Face Caucus SGN: Associating Solanaceae loci with phenotype

SGN: Associating Solanaceae loci with phenotypes

The Sol Genomics Network (SGN, http://www.sgn.cornell.edu/) is a Clade Oriented Database (COD) containing genomic, genetic and taxonomic information for species in the Euasterid clade.

We have recently added to SGN databases of Solanaceae genes and phenotypes, with a framework for simple and advanced searches by name, function, phenotype, map position, sequence, and ontology annotations. Phenotypes are represented as accessions of populations (mutants and mapping populations), and may be linked to one or more loci.

Loci may be linked to one or more phenotyped accessions related directly to the underlying gene or to a specific allele. Each locus and phenotype have a curated page with internal links to other SGN information pages, such as maps, markers, unigenes, and images, and external links to other databases, such as GenBank, PubMed, GO, and PO.

An on-line submission and feedback pipeline allows authorized Sol community-members to submit, edit, or obsolete database objects, data, images, and annotations. These permissions vary according to the user-type. The framework for editing the database is now being extended for developing an online ontology annotation tool, and storing complex quantitative and qualitative phenotype data.

The high level of conservation of genome organization in Solanaceae makes the family a unique subject to explore the basis of its phenotypic diversity. The small number of Solanaceae phenotypes with a known gene sequence calls for a comparative approach for revealing gene function and their associated phenotypes.