A methodology relying on two-dimensional (2D) electrophoresis and genetic mapping is proposed to dissect the genetic architecture of the quantitative control of gene products. Seventy-two anonymous polypeptide spots resolved using silver-stained high-resolution 2D gels of maize coleoptile extracts were automatically quantified for every individual of an F2 progeny between distant lines. A complete genetic linkage map, including 70 RFLP and 39 protein markers, allowed us to map Mendelian factors underlying quantitative variation for 42 polypeptides. One to 5 unlinked chromosomal regions were found to affect single polypeptides, 27% of which resulted in more than a doubling of the polypeptide spot intensity. Dominance was observed for half of the factors, with high amount dominant over low amount in most cases, which is consistent with the observation that the relative abundance of proteins in F1 hybrids is in average deviated to the high parental values. Epistatic interactions were shown to be involved in the control of 14% of the proteins. These features contrast sharply with the observations from 20 agromorphological traits measured in the same progeny, where limited substitution and dominance effects, and no epistatic interaction, were found.