DETECTING AND MAPPING SEQUENCE CHANGES IN DNA

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The goal of the current study is the generation of a map of the mouse genome in which all chromosomes are marked by loci, spaced approximately ten map units apart. These loci should be characterized by polymorphic variation, such that any given pair of strains which do not have a recent inbreeding history have different alleles at about half the loci. The single type of genetic marker which could fulfill these requirements is the restriction fragment length polymorphism in mouse DNA. We plan to map these variants using a variety of mapping techniques. The main emphasis will be on use of recombinant inbred strains. Other techniques will involve somatic hybrids segregating mouse chromosomes, the classical backcross and congenic strains of mice. We plan to probe the DNA with several kinds of cloned sequences. First, we will use identified cloned cDNA probes obtained from other laboratories. These have intrinsic interest as well as adding to the map. Second, we will use probes which we know hybridize to chromosomes which have very few polymorphic loci. These clones will be identified after hybridizing to DNA from a panel of mouse-hamster hybrid cell lines. They will be of two types. We will use random cDNA clones from libraries from a number of mouse organs. We also plan to use flanking regions to endogenous retroviruses which we will clone for genomic libraries of DNA from C57BL mouse strains. We have shown that these retroviruses occupy loci in C57BL which are not allelic to retroviral loci in other strains. This implies that they will hybridize to polymorphic DNA fragments. The fragment will contain a retrovirus in C57BL and will lack a retrovirus in other strains. As retroviruses appear to insert randomly in the mouse genome and mouse strains each have about 130 copies, they will be spaced about 12 cM apart on the mouse genome, and will be present on every chromosome. The achievement of a fully marked mouse map is essential to the full interpretation and analysis of regulatory genes, multigene phenotypes, and tumor susceptibility.