ARS | Publication request: A blackberry (Rubus L.) expressed sequence tag library for the development of simple sequence repeat markers

Submitted to: Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: May 29, 2008
Publication Date: July 16, 2008
Citation: Lewers, K.S., Saski, C.A., Cuthbertson, B.J., Henry, D.C., Staton, M.E., Main, D.S., Dhanaraj, A.L., Rowland, L.J., Tomkins, J.P. 2008. A blackberry (Rubus L.) expressed sequence tag library for the development of simple sequence repeat markers. Plant Science.8:69-76.

Interpretive Summary: Breeding of blackberries, a fruit which has many valuable nutritional and health benefits, is slow in part because seedlings that come from breeders¿ crosses must be grown to maturity for evaluation of many traits, including fruit quality. The breeding process would be greatly accelerated, and would be much more efficient, if a breeder could test a small seedling and know with confidence what traits that seedling will have if grown to maturity. A DNA based method, called ¿marker assisted selection¿ is available to accomplish this, but requires DNA ¿markers¿ that can be used to identify the seedlings the breeder should ¿select¿. This research reports the analysis of 3,000 blackberry genes and the discovery of 673 potential DNA markers. Results indicate that further analysis will provide many more markers. The gene sequences and markers will be deposited in a public database. Blackberry breeders and geneticists worldwide will use them.

Technical Abstract: A blackberry (Rubus L.) expressed sequence tag (EST) library was produced for developing simple sequence repeat (SSR) markers from the tetraploid blackberry cultivar, Merton Thornless, the source of the thornless trait in commercial cultivars. RNA was extracted from young expanding leaves and used for the construction of a cDNA library resulting in 18,432 clones. Of these, 3,884 were sequenced, and 3,000 high quality sequences were assembled into contigs, annotated, and searched for SSR regions. Among the most abundantly expressed genes were those involved with energy, cell structure, and defense. The sequences generated by this work were deposited in GenBank and the Genome Database for Rosaceae. A total of 673 primer pairs were identified, and a randomly chosen set of 33 was tested with two tetraploid blackberry cultivars. Of the 33 SSR primer pairs chosen for testing, 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 test marker assisted breeding in blackberry.