Plant & Animal Genome VII Conference

W133

GRAIN PROBES TO GrainGenes: ISSUES ON PROMOTING CANDIDATE GENES

¹ USDA ARS Western Regional Research Center, Albany, CA 94710-1105 USA
² USDA ARS, ³ Cornell University, Ithaca, New York 14853 USA

In the area of functional genomics, one goal is to be able to make sense of sequences derived from expressed sequence tags (ESTs). In many instances, the cDNAs used in these analyses are randomly derived from libraries differing by environment and tissue. However, in some cases, the origin of the ESTs are from clones used to construct physical maps (i.e. Heun et al., 1991). Another goal is to merge the information derived from EST analyses of sequences and match it up with loci defined in physical genome maps. Within the GrainGenes genome database, a standard has been followed for the naming of genes and loci for wheat (McIntosh et al., 1998), and in some cases, has also been applied to maps of other small grains species. Sequencing efforts are now analyzing ESTs used to develop these maps (Lazo et al., 1998; Sorrells et al. 1999) and beginning to deduce identities of the ESTs. The identities of these sequences are becoming evident through database screening against ever-growing genome sequence databases (Nucleotide Sequence Database Collaboration) using sequence similarity computer programs (i.e. BLAST, Altschul et al., 1990). Some changes in the naming conventions used to identify the mapped loci are proposed. Only experimental evidence can prove the identity of an EST, but such preliminary identities may serve as a template to infer functional expression within the plant. If the researcher can view the candidate identity effectively, this may lead to quick confirmation of the sequence. We hope to bring up issues concerned with dealing with these unconfirmed sequences, and elevating them from their candidate status.