyńska
- Institute of Biochemistry and Biophysics; Polish Academy of Sciences; Warsaw, Poland
| | - Agnieszka Sirko
- Institute of Biochemistry and Biophysics; Polish Academy of Sciences; Warsaw, Poland
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Abstract
Across animals, there is remarkable diversity in behavior. Modern genomic approaches have made it possible to identify the molecular underpinnings of varied behavioral phenotypes. By examining species with plastic phenotypes we have begun to understand the dynamic and flexible nature of neural transcriptomes and identified gene modules associated with variation in social and reproductive behaviors in diverse species. Importantly, it is becoming increasingly clear that some candidate genes and gene networks are involved in complex social behaviors across even divergent species, yet few comparative transcriptomics studies have been conducted that examine a specific behavior across species. We discuss the implications of a range of important and insightful studies that have increased our understanding of the neurogenomics of behavioral plasticity. Despite its successes, behavioral genomics has been criticized for its lack of hypotheses and causative insights. We propose here a novel avenue to overcome some of these short-comings by complementing "forward genomics" studies (i.e., from phenotype to behaviorally relevant gene modules) with a "reverse genomics" approach (i.e., manipulating novel gene modules to examine effects on behavior, hormones, and the genome itself) to examine the functional causes and consequences of differential gene expression patterns. We discuss how several established approaches (such as pharmacological manipulations of a novel candidate pathway, fine scale mapping of novel candidate gene expression in the brain, or identifying direct targets of a novel transcription factor of interest) can be used in combination with the analysis of the accompanying neurogenomic responses to reveal unexpected biological processes. The integration of forward and reverse genomics will move the field beyond statistical associations and yield great insights into the neural and molecular control of social behavior and its evolution.
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68
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Qi Y, Starker CG, Zhang F, Baltes NJ, Voytas DF. Tailor-made mutations in Arabidopsis using zinc finger nucleases. Methods Mol Biol 2014; 1062:193-209. [PMID: 24057367 DOI: 10.1007/978-1-62703-580-4_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Zinc finger nucleases (ZFNs) are proteins engineered to make site-specific double-strand breaks (DSBs) in a DNA sequence of interest. Imprecise repair of the ZFN-induced DSBs by the nonhomologous end-joining (NHEJ) pathway results in a spectrum of mutations, such as nucleotide substitutions, insertions, and deletions. Here we describe a method for targeted mutagenesis in Arabidopsis with ZFNs, which are engineered by context-dependent assembly (CoDA). This ZFN-induced mutagenesis method is an alternative to other currently available gene knockout or knockdown technologies and is useful for reverse genetic studies.
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Affiliation(s)
- Yiping Qi
- Department of Genetics, Cell Biology & Development and Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
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Kopecký D, Studer B. Emerging technologies advancing forage and turf grass genomics. Biotechnol Adv 2013; 32:190-9. [PMID: 24309540 DOI: 10.1016/j.biotechadv.2013.11.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 11/18/2013] [Accepted: 11/20/2013] [Indexed: 11/20/2022]
Abstract
Grassland is of major importance for agricultural production and provides valuable ecosystem services. Its impact is likely to rise in changing socio-economic and climatic environments. High yielding forage grass species are major components of sustainable grassland production. Understanding the genome structure and function of grassland species provides opportunities to accelerate crop improvement and thus to mitigate the future challenges of increased feed and food demand, scarcity of natural resources such as water and nutrients, and high product qualities. In this review, we will discuss a selection of technological developments that served as main drivers to generate new insights into the structure and function of nuclear genomes. Many of these technologies were originally developed in human or animal science and are now increasingly applied in plant genomics. Our main goal is to highlight the benefits of using these technologies for forage and turf grass genome research, to discuss their potentials and limitations as well as their relevance for future applications.
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Affiliation(s)
- David Kopecký
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, CZ-78371, Olomouc-Holice, Czech Republic
| | - Bruno Studer
- Forage Crop Genetics, Institute of Agricultural Sciences, ETH Zurich, Universitaetsstrasse 2, 8092 Zurich, Switzerland.
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Pflieger SP, Richard MMS, Blanchet S, Meziadi C, Geffroy VR. VIGS technology: an attractive tool for functional genomics studies in legumes. FUNCTIONAL PLANT BIOLOGY : FPB 2013; 40:1234-1248. [PMID: 32481191 DOI: 10.1071/fp13089] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 06/14/2013] [Indexed: 05/20/2023]
Abstract
Legume species are among the most important crops worldwide. In recent years, six legume genomes have been completely sequenced, and there is now an urgent need for reverse-genetics tools to validate genes affecting yield and product quality. As most legumes are recalcitrant to stable genetic transformation, virus-induced gene silencing (VIGS) appears to be a powerful alternative technology for determining the function of unknown genes. VIGS technology is based on the property of plant viruses to trigger a defence mechanism related to post-transcriptional gene silencing (PTGS). Infection by a recombinant virus carrying a fragment of a plant target gene will induce homology-dependent silencing of the endogenous target gene. Several VIGS systems have been developed for legume species since 2004, including those based on Bean pod mottle virus, Pea early browning virus, and Apple latent spherical virus, and used in reverse-genetics studies of a wide variety of plant biological processes. In this work, we give an overview of the VIGS systems available for legumes, and present their successful applications in functional genomics studies. We also discuss the limitations of these VIGS systems and the future challenges to be faced in order to use VIGS to its full potential in legume species.
