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Mining plant genomic and genetic data using the GnpIS information system

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Adam-Blondon, Anne-Francoise | Alaux, Michael | Durand, Sophie | Letellier, Thomas | Merceron, Guillaume | Mohellibi, Nacer | Pommier, Cyril | Steinbach, Delphine | Alfama-Depauw, Françoise | Amselem, Joëlle | Charruaud, Dorothée | Choisne, Nathalie | Flores, Raphaël-Gauthier | Guerche, Claire | Jamilloux, Véronique | Kimmel, Erik | Lapalu, Nicolas | Loaec, Mikaël | Michotey, Célia | Quesneville, Hadi

Edité par CCSD ; Springer -

GnpIS is an information system designed to help scientists working on plants and fungi to decipher the molecular and genetic architecture of trait variations by facilitating the navigation through genetic, genomic, and phenotypic information. The purpose of the present chapter is to illustrate how users can (1) explore datasets from phenotyping experiments in order to build new datasets for studying genotype × environment interactions in traits, (2) browse into the results of other genetic analysis data such as GWAS to generate or check working hypothesis about candidate genes or to identify important alleles and germplasms for breeding programs, and (3) explore the polymorphism in specific area of the genome using InterMine, JBrowse tools embedded in the GnpIS information system.

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