Managing banana genetic resources and genomic information with the Triplet Drupal/Tripal/Chado [P0944]

Unraveling the genetic diversity held in genebanks on a large scale is underway, given the advances in NGS-based technologies that produce high-density genetic markers for a large number of samples at low cost. As SNP markers are being mapped on the reference genomes, it is important to develop interoperable system for managing both genomic data and genetic resources. The latter are often managed through bespoke information systems. The Musa Germplasm Information System (MGIS), the main banana genetic resource website, has recently been developed to address those needs in a convenient and flexible way. First of all, we decided to head for a generic database schema, such as CHADO, and to use a robust content management system such as Drupal as the web interface. The Tripal module provides the "glue" between these two parts and drastically reduces development time. Using this trio, we were able to quickly recreate in few months a complete and scalable site and expand it with new features. We now have a germplasm management system allowing collection browsing, and accession browsing, searching and ordering. Accession passport data have been enriched by geographical data, phenotyping characterization data, and information from diversity studies based on molecular markers and SNPs. As a first-use case, such genotyping studies allow linking with the Banana Genome Hub (BGH) website to explore these data in the genome context. (Texte intégral

Musalogue: Catalogue de germoplasme de Musa. Plantains d’Afrique occidentale et centrale –Collection CARBAP

Ce Musalogue (3ème de la série) présente la remarquable collection de plantains (145 accessions) du CARBAP en Cameroun. Il vise à faciliter l’identification correcte des plantains africains et la diffusion des informations importantes sur leur extraordinaire diversité et leur potentiel agronomique ainsi que leurs qualités post-récolte afin de stimuler leur utilisation aussi bien par les chercheurs, les vulgarisateurs, les producteurs que par d’autres acteurs de la filière plantain. Le catalogue est une résultante de la collaboration entre une équipe scientifique pluridisciplinaire des institutions suivantes : CARBAP, Cirad et Bioversity International, qui ont activement participé à la réalisation du projet Food Security Thematic Programme Phase 2 (FSTP2) de l’Union Européenne qui a permis la collecte et l’analyse des données présentées dans ce catalogue. This Musalogue (3rd in the series) presents the remarkable plantain collection (145 accessions) of CARBAP in Cameroon. It aims to facilitate the correct identification of African plantains and disseminate the important information on their extraordinary diversity, agronomic potential, and post-harvest qualities, in order to encourage better use by researchers, extension workers, farmers and other actors in the plantain community. The catalogue is a result of collaboration by a multidisciplinary scientific team from the following institutes: CARBAP, Cirad and Bioversity International, who participated in the project Food Security Thematic Programme Phase 2 (FSTP2) of the European Union, which permitted the collection and analysis of the data presented in the catalogue

Correction to: Safeguarding and using global banana diversity: a holistic approach

An amendment to this paper has been published and can be accessed via the original article

A protocol for detection of large chromosome variations in Banana using next gGeneration sSequencing

Core activities of genebank operations include the preservation of germplasm identity and maintenance of genetic integrity. Some organisms such as banana are maintained by tissue culture that can foster accumulation of somatic mutations and loss of genetic integrity. Such changes can be reflected in their genome structure and thus be revealed by sequencing methods. Here, we propose a protocol for the detection of large chromosomal gains and/or losses that was applied to in vitro banana accessions with different levels of ploidy. Mixoploidy was detected in triploid (3x) accessions with chromosomal regions being diploid (2x) and tetraploid (4x) and in diploid accessions (2x) where large deletions resulted in partial haploidy (1x). Such abnormal molecular karyotypes can potentially explain phenotypic aberrations observed in off type material. With the affordable cost of Next Generation Sequencing (NGS) technologies and the release of the presented bioinformatic pipeline, we aim to promote the application of this methodology as a routine operation for genebank management as an important step to monitor the genetic integrity of distributed material. Moreover, genebank users can be also empowered to apply the methodology and check the molecular karyotype of the ordered material