title: Mining Plant Genomic and Genetic Data Using the GnpIS Information System.
abstract: 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.
authors.affiliation: Research Unit in Genomics-Info UR1164, INRA, Université Paris-Saclay, Versailles, Route de Saint-Cyr, 78026, Versailles Cedex, France. afadam@versailles.inra.fr.
authors.forename: A-F
authors.initials: AF
authors.lastname: Adam-Blondon
authors.affiliation: Research Unit in Genomics-Info UR1164, INRA, Université Paris-Saclay, Versailles, Route de Saint-Cyr, 78026, Versailles Cedex, France.
authors.forename: M
authors.initials: M
authors.lastname: Alaux
authors.affiliation: Research Unit in Genomics-Info UR1164, INRA, Université Paris-Saclay, Versailles, Route de Saint-Cyr, 78026, Versailles Cedex, France.
authors.forename: S
authors.initials: S
authors.lastname: Durand
authors.affiliation: Research Unit in Genomics-Info UR1164, INRA, Université Paris-Saclay, Versailles, Route de Saint-Cyr, 78026, Versailles Cedex, France.
authors.forename: T
authors.initials: T
authors.lastname: Letellier
authors.affiliation: Research Unit in Genomics-Info UR1164, INRA, Université Paris-Saclay, Versailles, Route de Saint-Cyr, 78026, Versailles Cedex, France.
authors.forename: G
authors.initials: G
authors.lastname: Merceron
authors.affiliation: Research Unit in Genomics-Info UR1164, INRA, Université Paris-Saclay, Versailles, Route de Saint-Cyr, 78026, Versailles Cedex, France.
authors.forename: N
authors.initials: N
authors.lastname: Mohellibi
authors.affiliation: Research Unit in Genomics-Info UR1164, INRA, Université Paris-Saclay, Versailles, Route de Saint-Cyr, 78026, Versailles Cedex, France.
authors.forename: C
authors.initials: C
authors.lastname: Pommier
authors.affiliation: Research Unit in Genomics-Info UR1164, INRA, Université Paris-Saclay, Versailles, Route de Saint-Cyr, 78026, Versailles Cedex, France.|Research Unit GQE-Le Moulon UMR 320, INRA, Université Paris-Sud, Université Paris-Saclay, CNRS, AgroParisTech, Ferme du Moulon, 91190, Gif-sur-Yvette, France.
authors.forename: D
authors.initials: D
authors.lastname: Steinbach
authors.affiliation: Research Unit in Genomics-Info UR1164, INRA, Université Paris-Saclay, Versailles, Route de Saint-Cyr, 78026, Versailles Cedex, France.
authors.forename: F
authors.initials: F
authors.lastname: Alfama
authors.affiliation: Research Unit in Genomics-Info UR1164, INRA, Université Paris-Saclay, Versailles, Route de Saint-Cyr, 78026, Versailles Cedex, France.
authors.forename: J
authors.initials: J
authors.lastname: Amselem
authors.affiliation: Research Unit in Genomics-Info UR1164, INRA, Université Paris-Saclay, Versailles, Route de Saint-Cyr, 78026, Versailles Cedex, France.|ADRINORD Espace Recherche Innovation, 2 rue des Canonniers, 59800, Lille, France.
authors.forename: D
authors.initials: D
authors.lastname: Charruaud
authors.affiliation: Research Unit in Genomics-Info UR1164, INRA, Université Paris-Saclay, Versailles, Route de Saint-Cyr, 78026, Versailles Cedex, France.
authors.forename: N
authors.initials: N
authors.lastname: Choisne
authors.affiliation: Research Unit in Genomics-Info UR1164, INRA, Université Paris-Saclay, Versailles, Route de Saint-Cyr, 78026, Versailles Cedex, France.
authors.forename: R
authors.initials: R
authors.lastname: Flores
authors.affiliation: Research Unit in Genomics-Info UR1164, INRA, Université Paris-Saclay, Versailles, Route de Saint-Cyr, 78026, Versailles Cedex, France.
authors.forename: C
authors.initials: C
authors.lastname: Guerche
authors.affiliation: Research Unit in Genomics-Info UR1164, INRA, Université Paris-Saclay, Versailles, Route de Saint-Cyr, 78026, Versailles Cedex, France.
authors.forename: V
authors.initials: V
authors.lastname: Jamilloux
authors.affiliation: Research Unit in Genomics-Info UR1164, INRA, Université Paris-Saclay, Versailles, Route de Saint-Cyr, 78026, Versailles Cedex, France.
authors.forename: E
authors.initials: E
authors.lastname: Kimmel
authors.affiliation: Research Unit in Genomics-Info UR1164, INRA, Université Paris-Saclay, Versailles, Route de Saint-Cyr, 78026, Versailles Cedex, France.|UMR BIOGER, UMR1290, INRA, AgroParisTech, 1 avenue Lucien Bretignières, 78850, Thiverval-Grignon, France.
authors.forename: N
authors.initials: N
authors.lastname: Lapalu
authors.affiliation: Research Unit in Genomics-Info UR1164, INRA, Université Paris-Saclay, Versailles, Route de Saint-Cyr, 78026, Versailles Cedex, France.
authors.forename: M
authors.initials: M
authors.lastname: Loaec
authors.affiliation: Research Unit in Genomics-Info UR1164, INRA, Université Paris-Saclay, Versailles, Route de Saint-Cyr, 78026, Versailles Cedex, France.
authors.forename: C
authors.initials: C
authors.lastname: Michotey
authors.affiliation: Research Unit in Genomics-Info UR1164, INRA, Université Paris-Saclay, Versailles, Route de Saint-Cyr, 78026, Versailles Cedex, France.
authors.forename: H
authors.initials: H
authors.lastname: Quesneville
mesh_terms: D019295:Computational Biology / Q000379:methods*; D057225:Data Mining / Q000379:methods; D030561:Databases, Nucleic Acid; D005658:Fungi / Q000235:genetics*; D014644:Genetic Variation; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D023281:Genomics / Q000379:methods; D005838:Genotype; D010641:Phenotype; D010944:Plants / Q000235:genetics* / Q000382:microbiology*; D014584:User-Computer Interface; D064878:Web Browser
keywords: GMOD genome browser; GWAS; Genetic resources; GnpIS; InterMine; Markers; Phenotypes; Polymorphism