Plant & Animal Genomes XIII Conference

January 15-19, 2005
Town & Country Convention Center
San Diego, CA

An Update On Gramene QTL Data Module

Junjian Ni¹ , Immanuel Yap¹ , Pankaj Jaiswal¹ , Edward Buckler³ , Doreen Ware² , Ken Clark² , Wei Zhao² , Liya Ren² , Lincoln Stein² , Susan McCouch¹

¹  Department of Plant Breeding, Cornell University, Ithaca, New York, 14853, USA

²  Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA

³  USDA-ARS, Institute for Genomic Diversity, Cornell University, Ithaca, New York, 14853, USA

We continue to curate and develop the QTL data module within Gramene. The current release of the QTL database houses trait and map position information for more than 7738 QTL. This includes most published QTL from rice, pearl millet and foxtail millet and some other QTL from maize, oat and barley. We are developing a set of standardized trait terms that are currently classified into nine different trait categories and used to organize and cluster the QTLs. These trait terms form the basis of Gramene’s Trait Ontology. Besides the previous simple searching and trait category browsing options, a new "QTL Power Search" interface has been developed to help users do more comprehensive queries to the database. We will continue to curate QTL studies for all cereal crops in coordination with other species databases such as MaizeGDB and GrainGenes. In the future, we plan more comprehensive curation for existing QTL, including methods of trait evaluation, descriptions of the environment, QTL statistics, allelic interactions, germplasm and population information, as well as the development of a repository for raw segregation data and phenotypic scores underlying QTL studies. Users are encouraged to participate in the improvement of the phenotype search through suggestions for search utilities and visual displays, as well as direct data submission and curation.