NEXTGEN : Next generation methods to preserve farm animal biodiversity by optimizing present and future breeding options

Project identifier 91-NEXTGEN
Project Status finished
Start date 2010-04-01
End date 2014-03-31
Roadmap Theme
  • Sustainable intensification: Identification and breeding of animals and crops to maintain/increase productivity
  • Type of Project Fundamental research project
    Type of Project Development and innovation oriented (research) project
    Programme FP7-KBBE
    Keyword genome; DNA analysis; adaptive variation; biobanking
    Location Uganda; Morocco; Iran (Islamic Republic of); United Kingdom of Great Britain and Northern Ireland
    Budget 3 758 355
    Main Funder Directorate-General for Research and Innovation (DG RTD) (FP7)
    Coordinator French National Centre for Scientific Research (CNRS)
    Partners
  • Cardiff University
  • Università Cattolica del Sacro Cuore
  • PTP Science Park
  • European Molecular Biology Laboratory (EMBL)
  • Ecole polytechnique federale de Lausanne (EPFL)
  • University of Teramo
  • Makerere University
  • Institut National de la Recherche Agronomique (INRA-MAROC)
  • Gorgan University of Agricultural Sciences and Natural Resources
  • Commonwealth Scientific and Industrial Research Organisation (CSIRO)
  • Project Web Site https://www.epfl.ch/labs/nextgen/
    Documents
  • Report (Cordis)
  • NextGen releases genomic data on sheep, goats and cattle
  • Description

    Executive Summary:

    We are currently experiencing a dramatic loss of farm animal. A significant number of breeds already disappeared in developed countries, and many are presently endangered. The same process is now progressively taking place in Africa and Asia. Based on whole genome data, the NEXTGEN global objective consists to develop cost-effective optimized methodologies for preserving farm-animal biodiversity, using cattle, sheep, and goats as model species.
    More specifically, NEXTGEN will:

    • - develop innovative bio-banking methods based on freeze-dried nuclei;
    • - produce whole genome data in selected populations;
    • - develop the necessary bioinformatics approaches; focusing on the identification of genomic regions under recent selection (adaptive / neutral variation);
    • - provide guidelines for studying disease resistance and genome/environment relationships in a spatial context;
    • - assess the value of wild ancestors and breeds from domestication centers as genetic resources.

    The tissue sampling for the genetic analyses has been carried out based on a grid system covering the whole country for Uganda (cattle) and for Morocco (sheep and goats). Such an innovative sampling approach opens new perspectives at the data analysis stage, as many different hypotheses can be tested using the same dataset.
    A total of 447 whole genomes of sheep (205), goats (208), and cattle (34) have been re-sequenced, with coverage of at least 10x. Additionally, a total of 1009 animals, mainly cattle from Uganda, have been genotyped with DNA chips.

    The main results are:
    • - new bio-banking perspectives based on freeze-dried nuclei;
    • - a collection of computer programs specifically developed for preserving farm animal biodiversity, either by optimizing the selection of individuals for breeding and biobanking (SELCAPRE program), or by identifying genes/environment relationships (Samada program);
    • - precise description of the geographical molecular diversity of cattle from Uganda, with the identification of selection signatures associated to disease tolerance/susceptibility;
    • - selection signatures associated to environmental parameters across Morocco for sheep and goats;
    • - precise assessment of the potential of different populations as genetic resources, including industrial breeds, traditional breeds within or outside of the domestication centers, and wild ancestors;
    • - general guideline for preserving farm animal biodiversity.