1. MGIS: managing banana (Musa spp.) genetic resources information and high-throughput genotyping data
- Author
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Valentin Guignon, L. Gueco, Agus Sutanto, T. Ayala-Silva, Christophe Jenny, K. Jelali, J. Adeka, Janet Paofa, P. Ngo Xuan, B. Dowiya, Rachel Chase, G. Vangu Paka, J. Daniells, Julie Sardos, Max Ruas, B. Effa effa, L. Herradura, G. Yi, Nicolas Roux, J. Kilangi, E. Kempenaers, C. Pavis, A. Andrieu, Tom Hazekamp, C. Tossou, J. Sandoval, H. Duvergey, Ibobondji. L., Guilhem Sempere, Mathieu Rouard, Yann Hueber, D. Thiemele, I. van den Houwe, C.P. Chao, S. Muhangi, Brian M. Irish, Parc Scientifique Agropolis II, Partenaires INRAE, South Green Bioinformatics Platform, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), USDA-ARS : Agricultural Research Service, University of Kisangani, Taiwan Banana Research Institute, Department of Agriculture, Fisheries and Forestry ( DAFF ), Institut de l'environnement et de recherches agricoles, Centre national de la recherche scientifique et technologique, University of the Philippines (UP System), Davao National Crop Research and Development Center, African Center for Research on Bananas and Plantains = Centre Africain de Recherches sur Bananiers et Plantains (CARBAP), Université Catholique de Louvain = Catholic University of Louvain (UCL), Agricultural Research Institute, National Agricultural Research Organization, Fruit and Vegetable Research Institute, Research Institute, Agrosystèmes tropicaux (ASTRO), Institut National de la Recherche Agronomique (INRA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre National de Recherche Agronomique de Côte d'Ivoire (CNRA), Institut National des Recherches Agricoles du Bénin (INRAB), Corporación Bananera Nacional (CORBANA), Indonesian Centre for Horticultural Research and Development, Guangdong Academy of Agricultural Sciences (GDAAS), Bioversity International [Montpellier], Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), CGIAR, CGIAR Research Program on Roots, Tubers and Bananas (RTB), CGIAR Research Programme for Managing and Sustaining Crop Collections (Genebanks Platform), Belgian Development Cooperation and Humanitarian Aid (DGD), German Ministry for Economic Cooperation and Development (BMZ) GIZ, Ruas, Max, Rouard, M., and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)
- Subjects
0106 biological sciences ,0301 basic medicine ,Germplasm ,Genotyping Techniques ,Computer science ,update ,[SDV]Life Sciences [q-bio] ,Interoperability ,Banque de gènes ,computer.software_genre ,01 natural sciences ,F30 - Génétique et amélioration des plantes ,[SHS]Humanities and Social Sciences ,collection ,Databases, Genetic ,Information system ,provides insights ,2. Zero hunger ,Database ,plants ,genomics ,evolution ,visualization ,exploration ,management ,rice ,Database schema ,High-Throughput Nucleotide Sequencing ,Schema (genetic algorithms) ,C30 - Documentation et information ,Système d'information ,[SDE]Environmental Sciences ,Seeds ,Data mining ,User interface ,General Agricultural and Biological Sciences ,Banque de données ,Génotype ,Information Systems ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,Ressource génétique végétale ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,Génie génétique ,Genetic diversity ,Génome ,Musa ,030104 developmental biology ,Database Tool ,computer ,Software ,010606 plant biology & botany - Abstract
Unraveling the genetic diversity held in genebanks on a large scale is underway, due to advances in Next-generation sequence (NGS) based technologies that produce high-density genetic markers for a large number of samples at low cost. Genebank users should be in a position to identify and select germplasm from the global genepool based on a combination of passport, genotypic and phenotypic data. To facilitate this, a new generation of information systems is being designed to efficiently handle data and link it with other external resources such as genome or breeding databases. The Musa Germplasm Information System (MGIS), the database for global ex situ-held banana genetic resources, has been developed to address those needs in a user-friendly way. In developing MGIS, we selected a generic database schema (Chado), the robust content management system Drupal for the user interface, and Tripal, a set of Drupal modules which links the Chado schema to Drupal. MGIS allows germplasm collection examination, accession browsing, advanced search functions, and germplasm orders. Additionally, we developed unique graphical interfaces to compare accessions and to explore them based on their taxonomic information. Accession-based data has been enriched with publications, genotyping studies and associated genotyping datasets reporting on germplasm use. Finally, an interoperability layer has been implemented to facilitate the link with complementary databases like the Banana Genome Hub and the MusaBase breeding database. Database URL: https://www.crop-diversity.org/mgis/
- Published
- 2017
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