The current challenge in biology is to link the rapidly accumulating sequence information to phenotypic information. The Sol Genomics Network (SGN, http://solgenomics.net) is a clade oriented database for the Solanaceae, including tomato, potato, pepper and petunia, and other Asterid plants. Genome to phenome linkages have been the focus of SGN for much of the past 10 years. Sequence data is obtained from large sequencing projects (tomato, potato) and resources such as Genbank, while the phenotypic data is obtained from sources such as the SolCAP project (http://solcap.msu.edu), and submissions by individual researchers. Currently, SGN has phenotypic information on more than 20,000 accessions, including free text descriptions, ontology based annotations, literature references, and images. To precisely describe the phenotypes of the Solanaceae, the Solanaceae Phenotype Ontology (SP) has been developed, as a pre-composed ontology linked to Plant Ontology (PO) and PATO. The phenotypic database at SGN is based on the Chado Natural Diversity module, which was co-developed by a number of databases, including SGN, the Genome Database for Roseaceae (GDR, http://rosaceae.org), and VectorBase. To link genotype to phenotype, the solQTL web tool was implemented in R and Perl that allows QTL analyses to be run on the fly on the website for a trait that has the required data (genotype and phenotype) in the database. Other approaches, such as Association Genetics, and application to breeders using Genomic Selection approaches, will be implemented in the future.
The Sol Genomics Nework (SGN, http://solgenomics.net) is a clade oriented database for the Solanaceae and closely related Asterids such as Rubiaceae, including coffee. Currently, SGN has several resources available for coffee, such as annotated transcript assemblies, a community curated set of over a hundred loci, and CoffeaCyc, a pathway database based on the Pathway Tools software suite. The SGN database has many further resources that as of yet do not contain coffee data. For example, SGN can store phenotypic and genotypic information for plant accessions. Currently, there are only a handful of coffee accessions in the database, and no genotypic information has been uploaded. Easy to use web interfaces for users to provide these data are available. If both genotypic and phenotypic information are in the database, for certain types of mapping populations, SGN can perform QTL and other analyses directly on the web. SGN also has a number of comparative features based on genetic maps, full genome sequences, and gene family data that we would like to apply to coffee in the near future.
solQTL (http://solgenomics.net/qtl) is a web application for dynamically linking phenotype of complex traits to their underlying genetic causes. It has a user-friendly web-interface to upload raw quantitative trait loci (QTL) data to the Sol Genomics Network (SGN, http://solgenomics.net) database and interactively runs QTL analyses using user-specified statistical methods. Predicted QTL regions are automatically and seamlessly cross-linked to annotated genomes and genetic maps, with tools such as GBrowse and SGN`s comparative map viewer. This deep cross-referencing of predicted QTLs to relevant genomic, expression, and phenotypic data at SGN and external databases will help researchers identify potential candidate genes and more closely linked markers, and better understand the underlying genetics of complex traits.
Also presented in poster: P0979, Monday January 16, 2012, 3:00 - 4:30 pm.