Abstract:
BACKGROUND:Plant breeding and genetics demand fast, exact and reproducible phenotyping. Efficient statistical evaluation of phenotyping data requires standardised data storage ensuring long-term data availability while maintaining intellectual property rights. This is state of the art at phenomics centres, which, however, are unavailable for most scientists. For them we developed a simple and cost-efficient system, the Phenotyper, which employs mobile devices or personal digital assistants (PDA) for on-site data entry and open-source software for data management. RESULTS:A graphical user interface (GUI) on a PDA replaces paper-based form sheet and data entry on a desktop. The user can define his phenotyping schemes in a web tool without in-depth knowledge of the system and thus adjust it more easily to new research aspects than in a classical laboratory information management system (LIMS). In the Phenotyper, schemes are built from controlled vocabulary gained from published ontologies. Vocabulary and schemes are stored in a database that also manages the user access. From the web page, schemes are downloaded as extended markup language (XML) files for the transfer to the PDA and the exchange between users. On the PDA, the GUI displays the schemes and stores data in comma separated value format and XML format. After manual quality control, data are uploaded via a web page to an independently hosted results database, in which data are stored in an entity-attribute-value structure to provide maximum flexibility. Datasets are linked to the original and curated data files stored on a file server. The ownership stamp, project affiliation and date stamp of a dataset are used to regulate data access, which is restricted to data belonging to the user or to his projects and data, for which the embargo period has ended. By export of standardised ASCII reports to long-term data storage facility, long-term accessibility allows searching, citing and use of raw data beyond the lifetime of the database. The Phenotyper is available to the scientific community for use and further development. CONCLUSIONS:The Phenotyper provides a well-structured, but flexible data acquisition and management structure for mobile on-site measurements for efficient evaluation and shared use of data.
journal_name
Plant Methodsjournal_title
Plant methodsauthors
Köhl K,Gremmels Jdoi
10.1186/s13007-015-0069-3subject
Has Abstractpub_date
2015-04-07 00:00:00pages
25issn
1746-4811pii
69journal_volume
11pub_type
杂志文章相关文献
Plant Methods文献大全abstract:BACKGROUND:A multitude of different imaging systems are already available to image genetically altered RNA species; however, only a few of these techniques are actually suitable to visualize endogenous RNA. One possibility is to use fluorescently-labelled and hybridization-sensitive probes. In order to yield more infor...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/1746-4811-10-15
更新日期:2014-05-31 00:00:00
abstract:Background:Measurements of rind and culm thickness and stem radius/diameter are important to biomechanical, ecological and physiological plant studies. However, many methods of measuring rind thickness and diameter are labor intensive and induce plant fatality. A novel rind puncture methodology for obtaining measuremen...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/s13007-020-00587-4
更新日期:2020-04-01 00:00:00
abstract:BACKGROUND:Microsatellites are popular molecular markers in many plant species due to their stable and highly polymorphic nature. A number of analysis methods have been described but analyses of these markers are typically performed on cumbersome polyacrylamide gels or more conveniently by capillary electrophoresis on ...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/1746-4811-4-8
更新日期:2008-05-19 00:00:00
abstract:BACKGROUND:The main aim of this study was to improve fungal resistance in bread wheat via transgenesis. Transgenic wheat plants harboring barley chitinase (chi26) gene, driven by maize ubi promoter, were obtained using biolistic bombardment, whereas the herbicide resistance gene, bar, driven by the CaMV 35S promoter wa...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/s13007-017-0191-5
更新日期:2017-05-22 00:00:00
abstract:Background:Non-contact resonant ultrasound spectroscopy (NC-RUS) has been proven as a reliable technique for the dynamic determination of leaf water status. It has been already tested in more than 50 plant species. In parallel, relative water content (RWC) is highly used in the ecophysiological field to describe the de...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/s13007-019-0511-z
更新日期:2019-11-07 00:00:00
abstract:Background:Most bacteria are not culturable, but can be identified through molecular methods such as metagenomics studies. Due to specific metabolic requirements and symbiotic relationships, these bacteria cannot survive on typical laboratory media. Many economically and medically important bacteria are unculturable; i...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/s13007-019-0465-1
更新日期:2019-07-31 00:00:00
abstract:BACKGROUND:Protoplasts isolated from leaves are useful materials in plant research. One application, the transient expression of recombinant genes using Arabidopsis mesophyll protoplasts (TEAMP), is currently commonly used for studies of subcellular protein localization, promoter activity, and in vivo protein-protein i...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/1746-4811-5-16
更新日期:2009-11-24 00:00:00
