Table 2 Haplotype effects of three ZmVTE4 SNPs identified with an optimal MLMM for αT levels
HaplotypeaZmVTE4 SNPsHaplotype FrequencyHaplotype Mean
ss196416269S5_200369481S5_200369534OverallTemperateTropicalαT, μg·g−1SD
A,C,GACG504463.022.48
G,C,GGCG151125269.184.01
A,G,GAGG113.51
G,G,GGGG28151315.953.90
G,C,TGCT22222.772.83
R2LR (%)b60.2
Partial R2LR (%)c48.4
P-valued2.2 × 10−38
Fold changee5.76
  • MLMM, multilocus mixed model; αT, alpha tocopherol; SNP, single-nucleotide polymorphism; SD, standard deviation of the untransformed BLUPs; BLUPs, best linear unbiased predictors;

  • a The most favorable allele for each of the ZmVTE4 SNPs is underlined.

  • b R2LR, likelihood-ratio based R2 statistic, percentage of total phenotypic variation explained by the unified mixed model.

  • c Partial R2LR, likelihood-ratio based partial R2 statistic, percentage of total phenotypic variation explained by the haplotypes.

  • d The P-value was from a unified mixed linear model that tested for an association between haplotypes and αT levels.

  • e Fold change was calculated as the ratio between the most favorable (G, G, G) and least favorable (G, C, T) haplotypes for αT levels.