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Affiliation(s)
- St Phanie Pflieger
- Institut de Biologie des Plantes, UMR8618, CNRS Université Paris-Sud, Saclay Plant Sciences, Rue Noetzlin, 91405 Orsay, France
| | - Manon M S Richard
- Institut de Biologie des Plantes, UMR8618, CNRS Université Paris-Sud, Saclay Plant Sciences, Rue Noetzlin, 91405 Orsay, France
| | - Sophie Blanchet
- Institut de Biologie des Plantes, UMR8618, CNRS Université Paris-Sud, Saclay Plant Sciences, Rue Noetzlin, 91405 Orsay, France
| | - Chouaib Meziadi
- Institut de Biologie des Plantes, UMR8618, CNRS Université Paris-Sud, Saclay Plant Sciences, Rue Noetzlin, 91405 Orsay, France
| | - Val Rie Geffroy
- Institut de Biologie des Plantes, UMR8618, CNRS Université Paris-Sud, Saclay Plant Sciences, Rue Noetzlin, 91405 Orsay, France
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Transcriptome comparative profiling of barley eibi1 mutant reveals pleiotropic effects of HvABCG31 gene on cuticle biogenesis and stress responsive pathways. Int J Mol Sci 2013; 14:20478-91. [PMID: 24129180 PMCID: PMC3821626 DOI: 10.3390/ijms141020478] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 09/26/2013] [Accepted: 09/26/2013] [Indexed: 01/03/2023] Open
Abstract
Wild barley eibi1 mutant with HvABCG31 gene mutation has low capacity to retain leaf water, a phenotype associated with reduced cutin deposition and a thin cuticle. To better understand how such a mutant plant survives, we performed a genome-wide gene expression analysis. The leaf transcriptomes between the near-isogenic lines eibi1 and the wild type were compared using the 22-k Barley1 Affymetrix microarray. We found that the pleiotropic effect of the single gene HvABCG31 mutation was linked to the co-regulation of metabolic processes and stress-related system. The cuticle development involved cytochrome P450 family members and fatty acid metabolism pathways were significantly up-regulated by the HvABCG31 mutation, which might be anticipated to reduce the levels of cutin monomers or wax and display conspicuous cuticle defects. The candidate genes for responses to stress were induced by eibi1 mutant through activating the jasmonate pathway. The down-regulation of co-expressed enzyme genes responsible for DNA methylation and histone deacetylation also suggested that HvABCG31 mutation may affect the epigenetic regulation for barley development. Comparison of transcriptomic profiling of barley under biotic and abiotic stresses revealed that the functions of HvABCG31 gene to high-water loss rate might be different from other osmotic stresses of gene mutations in barley. The transcriptional profiling of the HvABCG31 mutation provided candidate genes for further investigation of the physiological and developmental changes caused by the mutant.
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72
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Haro R, Fraile-Escanciano A, González-Melendi P, Rodríguez-Navarro A. The potassium transporters HAK2 and HAK3 localize to endomembranes in Physcomitrella patens. HAK2 is required in some stress conditions. PLANT & CELL PHYSIOLOGY 2013; 54:1441-1454. [PMID: 23825217 DOI: 10.1093/pcp/pct097] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The function of HAK transporters in high-affinity K+ uptake in plants is well established; this study aims to demonstrate that some transporters of the same family play important roles in endomembranes. The PpHAK2-PpHAK4 genes of Physcomitrella patens encode three transporters of high sequence similarity. Quantitative PCR showed that PpHAK2 and PpHAK3 transcripts are expressed at approximately the same level as the PpACT5 gene, while the expression of PpHAK4 seems to be restricted to specific conditions that have not been determined. KHA1 is an endomembrane K+/H+ antiporter of Saccharomyces cerevisiae, and the expression of the PpHAK2 cDNA, but not that of PpHAK3, suppressed the defect of a kha1 mutant. Transient expression of the PpHAK2-green fluorescent protein (GFP) and PpHAK3-GFP fusion proteins in P. patens protoplasts localized to the endoplasmic reticulum and Golgi complex, respectively. To determine the function of PpHAK2 and PpHAK3 in planta, we constructed ΔPphak2 and ΔPphak2 ΔPphak3 plants. ΔPphak2 plants were normal under all of the conditions tested except under K+ starvation or at acidic pH in the presence of acetic acid, whereupon they die. The defect observed under K+ starvation was suppressed by the presence of Na+. We propose that PpHAK2 may encode either a K(+)-H(+) symporter or a K+/H+ antiporter that mediates the transfer of H+ from the endoplasmic reticulum lumen to the cytosol. PpHAK2 may be a model of the second function of HAK transporters in plant cells. The disruption of the PpHAK3 gene in ΔPphak2 plants showed no effect.
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Affiliation(s)
- Rosario Haro
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Campus de Montegancedo, Carretera M-40, km 38, 28223 Pozuelo de Alarcón, Madrid, Spain.
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Time- and cost-efficient identification of T-DNA insertion sites through targeted genomic sequencing. PLoS One 2013; 8:e70912. [PMID: 23951038 PMCID: PMC3741346 DOI: 10.1371/journal.pone.0070912] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 06/24/2013] [Indexed: 12/13/2022] Open
Abstract
Forward genetic screens enable the unbiased identification of genes involved in biological processes. In Arabidopsis, several mutant collections are publicly available, which greatly facilitates such practice. Most of these collections were generated by agrotransformation of a T-DNA at random sites in the plant genome. However, precise mapping of T-DNA insertion sites in mutants isolated from such screens is a laborious and time-consuming task. Here we report a simple, low-cost and time efficient approach to precisely map T-DNA insertions simultaneously in many different mutants. By combining sequence capture, next-generation sequencing and 2D-PCR pooling, we developed a new method that allowed the rapid localization of T-DNA insertion sites in 55 out of 64 mutant plants isolated in a screen for gyrase inhibition hypersensitivity.
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Ravichandran S, Stone SL, Benkel B, Prithiviraj B. Purple Acid Phosphatase5 is required for maintaining basal resistance against Pseudomonas syringae in Arabidopsis. BMC PLANT BIOLOGY 2013; 13:107. [PMID: 23890153 PMCID: PMC3751912 DOI: 10.1186/1471-2229-13-107] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Accepted: 07/24/2013] [Indexed: 05/05/2023]
Abstract
BACKGROUND Plants have evolved an array of constitutive and inducible defense strategies to restrict pathogen ingress. However, some pathogens still manage to invade plants and impair growth and productivity. Previous studies have revealed several key regulators of defense responses, and efforts have been made to use this information to develop disease resistant crop plants. These efforts are often hampered by the complexity of defense signaling pathways. To further elucidate the complexity of defense responses, we screened a population of T-DNA mutants in Colombia-0 background that displayed altered defense responses to virulent Pseudomonas syringae pv. tomato DC3000 (Pst DC3000). RESULTS In this study, we demonstrated that the Arabidopsis Purple Acid Phosphatse5 (PAP5) gene, induced under prolonged phosphate (Pi) starvation, is required for maintaining basal resistance to certain pathogens. The expression of PAP5 was distinctly induced only under prolonged Pi starvation and during the early stage of Pst DC3000 infection (6 h.p.i). T-DNA tagged mutant pap5 displayed enhanced susceptibility to the virulent bacterial pathogen Pst DC3000. The pap5 mutation greatly reduced the expression of pathogen inducible gene PR1 compared to wild-type plants. Similarly, other defense related genes including ICS1 and PDF1.2 were impaired in pap5 plants. Moreover, application of BTH (an analog of SA) restored PR1 expression in pap5 plants. CONCLUSION Taken together, our results demonstrate the requirement of PAP5 for maintaining basal resistance against Pst DC3000. Furthermore, our results provide evidence that PAP5 acts upstream of SA accumulation to regulate the expression of other defense responsive genes. We also provide the first experimental evidence indicating the role PAP5 in plant defense responses.
