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A universal molecular method for identifying underground plant parts to species

Authors: 
Linder, CR, LA Moore, and RB Jackson
Year: 
2000
Journal: 
Molecular Ecology
Journal Volume/Pages: 
9:1549-1559

As part of a large project to determine rooting depth and resource uptake on the Edwards Plateau of central Texas, we developed a DNA-based technique that allows belowground parts of all plants to be identified to the level of genus and usually to species. Identification is achieved by comparing DNA sequences of the internal transcribed spacer (ITS) region of the 18S-26S nuclear ribosomal DNA repeat, derived from belowground plant material, with a reference ITS region database for plants at a site. The method will work throughout plants because the plant ITS region can be PCR amplified with a set of universal primers. Congeneric species can usually be identified because the ITS region evolves relatively rapidly. In our study all roots were easily identified to the level of genus; most congeneric species were identified solely by ITS sequence differences but some required a combination of ITS sequence data and aboveground surveys of species at a site. In addition to showing the feasibility and efficacy of our technique, we compare it to another DNA-based technique used to identify belowground plant parts. Finally, we also describe a DNA extraction and purification technique that reliably provides high quality DNA of sufficient quantity from roots so that PCR can be readily accomplished. Our technique should allow the belowground parts of plants in any system to be identified and thereby open new possibilities for the study of belowground plant communities.

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