Cartogratree: Enabling Forest Tree Genomics through Association Studies

Successfully identifying the genes and specific alleles associated with traits of interest in forest trees is dependent on the ability to access genotype, phenotype, and environmental data. The future of these association studies lies in next-generation sequence data, ontologically sound phenotypes, and geo-referenced measures.  Cartogratree leverages modern web technologies to interact with the Google Maps API on the front-end and web services, including SSWAP (Simple Semantic Web Architecture and Protocol), to connect to data points on the back-end.  CartograTree serves genomic and phenotype data from the TreeGenes database, phenotypes from the TRY-DB resource, and environmental data from Ameriflux and WorldClim. Combined, these resources amount to over 10,000 trees, 90,000 phenotypes, and 10 million genotypes. Along with the user’s ability to upload custom data in the form of phenotype or environmental measures, data mutability is supported by allowing the sub-setting and merging of sets of tree samples based on their phylogenies, previous studies, or geographical location. Custom parameterization (e.g. removing missing data) is also supported.  The user interface allows both simple and complex searches, and can be initiated based on functional information, sequence identifiers, and tree identifiers. The cornerstone feature is the integration of the iPlant Cyberinfrastructure’s SSWAP which connects the user to the data available for a given tree, as well as software that can take that data and perform association analysis, such as TASSEL. Explore Cartogratree at: http://dendrome.ucdavis.edu/cartogratree.