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Affiliation(s)
- Sridhar Ravichandran
- Department of Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 5E3, Canada
| | - Sophia L Stone
- Department of Biology, Dalhousie University, Halifax, NS B3H 4J1, Canada
| | - Bernhard Benkel
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 5E3, Canada
| | - Balakrishnan Prithiviraj
- Department of Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 5E3, Canada
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Brachi B, Faure N, Bergelson J, Cuguen J, Roux F. Genome-wide association mapping of flowering time in Arabidopsis thaliana in nature: genetics for underlying components and reaction norms across two successive years. ACTA BOTANICA GALLICA : BULLETIN DE LA SOCIETE BOTANIQUE DE FRANCE 2013; 160:205-219. [PMID: 24470785 PMCID: PMC3901435 DOI: 10.1080/12538078.2013.807302] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Often used as a proxy for the transition to reproduction, flowering time (FT) is an integrative trait of two successive biological processes, i.e. bolting time (BT) and the interval between bolting and flowering time (INT). In this study, we aimed to identify candidate genes associated with these composite traits in Arabidopsis thaliana using a field experiment. Genome-wide association (GWA) mapping was performed on BT, INT and FT based on a sample of 179 worldwide natural accessions genotyped for 216,509 SNPs. The high resolution conferred by GWA mapping indicates that FT is an integrative trait at the genetic level, with distinct genetics for BT and INT. BT is shaped largely by genes involved in the circadian clock whereas INT is shaped by genes involved in both the hormone pathways and cold acclimation. Finally, the florigen TSF appears to be the main integrator of environmental and internal signals in ecologically realistic conditions. Based on FT scored in a previous field experiment, we also studied the genetics underlying reaction norms across two years. Only four genes were common to both years, emphasizing the need to repeat field experiments. The gene regulation model appeared as the main genetic model for genotype × year interactions.
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Affiliation(s)
- Benjamin Brachi
- Laboratoire Génétique et Evolution des Populations Végétales, UMR CNRS 8198, Université des Sciences et Technologies de Lille – Lille 1, F-59655 Villeneuve d'Ascq cedex France
| | - Nathalie Faure
- Laboratoire Génétique et Evolution des Populations Végétales, UMR CNRS 8198, Université des Sciences et Technologies de Lille – Lille 1, F-59655 Villeneuve d'Ascq cedex France
| | - Joy Bergelson
- Department of Ecology and Evolution, University of Chicago, 1101 E. 57 Street, Chicago, IL 60637, USA
| | - Joël Cuguen
- Laboratoire Génétique et Evolution des Populations Végétales, UMR CNRS 8198, Université des Sciences et Technologies de Lille – Lille 1, F-59655 Villeneuve d'Ascq cedex France
| | - Fabrice Roux
- Laboratoire Génétique et Evolution des Populations Végétales, UMR CNRS 8198, Université des Sciences et Technologies de Lille – Lille 1, F-59655 Villeneuve d'Ascq cedex France
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Rigó G, Papdi C, Szabados L. Transformation using controlled cDNA overexpression system. Methods Mol Biol 2013; 913:277-90. [PMID: 22895767 DOI: 10.1007/978-1-61779-986-0_19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
The controlled cDNA overexpression system (COS) was developed to identify novel regulatory genes in model plants as well as in other species that might have a particular valuable trait. The COS system (Papdi et al. Plant Physiol 147:528-542, 2008) is composed of a random cDNA library prepared in a T-DNA plant expression vector, under the control of the estradiol-inducible XVE promoter. Large-scale genetic transformation of Arabidopsis thaliana generates a transgenic plant population with randomly inserted cDNA clones. Overexpression of the inserted cDNA can create selectable phenotypes, allowing the facile identification and cloning of the responsible genes. Here we describe protocols to create and use the COS system for diverse purposes in plant biology.
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Affiliation(s)
- Gábor Rigó
- Institute of Plant Biology, Biological Research Center, Szeged, Hungary
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Tanz SK, Castleden I, Hooper CM, Vacher M, Small I, Millar HA. SUBA3: a database for integrating experimentation and prediction to define the SUBcellular location of proteins in Arabidopsis. Nucleic Acids Res 2013; 41:D1185-91. [PMID: 23180787 PMCID: PMC3531127 DOI: 10.1093/nar/gks1151] [Citation(s) in RCA: 231] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 10/24/2012] [Accepted: 10/25/2012] [Indexed: 12/27/2022] Open
Abstract
The subcellular location database for Arabidopsis proteins (SUBA3, http://suba.plantenergy.uwa.edu.au) combines manual literature curation of large-scale subcellular proteomics, fluorescent protein visualization and protein-protein interaction (PPI) datasets with subcellular targeting calls from 22 prediction programs. More than 14 500 new experimental locations have been added since its first release in 2007. Overall, nearly 650 000 new calls of subcellular location for 35 388 non-redundant Arabidopsis proteins are included (almost six times the information in the previous SUBA version). A re-designed interface makes the SUBA3 site more intuitive and easier to use than earlier versions and provides powerful options to search for PPIs within the context of cell compartmentation. SUBA3 also includes detailed localization information for reference organelle datasets and incorporates green fluorescent protein (GFP) images for many proteins. To determine as objectively as possible where a particular protein is located, we have developed SUBAcon, a Bayesian approach that incorporates experimental localization and targeting prediction data to best estimate a protein's location in the cell. The probabilities of subcellular location for each protein are provided and displayed as a pictographic heat map of a plant cell in SUBA3.
