New approaches based on general mixed linear models were presented for analyzing complex quantitative traits in animal models, seed models and QTL (quantitative trait locus) mapping models. Variances and covariances can be appropriately estimated by MINQUE (minimum norm quadratic unbiased estimation) approaches. Random genetic effects can be predicted without bias by LUP (linear unbiased prediction) or AUP (adjusted unbiased prediction) methods. Mixed-model based composite interval mapping (MCIM) methods are suitable for efficiently searching QTLs along the whole genome. Bayesian methods and Markov Chain Monte Carlo (MCMC) methods can be applied in analyzing parameters of random effects as well as their variances.