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First published online May 7, 2009; doi:10.3732/ajb.0800246 American Journal of Botany 96: 1177-1189 (2009) © 2009 Botanical Society of America, Inc.

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DNA barcoding will frequently fail in complicated groups: An example in wild potatoes¹

USDA, Agricultural Research Service, Department of Horticulture, University of Wisconsin, 1575 Linden Drive, Madison, Wisconsin 53706-1590 USA

ABSTRACT

DNA barcoding ("barcoding") has been proposed as a rapid and practical molecular method to identify species via diagnostic variation in short orthologous DNA sequences from one or a few universal genomic regions. It seeks to address in a rapid and simple way the "taxonomic impediment" of a greater need for taxonomic identifications than can be supplied by taxonomists. Using a complicated plant group, Solanum sect. Petota (wild potatoes), I tested barcoding with the most variable and frequently suggested plant barcoding regions: the internal nontranscribed spacer of nuclear ribosomal DNA (ITS) and the plastid markers trnH-psbA intergenic spacer and matK. These DNA regions fail to provide species-specific markers in sect. Petota because the ITS has too much intraspecific variation and the plastid markers lack sufficient polymorphism. The complications seen in wild potatoes are common in many plant groups, but they have not been assessed with barcoding. Barcoding is a retroactive procedure that relies on well-defined species to function, is based solely on a limited number of DNA sequences that are often inappropriate at the species level, has been poorly tested with geographically well-dispersed replicate samples from difficult taxonomic groups, and discounts substantial practical and theoretical problems in defining species.

Key Words: DNA barcoding • ITS • matK • molecular phylogeny • potato • Solanum sect. Petota • trnH-psbA intergenic spacer

Received for publication 16 July 2008. Accepted for publication 30 January 2009.

FOOTNOTES

¹ The author thanks H. Ballard, F. Rodríguez, H. Ruess, and S. Stephenson for technical assistance; G. Anderson and L. Bohs for DNA samples; the staff of the US Potato Genebank and the C. M. Rick Tomato Genetic Resources Center for seed samples; and M. Ames, P. Bretting, K. Cameron, J. Doyle, K. Holmquist, A. Miller, J. C. Pires, N. I. Platnick, P. Raven, L. Rieseberg, and J. Wendel for discussion or review. This research was supported by USDA and NSF DEB 0316614 entitled "PBI Solanum: A worldwide treatment".

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