TABLE 1

Goodness-of-fit of different models and kinship matrices in explaining phenotypic variation of maize quantitative traits

Flowering timeEar heightEar diameter
MethodKinship matrix−2 (ML)BIC−2 (ML)BIC−2 (ML)BIC
SimpleNA1632.81643.92296.02307.11282.61293.5
MMSPAGeDi1524.31541.02237.72254.31254.21270.5
MMGenotype similarity1527.51544.22243.12259.81266.61282.9
MMPhylogenetic control1521.61538.62227.32243.91248.91265.2
SANA1525.71547.92248.92271.11276.91298.7
SA+MMSPAGeDi1494.91522.72220.32248.11253.61280.8
SA+MMGenotype similarity1500.91528.72227.12254.91266.51293.7
SA+MMPhylogenetic control1491.61519.42213.22241.01248.21275.4
• Comparison of the maximum likelihood (ML) and the Bayesian information criterion (BIC) of each model with different kinship matrices for maize quantitative traits. The model with the smaller BIC is preferred. Simple, the simple linear model without adjustment for population effect; SA, the model using the output from STRUCTURE as covariates; MM, the mixed model with different kinship matrices. The descriptions of kinship matrices are the same as in the Figure 1 legend.