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WIDDE: a Web-Interfaced next generation database for genetic diversity exploration, with a first application in cattle

Sempere Guilhem, Moazami-Goudarzi Katayoun, Eggen André, Laloë Denis, Gautier Mathieu, Flori Laurence. 2015. WIDDE: a Web-Interfaced next generation database for genetic diversity exploration, with a first application in cattle. BMC Genomics, 16 (940), 8 p.

Journal article ; Article de revue à facteur d'impact Revue en libre accès total
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Quartile : Q1, Sujet : BIOTECHNOLOGY & APPLIED MICROBIOLOGY / Quartile : Q2, Sujet : GENETICS & HEREDITY

Abstract : Background The advent and democratization of next generation sequencing and genotyping technologies lead to a huge amount of data for the characterization of population genetic diversity in model and non model-species. However, efficient storage, management, cross-analyzing and exploration of such dense genotyping datasets remain challenging. This is particularly true for the bovine species where many SNP datasets have been generated in various cattle populations with different genotyping tools. Description We developed WIDDE, a Web-Interfaced Next Generation Database that stands as a generic tool applicable to a wide range of species and marker types (http://widde.toulouse.inra.fr). As a first illustration, we hereby describe its first version dedicated to cattle biodiversity, which includes a large and evolving cattle genotyping dataset for over 750,000 SNPs available on 129 (89 public) different cattle populations representative of the world-wide bovine genetic diversity and on 7 outgroup bovid species. This version proposes an optional marker and individual filtering step, an export of genotyping data in different popular formats, and an exploration of genetic diversity through a principal component analysis. Users can also explore their own genotyping data together with data from WIDDE, assign their samples to WIDDE populations based on distance assignment method and supervised clustering, and estimate their ancestry composition relative to the populations represented in the database. Conclusion The cattle version of WIDDE represents to our knowledge the first database dedicated to cattle biodiversity and SNP genotyping data that will be very useful for researchers interested in this field. As a generic tool applicable to a wide range of marker types, WIDDE is overall intended to the genetic diversity exploration of any species and will be extended to other species shortly. The structure makes it easy to include additional output formats and new tools dedicated to genetic diversity exploration. (Résumé d'auteur)

Mots-clés Agrovoc : Banque de données, Internet, Bioinformatique, Variation génétique, Polymorphisme génétique, Distance génétique, Génétique des populations, Ressource génétique animale, Génotype, Marqueur génétique, ACP, Bovin

Classification Agris : L10 - Animal genetics and breeding
C30 - Documentation and information
U30 - Research methods

Champ stratégique Cirad : Axe 1 (2014-2018) - Agriculture écologiquement intensive

Auteurs et affiliations

  • Sempere Guilhem, CIRAD-BIOS-UMR INTERTRYP (FRA)
  • Moazami-Goudarzi Katayoun, INRA (FRA)
  • Eggen André, Illumina Inc. (USA)
  • Laloë Denis, INRA (FRA)
  • Gautier Mathieu, INRA (FRA)
  • Flori Laurence, CIRAD-BIOS-UMR INTERTRYP (FRA)

Source : Cirad-Agritrop (https://agritrop.cirad.fr/578132/)

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