TOBIOJ The Open Biology Journal Open Bio. J. 1874-1967 Bentham Open TOBIOJ-1-35 10.2174/1874196700801010035 Biology DNA Barcoding in a Crop Genebank: The Capsicum annuum Species Complex Jarret Robert L. * USDA/ARS/PGRCU, 1109 Experiment Street, Griffin, GA 30223. Address correspondence to this author at the USDA/ARS/PGRCU, 1109 Experiment Street, Griffin, GA 30223; Tel: 770 228 7303; Fax: 770 228 7282; E-mail: bob.jarret@ars.usda.gov 28 10 2008 2008 1 35 42 06 05 2008 31 07 2008 22 08 2008 © 2008 Jarret et al. 2008 Robert L. Jarret

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Variability within eight cpDNA introns including trnS-trnfM, trnL-trnT, trnH-psbA, trnF-trnL, trnD-trnT, trnCrpoB, rps16 and matK, and the nuclear waxy introns was examined in seven species of Capsicum (C. annuum, C. baccatum, C. chinense, C. frutescens, C. pubescens, C. chacoense and C. rhomboideum) in order to evaluate the feasibility of utilizing these loci for DNA barcoding within the C. annuum complex. Numerous insertions/deletions (indels) and substitutions were detected in all cpDNA introns. However, none was sufficient to differentiate the individual members of the C. annuum complex (C. annuum, C. chinense and C. frutescens). Variation within trnL-trnT, trnF-trnL and trnH-psbA enabled the differentiation of the complex from the other taxa examined. In contrast, single base indels and substitutions within the waxy introns permitted the differentiation of all taxa within the plant materials examined. The use of trnH-psbA or trnL-trnT, and the waxy introns is proposed for barcoding members of the C. annuum complex.