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United States Department of Agriculture

Agricultural Research Service

Research Project: MANAGEMENT OF TEMPERATE FRUIT NUT AND SPECIALTY CROP GENETIC RESOURCES Title: Transferability of Rubus Microsatellite Markers to Black Raspberry

Authors
item Dossett, Michael -
item Bassil, Nahla
item Finn, Chad

Submitted to: Acta Horticulturae
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: December 20, 2009
Publication Date: April 1, 2010
Citation: Dossett, M., Bassil, N.V., Finn, C.E. 2010. Transferability of Rubus Microsatellite Markers to Black Raspberry. Acta Horticulturae. 859:103-109.

Interpretive Summary: Microsatellites or simple sequence repeats (SSRs) are DNA markers with a variety of applications for genetic studies. To date, SSR marker development in brambles has focused on red raspberry and also in blackberry. The objective of this study was to determine the suitability of these SSR markers for use in black raspberry. The ability of 112 SSR primer pairs from red raspberry and blackberry to work in black raspberry was tested in the black raspberry cultivar ‘Munger.’ A panel of eleven cultivated and four wild additional black raspberry genotypes was then used to evaluate these SSR primers for differences between individuals. This led to the identification of 20 SSR primer pairs that were evaluated in all 16 individuals for DNA fragment size. Analysis of these marker differences showed that all 12 black raspberry cultivars were much more closely related to each other than they were to any of the four wild plants, suggesting a much lower rate of genetic diversity in cultivated black raspberry than in the wild. Analysis of marker quality led to the identification of several markers that may be useful for genetic fingerprinting and genetic diversity studies.

Technical Abstract: Microsatellite or simple sequence repeat (SSR) markers have been developed from genomic and expressed sequence tag (EST) libraries in red raspberry (Rubus idaeus L., subgenus Idaeobatus) and also in blackberry (Rubus L. subgenus Rubus). Recently, there has also been increased interest in the use of SSR markers in black raspberry (R. occidentalis L. 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 generated 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.

Last Modified: 12/20/2014