Mapping new murine polymorphisms detected by random amplified polymorphic DNA (RAPD) PCR

Random amplified polymorphic DNA polymerase chain reaction (RAPD PCR) uses a single primer of arbitrary nucleotide sequence to amplify DNA. Amplification occurs when two complementary sites for the primer exist in the correct orientation to each other. Prior knowledge of the target DNA sequence is not needed, and a single primer may amplify a number of DNA fragments. Random nonpalindromic DNA sequences 12 bases in length and 58% in GC content were generated by a computer program and used as PCR primers. Several polymorphisms detected and mapped with these primers have been reported; we now add 17 additional loci. Table 1 lists the primer names, sequence, estimated band size, and final locus name. If a primer detected more than one polymorphic band between strains A/J (A) and C57BL/6J (B), the bands were assigned a temporary designation. Most polymorphisms were scored by the presence or absence of a band except for D10J2, which was a length polymorphism. The two bands of this length polymorphism cosegregated in all RI strains, so we concluded that they were allelic. D2J3 is a PCR product that is present in A and absent in B, but another PCR product migrates close to this one so the polymorphism appears to be a double band in strain A compared with a single band in strain B.