A Breeder-friendly DNA Fingerprinting Protocol for Blackberry Fruit

In the event of alleged inappropriate use or an error in propagation of a cultivar, fruit breeders need easy and low-cost methods of identifying products from their breeding programs. Particularly important is the ability to identify the cultivar by fruit samples, since fruit samples may be the only plant part available to investigate a propagation or use concern. Blackberry fruit has substantial maternal tissue in the receptacle, or torus, that can be used for DNA extraction. Microsatellite DNA polymorphisms provide a reliable opportunity for the exploitation, or “fingerprinting,” of blackberry cultivars by using either fruit or leaf samples. A DNA-based identification protocol would ideally be fast and inexpensive and would use readily available tools in any standard molecular laboratory.  In this study, we used fruit receptacle tissue for our cultivar differentiation and identification. Further, we used a low PCR annealing temperature of 50°C. We were able to identify over 30 blackberry cultivars developed at the University of Arkansas by using as few as three microsatellite primer pairs with agarose-based gel electrophoresis. This project emphasizes the low-cost and efficiency of being able to use an in-house protocol to identify specific cultivars from one’s own breeding program.