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Affiliation(s)
- Sandra K. Tanz
- Centre of Excellence in Computational Systems Biology, ARC Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis on Biomolecular Networks (CABiN), The University of Western Australia, Perth, WA 6009, Australia
| | - Ian Castleden
- Centre of Excellence in Computational Systems Biology, ARC Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis on Biomolecular Networks (CABiN), The University of Western Australia, Perth, WA 6009, Australia
| | - Cornelia M. Hooper
- Centre of Excellence in Computational Systems Biology, ARC Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis on Biomolecular Networks (CABiN), The University of Western Australia, Perth, WA 6009, Australia
| | - Michael Vacher
- Centre of Excellence in Computational Systems Biology, ARC Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis on Biomolecular Networks (CABiN), The University of Western Australia, Perth, WA 6009, Australia
| | - Ian Small
- Centre of Excellence in Computational Systems Biology, ARC Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis on Biomolecular Networks (CABiN), The University of Western Australia, Perth, WA 6009, Australia
| | - Harvey A. Millar
- Centre of Excellence in Computational Systems Biology, ARC Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis on Biomolecular Networks (CABiN), The University of Western Australia, Perth, WA 6009, Australia
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Juvale PS, Hewezi T, Zhang C, Kandoth PK, Mitchum MG, Hill JH, Whitham SA, Baum TJ. Temporal and spatial Bean pod mottle virus-induced gene silencing in soybean. MOLECULAR PLANT PATHOLOGY 2012; 13:1140-8. [PMID: 22738403 PMCID: PMC6638800 DOI: 10.1111/j.1364-3703.2012.00808.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Virus-induced gene silencing (VIGS) is a powerful reverse genetics tool in plant science. In this study, we investigated the temporal and spatial silencing patterns achieved by Bean pod mottle virus (BPMV)-based VIGS in soybean using virus constructs targeting green fluorescence protein (GFP). Silencing GFP enabled an in-depth analysis of silencing in soybean tissues over time in a transgenic line constitutively expressing GFP. We discovered evidence for variable GFP silencing based on insert orientation and targeted region in the coding sequence. A 3' sequence in reverse orientation produced the strongest silencing phenotypes. Furthermore, we documented that BPMV VIGS can achieve widespread silencing in a broad range of tissues, including leaves, stems, flowers and roots. Near-complete silencing was attained in leaves and flowers. Although weaker than in shoots, the observed gene silencing in soybean roots will also allow reverse genetics studies in this tissue. When GFP fluorescence was assayed in cross-sections of stems and leaf petioles, near-complete and uniform silencing was observed in all cell types. Silencing was observed from as early as 2 weeks post-virus inoculation in leaves to 7 weeks post-virus inoculation in flowers, suggesting that this system can induce and maintain silencing for significant durations.
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Affiliation(s)
- Parijat S Juvale
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, USA
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79
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Baldazzi V, Bertin N, de Jong H, Génard M. Towards multiscale plant models: integrating cellular networks. TRENDS IN PLANT SCIENCE 2012; 17:728-36. [PMID: 22818768 DOI: 10.1016/j.tplants.2012.06.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Revised: 06/22/2012] [Accepted: 06/26/2012] [Indexed: 05/22/2023]
Abstract
One of the ambitions of 'crop systems biology' is to combine information from molecular biology with a broader view of plant development and growth. In the context of modeling, this calls for a multiscale perspective that focuses on the interplay between cellular and macroscopic studies. With this in mind, in this review we aim to draw attention to a panel of approaches that were developed in the context of systems biology and are used for analyzing and describing the behavior of cellular networks. Ultimately, insights obtained from these methods can be exploited to refine the description of plant processes, leading to integrated plant-cellular models.
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Affiliation(s)
- Valentina Baldazzi
- INRA, UR 1115 Plantes et Systèmes de Culture Horticoles, Domaine St Paul, Site Agroparc, F-84941 Avignon Cedex 9, France.
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80
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Baldazzi V, Bertin N, de Jong H, Génard M. Towards multiscale plant models: integrating cellular networks. TRENDS IN PLANT SCIENCE 2012. [PMID: 22818768 DOI: 10.1016/j.tplants.2012.06.012 [epub ahead of print]] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
One of the ambitions of 'crop systems biology' is to combine information from molecular biology with a broader view of plant development and growth. In the context of modeling, this calls for a multiscale perspective that focuses on the interplay between cellular and macroscopic studies. With this in mind, in this review we aim to draw attention to a panel of approaches that were developed in the context of systems biology and are used for analyzing and describing the behavior of cellular networks. Ultimately, insights obtained from these methods can be exploited to refine the description of plant processes, leading to integrated plant-cellular models.
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Affiliation(s)
- Valentina Baldazzi
- INRA, UR 1115 Plantes et Systèmes de Culture Horticoles, Domaine St Paul, Site Agroparc, F-84941 Avignon Cedex 9, France.
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81
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Formighieri C, Franck F, Bassi R. Regulation of the pigment optical density of an algal cell: Filling the gap between photosynthetic productivity in the laboratory and in mass culture. J Biotechnol 2012; 162:115-23. [DOI: 10.1016/j.jbiotec.2012.02.021] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Revised: 02/27/2012] [Accepted: 02/29/2012] [Indexed: 11/26/2022]
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82
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Valentine ME, Wolyniak MJ, Rutter MT. Extensive phenotypic variation among allelic T-DNA inserts in Arabidopsis thaliana. PLoS One 2012; 7:e44981. [PMID: 23028719 PMCID: PMC3441624 DOI: 10.1371/journal.pone.0044981] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 08/15/2012] [Indexed: 11/19/2022] Open
Abstract
T-DNA insertion mutants are a tool used widely in Arabidopsis thaliana to disrupt gene function. We phenotyped multiple homozygous T-DNA A. thaliana mutants at each of two loci (AT1G11060 and AT4G00210). We measured life history traits, including germination, size at reproduction and fruit production. Allelic T-DNA lines differed for most traits at AT1G11060 but not at AT4G00210. However, insertions in exons differed from other insertion positions in AT4G00210 but not in AT1G11060. We found evidence for additional insertions in approximately half of the lines, but found few phenotypic consequences. In general, our results suggest that a cautious interpretation of T-DNA phenotypes is warranted.
