Genome Wide Association of QTLs for Size and Conformational Traits in Horses

Identification of loci for body size QTLs is important to understand the genetic architecture of basic quantitative traits and morphologic changes undergone during domestication. Using the Illumina 54K SNP chip, we genotyped 48 Thoroughbreds and 48 horses from 16 breeds that represent extremes in body size. Previously, we defined conformational phenotypes using principle components analysis of 35 individual body measures.  The first component (trait PC1) corresponded to the overall body size variation, while PC2 captured variation in skeletal thickness between horses. We applied test statistics for genome wide association based on linear regression, a very powerful tool for mapping QTLs. However, the presence of population substructure in this diverse dataset could reduce power and mask real QTL effects. We successfully corrected for population structure using a mixed model approach that takes into account the genomic relationship between animals using EMMA software. Building on the successful identification of 4 major loci for body size, we have now continued the analysis using different genetic models (additive, dominance and recessive). Bonferroni-corrected genome-wide significant associations were detected in chromosomes 1, 2, 3, 28, 6 and 14. Polymorphisms from these newly identified loci will be genotyped in a larger sample set to validate the association and verify the causal mutations.