Exploring non-additive variance using genome-wide dense SNP in four French and Nordic dairy cattle breeds A. Marete1,2, L. Janns,2, B. Guldbrandtsen2, Hoze C1,3, G. Sahana2, D. Boichard1, M. S. Lund2 1GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France 2Aarhus University, Center for Quantitative Genetics and Genomics, Denmark 3Allice, 75595 Paris, France andrew.marete@mbg.au.dk (Corresponding Author) Non-additive genetic variation is usually ignored in studies of the genetic architecture and genomic prediction of complex traits. However, non-additive genetic effects may have an important contribution to total genetic variation. This study presented a Bayesian mixed model including additive and non-additive genetic effects, with corresponding genetic relationship matrices obtained from genome-wide dense SNPs. The amounts of additive genetic and dominance variance were estimated from all SNPs whereas epistatic variance was estimated for a set of pre-selected markers with a major effect. Variances were estimated for milk, fat, and protein yields from 54,862 cows in four dairy populations. In general, variation due to non-additive effects was present in all the four breeds with Montbeliarde and Holstein breeds having more dominance and epistatic variation. Dominance variance was quite consistent across breeds and traits and represented about 20% of the additive genetic variance. The epistatic variance estimates were more variable, from nearly zero to 19% of the additive genetic variance, with an average of 7%. Keywords: andrew marete, non-additive, epistasis, SNP-by-SNP interaction, bovine, genomics

Andrew G Marete, Luc Janss, Goutam Sahana, Bernt Guldbrandtsen, Chris Hoze, Mogens Sando Lund, Didier Boichard

Proceedings of the World Congress on Genetics Applied to Livestock Production, Volume Biology & Species - Bovine (dairy) 1, , 70, 2018
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