PAG-XI  Plant & Animal Genomes XI Conference

January 11-15, 2003
Town & Country Convention Center
San Diego, CA

Workshop: Allele Mining
            

W9

GENE-MINEing AGRONOMICALLY IMPORTANT TRAITS IN GERMPLASM

Guy Davenport1 , William D. Beavis2 , Marco C.A.M. Bink3 , Klaus J. Dehmer4 , Jo Dicks1 , David S. Dixon2 , Vanessa Fens5 , Matthias Frisch6 , Gerrit Gort3 , Eva Křístová7 , Aleš Lebeda8 , Thomas Metz9 , Albrecht E. Melchinger6 , Johan Peleman10 , David Pink11 , Jochen Reif6 , Jeroen Rouppe van der Voort10 , Rob van Treuren5 , Theo J.L. van Hintum5

1 John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, United Kingdom
2 National Centre for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, New Mexico 870505, USA
3 Plant Research International, The Netherlands P.O. Box 16, 6700 AA, Wageningen, The Netherlands
4 Institute of Plant Genetics and Crop Plant Research, GeneBank, Correnstrasse 3, D-06466 Gatersleben, Germany
5 Centre for Genetic Resources, P.O. Box 16, 6700 AA, The Netherlands
6 University of Hohenheim, Fruwirthstrasse 21, 70593 Stuttgart, Germany
7 Research Institute of Crop Production Praha-Ruzyně, Division of Genetics and Plant Breeding, Dept. of Gene Bank, Šlechtitelů 11, CZ-783 71 Olomouc-Holice, Czech Republic
8 Palacký University Olomouc, Faculty of Science, Dept of Botany, Šlechtitelů 11, CZ-783 71 Olomouc-Holice, Czech Republic
9 International Plant Genetic Resources Institute (IPGRI), Via dei Tre Denari 472/a, 00057 Maccarese, Rome, Italy
10 KeyGene N.V., Agro Business Park, 6708 PW Wageningen, The Netherlands
11 Horticultural Research International, Wellsebourne Plant Genetics and Biotechnology Dept, Warwick CV35 9EF, United Kingdom

The objective of GENE-MINE (http://www.gene-mine.org) is to develop and evaluate an integrative information system for the analysis and exploitation of plant germplasm collections. The system includes new analysis methods that reveal the relationships between large-scale molecular marker data, phenotypic traits and environmental data in order to establish a more productive, informative and cost-effective collection.

  1. Integrating disparate data sources

    We have developed a generic extensible model for associating properties, such as traits, genetic data and molecular data with accession data.

  2. Asking biological questions of the data

    A user-friendly germplasm query management system is currently under development. It will allow users to perform complex queries on the data using simple germplasm related terms.

  3. Analysing the data in novel ways

    Since often the analysis needed does not exist yet, or is only suited for small data sets, a range of new methods and algorithms are being developed that will be allow the answering genebank questions.

  4. Visualising the results

    We are developing novel ways to visualise the results from analyses of large data sets.

  5. Study properties of the strategies developed

    In addition to assessing the effectiveness of the different strategies developed in the project, we are currently investigating the accessibility, redundancy and genetic diversity in wild Lactuca genebank collections.

    6.

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