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Title: Developing expressed sequence tag libraries and the discovery of simple sequence repeat markers for two species of raspberry (Rubus L.)

item Bushakra, Jill
item Lewers, Kimberly
item STATON, MARGARET - University Of Tennessee
item ZHEBENTYAEVA, TETYANA - Clemson University
item SASKI, CHRISTOPHER - Clemson University

Submitted to: BMC Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/28/2015
Publication Date: 10/26/2015
Publication URL:
Citation: Bushakra, J., Lewers, K.S., Staton, M.E., Zhebentyaeva, T., Saski, C.A. 2015. Developing expressed sequence tag libraries and the discovery of simple sequence repeat markers for two species of raspberry (Rubus L.). Biomed Central (BMC) Plant Biology. 15:258-269.

Interpretive Summary: Breeding of raspberries, 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 with desirable traits. This research reports the analysis of 3,507 raspberry genes potentially associated with desirable raspberry traits and the discovery of 351 potential DNA markers for those genes. Raspberry breeders and geneticists worldwide will use this information for breeding improved blackberry.

Technical Abstract: Background: Due to a relatively high level of codominant inheritance and transferability within and among taxonomic groups, simple sequence repeat (SSR) markers are important elements in comparative mapping and delineation of genomic regions associated with traits of economic importance. Expressed Sequence Tags (ESTs) are a source of SSRs that can be used to develop markers to facilitate plant breeding and for more basic research across genera and higher plant orders. Results: To accelerate development of EST-SSRs in the genus Rubus (Rosaceae), 1,149 and 2,358 cDNA sequences were generated from red raspberry (R. idaeus) and black raspberry (R. occidentalis), respectively. The sequences were screened for SSRs, and primers were designed from the surrounding sequences. Using rigorous criteria for filtering, 113 and 238 EST-SSRs were designed for red and black raspberry, respectively. ESTs containing SSRs were functionally annotated using the GenBank non-redundant (nr) database and further classified using the Gene Ontology database. Conclusion: This resource of Rubus-specific, gene-derived markers will facilitate the construction of linkage maps composed of transferable markers for studying and manipulating important traits in this economically important genus.