ARS | Publication request: CROSS-SPECIES AMPLIFICATION OF SSR LOCI IN VACCINIUM

Submitted to: Acta Horticulturae
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: February 28, 2004
Publication Date: January 20, 2006
Citation: Boches, P., Rowland, L.J., Hummer, K.E., Bassil, N.V. 2006. Cross-species amplification of ssr loci in vaccinium. Acta Horticulturae. 715:119-128.

Interpretive Summary: Out of 1000 highbush blueberry DNA sequences isolated by Dr. Rowland, 28 contained short repeated pieces of DNA that could serve as markers for paternity testing and fingerprinting. We extracted DNA from wild blueberry relatives and compared the size of these 28 specific short sequences of DNA. We looked at groups of wild blueberry relatives from South America, eastern and western United States, as well as Asia. We examined the DNA from widely different species within the blueberry genus. About 42% of the short DNA sections examined matched across the species, where ever the blueberries originated. About 90% of the short DNA pieces were common to the close relatives in the blueberry section. About 40 to 50% of the DNA pieces were common to the relatives that were further removed. The more distant the blueberry relative was, the lower the amount of DNA cross-amplified. Our laboratory will be looking for additional short DNA sequences that can be used as markers that will be useful for blueberry breeding and development.

Technical Abstract: Primers were designed to amplify 28 simple sequence repeat (SSR) sequences discovered in an expressed sequence tag (EST) library derived from the highbush blueberry, Vaccinium corymbosum L. Cross-species amplification was evaluated in species belonging to sections Cyanococcus, Pyxothamnus, Batodendron, and Ciliata of the genus Vaccinium. Amplification was tested in one or more representatives of V. virgatum Aiton = V. ashei Reade, V. ovatum Pursh, V. arboreum Marshall, V. oldhamii Miq., V. elliotii Chapm., V. simulatum Small, V. corymbosum hybrid cv. Flordablue, and V. bracteatum Thunb. Of 22 primer pairs that amplified a fragment of the expected size in V. corymbosum, 7 (42%) resulted in cross-species amplification regardless of section. However, primers designed in V. corymbosum were most easily transferred to V. simulatum and V. elliotii (90% of primers cross-amplified) and least easily transferred to V. ovatum, V. arboreum, and V. oldhamii (40%, 50%, and 50% of primers cross-amplified, respectively). These results were expected because V. simulatum, V. elliotti, and V. corymbosum belong to section Cyanococcus; whereas V. ovatum, V. arboreum, and V. oldhamii belong to the more distantly related sections Pyxothamnus, Batodendron, and Ciliata, respectively. Single factor analysis of variance indicated a significant difference (p <0.02). Additional SSR primers from EST and genomic (enriched library) sources are under development.