ARS | Publication request: DNA Barcoding in a Crop Genebank: Resolving the Capsicum Annuum Species Complex.

Submitted to: The Open Biology Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: July 31, 2008
Publication Date: August 22, 2008
Citation: Jarret, R.L. 2008. DNA Barcoding in a Crop Genebank: Resolving the Capsicum annuum Species Complex.. The Open Biology Journal. 1:35-42.

Interpretive Summary: Three cultivated species of pepper (Capsicum annuum, C. frutescens and C. chinense) can be difficult to differentiate from one another as many of the morphological characteristics that are used to identify species of pepper are shared among these three. We analyzed DNA variability within eight non-coding regions of the chloroplast genome in order to detect changes in these regions that were specific to each species. While no DNA sequence variation in these regions was found to be unique to each species, unique regions were identified in the non-coding waxy intron. Variability within the latter region may prove useful for the identification of pepper species.

Technical Abstract: Variability within eight cpDNA introns including trnS-trnfM, trnL-trnT, trnH-psbA, trnF-trnL, trnD-trnT, trnC-rpoB, rps16, and matK, and the nuclear waxy intron 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 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 intron permitted the identification of all taxa within the plant materials examined. The use of trnH-psbA or trnL-trnT, and waxy is proposed for barcoding members of the C. annuum complex.