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

item Lewers, Kimberly
item SASKI, C
item HENRY, D
item STATON, M
item MAIN, D
item Rowland, Lisa

Submitted to: BMC Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/29/2008
Publication Date: 7/16/2008
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., Tompkins, J.P. 2008. A blackberry (Rubus L.) expressed sequence tag library for the development of simple sequence repeat markers. Biomed Central (BMC) Plant Biology.8:69-76.

Interpretive Summary: Breeding of blackberries, a fruit which has many valuable nutritional and health-promoting properties, is slow in part because seedlings derived 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 to develop new blackberry varieties.

Technical Abstract: Background: 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. Results: 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. Conclusions: 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.