Internet Resources for Gene Expression Analysis in Arabidopsis thaliana

The number of online databases and web-tools for gene expression analysis in Arabidopsis thaliana has increased tremendously during the last years. These resources permit the database-assisted identification of putative cis-regulatory DNA sequences, their binding proteins, and the determination of common cis-regulatory motifs in coregulated genes. DNA binding proteins may be predicted by the type of cis-regulatory motif. Further questions of combinatorial control based on the interaction of DNA binding proteins and the colocalization of cis-regulatory motifs can be addressed. The database-assisted spatial and temporal expression analysis of DNA binding proteins and their target genes may help to further refine experimental approaches. Signal transduction pathways upstream of regulated genes are not yet fully accessible in databases mainly because they need to be manually annotated. This review focuses on the use of the AthaMap and PathoPlant® databases for gene expression regulation analysis and discusses similar and complementary online databases and web-tools. Online databases are helpful for the development of working hypothesis and for designing subsequent experiments

Anaerobic and pathogen-induced resistance gene expression in transgenic potatoes

Das phytopathogene Bakterium Erwinia carotovora verursacht die Kartoffelkrankheiten Schwarzbeinigkeit und Knollennaßfäule. Das Bakterium verbreitet sich in Kartoffelknollen bevorzugt unter sauerstoffarmen Bedingungen. Deshalb wurde eine gentechnische Resistenzstrategie entwickelt, welche die Expression eines antimikrobiellen Faktors gezielt unter anaeroben Bedingungen vorsieht. Zur anaeroben Fremdproteinsynthese wurde der in Tabak anaerob induzierbare Mais GapC4 Promotor gewählt. Zur Untersuchung des Induktionsverhaltens dieses Promotors in der Kartoffel wurden transgene GapC4-GUS Pflanzen hergestellt. Dabei stellte sich heraus, daß der Promotor unter anaeroben Bedingungen in allen Teilen der Pflanze stark induziert wird, während er aerob nicht aktiv ist. Nach der Infektion von Knollenscheiben mit Erwinia carotovora zeigte sich ebenfalls eine Induzierbarkeit des Promotors. Dabei beschränkte sich die Induktion des Promotors nicht nur auf infiziertes Knollengewebe, sondern auch in benachbartem noch intaktem Gewebe wurden Signale festgestellt. Auch sterile Erwinia-Extrakte und aufgereinigte pektolytische Enzyme waren in der Lage, den Promotor in Knollenscheiben zu induzieren. Als Resistenzgenkonstrukt wurde der GapC4 Promotor mit dem Gen für T4-Lysozym fusioniert. Dieses Konstrukt wurde zur Transformation von Kartoffel eingesetzt. Zehn transgene Linien wurden in fünf Knollenscheibentests auf Resistenz gegenüber Erwinia carotovora getestet. Dabei zeigten sich in vielen Linien signifikante Resistenzsteigerungen verglichen mit den Kontrollen. Bei einigen Linien wurde ein ähnlich gutes Resistenzverhalten im Vergleich zu einer Kontrolle mit erhöhter Resistenz festgestellt, bei der das T4-Lysozym unter der Kontrolle des 35S Promotors exprimiert wird.The phytopathogenic bacterium Erwinia carotovora causes the potato diseases black leg and soft rot. In potato tubers, this bacterium preferentially spreads under low oxygen conditions. Therefore, a genetic resistance engineering strategy was developed, which comprises the expression of an antimicrobial factor specifically under anaerobic conditions. The maize GapC4 promoter was chosen for anaerobic foreign protein synthesis. Transgenic GapC4-GUS plants were produced to analyze the induction pattern of this promoter in the potato. The promoter is strongly induced under anaerobic conditions in all tissues of the potato plant, while it is not aerobically active. The promoter is also induced after infection of tuber disks with Erwinia carotovora. Additionally, promoter induction was not only limited to infected tuber tissue, but was detected also in neighboring still intact tissue. Also sterile Erwinia extract and isolated pectolytic enzymes were able to induce the promoter in tuber disks. The resistance gene construct consisted in a fusion of the GapC4 promoter with the gene for T4 lysozyme. This construct was employed for transformation of potato. Ten transgenic lines were tested in five tuber disk tests for resistance to Erwinia carotovora. Significant increases of resistance were observed in many lines compared to control lines. A similarly good resistance level was detected in some lines in comparison to a control with increased resistance, which harbors the T4 lysozyme gene under the control of the 35S promoter

