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 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.