CHARACTERIZATION OF CR-1 REPEAT RANDOM PCR MARKERS FOR MAPPING THE CHICKEN GENOME

Polymerase chain reaction (PCR) primers complementary to portions of t he chicken repetitive element CR1 have been used previously to generat e useful markers on the chicken genome linkage map. To understand bett er the genetic basis for this technique and to convert CR1-PCR loci to markers useful in physical genome mapping, five polymorphic CR1-PCR-g enerated DNAs were cloned and partially sequenced. Inverse PCR was the n employed to clone the corresponding region of the genomes of both th e Jungle Fowl (JF) and White Leghorn (WL) parental DNA templates. Our results demonstrate that some of the CR1-PCR-generated DNAs arise from priming at an endogenous CR1 element, whereas others are due to chanc e complementarity between the CR1-PCR primer in use and random anneali ng sites in the genome, unrelated to a demonstrable CR1 element. In al l five instances, it was possible to identify the sequence difference between the JF and WL parental DNAs that gave rise to the initial poly morphism and design allele-specific PCR primer sets that uniquely det ect that polymorphism. In four of the five instances, the polymorphism was a one or two basepair sequence difference within the primer annea ling site, but in the fifth case the responsible difference was outsid e, but very close to, the annealing site. In all instances the allele- specific PCR for the sequence polymorphism mapped identically with the corresponding CRI-PCR amplification polymorphism. We conclude that CR 1-PCR provides an efficient and reliable mechanism for genome mapping in avians that can correlate linkage and physical mapping approaches.