Anaerobiosis results in the selective synthesis of a particular set of polypeptides in the maize root including the two alcohol dehydrogenases (Sachs, M. M., Freeling, M., and Okimoto, R. (1980) Cell 20, 761-768), pyruvate decarboxylase (Wignarajah, K., and Greenway, H. (1976) New Phytol. 77, 575-584; Laszlo, A., and St. Lawrence, P. (1983) Mol. Gen. Genet. 192, 110-117), glucose phosphate isomerase (Kelley, P. M., and Freeling, M. (1984) J. Biol. Chem. 259, 673-677) and aldolase (Kelley, P. M., and Freeling, M. (1984) J. Biol. Chem. 259, 14180-14183). This report describes the identification and characterization of cDNA clones to five different mRNA species induced upon anaerobic shock. Immunoprecipitation of hybrid-selected translation polypeptides has determined the identity of the cDNA clone for fructose-1,6-diphosphate aldolase mRNA. Quantitative hybridization analysis of anaerobic mRNAs using the cDNA clones has shown that there is not a simultaneous accumulation of anaerobic mRNAs. Upon reintroduction of air, the anaerobic mRNAs disappear rapidly and at approximately the same rate. A translocation line that generates progeny that contain 1, 2, and 3 doses of the long arm of chromosome one (1L) allowed us to test for clustering of the anaerobic genes; two of the anaerobic genes tested do not reside with Adh 1 and Phi 1 on the long arm of chromosome 1.