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Affiliation(s)
- Megan E. Valentine
- Department of Biology, College of Charleston, Charleston, South Carolina, United States of America
| | - Michael J. Wolyniak
- Department of Biology, Hampden-Sydney College, Hampden-Sydney, Virginia, United States of America
| | - Matthew T. Rutter
- Department of Biology, College of Charleston, Charleston, South Carolina, United States of America
- * E-mail:
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83
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Balu B. Moving "Forward" in Plasmodium Genetics through a Transposon-Based Approach. J Trop Med 2012; 2012:829210. [PMID: 22649460 PMCID: PMC3356940 DOI: 10.1155/2012/829210] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2011] [Revised: 02/07/2012] [Accepted: 02/20/2012] [Indexed: 01/07/2023] Open
Abstract
The genome sequence of the human malaria parasite, Plasmodium falciparum, was released almost a decade ago. A majority of the Plasmodium genome, however, remains annotated to code for hypothetical proteins with unknown functions. The introduction of forward genetics has provided novel means to gain a better understanding of gene functions and their associated phenotypes in Plasmodium. Even with certain limitations, the technique has already shown significant promise to increase our understanding of parasite biology needed for rationalized drug and vaccine design. Further improvements to the mutagenesis technique and the design of novel genetic screens should lead us to some exciting discoveries about the critical weaknesses of Plasmodium, and greatly aid in the development of new disease intervention strategies.
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Affiliation(s)
- Bharath Balu
- Tropical Disease Research Program, Center for Infectious Disease and Biodefense Research, SRI International, Harrisonburg, VA 22802, USA
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84
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Păcurar DI, Păcurar ML, Street N, Bussell JD, Pop TI, Gutierrez L, Bellini C. A collection of INDEL markers for map-based cloning in seven Arabidopsis accessions. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:2491-501. [PMID: 22282537 PMCID: PMC3346218 DOI: 10.1093/jxb/err422] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The availability of a comprehensive set of resources including an entire annotated reference genome, sequenced alternative accessions, and a multitude of marker systems makes Arabidopsis thaliana an ideal platform for genetic mapping. PCR markers based on INsertions/DELetions (INDELs) are currently the most frequently used polymorphisms. For the most commonly used mapping combination, Columbia×Landsberg erecta (Col-0×Ler-0), the Cereon polymorphism database is a valuable resource for the generation of polymorphic markers. However, because the number of markers available in public databases for accessions other than Col-0 and Ler-0 is extremely low, mapping using other accessions is far from straightforward. This issue arose while cloning mutations in the Wassilewskija (Ws-4) background. In this work, approaches are described for marker generation in Ws-4 x Col-0. Complementary strategies were employed to generate 229 INDEL markers. Firstly, existing Col-0/Ler-0 Cereon predicted polymorphisms were mined for transferability to Ws-4. Secondly, Ws-0 ecotype Illumina sequence data were analyzed to identify INDELs that could be used for the development of PCR-based markers for Col-0 and Ws-4. Finally, shotgun sequencing allowed the identification of INDELs directly between Col-0 and Ws-4. The polymorphism of the 229 markers was assessed in seven widely used Arabidopsis accessions, and PCR markers that allow a clear distinction between the diverged Ws-0 and Ws-4 accessions are detailed. The utility of the markers was demonstrated by mapping more than 35 mutations in a Col-0×Ws-4 combination, an example of which is presented here. The potential contribution of next generation sequencing technologies to more traditional map-based cloning is discussed.
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Affiliation(s)
- Daniel Ioan Păcurar
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-90183 Umeå, Sweden.
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85
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Weigel D. Natural variation in Arabidopsis: from molecular genetics to ecological genomics. PLANT PHYSIOLOGY 2012; 158:2-22. [PMID: 22147517 PMCID: PMC3252104 DOI: 10.1104/pp.111.189845] [Citation(s) in RCA: 242] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Accepted: 12/05/2011] [Indexed: 05/18/2023]
Affiliation(s)
- Detlef Weigel
- Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany.
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86
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Understanding the mode of phytohormones' action in plants. SCIENCE CHINA. LIFE SCIENCES 2011; 54:1062-3. [PMID: 22173314 DOI: 10.1007/s11427-011-4246-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Accepted: 12/04/2011] [Indexed: 10/14/2022]
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87
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Azevedo H, Silva-Correia J, Oliveira J, Laranjeira S, Barbeta C, Amorim-Silva V, Botella MA, Lino-Neto T, Tavares RM. A strategy for the identification of new abiotic stress determinants in Arabidopsis using web-based data mining and reverse genetics. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2011; 15:935-47. [PMID: 22136640 DOI: 10.1089/omi.2011.0083] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Since the sequencing of the Arabidopsis thaliana genome in 2000, plant researchers have faced the complex challenge of assigning function to thousands of genes. Functional discovery by in silico prediction or homology search resolved a significant number of genes, but only a minor part has been experimentally validated. Arabidopsis entry into the post-genomic era signified a massive increase in high-throughput approaches to functional discovery, which have since become available through publicly-available web-based resources. The present work focuses on an easy and straightforward strategy that couples data-mining to reverse genetics principles, to allow for the identification of new abiotic stress determinant genes. The strategy explores systematic microarray-based transcriptomics experiments, involving Arabidopsis abiotic stress responses. An overview of the most significant resources and databases for functional discovery in Arabidopsis is presented. The successful application of the outlined strategy is illustrated by the identification of a new abiotic stress determinant gene, HRR, which displays a heat-stress-related phenotype after a loss-of-function reverse genetics approach.
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Affiliation(s)
- Herlânder Azevedo
- Center for Biodiversity, Functional & Integrative Genomics (BioFIG), CBFP/Department of Biology, University of Minho, Campus de Gualtar, Braga, Portugal.
