TRANSFERABILITY OF RUBUS MICROSATELLITE MARKERS TO BLACK RASPBERRY

Abstract

Microsatellite or simple sequence repeat (SSR) markers have been developed from genomic and expressed sequence tag (EST) libraries in red raspberry (Rubus idaeus, subgenus Idaeobatus) and also in blackberry (Rubus subgenus Rubus). Recently, there has also been increased interest in the use of SSR markers in black raspberry (R. occidentalis subgenus Idaeobatus) to aid in the identification and characterization of new sources of genetic diversity for breeding, and to aid in the development of a core collection of the 208 seed and clonal accessions at the US Department of Agriculture, Agricultural Research Service, National Clonal Germplasm Repository in Corvallis, Oregon. The objective of this study was to determine the suitability of SSR markers developed in other Rubus species for use in black raspberry. Amplification and optimum annealing temperatures of 112 Rubus SSR primer pairs were 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, using 3% agarose gel electrophoresis. This led to the identification of 27 primer pairs that appeared to generate polymorphic markers. Marker quality and genetic relationships were evaluated by fragment analysis in 12 cultivated and 4 wild genotypes using 20 of these markers after separation by capillary electrophoresis.