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.
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Acknowledgments
We gratefully thank Aminah-Olivia Keliet, Btissam Aissaoui, Laura Burlot, Loic Couderc, Guillaume Cornut, Mathieu Labernardière, Mathilde Lainé, Aristide Lebreton, Florian Philippe, Sandrine Nsigue-Meilo, and Daphnée Verdelet for their help in some developments, data insertion, and trainings on GnpIS in the last 4 years. We also warmly thank our past and present projects’ partners who are providing the data inserted in the database and who are at the origin of many improvements. For the most important recent improvements, we specially thank Stephane Nicolas, Mathilde Causse, Christopher Sauvage, Jacques Le Gouis, Alain Charcosset, Patrice This, Thierry Lacombe, Gilles Charmet, François-Xavier Oury, Arnaud Gauffreteau, Etienne Paux, and Frédéric Choulet. GnpIS has been developed in the last 4 years with the support of INRA, the ANR p rojects of the “Investment for the Future” call Phenome (https://www.phenome-fppn.fr/), Aker (http://www.aker-betterave.fr/en/), Amaizing (ANR-10-BTBR-03), Breedwheat (ANR-10-BTBR-02) and Peamust (ANR-11-BTBR-02), the ANR project GnpAsso (ANR-10-GENM-0006), the TransPLANT FP7 European infrastructure project (project no 283496).
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Adam-Blondon, AF. et al. (2017). Mining Plant Genomic and Genetic Data Using the GnpIS Information System. In: van Dijk, A. (eds) Plant Genomics Databases. Methods in Molecular Biology, vol 1533. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6658-5_5
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DOI: https://doi.org/10.1007/978-1-4939-6658-5_5
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