Two alternative haplotypes at the complex locus controlling hemoglobin a chain synthesis in Mus musculus were compared at the DNA level. As expected, Hbbd homozygotes-which as adults synthesize two species of 13 chain-have two genes for d3 globin. Adult mice homozygous for the Hbbs haplotype make only a single type of 1 polypeptide, yet they also have two 13 globin genes. Apparently the two Hbbs genes encode identical proteins, or one of the two genes is not detectably expressed. The Hbbs and Hbbd haplotypes are thus more similar at the DNA level than studies of their polypeptide products have indicated.The synthesis of the hemoglobin 1 chain in the laboratory mouse Mus musculus musculus is controlled by the Hbb locus, at which a number of allelic alternatives, or haplotypes, have been described (1). These are of two general types: Hbbs and Hbbd. The Hbbs haplotype determines the synthesis of a single 13 globin polypeptide, /ls, in the adult mouse. Two types of /3 globin are specified by the Hbbd complex: Mdmai and (3dmin; the relative amount of these two proteins is developmentally regulated (2). Variation within these two classes of haplotype is also known. The Hbbs allele of SWR mice (3, 4) has been shown by protein sequence analysis to produce a slightly different ,B sequence than that of C57BL mice. Au/SsJ mice carry the HbbP haplotype, which is distinct from Hbbd in that it specifies a slightly different minor chain (5). Finally, the Hbbd-like alleles of the interbreeding subspecies M. m. castaneus and M. m. molossinus produce minor chains that vary slightly from those of M. m. musculus (6). Closely linked to the Hbb locus are the genes for the ,B-like embryonic globin y (7,8).Digestion of a mammalian genome by the restriction endonuclease EcoRI generates several million fragments (9). Jeffreys and Flavell (10) were able to identify the EcoRI fragments of rabbit DNA that contained 3 globin sequences after spreading the fragments in a single dimension. They electrophoresed a denatured digest through an agarose gel (denaturation allows a larger amount of DNA to be loaded), transferred the DNA to a nitrocellulose membrane, and hybridized it with a cloned cDNA copy of ,B globin mRNA labeled in vitro with 32P by nick-translation. A similar analysis of human ,B globin genes has been reported by Mears et al. (11). The sensitivity and resolution afforded by such analyses may be considerably enhanced by spreading the digested DNA in two dimensions. The DNA is first subjected to reverse-phase chromatography on RPC-5 (12, 13), and the fractions so obtained are then run in an analytical agarose slab gel. The DNA in the pattern, or "spread," is denatured in situ, transferred to nitrocellulose (14) Hybridization probes were labeled with 32P by nick-translation to a specific activity of 50-200 cpm/pg (18). The probe for 1 globin was obtained by digesting the plasmid pCR1IBM9 (19), which contains a cloned cDNA copy of mouse 13 globin mRNA, with the endonuclease Hha I. The fragment bearing the inserted cDNA sequenc...