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Experience from large scale use of the EuroGenomics custom SNP chip in cattle

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  • Didier A Boichard, INRA, UMR1313 Génétique Animale et Biologie Intégrative, France
  • Mekki Boussaha, Animal Genetics and Integrative Biology, UMR 1313 GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France., France
  • Aurélien Capitan, INRA, UMR1313 Génétique Animale et Biologie Intégrative, Universite Paris-Saclay, Allice, France
  • Dominique Rocha, INRA, UMR1313 Génétique Animale et Biologie Intégrative, France
  • Chris Hoze, UMR 1313 GABI, INRA, AgroParis Tech, Université Paris-Saclay, Jouy-en-Josas, Universite Paris-Saclay, Allice, France
  • Marie-Pierre Sanchez, Universite Paris-Saclay
  • ,
  • Thierry Tribout, Universite Paris-Saclay
  • ,
  • Rabia Letaief, INRA, UMR1313 Génétique Animale et Biologie Intégrative (GABI), , France
  • Pascal Croiseau, Universite Paris-Saclay, France
  • Cécile Grohs, INRA, UMR1313 Génétique Animale et Biologie Intégrative, France
  • Wanbo Li, GIGA-R & Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium, Belgium
  • Chad Harland, GIGA-R & Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium, Belgium
  • Carole Charlier, Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Belgium
  • Mogens Sandø Lund
  • Goutam Sahana
  • Michel Georges, Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Belgium
  • Stephane Barbier, Valogene, 75012 Paris, France
  • ,
  • Wouter Coppieters, GIGA-R & Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium, Belgium
  • Sebastian Fritz, Animal Genetics and Integrative Biology, UMR 1313 GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France., Allice, France
  • Bernt Guldbrandtsen
This article presents the strategy to evaluate candidate mutations underlying QTL or responsible for genetic defects, based upon the design and large-scale use of the Eurogenomics custom SNP chip set up for bovine genomic selection. Some variants under study originated from mapping genetic defects, embryonic lethals, or QTL by GWAS. Other variants originated from a reverse genetics approach and were selected according to their annotation. Because of the limitation in chip size, these variants were severely selected. For instance, structural variants were required to affect a gene. Loss-of-function variants were preferred to deleterious non synonymous variants. An incremental process was used, with one or two chip versions each year, the less informative variants being replaced by new candidates. Many examples are presented. Expected results are: confirmation of effects in large independent populations; estimation of allelic frequencies in different breeds; accumulation of individual genotypes. When confirmed, a variant can be used in a straightforward way by the industry in breeding programs by switching its status on the chip. Keywords: bovine, custom chip, causal variant, genetic defect, GWAS analysis
Original languageEnglish
Title of host publicationProceedings of the World Congress on Genetics Applied to Livestock Production : Volume Molecular Genetics 4
Number of pages6
Volume11
Publication year2018
Article number11.675
Publication statusPublished - 2018
EventThe 11th World Congress on Genetics Applied to Livestock Production - Aotea Centre, Auckland 1010, Auckland, New Zealand
Duration: 11 Feb 201816 Feb 2018
Conference number: 11

Conference

ConferenceThe 11th World Congress on Genetics Applied to Livestock Production
Nummer11
LocationAotea Centre, Auckland 1010
LandNew Zealand
ByAuckland
Periode11/02/201816/02/2018

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