abstract:Background:Functional genomic studies using genetics approaches of conifers are hampered by the complex and enormous genome, long vegetative growth period, and exertion in genetic transformation. Thus, the research carried out on gene function in Pinus tabuliformis is typically performed by heterologous expression base...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/s13007-020-00594-5
更新日期:2020-04-10 00:00:00
abstract:BACKGROUND:The inability to genetically transform any fern species has been a major technical barrier to unlocking fern biology. Initial attempts to overcome this limitation were based on transient transformation approaches or achieved very low efficiencies. A highly efficient method of stable transformation was recent...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/s13007-015-0080-8
更新日期:2015-07-03 00:00:00
abstract:BACKGROUND:The cultivar Micro-Tom (MT) is regarded as a model system for tomato genetics due to its short life cycle and miniature size. However, efforts to improve tomato genetic transformation have led to protocols dependent on the costly hormone zeatin, combined with an excessive number of steps. RESULTS:Here we re...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/1746-4811-6-23
更新日期:2010-10-07 00:00:00
abstract:Motivation:In 2005, researchers from the French National Research Institute for Agriculture, Food and Environment (Institut national de recherche pour l'agriculture, l'alimentation et l'environnement, INRAE) started a collaboration with the French farmers' seed network Réseau Semences Paysannes (RSP) on bread wheat par...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/s13007-020-00640-2
更新日期:2020-07-23 00:00:00
abstract:Background:Plant roots release a variety of organic compounds into the soil which alter the physical, chemical and biological properties of the rhizosphere. Root exudates are technically challenging to measure in soil because roots are difficult to access and exudates can be bound by minerals or consumed by microorgani...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/s13007-018-0380-x
更新日期:2018-12-20 00:00:00
abstract: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 th...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/s13007-016-0135-5
更新日期:2016-06-24 00:00:00
abstract:Background:Root is the principal part of plants to absorb water and nutrient, anchor the plant and affect yield and quality. Non-destructive detection of root traits is difficult to perform due to the hidden nature of the root. Therefore, improved methods to measure roots are necessary to support plant breeding, and op...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/s13007-019-0414-z
更新日期:2019-03-23 00:00:00
abstract:Background:Plant root apex is the major part to direct the root growth and development by responding to various signals/cues from internal and soil environments. To study and understand root system biology particularly at a molecular and cellular level, an Arabidopsis T-DNA insertional enhancer trap line J3411 expressi...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/s13007-019-0393-0
更新日期:2019-01-31 00:00:00
abstract:BACKGROUND:In the contexts of genomics, post-genomics and systems biology approaches, data integration presents a major concern. Databases provide crucial solutions: they store, organize and allow information to be queried, they enhance the visibility of newly produced data by comparing them with previously published r...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/1746-4811-7-8
更新日期:2011-03-29 00:00:00
abstract:BACKGROUND:Identifying cis-regulatory elements is critical in understanding the direct and indirect regulatory mechanisms of gene expression. Current approaches include DNase-seq, a technique that combines sensitivity to the nonspecific endonuclease DNase I with high throughput sequencing to identify regions of regulat...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/s13007-015-0087-1
更新日期:2015-09-04 00:00:00
abstract:BACKGROUND:Kinome profiling aims at the parallel analysis of kinase activities in a cell. Novel developed arrays containing consensus substrates for kinases are used to assess those kinase activities. The arrays described in this paper were already used to determine kinase activities in mammalian systems, but since sub...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/1746-4811-3-3
更新日期:2007-02-12 00:00:00
abstract:Background:Deep rooting is one of the most promising plant traits for improving crop yield under water-limited conditions. Most root phenotyping methods are designed for laboratory-grown plants, typically measuring very young plants not grown in soil and not allowing full development of the root system. Results:This s...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/s13007-019-0533-6
更新日期:2019-12-09 00:00:00
abstract:BACKGROUND:Effects of abiotic and biotic stresses on plant photosynthetic performance lead to fitness and yield decrease. The maximum quantum efficiency of photosystem II (F v/F m) is a parameter of chlorophyll fluorescence (ChlF) classically used to track changes in photosynthetic performance. Despite recent technical...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/s13007-015-0067-5
更新日期:2015-03-26 00:00:00
abstract::Over the last 10 years, high-density SNP arrays and DNA re-sequencing have illuminated the majority of the genotypic space for a number of organisms, including humans, maize, rice and Arabidopsis. For any researcher willing to define and score a phenotype across many individuals, Genome Wide Association Studies (GWAS)...
