2015
Plant and Animal Genome (2015-01-10-2015-01-14) San Diego (USA). In : Plant and Animal Genome XXIII. 2015. n.p.
08 Jul 2015 GnpIS-Asso : A Generic Database for Managing and Exploiting Plant Genetic Association Studies Results Using High Throughput Genotyping and Phenotyping DataSteinbach, D. ; Merceron, G. ; Michotey, C. ; Flores, R.-G. ; Mohellibi, N. ; Pommier, C. ; Sauvage, C. ; Nicolas, S. ; Dubreuil, P. ; Le Gouis, J.
We will present a new functionality developed in GnpIS information system to manage association studies data (GWAS). A query form is available on http://urgi.versailles.inra.fr/gnpis portal and directly at this URL https://urgi.versailles.inra.fr/association/association/viewer.do#form. The tool allows plant scientists or breeders to get associations values between traits and markers obtained in several association studies. Several filters are available to refine the query, such as the species, trait (s), or marker (s) or panel of germplasms. The tool gives also the possibility in a second round of analysis, to add a new set of filters, i) on statistical values, or ii) on treatment done in the study, or iii) on the location and iv) year of the phenotyping trial or according to the v) statistical model chosen to do the analysis. It allows to view graphically the results with dedicated plots (QQPlot, Manhattan Plot), generated dynamically and to extract data in files to continue the analysis with external tools. After selecting the best markersassociated to trait of interest, the tool allows also to automatically jump on the genome to find where this marker is located on chromosomes and to identify in a very simpler way which genes or other markers or features of interest are near it. This tool is already now used for dealing GWAS studies (association, genotyping and phenotyping data) for 2 species: tomato and maize, data that are already referenced in two 2 publications and will also manage wheat data in 2015.
Creation date: 20 Oct 2015
eZ PublishPublication supervisor: A-F. Adam-Blondon
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