Breeders of cole crops (Brassica oleracea L.) have an interest in utilizing current and emerging PCR-based marker systems to differentiate elite germplasm. However, until efficiency and cost-effectiveness are determined, most breeders are hesitant to change methods. In this study, our goal was to compare simple sequence repeat (SSR), amplified fragment-length polymorphism (AFLP), and sequence-related amplified polymorphism (SRAP) marker systems for their effectiveness in differentiating a diverse population of 24 elite broccoli (B. oleracea Italica Group) inbreds. Published SSR primer sequences for Brassica L. species were used along with AFLP and SRAP primer combinations. Several SSR primers failed to amplify DNA in the broccoli population, but all AFLP and SRAP primer combinations produced multiple bands. Twenty-nine percent of the SSR primers were monomorphic, while most of the remaining primers detected only one or two differences among inbreds. AFLP and SRAP methods produced multiple differences per primer in almost every case. Phenetic analysis revealed that the type of marker affected the classification of the genotypes. All three marker systems were able to successfully differentiate between the 24 elite inbreds, however, AFLPs and SRAPs were more efficient, making them better alternatives than SSRs over other established methods for fingerprinting B. oleracea inbreds.
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