PathoPlant(®): a platform for microarray expression data to analyze co-regulated genes involved in plant defense responses

Plants react to pathogen attack by expressing specific proteins directed toward the infecting pathogens. This involves the transcriptional activation of specific gene sets. PathoPlant(®), a database on plant–pathogen interactions and signal transduction reactions, has now been complemented by microarray gene expression data from Arabidopsis thaliana subjected to pathogen infection and elicitor treatment. New web tools enable identification of plant genes regulated by specific stimuli. Sets of genes co-regulated by multiple stimuli can be displayed as well. A user-friendly web interface was created for the submission of gene sets to be analyzed. This results in a table, listing the stimuli that act either inducing or repressing on the respective genes. The search can be restricted to certain induction factors to identify, e.g. strongly up- or down-regulated genes. Up to three stimuli can be combined with the option of induction factor restriction to determine similarly regulated genes. To identify common cis-regulatory elements in co-regulated genes, a resulting gene list can directly be exported to the AthaMap database for analysis. PathoPlant is freely accessible at

A MAGIC population as an approach to the conservation and development of genetic diversity of winter barley for breeding purposes by on-farm management

Zusätzliche genetische Diversität in Züchtungsprogrammen und im Wintergerstenanbau sind erforderlich, um den Auswirkungen des Klimawandels besser begegnen zu können. Um bestehende Aktivitäten der Wintergerstenzüchter zu ergänzen, wurde 2008 mit einem Programm zur Populationszüchtung begonnen. Von insgesamt 227 deutschen Wintergerstesorten, die im Zeitraum von 1914 bis 2003 eine Sortenzulassung erlangten, wurden 58 Sorten mit SSR-Markern genetisch analysiert. Davon wurden 32 möglichst divergente Elternlinien ausgewählt und anschließend über 6 Generationen nach einem multiparentalen Kreuzungsschema (MAGIC) miteinander gekreuzt. Die daraus resultierenden 324 Linien wurden zu einer heterogenen MAGIC-Population vereint. Um sich an regionale Bedingungen anzupassen und auszudifferenzieren, werden derzeit MAGIC-Subpopulationen in einem Netzwerk bestehend aus 12 unterschiedlichen, ökogeografisch kontrastierenden Standorten in Deutschland an- und nachgebaut und somit als Evolutionsramsche einer natürlichen standortbedingten Selektion unter­zogen. Der Nachbau wird über einen Zeitraum von 6 bis 8 Jahren erfolgen und beinhaltet für jeden Standort zwei unterschiedliche Intensitätsstufen bezüglich Düngung und Pflanzenschutzmaßnahmen. Für die Protokollierung der Anbaubedingungen, die Erfassung von Evaluierungsdaten, aber auch zur Dokumentation des MAGIC-Kreuzungsschemas sowie für nachfolgende Datenanalysen wurde das Informationssystem ROBUSTUM entwickelt. Der beschriebene Ansatz erlaubt eine kontinuierliche und dynamische Anpassung der natürlichen genetischen Vielfalt in unseren Kulturpflanzen an klimatische und standortbedingte agronomische Veränderungen. Damit eignen sich Evolutionsramsche besonders für den ökologischen Anbau, aber auch für Grenzlagen und Standorte mit ungünstigen Boden- und Witterungs­bedingungen. Vor dem Hintergrund zunehmender extremer Klima­bedingungen können diese Eigenschaften in Zukunft noch eine weitaus größere Bedeutung für die Landwirtschaft erlangen. Populationen tragen ferner zum Erhalt bzw. Aufbau einer möglichst breiten genetischen Vielfalt bei. Mit diesem Ansatz lässt sich das Potenzial von Evolutionsramschen abschätzen, das zur Entwicklung nachhaltiger landwirtschaftlicher Produktionssysteme beitragen kann.Additional genetic diversity in crop breeding programmes and in crop production is required to better cope with the impact of climate change. To complement ongoing activities of winter barley breeders, an evolutionary plant breeding programme has been initiated in 2008. Out of 227 German winter barley varieties released between 1914 and 2003, a set of 58 varieties was genetically analysed using SSR markers. Among these, 32 genotypes representing the genetic diversity of the whole set were crossed according to the Multi-parent Advanced Generation Inter-Cross scheme (MAGIC) over six generations. The resulting 324 lines were combined to form a heterogeneous MAGIC winter barley population. In order to adapt to regional agricultural conditions, MAGIC sub-­­­populations are currently being cultivated within a network of 12 eco-geographically contrasting locations and subjected to natural site-related selection as evolutionary bulks. Cultivation and seed saving will take place over a period of 6 to 8 years under high and low input production conditions. An information system named ROBUSTUM has been developed for consistent recording of cultivation conditions, of characterisation and evaluation data as well as for documentation of the pedigree and for sub­sequent data analyses. The present approach enables a continuous and dynamic adaptation of the natural genetic diversity present in our crops to climatic and site-related agronomic changes. This makes the evolutionary bulk particularly suitable for organic cultivation, but also for marginal sites and locations with unfavourable soil and weather conditions. In view of increasingly extreme climatic conditions, these properties may become even more important for agriculture in the future. Populations also contribute to the maintenance and development of a genetic diversity as broad as possible. This approach enables estimation of the potential of evolutionary bulks to contribute to the development of sustainable agricultural production systems

