Data Collection, Processing and Integration for Systems Biology Research on Drought Tolerance

The subject of the POLAPGEN-BD* project is systems biology research on drought tolerance in barley. The plant material comprises three populations of RILs obtained from crosses between European and Asian varieties, their parents and a pool of varieties registered in Poland. They are observed in control and drought conditions in field and greenhouse experiments, both during stress and on harvest, for transcriptomic, proteomic, metabolomic, physiological, anatomical and yield-related traits; they are also SSR- and SNP-genotyped. The results of the project will consist of genetic markers, tolerance measurement and testing methods, and a catalogue varieties' allelic information. For data collection an instance of MySQL Germinate database schema has been developed, with a search facility and a Biomart user interface. Genotypic and phenotypic data obtained by partners are verified and deposited using a custom Java application. Trait names are standardised and have been submitted as a barley-related set to Crop Ontology. Data are processed using commercial (Joinmap, Genevestigator, ImageMaster 2D) or publicly available programs (MetAlign, TargetSearch, Mapman, Cytoscape), or own scripts in R and Genstat (e.g. for processing of UPLC/UV secondary metabolite profiles). The developed data storage and processing infrastructure is crucial for achievement of the project’s objectives and presents a set of solutions which will be also used in other systems biology investigations performed by the Consortium.

*POLAPGEN-BD project no. WND-POIG.01.03.01-00-101/08 (www.polapgen.eu) is co-financed by the EU Cohesion Fund through the Polish Innovative Economy Program 2007-2013; some results obtained in collaboration with EC FP7 transPlant project no. RI-283496 (www.transplantdb.eu)