Open Access Research article

A blackberry (Rubus L.) expressed sequence tag library for the development of simple sequence repeat markers

Kim S Lewers1*, Chris A Saski2, Brandon J Cuthbertson23, David C Henry2, Meg E Staton2, Dorrie S Main24, Anik L Dhanaraj15, Lisa J Rowland1 and Jeff P Tomkins2

Author Affiliations

1 USDA-ARS, Beltsville Agricultural Research Center, Genetic Improvement of Fruits and Vegetables Lab, Bldg. 010A, BARC-West, 10300 Baltimore Ave., Beltsville, MD 20705-2350, USA

2 Clemson University Genomics Institute, 51 New Cherry St., 304 Biosystems Research Complex, Clemson University, Clemson, SC 29634, USA

3 National Institutes of Health/National Institute of Environmental Health Sciences, Laboratory of Signal Transduction, Peptide Hormone Action Group, 111 TW Alexander Drive, PO Box 12233, MD F3-04 Research Triangle Park, NC 27709-2233, USA

4 Center for Integrated Biotechnology, Dept of Horticulture and Landscape Architecture, Washington State University, 45 Johnson Hall, Pullman, WA 99164-6414, USA

5 Monsanto Research Centre, Biotech Product Support, 44/2A Bellary Road, NH-7, Hebbal, Bangalore 560 092, India

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BMC Plant Biology 2008, 8:69  doi:10.1186/1471-2229-8-69

Published: 20 June 2008



The recent development of novel repeat-fruiting types of blackberry (Rubus L.) cultivars, combined with a long history of morphological marker-assisted selection for thornlessness by blackberry breeders, has given rise to increased interest in using molecular markers to facilitate blackberry breeding. Yet no genetic maps, molecular markers, or even sequences exist specifically for cultivated blackberry. The purpose of this study is to begin development of these tools by generating and annotating the first blackberry expressed sequence tag (EST) library, designing primers from the ESTs to amplify regions containing simple sequence repeats (SSR), and testing the usefulness of a subset of the EST-SSRs with two blackberry cultivars.


A cDNA library of 18,432 clones was generated from expanding leaf tissue of the cultivar Merton Thornless, a progenitor of many thornless commercial cultivars. Among the most abundantly expressed of the 3,000 genes annotated were those involved with energy, cell structure, and defense. From individual sequences containing SSRs, 673 primer pairs were designed. Of a randomly chosen set of 33 primer pairs tested with two blackberry cultivars, 10 detected an average of 1.9 polymorphic PCR products.


This rate predicts that this library may yield as many as 940 SSR primer pairs detecting 1,786 polymorphisms. This may be sufficient to generate a genetic map that can be used to associate molecular markers with phenotypic traits, making possible molecular marker-assisted breeding to compliment existing morphological marker-assisted breeding in blackberry.