Characterization of CR1 repeat random PCR markers for mapping the chicken genome

Animal Genetics
R OkimotoJ B Dodgson

Abstract

Polymerase chain reaction (PCR) primers complementary to portions of the chicken repetitive element CR1 have been used previously to generate useful markers on the chicken genome linkage map. 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 region 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, whereas 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 instances, 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 instances, the polymorphism was a one or two basepair sequence difference within the primer annealing site, but in the fifth case the responsible differenc...Continue Reading

Citations

Aug 9, 2001·Animal Genetics·C KnorrJ B Dodgson
Mar 2, 1999·Animal Genetics·C KnorrJ B Dodgson

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