Documentation system for plant transformation service and research

Background: In plant transformation, method compliance is critical for success. Transformation methods are complicated and tend to evolve over time. Until the complete method is published, method details are often partially orally transmitted and thus bound to a few people. Their documentation in text files are often a mixture of material and method description with many references to other sources especially to media description. These media are complex and often composed from several commercially available mixtures plus individually prepared stocks. The actual transformation experiment is generally documented in lab books, in which deviations from the methods and results are reported. Additionally, work schedules are planned in diaries. Both paper-based sources lack backup copies and miss unambiguous links to method descriptions and media recipes. Description: To solve the problem, we devised a standard-operation-procedure system based on a Microsoft Access database containing the interlinked modules 'Media', 'Methods' and 'Experiments'. The Media module contains all basic chemicals, stocks and complex media. In this module, complex media are composed from other elements of the Media module, thus mimicking the workflows of media preparation in the lab. The Media module is made attractive to the user by functions that generate file cards and labels. The Methods module describes each method stepwise and links the steps to the media. Copy functions allow cloning of old methods to document method evolution without alteration of the old methods. Activation and inactivation functions in the Media and the Methods module remove outdated entries from active use. The Experiments module links the method to experiment specific information. This module generates a lab-book like user interface and a work schedule, and it contains a simple result section. Conclusion: The system has been evolved and tested over several years in a transformation service unit, where it increased efficiency. Additionally, the system provided rapid access to data for quality control and decision making. The system can be easily modified for the use in other research environments

Expression profiling of rice cultivars differing in their tolerance to long-term drought stress

Understanding the molecular basis of plant performance under water-limiting conditions will help to breed crop plants with a lower water demand. We investigated the physiological and gene expression response of drought-tolerant (IR57311 and LC-93-4) and drought-sensitive (Nipponbare and Taipei 309) rice (Oryza sativa L.) cultivars to 18 days of drought stress in climate chamber experiments. Drought stressed plants grew significantly slower than the controls. Gene expression profiles were measured in leaf samples with the 20 K NSF oligonucleotide microarray. A linear model was fitted to the data to identify genes that were significantly regulated under drought stress. In all drought stressed cultivars, 245 genes were significantly repressed and 413 genes induced. Genes differing in their expression pattern under drought stress between tolerant and sensitive cultivars were identified by the genotype × environment (G × E) interaction term. More genes were significantly drought regulated in the sensitive than in the tolerant cultivars. Localizing all expressed genes on the rice genome map, we checked which genes with a significant G × E interaction co-localized with published quantitative trait loci regions for drought tolerance. These genes are more likely to be important for drought tolerance in an agricultural environment. To identify the metabolic processes with a significant G × E effect, we adapted the analysis software MapMan for rice. We found a drought stress induced shift toward senescence related degradation processes that was more pronounced in the sensitive than in the tolerant cultivars. In spite of higher growth rates and water use, more photosynthesis related genes were down-regulated in the tolerant than in the sensitive cultivars

Confounding Factors in Container-Based Drought Tolerance Assessments in Solanum tuberosum

Potato is an important food crop with high water-use-efficiency but low drought tolerance. The bottleneck in drought tolerance breeding is phenotyping in managed field environments. Fundamental research on drought tolerance is predominantly done in container-based test systems in controlled environments. However, the portability of results from these systems to performance under field conditions is debated. Thus, we analyzed the effects of climate conditions, container size, starting material, and substrate on yield and drought tolerance assessment of potato genotypes compared to field trials. A leave one out assessment indicated a minimum of three field trials for stable tolerance prediction. The tolerance ranking was highly reproducible under controlled-conditions, but weakly correlated with field performance. Changing to variable climate conditions, increasing container size, and substituting cuttings by seed tubers did not improve the correlation. Substituting horticultural substrate by sandy soil resulted in yield and tuber size distributions similar to those under field conditions. However, as the effect of the treatment × genotype × substrate interaction on yield was low, drought tolerance indices that depend on relative yields can be assessed on horticultural substrate also. Realistic estimates of tuber yield and tuber size distribution, however, require the use of soil-based substrates

