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Plant Methods

Donna M Bond, Nick W Albert, Robyn H Lee, Gareth B Gillard, Chris M Brown, Roger P Hellens, Richard C Macknight
BACKGROUND: Transcription factors (TFs) coordinate precise gene expression patterns that give rise to distinct phenotypic outputs. The identification of genes and transcriptional networks regulated by a TF often requires stable transformation and expression changes in plant cells. However, the production of stable transformants can be slow and laborious with no guarantee of success. Furthermore, transgenic plants overexpressing a TF of interest can present pleiotropic phenotypes and/or result in a high number of indirect gene expression changes...
2016: Plant Methods
Chantal Le Marié, Norbert Kirchgessner, Patrick Flütsch, Johannes Pfeifer, Achim Walter, Andreas Hund
BACKGROUND: Phenotyping of genotype-by-environment interactions in the root-zone is of major importance for crop improvement as the spatial distribution of a plant's root system is crucial for a plant to access water and nutrient resources of the soil. However, so far it is unclear to what extent genetic variations in root system responses to spatially varying soil resources can be utilized for breeding applications. Among others, one limiting factor is the absence of phenotyping platforms allowing the analysis of such interactions...
2016: Plant Methods
Guo-Qian Yang, Yun-Mei Chen, Jin-Peng Wang, Cen Guo, Lei Zhao, Xiao-Yan Wang, Ying Guo, Li Li, De-Zhu Li, Zhen-Hua Guo
BACKGROUND: The double digest restriction-site associated DNA sequencing technology (ddRAD-seq) is a reduced representation sequencing technology by sampling genome-wide enzyme loci developed on the basis of next-generation sequencing. ddRAD-seq has been widely applied to SNP marker development and genotyping on animals, especially on marine animals as the original ddRAD protocol is mainly built and trained based on animal data. However, wide application of ddRAD-seq technology in plant species has not been achieved so far...
2016: Plant Methods
Patrick C Boyle, Simon Schwizer, Sarah R Hind, Christine M Kraus, Susana De la Torre Diaz, Bin He, Gregory B Martin
BACKGROUND: The plant plasma membrane is a key battleground in the war between plants and their pathogens. Plants detect the presence of pathogens at the plasma membrane using sensor proteins, many of which are targeted to this lipophilic locale by way of fatty acid modifications. Pathogens secrete effector proteins into the plant cell to suppress the plant's defense mechanisms. These effectors are able to access and interfere with the surveillance machinery at the plant plasma membrane by hijacking the host's fatty acylation apparatus...
2016: Plant Methods
Mitchell A Ellison, Michael B McMahon, Morris R Bonde, Cristi L Palmer, Douglas G Luster
BACKGROUND: Rust fungi are obligate pathogens with multiple life stages often including different spore types and multiple plant hosts. While individual rust pathogens are often associated with specific plants, a wide range of plant species are infected with rust fungi. To study the interactions between these important pathogenic fungi and their host plants, one must be able to differentiate fungal tissue from plant tissue. This can be accomplished using the In situ hybridization (ISH) protocol described here...
2016: Plant Methods
Filippo Biscarini, Nelson Nazzicari, Chiara Broccanello, Piergiorgio Stevanato, Simone Marini
BACKGROUND: Noise (errors) in scientific data is endemic and may have a detrimental effect on statistical analyses and experimental results. The effects of noisy data have been assessed in genome-wide association studies for case-control experiments in human medicine. Little is known, however, on the impact of noisy data on genomic predictions, a widely used statistical application in plant and animal breeding. RESULTS: In this study, the sensitivity to noise in the data of five classification methods (K-nearest neighbours-KNN, random forest-RF, ridge logistic regression-LR, and support vector machines with linear or radial basis function kernels) was investigated...
2016: Plant Methods
Atena Haghighattalab, Lorena González Pérez, Suchismita Mondal, Daljit Singh, Dale Schinstock, Jessica Rutkoski, Ivan Ortiz-Monasterio, Ravi Prakash Singh, Douglas Goodin, Jesse Poland
BACKGROUND: Low cost unmanned aerial systems (UAS) have great potential for rapid proximal measurements of plants in agriculture. In the context of plant breeding and genetics, current approaches for phenotyping a large number of breeding lines under field conditions require substantial investments in time, cost, and labor. For field-based high-throughput phenotyping (HTP), UAS platforms can provide high-resolution measurements for small plot research, while enabling the rapid assessment of tens-of-thousands of field plots...