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88
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Singh S, Tan HQ, Singh J. Mutagenesis of barley malting quality QTLs with Ds transposons. Funct Integr Genomics 2011; 12:131-41. [DOI: 10.1007/s10142-011-0258-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Revised: 10/25/2011] [Accepted: 11/02/2011] [Indexed: 11/28/2022]
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89
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Bolle C, Schneider A, Leister D. Perspectives on Systematic Analyses of Gene Function in Arabidopsis thaliana: New Tools, Topics and Trends. Curr Genomics 2011; 12:1-14. [PMID: 21886450 PMCID: PMC3129038 DOI: 10.2174/138920211794520187] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Revised: 10/28/2010] [Accepted: 11/23/2010] [Indexed: 11/22/2022] Open
Abstract
Since the sequencing of the nuclear genome of Arabidopsis thaliana ten years ago, various large-scale analyses of gene function have been performed in this model species. In particular, the availability of collections of lines harbouring random T-DNA or transposon insertions, which include mutants for almost all of the ~27,000 A. thaliana genes, has been crucial for the success of forward and reverse genetic approaches. In the foreseeable future, genome-wide phenotypic data from mutant analyses will become available for Arabidopsis, and will stimulate a flood of novel in-depth gene-function analyses. In this review, we consider the present status of resources and concepts for systematic studies of gene function in A. thaliana. Current perspectives on the utility of loss-of-function and gain-of-function mutants will be discussed in light of the genetic and functional redundancy of many A. thaliana genes.
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Affiliation(s)
- C Bolle
- Lehrstuhl für Molekularbiologie der Pflanzen (Botanik), Department Biologie I, Ludwig-Maximilians-Universität München, Großhaderner Str. 2, D-82152 Planegg-Martinsried, Germany
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90
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Kurowska M, Daszkowska-Golec A, Gruszka D, Marzec M, Szurman M, Szarejko I, Maluszynski M. TILLING: a shortcut in functional genomics. J Appl Genet 2011; 52:371-90. [PMID: 21912935 PMCID: PMC3189332 DOI: 10.1007/s13353-011-0061-1] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Revised: 08/16/2011] [Accepted: 08/17/2011] [Indexed: 11/01/2022]
Abstract
Recent advances in large-scale genome sequencing projects have opened up new possibilities for the application of conventional mutation techniques in not only forward but also reverse genetics strategies. TILLING (Targeting Induced Local Lesions IN Genomes) was developed a decade ago as an alternative to insertional mutagenesis. It takes advantage of classical mutagenesis, sequence availability and high-throughput screening for nucleotide polymorphisms in a targeted sequence. The main advantage of TILLING as a reverse genetics strategy is that it can be applied to any species, regardless of its genome size and ploidy level. The TILLING protocol provides a high frequency of point mutations distributed randomly in the genome. The great mutagenic potential of chemical agents to generate a high rate of nucleotide substitutions has been proven by the high density of mutations reported for TILLING populations in various plant species. For most of them, the analysis of several genes revealed 1 mutation/200-500 kb screened and much higher densities were observed for polyploid species, such as wheat. High-throughput TILLING permits the rapid and low-cost discovery of new alleles that are induced in plants. Several research centres have established a TILLING public service for various plant species. The recent trends in TILLING procedures rely on the diversification of bioinformatic tools, new methods of mutation detection, including mismatch-specific and sensitive endonucleases, but also various alternatives for LI-COR screening and single nucleotide polymorphism (SNP) discovery using next-generation sequencing technologies. The TILLING strategy has found numerous applications in functional genomics. Additionally, wide applications of this throughput method in basic and applied research have already been implemented through modifications of the original TILLING strategy, such as Ecotilling or Deletion TILLING.
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Affiliation(s)
- Marzena Kurowska
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Jagiellonska 28, 40-032 Katowice, Poland
| | - Agata Daszkowska-Golec
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Jagiellonska 28, 40-032 Katowice, Poland
| | - Damian Gruszka
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Jagiellonska 28, 40-032 Katowice, Poland
| | - Marek Marzec
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Jagiellonska 28, 40-032 Katowice, Poland
| | - Miriam Szurman
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Jagiellonska 28, 40-032 Katowice, Poland
| | - Iwona Szarejko
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Jagiellonska 28, 40-032 Katowice, Poland
| | - Miroslaw Maluszynski
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Jagiellonska 28, 40-032 Katowice, Poland
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91
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Abstract
Genome walking is a molecular procedure for the direct identification of nucleotide sequences from purified genomes. The only requirement is the availability of a known nucleotide sequence from which to start. Several genome walking methods have been developed in the last 20 years, with continuous improvements added to the first basic strategies, including the recent coupling with next generation sequencing technologies. This review focuses on the use of genome walking strategies in several aspects of the study of eukaryotic genomes. In a first part, the analysis of the numerous strategies available is reported. The technical aspects involved in genome walking are particularly intriguing, also because they represent the synthesis of the talent, the fantasy and the intelligence of several scientists. Applications in which genome walking can be employed are systematically examined in the second part of the review, showing the large potentiality of this technique, including not only the simple identification of nucleotide sequences but also the analysis of large collections of mutants obtained from the insertion of DNA of viral origin, transposons and transfer DNA (T-DNA) constructs. The enormous amount of data obtained indicates that genome walking, with its large range of applicability, multiplicity of strategies and recent developments, will continue to have much to offer for the rapid identification of unknown sequences in several fields of genomic research.
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Affiliation(s)
- Claudia Leoni
- Department of Biochemistry and Molecular Biology, University of Bari, Bari, Italy
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92
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Barkley NA, Wang ML. Application of TILLING and EcoTILLING as Reverse Genetic Approaches to Elucidate the Function of Genes in Plants and Animals. Curr Genomics 2011; 9:212-26. [PMID: 19452039 PMCID: PMC2682938 DOI: 10.2174/138920208784533656] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2008] [Revised: 04/24/2008] [Accepted: 04/28/2008] [Indexed: 11/22/2022] Open
Abstract
With the fairly recent advent of inexpensive, rapid sequencing technologies that continue to improve sequencing efficiency and accuracy, many species of animals, plants, and microbes have annotated genomic information publicly available. The focus on genomics has thus been shifting from the collection of whole sequenced genomes to the study of functional genomics. Reverse genetic approaches have been used for many years to advance from sequence data to the resulting phenotype in an effort to deduce the function of a gene in the species of interest. Many of the currently used approaches (RNAi, gene knockout, site-directed mutagenesis, transposon tagging) rely on the creation of transgenic material, the development of which is not always feasible for many plant or animal species. TILLING is a non-transgenic reverse genetics approach that is applicable to all animal and plant species which can be mutagenized, regardless of its mating / pollinating system, ploidy level, or genome size. This approach requires prior DNA sequence information and takes advantage of a mismatch endonuclease to locate and detect induced mutations. Ultimately, it can provide an allelic series of silent, missense, nonsense, and splice site mutations to examine the effect of various mutations in a gene. TILLING has proven to be a practical, efficient, and an effective approach for functional genomic studies in numerous plant and animal species. EcoTILLING, which is a variant of TILLING, examines natural genetic variation in populations and has been successfully utilized in animals and plants to discover SNPs including rare ones. In this review, TILLING and EcoTILLING techniques, beneficial applications and limitations from plant and animal studies are discussed.
