RT Journal Article
SR Electronic
T1 Comparative architectures of direct and social genetic effects from the genome-wide association study of 170 phenotypes in outbred laboratory mice
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 302349
DO 10.1101/302349
A1 Amelie Baud
A1 Francesco Paolo Casale
A1 Jerome Nicod
A1 Oliver Stegle
YR 2019
UL http://biorxiv.org/content/early/2019/01/21/302349.abstract
AB Social genetic effects (SGE, also called indirect genetic effects) are associations between genotypes of one individual and phenotype of another. SGE can arise when two individuals interact and heritable traits of one influence the phenotype of the other. To better understand how SGE arise from individual genetic loci, we have derived statistical strategies for the joint analysis of SGE and traditional direct genetic effects (DGE, effects of an individual's genotypes on its own phenotype), which we applied to a dataset of 170 behavioural, physiological and morphological phenotypes measured in 1,812 outbred laboratory mice. Genome-wide association study of SGE and DGE identified 24 and 120 genome-wide significant loci respectively (FDR < 10). We found no overlap between genome-wide significant SGE and DGE loci acting on the same phenotype, and a moderate correlation between SGE and DGE genome-wide, demonstrating that sgeGWAS has the potential to identify novel genetic loci contributing to inter-individual differences. We focused on two such loci to illustrate how individual SGE loci may help identify traits of social partners mediating social effects. Finally, we contrasted the effect sizes of genome-wide significant SGE and DGE loci and found smaller effect sizes for the former: SGE associations explained a maximum of 2.5% of phenotypic variance when eleven genome-wide significant DGE associations explained more than 5% of phenotypic variance. Our results and the presented methods will guide the design and analysis of future sgeGWAS.