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The differential induction of alpha-fetoprotein (AFP) mRNA during liver regeneration in three inbred strains of mice was examined to determine the genetic and molecular bases for the differences in protein production. BALB/cJ, C3H/He, and C57BL/6 mice, previously identified as high, intermediate, and low AFP producers, respectively, were used. Liver AFP mRNA concentrations during normal development and after carbon tetrachloride administration were measured and shown to correlate exactly with the serum protein concentrations. By performing a series of genetic crosses, we identified two unlinked genetic loci that acted independently to affect the inducibility of AFP mRNA. The raf gene, previously identified by Olsson et al. (J. Exp. Med. 145:819-827, 1977), determines the adult basal level of AFP mRNA, and the Rif gene affects its inducibility during regeneration. By using a polymorphic restriction endonuclease site within the albumin-AFP structural gene region, we show that neither regulatory gene is closely linked to the structural genes. In addition, neither gene affects the concentration of albumin mRNA during development or liver regeneration.