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Affiliation(s)
- N A Barkley
- USDA-ARS, Plant Genetic Resources Conservation Unit (PGRCU), 1109 Experiment Street, Griffin, GA 30223, USA
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93
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Xiang D, Venglat P, Tibiche C, Yang H, Risseeuw E, Cao Y, Babic V, Cloutier M, Keller W, Wang E, Selvaraj G, Datla R. Genome-wide analysis reveals gene expression and metabolic network dynamics during embryo development in Arabidopsis. PLANT PHYSIOLOGY 2011; 156:346-56. [PMID: 21402797 PMCID: PMC3091058 DOI: 10.1104/pp.110.171702] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Accepted: 03/11/2010] [Indexed: 05/18/2023]
Abstract
Embryogenesis is central to the life cycle of most plant species. Despite its importance, because of the difficulty associated with embryo isolation, global gene expression programs involved in plant embryogenesis, especially the early events following fertilization, are largely unknown. To address this gap, we have developed methods to isolate whole live Arabidopsis (Arabidopsis thaliana) embryos as young as zygote and performed genome-wide profiling of gene expression. These studies revealed insights into patterns of gene expression relating to: maternal and paternal contributions to zygote development, chromosomal level clustering of temporal expression in embryogenesis, and embryo-specific functions. Functional analysis of some of the modulated transcription factor encoding genes from our data sets confirmed that they are critical for embryogenesis. Furthermore, we constructed stage-specific metabolic networks mapped with differentially regulated genes by combining the microarray data with the available Kyoto Encyclopedia of Genes and Genomes metabolic data sets. Comparative analysis of these networks revealed the network-associated structural and topological features, pathway interactions, and gene expression with reference to the metabolic activities during embryogenesis. Together, these studies have generated comprehensive gene expression data sets for embryo development in Arabidopsis and may serve as an important foundational resource for other seed plants.
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94
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Bolon YT, Haun WJ, Xu WW, Grant D, Stacey MG, Nelson RT, Gerhardt DJ, Jeddeloh JA, Stacey G, Muehlbauer GJ, Orf JH, Naeve SL, Stupar RM, Vance CP. Phenotypic and genomic analyses of a fast neutron mutant population resource in soybean. PLANT PHYSIOLOGY 2011; 156:240-53. [PMID: 21321255 PMCID: PMC3091049 DOI: 10.1104/pp.110.170811] [Citation(s) in RCA: 110] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2010] [Accepted: 02/11/2011] [Indexed: 05/18/2023]
Abstract
Mutagenized populations have become indispensable resources for introducing variation and studying gene function in plant genomics research. In this study, fast neutron (FN) radiation was used to induce deletion mutations in the soybean (Glycine max) genome. Approximately 120,000 soybean seeds were exposed to FN radiation doses of up to 32 Gray units to develop over 23,000 independent M2 lines. Here, we demonstrate the utility of this population for phenotypic screening and associated genomic characterization of striking and agronomically important traits. Plant variation was cataloged for seed composition, maturity, morphology, pigmentation, and nodulation traits. Mutants that showed significant increases or decreases in seed protein and oil content across multiple generations and environments were identified. The application of comparative genomic hybridization (CGH) to lesion-induced mutants for deletion mapping was validated on a midoleate x-ray mutant, M23, with a known FAD2-1A (for fatty acid desaturase) gene deletion. Using CGH, a subset of mutants was characterized, revealing deletion regions and candidate genes associated with phenotypes of interest. Exome resequencing and sequencing of PCR products confirmed FN-induced deletions detected by CGH. Beyond characterization of soybean FN mutants, this study demonstrates the utility of CGH, exome sequence capture, and next-generation sequencing approaches for analyses of mutant plant genomes. We present this FN mutant soybean population as a valuable public resource for future genetic screens and functional genomics research.
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Affiliation(s)
- Yung-Tsi Bolon
- Plant Science Research Unit, United States Department of Agriculture-Agricultural Research Service, St. Paul, Minnesota 55108, USA.
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95
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Zhou R, Benavente LM, Stepanova AN, Alonso JM. A recombineering-based gene tagging system for Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 66:712-723. [PMID: 21294796 DOI: 10.1111/j.1365-313x.2011.04524.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
One of the most information-rich aspects of gene functional studies is characterization of gene expression profiles at cellular resolution, and subcellular localization of the corresponding proteins. These studies require visualization of the endogenous gene products using specific antibodies, or, more commonly, generation of whole-gene translational fusions with a reporter gene such as a fluorescent protein. To facilitate the generation of such translational fusions and to ensure that all cis-regulatory sequences are included, we have used a bacterial homologous recombination system (recombineering) to insert fluorescent protein tags into genes of interest harbored by transformation-competent bacterial artificial chromosomes (TACs). This approach has several advantages compared to other classical strategies. First, the researcher does not have to guess what the regulatory sequences of a gene are, as tens of thousands of base pairs flanking the gene of interest can be included in the construct. Second, because the genes of interest are not amplified by PCR, there are practically no limits to the size of a gene that can be tagged. Third, there are no restrictions on the location in which the fluorescent protein can be inserted, as the position is determined by sequence homology with the recombination primers. Finally, all of the required strains and TAC clones are publically available, and the experimental procedures described here are simple and robust. Thus, we suggest that recombineering-based gene tagging should be the gold standard for gene expression studies in Arabidopsis.
