Fig. 3

Performance of different models in terms of genomic prediction, heritability estimation, and model fit based on the medium-density (50K SNPs) and high-density (300K SNPs) panels. The three plots in the upper half represent the results for genomic prediction (a), heritability estimation (b) and model fit (c) for phenotypes that are controlled by weakly tagged causal variants. The three plots in the lower half represent the results for genomic prediction (d), heritability estimation (e) and model fit (f) for phenotypes that are controlled by strongly tagged causal variants. Paired t-test was applied to compare the difference between methods, with P values adjusted by Bonferroni correction. *** indicates significant differences at P < 0.001, ** significant differences at 0.001 < P < 0.01, * significant differences at 0.01 < P < 0.05, and ns indicates no statistically significant difference