Haematological traits were analysed for an association with SNPs using a mixed-model analysis of variance in JMP Genomics (SAS Institute, Cary, NC, USA). Mixed-model analysis tests an association between traits and a single SNPs and simultaneously adjusts for population structure and family relatedness [13 (link)]. The genetic similarity matrix between individuals was first computed as identity by descent of each pair for the k-matrix. This genome wide relatedness and the slaughter day were used as random effects. For controlling of population stratification, the correlation-selected principal components analysis was used [14 (link), 15 (link)]. Significant correlations at a false discovery rate (FDR) of 5% were considered as covariates. Additionally, genotype and gender were used as fixed effects, age and carcass weight were considered as covariates. Significantly associated SNP markers were reported at a threshold of NegLog10 (p-value) > 5. In order to consider multiple testing issues, a false discovery rate (FDR) was estimated (FDR < 5% corresponding to NegLog10 (p-value) > 6).
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