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Affiliation(s)
- Rongrong Zhou
- Department of Genetics, North Carolina State University, Raleigh, NC 27695, USA
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96
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Abstract
We report here an efficient method for making targeted mutations in Arabidopsis thaliana genes. The approach uses zinc-finger nucleases (ZFNs) - enzymes engineered to create DNA double-strand breaks at specific target loci. Imprecise repair of double-strand breaks by nonhomologous end-joining generates small insertions or deletions at the cleavage site. In this protocol, constructs encoding ZFNs for specific loci are transformed into Arabidopsis by Agrobacterium-mediated transformation. ZFN expression is induced during germination to initiate mutagenesis of the target locus. Typically, more than 20% of the primary transgenics segregate loss-of-function mutations in the next generation. ZFNs make it possible to expand the range of Arabidopsis mutants available for study and to create mutations in genes missed by random mutagenesis approaches, such as those using T-DNA, transposons, or chemical mutagens.
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97
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Keurentjes JJB, Angenent GC, Dicke M, Dos Santos VAPM, Molenaar J, van der Putten WH, de Ruiter PC, Struik PC, Thomma BPHJ. Redefining plant systems biology: from cell to ecosystem. TRENDS IN PLANT SCIENCE 2011; 16:183-90. [PMID: 21215676 DOI: 10.1016/j.tplants.2010.12.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Revised: 12/03/2010] [Accepted: 12/08/2010] [Indexed: 05/06/2023]
Abstract
Molecular biologists typically restrict systems biology to cellular levels. By contrast, ecologists define biological systems as communities of interacting individuals at different trophic levels that process energy, nutrient and information flows. Modern plant breeding needs to increase agricultural productivity while decreasing the ecological footprint. This requires a holistic systems biology approach that couples different aggregation levels while considering the variables that affect these biological systems from cell to community. The challenge is to generate accurate experimental data that can be used together with modelling concepts and techniques that allow experimentally verifying in silico predictions. The coupling of aggregation levels in plant sciences, termed Integral Quantification of Biological Organization (IQ(BiO)), might enhance our abilities to generate new desired plant phenotypes.
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Affiliation(s)
- Joost J B Keurentjes
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
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Elwell AL, Gronwall DS, Miller ND, Spalding EP, Brooks TLD. Separating parental environment from seed size effects on next generation growth and development in Arabidopsis. PLANT, CELL & ENVIRONMENT 2011; 34:291-301. [PMID: 20955226 DOI: 10.1111/j.1365-3040.2010.02243.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Plant growth and development is profoundly influenced by environmental conditions that laboratory experimentation typically attempts to control. However, growth conditions are not uniform between or even within laboratories and the extent to which these differences influence plant growth and development is unknown. Experiments with wild-type Arabidopsis thaliana were designed to quantify the influences of parental environment and seed size on growth and development in the next generation. A single lot of seed was planted in six environmental chambers and grown to maturity. The seed produced was mechanically sieved into small and large size classes then grown in a common environment and subjected to a set of assays spanning the life cycle. Analysis of variance demonstrated that seed size effects were particularly significant early in development, affecting primary root growth and gravitropism, but also flowering time. Parental environment affected progeny germination time, flowering and weight of seed the progeny produced. In some cases, the parental environment affected the magnitude of (interacted with) the observed seed size effects. These data indicate that life history circumstances of the parental generation can affect growth and development throughout the life cycle of the next generation to an extent that should be considered when performing genetic studies.
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Affiliation(s)
- Angela L Elwell
- Department of Botany, University of Wisconsin, 430 Lincoln Drive, Madison, WI 53706, USA
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Bergelson J, Roux F. Towards identifying genes underlying ecologically relevant traits in Arabidopsis thaliana. Nat Rev Genet 2010; 11:867-79. [PMID: 21085205 DOI: 10.1038/nrg2896] [Citation(s) in RCA: 210] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A major challenge in evolutionary biology and plant breeding is to identify the genetic basis of complex quantitative traits, including those that contribute to adaptive variation. Here we review the development of new methods and resources to fine-map intraspecific genetic variation that underlies natural phenotypic variation in plants. In particular, the analysis of 107 quantitative traits reported in the first genome-wide association mapping study in Arabidopsis thaliana sets the stage for an exciting time in our understanding of plant adaptation. We also argue for the need to place phenotype-genotype association studies in an ecological context if one is to predict the evolutionary trajectories of plant species.
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Affiliation(s)
- Joy Bergelson
- Department of Ecology and Evolution, University of Chicago, Illinois 60637, USA.
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Detection of a gravitropism phenotype in glutamate receptor-like 3.3 mutants of Arabidopsis thaliana using machine vision and computation. Genetics 2010; 186:585-93. [PMID: 20647506 DOI: 10.1534/genetics.110.118711] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Gene disruption frequently produces no phenotype in the model plant Arabidopsis thaliana, complicating studies of gene function. Functional redundancy between gene family members is one common explanation but inadequate detection methods could also be responsible. Here, newly developed methods for automated capture and processing of time series of images, followed by computational analysis employing modified linear discriminant analysis (LDA) and wavelet-based differentiation, were employed in a study of mutants lacking the Glutamate Receptor-Like 3.3 gene. Root gravitropism was selected as the process to study with high spatiotemporal resolution because the ligand-gated Ca(2+)-permeable channel encoded by GLR3.3 may contribute to the ion fluxes associated with gravity signal transduction in roots. Time series of root tip angles were collected from wild type and two different glr3.3 mutants across a grid of seed-size and seedling-age conditions previously found to be important to gravitropism. Statistical tests of average responses detected no significant difference between populations, but LDA separated both mutant alleles from the wild type. After projecting the data onto LDA solution vectors, glr3.3 mutants displayed greater population variance than the wild type in all four conditions. In three conditions the projection means also differed significantly between mutant and wild type. Wavelet analysis of the raw response curves showed that the LDA-detected phenotypes related to an early deceleration and subsequent slower-bending phase in glr3.3 mutants. These statistically significant, heritable, computation-based phenotypes generated insight into functions of GLR3.3 in gravitropism. The methods could be generally applicable to the study of phenotypes and therefore gene function.
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