Mapping DNA polymorphisms using PCR primers derived from the sequence of an avian CR1 element

Primers complementary to the chicken middle repetitive sequence element CR1 were used to generate and simultaneously map polymorphic polymerase chain reaction products (CR1-PCR) with various chicken DNAs as templates. Ten primers were prepared using the sequence of a single CR1 element as a guide. These 10 primers generated 23 polymorphic CR1-PCR products. The average number of polymorphic CR1-PCR products generated using single primers (1.1 per primer) was significantly higher than the average number observed using combinations of two primers (0.3 per primer combination). The polymorphic CR1-PCR products were mapped in a subset of a reference backcross population designed for the genetic linkage analysis of the chicken. Nineteen of the polymorphic CR1-PCR products identified were assigned to 13 of 19 linkage groups characterized thus far in this population; three have yet to be linked to a specific map location. One of the CR1-PCR markers mapped to the chicken Z chromosome. There was no evidence for a significant clustering of CR1-PCR markers within the map, even at the site of the CR1 element whose sequence was used for primer design.