Fig. 3

Representative allele screening of polymorphic loci. PCR screens of a subset of non-reference CfERV-Fc1(a) integrants. Validation of insertionally polymorphic sites was performed for seven candidate sites across genomic DNA from a panel of breed dogs. a Strategy for primer design and allele detection. Primers were designed to target within 250 bp of the insertion coordinates based on re-mapping of the assembled breakpoints to the CanFam3.1 reference. Two primers sets were used for each locus: one utilized an internal and flanking primer to amplify the 5′ LTR of a full-length element; another set was used for detection of the pre-integration (unoccupied) or solo LTR alleles each locus. b Banding patterns supporting the unoccupied, solo LTR, or full-length alleles. The chromosomal location of each integrant is indicated at left; allele presence is indicated at right: (+) insertion presence and detected allele; (−) insertion absence. Samples: A, boxer; B, Labrador retriever; C, golden retriever; D, Springer spaniel; E, standard poodle; F, German shepherd; G, shar-pei