Transferability of Rubus Microsatellite Markers for Use In Black Raspberry

Microsatellites or simple sequence repeats (SSRs) are valuable as co-dominant genetic markers with a variety of applications such as DNA fingerprinting, linkage mapping, and population structure analysis. To date, SSR marker development in Rubus has focused on red raspberry (Rubus idaeus L., subgenus Idaeobatus) and more recently in blackberry (Rubus L. subgenus Rubus). The objective of this study was to determine the suitability of SSR markers developed in other Rubus species for use in black raspberry (R. occidentalis L., subgenus Idaeobatus). The amplification and optimum annealing temperature of 109 Rubus SSR primer pairs was determined in the black raspberry ‘Munger’ by gradient polymerase chain reaction. A panel of 15 cultivars and wild black raspberry accessions was used to evaluate these SSR primers for polymorphism visually, using 3% agarose gel electrophoresis. Transferability of SSR markers was better for those developed in red raspberry than blackberry, with a higher percentage successfully amplifying products (88% and 74%, respectively) and a higher percentage of polymorphic markers among those amplifying products (32% and 22%, respectively). The percentage of polymorphic markers was also higher for those developed from red raspberry genomic libraries (35%) than from blackberry genomic libraries (29%) while the percentage for those developed from genic regions (EST, cDNA) was similar (20% and 19%, respectively). Of the 25 red raspberry SSR markers tested, seven amplified products that were polymorphic, while 12 of the 83 blackberry SSR markers tested were polymorphic. These 19 SSR markers will be useful for studying diversity in black raspberry germplasm.