Genetic characterization of the Hooded locus in ACI, BN, COP, Con1 and Con2 rats.

The Hooded coat color phenotype exhibited by COP rats results from the insertion of an endogenous retrovirus (ERV) into intron 1 of Kit. The Irish phenotype characteristic of ACI rats results from the presence of a solitary ERV long terminal repeat (LTR) at the same location within Kit intron 1. A. This panel illustrates the site and antisense orientation of the ERV insertion relative to Kit. Also illustrated are the relative positions of the sequences that correspond to the AB and CD primer pairs used to evaluate the site and type of ERV/LTR insertion. B.Left five lanes. The AB primer pair generated a 1006 bp PCR product from BN (Self allele at Hooded) genomic DNA template. The 1590 bp PCR product generated from ACI, Con1 and Con2 genome DNA is consistent with the presence of a solitary LTR within Kit intron 1 (Irish allele at Hooded). No product was generated when the AB primer pair was used to amplify genomic DNA from COP, due to the large size of the inserted ERV (Hooded allele). Right five lanes. The CD primer pair generated a 997 bp PCR product from COP (Hooded allele) genomic DNA. No product was generated from the CD primer pair upon amplification of genomic DNA from BN (Self allele), ACI, Con1 or Con2 (all Irish allele) rats, because primer D is within the inserted ERV element unique to the Hooded allele. Center lane. A 100 bp ladder (New England Biolabs) served as a marker for DNA fragment size. C. The illustrated nucleotide sequences flanking the ERV/LTR insertion site were confirmed by Sanger based capillary sequencing of PCR products generated using primer pair AB for BN, ACI, Con1 and Con2 rats, and primer pairs CD for COP rats. The upward arrow indicates the site of ERV insertion at nucleotide position 34,957,384 (rat genome assembly Rnor_5.0).