Evaluation of RAPD analysis for identification of polymorphisms in canine genomic DNA

Random amplified polymorphic DNA (RAPD) analysis was assessed as a method to identify polymorphic markers in dogs for potential use in linkage analysis of traits segregating in specific pedigrees. Three sets of primers were evaluated: 294 ten‐nucleotide long arbitrary primers from sets commonly used in RAPD analysis; 40 primers containing simple repeat elements; and 10 long random primers (19‐24 nucleotides). Of the 294 10‐mer RAPD primers, 220 (75%) amplified DNA segments from template DNA yielding primarily of 4‐5 DNA bands. Furthermore, only a few of the primers containing simple repeat elements produced discrete DNA fragments on amplification. On the other hand, all ten of the longer primers yielded amplification products with an average of 10 bands. Polymorphic bands were identified among the test DNA samples in 30% of reactions using 10‐mer RAPD primers, and in 50% of cases utilizing the long primers. RAPD primers with higher GC content amplified more polymorphic DNA fragments. Characteristic differences in amplification patterns were noted among breeds with several of these primers. We conclude from this study that by selecting primers with high GC content RAPD analysis can be successfully applied to identify polymorphic markers even in relatively inbred dog populations, and offers a promising method to search for markers linked to genetic traits of interest.