journal_title:Plant methods
pub_type: 杂志文章,评审
doi:10.1186/1746-4811-9-29
更新日期:2013-07-22 00:00:00
abstract:BACKGROUND:Pentatricopeptide-repeat proteins (PPRs) characterized by tandem arrays of a degenerate 35-amino-acid repeat (PPR motif) can bind a single strand RNA and regulate organelle gene expression at the post-transcriptional level, including RNA cleavage, splicing, editing and stability etc. PPRs are conserved in al...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/s13007-020-00696-0
更新日期:2020-11-18 00:00:00
abstract:BACKGROUND:The elucidation of complex biological systems requires integration of multiple molecular parameters. Accordingly, high throughput methods like transcriptomics, proteomics, metabolomics and lipidomics have emerged to provide the tools for successful system-wide investigations. Unfortunately, optimized analysi...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/s13007-016-0146-2
更新日期:2016-11-10 00:00:00
abstract:Background:To investigate potential effects of herbicide phytotoxic on crops, a major challenge is a lack of non-destructive and rapid methods to detect plant growth that could allow characterization of herbicide-resistant plants. In such a case, hyperspectral imaging can quickly obtain the spectrum for each pixel in t...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/s13007-020-00576-7
更新日期:2020-03-05 00:00:00
abstract: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 trans...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/s13007-016-0141-7
更新日期:2016-10-19 00:00:00
abstract:BACKGROUND:Starch is the most important source of calories for human nutrition and the majority of it is produced by cereal farming. Starch is also used as a renewable raw material in a range of industrial sectors. It can be chemically modified to introduce new physicochemical properties. In this way starch is adapted ...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/1746-4811-8-36
更新日期:2012-09-07 00:00:00
abstract::[This corrects the article DOI: 10.1186/s13007-017-0166-6.]. ...
journal_title:Plant methods
pub_type: 杂志文章,已发布勘误
doi:10.1186/s13007-017-0249-4
更新日期:2017-11-16 00:00:00
abstract:Background:Low pollen viability may limit grapevine yield under certain conditions, causing relevant economic losses to grape-growers. It is usually evaluated by the quantification of the number of viable and non-viable pollen grains that are present in a sample after an adequate pollen grain staining procedure. Althou...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/s13007-017-0267-2
更新日期:2018-01-09 00:00:00
abstract:BACKGROUND:The data generated during a course of a biological experiment/study can be sometimes be massive and its management becomes quite critical for the success of the investigation undertaken. The accumulation and analysis of such large datasets often becomes tedious for biologists and lab technicians. Most of the...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/1746-4811-5-18
更新日期:2009-12-10 00:00:00
abstract:BACKGROUND:Leaf rust (LR), caused by Puccinia triticina and is an important disease of wheat (Triticum aestivum L.). The most sustainable method for controlling rust diseases is deployment of cultivars incorporating adult plant resistance (APR). However, phenotyping breeding populations or germplasm collections for res...
journal_title:Plant methods
pub_type: 杂志文章
doi:10.1186/s13007-016-0117-7
更新日期:2016-03-02 00:00:00