2016: Plant Methods
Michal Slota, Miroslaw Maluszynski, Iwona Szarejko
BACKGROUND: Genetic studies on the molecular mechanisms of the regulation of root growth require the characterisation of a specific root phenotype to be linked with a certain genotype. Such studies using classical labour-intensive methods are severely hindered due to the technical limitations that are associated with the impeded observation of the root system of a plant during its growth. The aim of the research presented here was to develop a reliable, cost-effective method for the analysis of a plant root phenotype that would enable the precise characterisation of the root system architecture of cereals...
2016: Plant Methods
François Postic, Claude Doussan
BACKGROUND: To face climate change and subsequent rainfall instabilities, crop breeding strategies now include root traits phenotyping. Rapid estimation of root traits in controlled conditions can be achieved by using parallel electrical capacitance and its linear correlation with root dry mass. The aim of the present study was to improve robustness and efficiency of methods based on capacitance and other electrical variables, such as serial/parallel resistance, conductance, impedance or reactance...
2016: Plant Methods
Peter Lootens, Tom Ruttink, Antje Rohde, Didier Combes, Philippe Barre, Isabel Roldán-Ruiz
BACKGROUND: Genetic studies and breeding of agricultural crops frequently involve phenotypic characterization of large collections of genotypes grown in field conditions. These evaluations are typically based on visual observations and manual (destructive) measurements. Robust image capture and analysis procedures that allow phenotyping large collections of genotypes in time series during developmental phases represent a clear advantage as they allow non-destructive monitoring of plant growth and performance...
2016: Plant Methods
Christian Jeudy, Marielle Adrian, Christophe Baussard, Céline Bernard, Eric Bernaud, Virginie Bourion, Hughes Busset, Llorenç Cabrera-Bosquet, Frédéric Cointault, Simeng Han, Mickael Lamboeuf, Delphine Moreau, Barbara Pivato, Marion Prudent, Sophie Trouvelot, Hoai Nam Truong, Vanessa Vernoud, Anne-Sophie Voisin, Daniel Wipf, Christophe Salon
BACKGROUND: In order to maintain high yields while saving water and preserving non-renewable resources and thus limiting the use of chemical fertilizer, it is crucial to select plants with more efficient root systems. This could be achieved through an optimization of both root architecture and root uptake ability and/or through the improvement of positive plant interactions with microorganisms in the rhizosphere. The development of devices suitable for high-throughput phenotyping of root structures remains a major bottleneck...
2016: Plant Methods
Martin Schäfer, Christoph Brütting, Ian T Baldwin, Mario Kallenbach
BACKGROUND: Plant metabolites are commonly functionally classified, as defense- or growth-related phytohormones, primary and specialized metabolites, and so forth. Analytical procedures for the quantifications of these metabolites are challenging because the metabolites can vary over several orders of magnitude in concentrations in the same tissues and have very different chemical characteristics. Plants clearly adjust their metabolism to respond to their prevailing circumstances in very sophisticated ways that blur the boundaries among these functional or chemically defined classifications...
2016: Plant Methods
David Dobnik, Ana Lazar, Tjaša Stare, Kristina Gruden, Vivianne G A A Vleeshouwers, Jana Žel
BACKGROUND: Virus-induced gene silencing (VIGS) is an optimal tool for functional analysis of genes in plants, as the viral vector spreads throughout the plant and causes reduced expression of selected gene over the whole plant. Potato (Solanum tuberosum) is one of the most important food crops, therefore studies performing functional analysis of its genes are very important. However, the majority of potato cultivars used in laboratory experimental setups are not well amenable to available VIGS systems, thus other model plants from Solanaceae family are used (usually Nicotiana benthamiana)...