Finding Phenotypic Biomarkers for Drought Tolerance in <i>Solanum tuberosum</i>

Climate change models predict increased drought frequencies. Maintaining yield stability necessitates drought-tolerant crops. However, their breeding is challenging; drought tolerance is a multigene trait with significant environment interaction. Thus, the training of genomic selection models requires phenotyping a large genotype population under arid conditions. We aimed to identify phenotypic tolerance traits that facilitate the screening of large populations in the field. We performed three trials on 20 tetraploid Solanum tuberosum ssp. tuberosum genotypes with significant drought tolerance variation. Plants were subjected to early, late and long-term drought under variable climate conditions. For each stress scenario, the drought tolerance index DRYMp was calculated from the relative tuber starch yield. A laser scanner system measured canopy development continuously over the crop’s lifecycle and provided estimates of leaf movement and canopy growth features. Growth curves were evaluated by logistic regression. Different multiple regression approaches were compared for their ability to predict tolerance from phenotype data of optimally watered or stressed plants. We established that early short-term stress can be used as a proxy for long-term stress in the absence of genetic variation for drought stress recovery or memory. The gen-otypes varied significantly in most canopy features. Leaf-area-based features combined significant genotype effects with environmental stability. Multiple regression models based on single-day data outperformed those based on the regression curve parameter. The models included leaf area and leaf position parameters and partially reproduced prior findings on siblings in a genetically more diverse population

A plant resource and experiment management system based on the Golm Plant Database as a basic tool for omics research

<p>Abstract</p> <p>Background</p> <p>For omics experiments, detailed characterisation of experimental material with respect to its genetic features, its cultivation history and its treatment history is a requirement for analyses by bioinformatics tools and for publication needs. Furthermore, meta-analysis of several experiments in systems biology based approaches make it necessary to store this information in a standardised manner, preferentially in relational databases. In the Golm Plant Database System, we devised a data management system based on a classical Laboratory Information Management System combined with web-based user interfaces for data entry and retrieval to collect this information in an academic environment.</p> <p>Results</p> <p>The database system contains modules representing the genetic features of the germplasm, the experimental conditions and the sampling details. In the germplasm module, genetically identical lines of biological material are generated by defined workflows, starting with the import workflow, followed by further workflows like genetic modification (transformation), vegetative or sexual reproduction. The latter workflows link lines and thus create pedigrees. For experiments, plant objects are generated from plant lines and united in so-called cultures, to which the cultivation conditions are linked. Materials and methods for each cultivation step are stored in a separate ACCESS database of the plant cultivation unit. For all cultures and thus every plant object, each cultivation site and the culture's arrival time at a site are logged by a barcode-scanner based system. Thus, for each plant object, all site-related parameters, e.g. automatically logged climate data, are available. These life history data and genetic information for the plant objects are linked to analytical results by the sampling module, which links sample components to plant object identifiers. This workflow uses controlled vocabulary for organs and treatments. Unique names generated by the system and barcode labels facilitate identification and management of the material. Web pages are provided as user interfaces to facilitate maintaining the system in an environment with many desktop computers and a rapidly changing user community. Web based search tools are the basis for joint use of the material by all researchers of the institute.</p> <p>Conclusion</p> <p>The Golm Plant Database system, which is based on a relational database, collects the genetic and environmental information on plant material during its production or experimental use at the Max-Planck-Institute of Molecular Plant Physiology. It thus provides information according to the MIAME standard for the component 'Sample' in a highly standardised format. The Plant Database system thus facilitates collaborative work and allows efficient queries in data analysis for systems biology research.</p

In the Sample Composer, a component of a sample is defined by selecting one plant object from the filtered object list and combining it with information about sampling time, organ and treatment information

Definitions of the ontology terms, identifier and alias of the selected plant object are displayed at the bottom of the page. The example shows four samples, the fourth sample has three components.<p><b>Copyright information:</b></p><p>Taken from "A plant resource and experiment management system based on the Golm Plant Database as a basic tool for omics research"</p><p>http://www.plantmethods.com/content/4/1/11</p><p>Plant Methods 2008;4():11-11.</p><p>Published online 21 May 2008</p><p>PMCID:PMC2409336.</p><p></p