Single variant analysis was conducted for each SNP and each phenotype. To account for family structure we used a mixed model(33) where the kinship matrix was fixed according to the known pedigree structure. The model was estimated with an implementation of FaST-LMM(34). Mixed models allow an estimate of phenotypic heritability, where the phenotypic variance-covariance matrix is partitioned into: Cov(y) = σg2K+σe2I, where Cov(y) is the N×N phenotypic matrix, K is the N×N kinship matrix fixed according to the known pedigree structure, σg is the heritability variance component, σe is the error variance, and I is an N×N identity matrix.