2016: Plant Methods
Michal Goralski, Paula Sobieszczanska, Aleksandra Obrepalska-Steplowska, Aleksandra Swiercz, Agnieszka Zmienko, Marek Figlerowicz
BACKGROUND: Nicotiana benthamiana has been widely used in laboratories around the world for studying plant-pathogen interactions and posttranscriptional gene expression silencing. Yet the exploration of its transcriptome has lagged behind due to the lack of both adequate sequence information and genome-wide analysis tools, such as DNA microarrays. Despite the increasing use of high-throughput sequencing technologies, the DNA microarrays still remain a popular gene expression tool, because they are cheaper and less demanding regarding bioinformatics skills and computational effort...
2016: Plant Methods
Abdul Kareem, Dhanya Radhakrishnan, Xin Wang, Subhikshaa Bagavathiappan, Zankhana B Trivedi, Kaoru Sugimoto, Jian Xu, Ari Pekka Mähönen, Kalika Prasad
BACKGROUND: Plants have the remarkable property to elaborate entire body plan from any tissue part. The conversion of lateral root primordium (LRP) to shoot is an ideal method for plant propagation and for plant researchers to understand the mechanism underlying trans-differentiation. Until now, however, a robust method that allows the efficient conversion of LRP to shoot is lacking. This has limited our ability to study the dynamic phases of reprogramming at cellular and molecular levels...
2016: Plant Methods
Chathura Gunasekara, Avinash Subramanian, Janaki Venkata Ram Kumar Avvari, Bin Li, Su Chen, Hairong Wei
BACKGROUND: Plant biologists frequently need to examine if a sequence motif bound by a specific transcription or translation factor is present in the proximal promoters or 3' untranslated regions (3' UTR) of a set of plant genes of interest. To achieve such a task, plant biologists have to not only identify an appropriate algorithm for motif searching, but also manipulate the large volume of sequence data, making it burdensome to carry out or fulfill. RESULT: In this study, we developed a web portal that enables plant molecular biologists to search for DNA motifs especially degenerate ones in custom sequences or the flanking regions of all genes in the 50 plant species whose genomes have been sequenced...
2016: Plant Methods
Muhammad Shahzad Anjam, Yvonne Ludwig, Frank Hochholdinger, Chisato Miyaura, Masaki Inada, Shahid Siddique, Florian M W Grundler
BACKGROUND: Cyst nematodes are biotrophs that form specialized feeding structures in the roots of host plants, which consist of a syncytial fusion of hypertrophied cells. The formation of syncytium is accompanied by profound transcriptional changes and active metabolism in infected tissues. The challenge in gene expression studies for syncytium has always been the isolation of pure syncytial material and subsequent extraction of intact RNA. Root fragments containing syncytium had been used for microarray analyses...
2016: Plant Methods
Petr Cápal, Takashi R Endo, Jan Vrána, Marie Kubaláková, Miroslava Karafiátová, Eva Komínková, Isabel Mora-Ramírez, Winfriede Weschke, Jaroslav Doležel
BACKGROUND: Identification of transgene insertion sites in plant genomes has practical implications for crop breeding and is a stepping stone to analyze transgene function. However, single copy sequences are not always easy to localize in large plant genomes by standard approaches. RESULTS: We employed flow cytometric chromosome sorting to determine chromosomal location of barley sucrose transporter construct in three transgenic lines of common wheat. Flow-sorted chromosomes were used as template for PCR and fluorescence in situ hybridization to identify chromosomes with transgenes...
2016: Plant Methods
Wenhao Yan, Dijun Chen, Kerstin Kaufmann
BACKGROUND: The efficiency of multiplex editing in plants by the RNA-guided Cas9 system is limited by efficient introduction of its components into the genome and by their activity. The possibility of introducing large fragment deletions by RNA-guided Cas9 tool provides the potential to study the function of any DNA region of interest in its 'endogenous' environment. RESULTS: Here, an RNA-guided Cas9 system was optimized to enable efficient multiplex editing in Arabidopsis thaliana...
2016: Plant Methods
Anna Ostendorp, Steffen Pahlow, Jennifer Deke, Melanie Thieß, Julia Kehr
BACKGROUND: Grafting is a well-established technique for studying long-distance transport and signalling processes in higher plants. While oilseed rape has been the subject of comprehensive analyses of xylem and phloem sap to identify macromolecules potentially involved in long-distance information transfer, there is currently no standardised grafting method for this species published. RESULTS: We developed a straightforward collar-free grafting protocol for Brassica napus plants with high reproducibility and success rates...
2016: Plant Methods
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