Isolation of polymorphic AGC repeats located 3' to bovine SINEs

A bovine genomic library was screened for the presence of (AGC)n repeats. All isolated AGC repeats were located adjacent to the 3′ end of bovine short interspersed nuclear elements (SINE). Polymerase chain reactions (PCR) using either two unique primers or one unique and one SINE primer produced high-resolution products without the secondary artifact ladders typical of dinucleotide microsatellites. Four AGC microsatellites were found to be polymorphic with 2–4 alleles each and polymorphism information context (PIC) values ranging between 0.26 and 0.49. One microsatellite, AR025, was mapped to chromosome 26 with the CSIRO reference families. Because of their strong association with AGC repeats and high frequency in the genome, SINE-3′ PCR may prove to be a novel source of polymorphic trinucleotide markers in the bovine genome.