Submitted to: Animal Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/30/1997
Publication Date: N/A
Interpretive Summary: The chicken contains around 100,000 copies of a particular repetitive DNA element known as CR1 scattered throughout its genome. The presence of these CR1 elements provides an opportunity to place genetic markers using DNA sequence from the CR1 element. This paper demonstrates that genetic markers based on CR1 elements is possible. Furthermore, these genetic markers are highly reproducible which means that they can be used to combine the chicken genetic and physical maps. Tying together the two maps will help academic research efforts to identify and clone genes of economic importance. Ultimately, the consumer will benefit from the efficient production of superior poultry.
Technical Abstract: PCR primers complementary to portions of the chicken repetitive element CR1 have been previously used to generate useful markers on the chicken genome linkage map. In order to understand better the genetic basis for this technique and to convert CR1-PCR loci to markers useful in physical genome mapping, five polymorphic CR1-PCR-generated DNAs were cloned and partially sequenced. Inverse PCR was then employed to clone the corresponding regio of the genomes of both the 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, while others are due to chance complementarity between the CR1-PCR primer in use and random annealing sites in the genome, unrelated to a demonstrable CR1 element. In all five cases, it was possible to identify the sequence difference between the JF and WL parental DNAs that gave rise to the initial polymorphism and design allele-specific PCR primer sets that uniquely detect that polymorphism. In four of the five cases, the polymorphism was a one or two base pair sequence difference within the primer annealing site, but in the fifth case the responsible difference was outside of, but very close to, the annealing site. In all cases the allele-specific PCR reaction for the sequence polymorphism mapped identically with the corresponding CR1-PCR amplification polymorphism. We conclude that CR1-PCR provides an efficient and reliable mechanism for genome mapping in chickens that can correlate linkage and physical mapping approaches.