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
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 language
English
Title of host publication
Proceedings of the World Congress on Genetics Applied to Livestock Production : Volume Molecular Genetics 4
Number of pages
6
Volume
11
Publication year
2018
Article number
11.675
Publication status
Published - 2018
Event
The 11th World Congress on Genetics Applied to Livestock Production - Aotea Centre, Auckland 1010, Auckland, New Zealand Duration: 11 Feb 2018 → 16 Feb 2018 Conference number: 11
Conference
Conference
The 11th World Congress on Genetics Applied to Livestock Production