A statistical method for mapping quantitative trait loci （QTLs） underlying endosperm traits is proposed. The method is based on a genetic model containing both the direct effects and maternal effects of an endosperm QTL and on an experimental design termed two-stage hierarchical design, in which the trait information is obtained from F3 endosperms and molecular marker information is obtained from F2 plants and F3 embryos （plants）. Results of computer simulations indicate that the method can efficiently map endosperm QTLs and precisely estimate both the direct and maternal effects of endosperm QTLs when the sample size is sufficiently large.
