MGIS: Managing banana (Musa spp.) genetic resources information and high-throughput genotyping data

Authors: RUAS, MAX - Bioversity International; GUIGNON, VALENTIN - Bioversity International; SEMPERE, GUILHEM - Cirad, France; SARDOS, JULIE - Bioversity International; HUEBER, YANN - Bioversity International; DUVERHEY, HUGO - Bioversity International; ANDRIEU, ALEXIS - Bioversity International; CHASE, RACHEL - Bioversity International; JENNY, CRISTOPHE - Cirad, France; HAZEKAMP, TOM - Bioversity International; JELALI, KAIS - Bioversity International; ADEKA, JOSEPH - University Of Kisangani; Ayala Silva, Tomas; CHAO, CHIH-PING - Agricultural Research Institute Of Taiwan; DANIELS, JEFF - Queensland Department Of Primary Industries & Fisheries; DOWLYA, BENJAMIN - Bioversity International; EFFA EFFA, BRANLY - Centre National De La Recherche Scientifique; GUECO, LAVERN - University Of The Philippines Los Banos; KEMPENAERS, ELS - Katholieke University; HERRADURA, LORNA - Department Of Agriculture-Bureau Of Plant Industry; IBOBONDJI, LUCIEN - Centre Africain De Recherche Sur Bananiers Et Plantains (CARBAP); Irish, Brian; KILANGI, JASMECK - Agricultural Research Institute - Naliendele; MUHANGI, SEDRACH - National Agricultural Research Organization - Uganda; NGO XUAN, PHONG - Vietnam Academy Of Agricultural Sciences (VAAS); PAOFA, JANET - Papua New Guinea National Agricultural Research Institute (NARI); PAVIS, CLAUDE - Institut National De La Recherche Agronomique (INRA); SANDOVAL JORGE - National Banana Corporation (CORBANA); SUTANTO, AGUS - Indonesian Agency For Agricultural Research And Development; THIEMELE, DELESS - Centre National De Recherche Agronomique (NCAR); TOSSOU, CHRISTOPHE - Institut National Des Recherches Agricoles Du Benin (INRAB); VANGU PAKA, GERMAINE - Institut National De La Recherche Agronomique (INRA); GANJUN, YI - Guangdong Academy Of Agricultural Sciences; VAN DEN HOUWE, INES - Bioversity International; ROUX, NICOLAS - Bioversity International; ROUARD, MATHIEU - Bioversity International

Submitted to: Database: The Journal of Biological Databases and Curation
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/12/2017
Publication Date: 6/11/2017
Citation: Ruas, M., Guignon, V., Sempere, G., Sardos, J., Hueber, Y., Duverhey, H., Andrieu, A., Chase, R., Jenny, C., Hazekamp, T., Jelali, K., Adeka, J., Ayala Silva, T., Chao, C., Daniels, J., Dowlya, B., Effa Effa, B., Gueco, L., Kempenaers, E., Herradura, L., Ibobondji, L., Irish, B.M., Kilangi, J., Muhangi, S., Ngo Xuan, P., Paofa, J., Pavis, C., Sandoval Jorge, Sutanto, A., Thiemele, D., Tossou, C., Vangu Paka, G., Ganjun, Y., Van Den Houwe, I., Roux, N., Rouard, M. 2017. MGIS: Managing banana (Musa spp.) genetic resources information and high-throughput genotyping data. Database: The Journal of Biological Databases and Curation. doi:10.1093/database/bax046.

Interpretive Summary: Important agricultural crop collections in the world are maintained in genebanks. Plants in these collections are conserved long-term and require a detailed cataloging system to help keep information well-organized. Digital databases aid in managing information in genebanks and continue to evolve as software platforms are developed and as new information associated with the conserved plant collections increases. The Musa Germplasm Information System is the information management tool for the world’s international banana germplasm collection as well as national germplasm collections including USDA’s (https://www.crop-diversity.org/mgis/collection/01USA108). MGIS has recently been updated with substantial data from these global banana germplasm collections and has been redesigned to add many useful features and functions to its user base. Improvements to MGIS include software that is customizable which allows continual adapting and adopting of new features to the databases including molecular data searches. In addition, options for comparison among plants in the collections, updated scientific publications linked to collection holdings as well as linkage and interoperability between several plant databases and breeding platforms were included in the improved version of MGIS. Plant scientists, breeders and custodians of banana collections around the world benefit from the increased information and functions provided by MGIS.

Technical Abstract: Unraveling genetic diversity held in genebanks on a large scale is underway, due to the advances in Next-generation sequence-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. A new generation of information systems has to be designed to efficiently handle this data and link it with other external resources such as genome or breeding databases. The Musa Germplasm Information System (MGIS) is the database for global ex situ held banana genetic resources which has been developed to address those needs in a user-friendly way. In developing MGIS, we firstly decided to select a generic database schema (Chado) and to use a robust content management system such as Drupal for the user interface front-end with the Tripal module as an effective layer between these two. MGIS allows germplasm collection examination, accession browsing, faceted searches and germplasm requesting. Additionally, we developed unique graphical interfaces to compare accessions and to explore taxonomic data. Accession-based data has been enriched with publications, genotyping studies and associated genotyping datasets reporting on germplasm use. Finally, an interoperability layer was implemented to facilitate the link with complementary databases like the Banana Genome Hub or the MusaBase breeding database.