Modules of the PGRC

Service and research of the PGRC is organized in 7 modules that usually comprise more than one research group of the institute.
For more information, please contact the corresponding module coordinator.

• Module 1, Genomics Service
• Module 2, Bioinformatics
• Module 3, Genetic Diversity and Genome Mapping
• Module 4, Gene Isolation
• Module 5, Transcriptome Analysis and Functional Genomics
• Module 6, Proteome analysis
• Module 7, Genetic Engineering

Module 1, Genomics Service

Service activities for all scientific groups of the Institute of Plant Genetics and Crop Plant Research inlcude sequencing (MegaBace 1000 capillary sequencer) with or without DNA template preparation, PCR amplification and spotting of DNA on nylon-based macroarrays, maintenance of EST clone collections and clone picking. The picking and shipping of single EST clones or small clone collections is offered to the scientific community free of charge. The PGRC service activities are adjusted in regular intervals to the needs of scientific groups of the institute.

Coordinator Module 1: Patrick Schweizer (schweiz@ipk-gatersleben.de)

Module 2, Bioinformatics

This modul supports IPK biologists with the development and maintenance of molecular biological databases, molecular biological data integration, installation of bioinformatics tools for various in silico analysis tasks and consulting in all these fields.

Coordinator Module 2: Uwe Scholz (scholz@ipk-gatersleben.de)

Module 3, Genetic Diversity and Genome Mapping

The IPK genebank holds about 145,000 accessions of different crop species and their wild relatives. The analysis of genetic diversity in these materials allows the inference of, e.g., domestication modes, geographical differentiation and local adaptations within crops, or the identification of traits linked with cultivation. Ample experience exists for the generation and analysis of genetic diversity at the molecular level using markers such as AFLPs, SSRs and SNPs or DNA sequence analysis. Linkage mapping is performed mainly in barley and wheat in various mapping populations. For analysis of quantitative traits (QTLs), besides classical symmetrical mapping populations, the advanced backcross strategy has been applied and is used for the development of specific introgression and nearly isogenic lines.

Coordinators Module 3: Frank Blattner (Genetic Diversity; blattner@ipk-gatersleben.de) and Marion Röder (Genome Mapping; roder@ipk-gatersleben.de)

Module 4, Gene Isolation

The module provides the coordination of resources and expertise for gene isolation in cereal crops, with emphasis on barley. Resources available on the basis of co-operations are a BAC library of the barley cultivar Morex (CUGI, USA) together with high-density colony filters and BAC-DNA pools (from GABI-PLANT, L. Altschmied) for screening by hybridisation or PCR, respectively. Further BAC libraries from cereal (Secale cereale) and other plant species are expected to become available either as IPK resource or within international co-operations in year 2005/2006. Standard technology for BAC-contig analysis is available including know-how about sub-cloning strategies and marker development for chromosome walking.

As an additional resource for gene isolation, a TILLING population is under development in the barley cultivar Barke (GABI-TILL) and will be open to customised screens on the basis of co-operations. Access to additional TILLING populations developed by the SCRI (Dundee, Scotland) is planned on the basis of the PGRC-Barley Genome Net co-operative.

Coordinator Module 4: Nils Stein (stein@ipk-gatersleben.de)

Module 5, Transcriptome Analysis and Functional Genomics

A collection of approximately 200,000 EST sequences from many tissues of barley has been established at the PGRC. This resource has been used e.g. for the establishment of a transcript map of barley, for the production of a 10K cDNA array (barleyPGRC1), besides for supporting the design of the Barley1 chip of Affymetrix Co.. Moreover,a high-throughput RNAi screening system has been established in order to address gene function in pathogen-attacked or drough-stressed barley.

Coordinator Module 5: Lothar Altschmied (lothar@ipk-gatersleben.de)

Module 6, Proteome analysis

Proteome analysis has been established for various tissues of Arabidopsis, barley and tobacco. Separation of complex protein mixtures is based on 2-D gel electrophoresis using different pH gradients in the first dimension and SDS-PAGE in the second dimension. Relevant spots are identified by mass spectrometry. Peptide mass fingerprinting is performed by MALDI-TOF-MS. Additional information on peptides is obtained by ESI-MS/MS including de novo sequencing capability. Database searches are performed using public or internal databases and are assisted by module 2 (Bioinformatics). Major projects deal with the investigation of the protein content and composition in barley seeds.

Coordinator Module 6: Hans-Peter Mock (mock@ipk-gatersleben.de)

Module 7, Genetic Engineering

Agrobacterium-based genetic transformation of barley, wheat, pea, carrot and Nicotiana benthamiana is performed preferably in cooperation with IPK-internal research groups but also with the scientific community. The service includes allocation of appropriate generic vectors, advice on binary vector construction, generation of transgenic plants as well as molecular proof of their transgenic nature. In barley, T_1 -seeds homozygous for the transgene can be provided within about 10 month via transformation of androgenetic pollen cultures.

Coordinator Module 7: Jochen Kumlehn (kumlehn@ipk-gatersleben.de)