AthaMap web tools for the analysis and identification of co-regulated genes

The AthaMap database generates a map of cis-regulatory elements for the whole Arabidopsis thaliana genome. This database has been extended by new tools to identify common cis-regulatory elements in specific regions of user-provided gene sets. A resulting table displays all cis-regulatory elements annotated in AthaMap including positional information relative to the respective gene. Further tables show overviews with the number of individual transcription factor binding sites (TFBS) present and TFBS common to the whole set of genes. Over represented cis-elements are easily identified. These features were used to detect specific enrichment of drought-responsive elements in cold-induced genes. For identification of co-regulated genes, the output table of the colocalization function was extended to show the closest genes and their relative distances to the colocalizing TFBS. Gene sets determined by this function can be used for a co-regulation analysis in microarray gene expression databases such as Genevestigator or PathoPlant. Additional improvements of AthaMap include display of the gene structure in the sequence window and a significant data increase. AthaMap is freely available at

AthaMap web tools for database-assisted identification of combinatorial cis-regulatory elements and the display of highly conserved transcription factor binding sites in Arabidopsis thaliana

The AthaMap database generates a map of cis-regulatory elements for the Arabidopsis thaliana genome. AthaMap contains more than 7.4 × 10(6) putative binding sites for 36 transcription factors (TFs) from 16 different TF families. A newly implemented functionality allows the display of subsets of higher conserved transcription factor binding sites (TFBSs). Furthermore, a web tool was developed that permits a user-defined search for co-localizing cis-regulatory elements. The user can specify individually the level of conservation for each TFBS and a spacer range between them. This web tool was employed for the identification of co-localizing sites of known interacting TFs and TFs containing two DNA-binding domains. More than 1.8 × 10(5) combinatorial elements were annotated in the AthaMap database. These elements can also be used to identify more complex co-localizing elements consisting of up to four TFBSs. The AthaMap database and the connected web tools are a valuable resource for the analysis and the prediction of gene expression regulation at