Plant & Animal Genome V Conference
Town & Country Hotel, San Diego, CA, January 12-16, 1997.
PAG-V: W43 - A GRASS COMPARATIVE MAPPING DATA COOPERATIVE: DISCUSSION PANEL AT THE IGGI WORKSHOP
W43
A GRASS COMPARATIVE MAPPING DATA COOPERATIVE: DISCUSSION PANEL AT THE IGGI WORKSHOP
CARTINHOUR, SAM(1), DAVE MATTHEWS(2), EDIE PAUL(2), MARY POLACCO(3), JO DICKS(4)
1. Crop Biotechnology Center and , Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843 USA
2. Dept. of Plant Breeding and Biometry, Cornell University, Ithaca, NY 14853 USA
3. Plant Genetics Research Unit, USDA-ARS, University of Missouri, Columbia, MO 65211 USA
4. Bioinformatics Group, Department of Computing, John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK
The comparison of grass genetic maps relies on detailed, high-quality data representing the relationships between genomes. Several database groups are currently compiling comparative data and integrating it into their databases. However, given the scope of data and the amount of time required for curation, it would be advantageous to coordinate individual efforts and focus together on constructing a single comparative data set. The result would be a more complete resource which could be used to add value to each database, reference data across databases, resolve problems in nomenclature, and design new displays for presenting comparative maps. The purpose of the panel is to stimulate discussion of how such a collaboration could be implemented. There are several interesting scientific and informatics issues that such a cooperative would need to address. For example, putative homologies between genomes can be based on different kinds of evidence such as probe cross-hybridization, sequence analysis, biochemical function and naked-eye phenotype. Each of these types of homology requires different methods for detection and documentation and is amenable to varying degrees of automation by computer methods. Also, some loci are less precisely mapped than others (e.g., mapped to chromosomal regions by deletions or as QTLs) and these may need special handling. Clusters of loci as well as individual loci will also be related, and criteria for clustering and relationships between cluster members may need close attention. Dealing with these complexities will require a serious investment of resources by those groups who agree to participate in the cooperative, including substantial involvement by geneticists and physiologists as well as informatics specialists.