Plant & Animal Genome VI Conference

P5

ASSIGNING PUTATIVE GENE FUNCTIONS TO MAPPED PROBE LOCI IN THE GRAINGENES GENOME DATABASE AND SEQUENCING OF WHEAT ENDOSPERM cDNAs

1. USDA ARS, Western Regional Research Center, Albany, CA 94710-1105
2. Department of Plant Breeding & Biometry, Cornell University, Ithaca, NY 14853
3. Stanford DNA Sequence and Technology Center, Palo Alto, CA 94304

The genome database GrainGenes has been a useful tool for collecting and displaying research information for the cereals community. A major component of the data in GrainGenes is genetic maps and the associated information on probes used to construct those maps. In many instances the probes were derived from random cDNAs. Although these cDNAs were used as probes to map specific genes, nothing was known of their identity and/or function. Efforts were taken to gain sequence data from these mapped probes. In addition, random cDNAs from a wheat endosperm library were single-pass sequenced to evaluate the usefulness of such data and to assess some of the parameters that would be involved in a larger-scale expressed sequence tag (EST) program. In this effort sequences were compared against NCBI genome data banks using BLAST search programs. To date, over 1000 sequences have been analyzed. About 26% of the mapped sequences and 49% of the wheat endosperm library sequences had good matches to archived database sequences. Many of the mapped sequences were unique. Some of the endosperm sequences were represented more than once, and were associated with storage proteins and common housekeeping enzymes. Sequences which did not match wheat sequences in the database often matched sequences of closely related cereals. This data is being integrated into the GrainGenes database and display tools are being developed to make searches within the database more informative.