Impact of QTL properties on the accuracy of multi-breed genomic prediction
Yvonne CJ Wientjes, Mario PL Calus, Michael E Goddard, Ben J Hayes
GENETICS SELECTION EVOLUTION | BMC | Published : 2015
BACKGROUND: Although simulation studies show that combining multiple breeds in one reference population increases accuracy of genomic prediction, this is not always confirmed in empirical studies. This discrepancy might be due to the assumptions on quantitative trait loci (QTL) properties applied in simulation studies, including number of QTL, spectrum of QTL allele frequencies across breeds, and distribution of allele substitution effects. We investigated the effects of QTL properties and of including a random across- and within-breed animal effect in a genomic best linear unbiased prediction (GBLUP) model on accuracy of multi-breed genomic prediction using genotypes of Holstein-Friesian an..View full abstract
Awarded by Breed4Food
Awarded by EU
The authors thank Roel Veerkamp, Chris Schrooten and Henk Bovenhuis for their useful comments. This study was financially supported by Breed4Food (KB-12-006.03-005-ASG-LR), a public-private partnership in the domain of animal breeding and genomics, the cooperative cattle improvement organization CRV BV (Arnhem, The Netherlands), and EU FP7 IRSES SEQSEL (Grant no. 317697) by funding the research visit of Yvonne Wientjes at the Department of Environmental and Primary Industries in Victoria, Australia. The 1000 bulls genomes consortium is acknowledged for providing the sequence data, and in particular Paul Stothard for providing the annotations.