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, Frankrig
  • Mekki Boussaha, Animal Genetics and Integrative Biology, UMR 1313 GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France., Frankrig
  • Aurélien Capitan, INRA, UMR1313 Génétique Animale et Biologie Intégrative, Université Paris-Saclay, Allice, Frankrig
  • Dominique Rocha, INRA, UMR1313 Génétique Animale et Biologie Intégrative, Frankrig
  • Chris Hoze, UMR 1313 GABI, INRA, AgroParis Tech, Université Paris-Saclay, Jouy-en-Josas, Université Paris-Saclay, Allice, Frankrig
  • Marie-Pierre Sanchez, Université Paris-Saclay
  • ,
  • Thierry Tribout, Université Paris-Saclay
  • ,
  • Rabia Letaief, INRA, UMR1313 Génétique Animale et Biologie Intégrative (GABI), , Frankrig
  • Pascal Croiseau, Université Paris-Saclay, Frankrig
  • Cécile Grohs, INRA, UMR1313 Génétique Animale et Biologie Intégrative, Frankrig
  • Wanbo Li, GIGA-R & Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium, Belgien
  • Chad Harland, GIGA-R & Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium, Belgien
  • Carole Charlier, Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Belgien
  • Mogens Sandø Lund
  • Goutam Sahana
  • Michel Georges, Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Belgien
  • Stephane Barbier, Valogene, 75012 Paris, France
  • ,
  • Wouter Coppieters, GIGA-R & Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium, Belgien
  • Sebastian Fritz, Animal Genetics and Integrative Biology, UMR 1313 GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France., Allice, Frankrig
  • 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
OriginalsprogEngelsk
TitelProceedings of the World Congress on Genetics Applied to Livestock Production : Volume Molecular Genetics 4
Antal sider6
Vol/bind11
Udgivelsesår2018
Artikelnummer11.675
StatusUdgivet - 2018
BegivenhedThe 11th World Congress on Genetics Applied to Livestock Production - Aotea Centre, Auckland 1010, Auckland, New Zealand
Varighed: 11 feb. 201816 feb. 2018
Konferencens nummer: 11

Konference

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

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