Mapping QTLs with epistatic effects and QTLxenvironment interactions by mixed linear model approaches

A new methodology based on mixed linear models was developed for mapping QT Ls with digenic epistasis and QTL x environment (QE) interactions. Reliable estimates of QTL main effects (additive and epistasis effects) can be obta ined by the maximum-likelihood estimation method, while QE interaction effe cts (additive x environment interaction and epistasis x environment interac tion) can be predicted by the-best-linear-unbiased-prediction (BLUP) method . Likelihood ratio and t statistics were combined for testing hypotheses ab out QTL effects and QE interactions. Monte Carlo simulations were conducted for evaluating the unbiasedness, accuracy, and power for parameter estimat ion in QTL mapping. The results indicated that the mixed-model approaches c ould provide unbiased estimates for both positions and effects of QTLs, as well as unbiased predicted values for QE interactions. Additionally, the mi xed-model approaches also showed high accuracy and power in mapping QTLs wi th epistatic effects and QE interactions. Based on the models and the metho dology, a computer software program (QTLMapper version 1.0) was developed, which is suitable for interval mapping of QTLs with additive, additive x ad ditive epistasis, and their environment interactions.