Genome wide association analysis of the QTL MAS 2012 data investigating pleiotropy

Different genome wide association methods (GWAS) including multivariate analysis techniques were applied to identify quantitative trait loci (QTL) and pleiotropy in the simulated data set provided by the QTL-MAS workshop 2012 held in Alghero (Italy).

Genetic correlations and heritabilities for all three quantitative traits were obtained by a multivariate animal model. In a second step the data were corrected for a polygenic component containing the genomic-based kinship matrix. Residuals from this model were later used for QTL detection in a regression analysis, to achieve genome-wide rapid association (GRAMMAR). In order to take pleiotropic effects into account, all three traits were condensed via principle component techniques to two principal components (PC) which reflect the phenotypic variance covariance structure of all traits. The PCs were analyzed by single trait analysis by GRAMMAR. As an alternative to GRAMMAR, the data set was analyzed by Bayesian methods implemented in the package snptest. The program allows the analysis of the data in a univariate and a multivariate way, where all three traits are investigated simultaneously.

According to the polygenic model, analyses the three traits revealed high heritability (0.56, 0.55, and 0.66). Traits 1 and 2 were highly correlated (rg = 0.84). All applied GWAS revealed 10 QTL on four different chromosomes. No QTL was detected on chromosome 5. The Bayesian multivariate analysis revealed significant pleiotropic SNPs.

Principal component and multivariate analyses seem to be promising in order to characterize the genetic basis of trait relationships.