DNA Barcoding in a Crop Genebank: The Capsicum annuum Species Complex

Robert L Jarret

doi:10.2174/1874196700801010035

Abstract

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.

Highlights

Crop genebanks provide research materials that are essential for the study of crop domestication/evolution, as well as for crop improvement, archeological, ecological, botanical, etc. research worldwide [1]
Accessions of C. annuum in Group I were differentiated from C. chinense and C. frutescens based on the presence or absence of a 7 or a 13 bp indel
Crop genebanks contain a limited number of plant families each containing one or more genera and are typically assembled around a single crop species (i.e. C. annuum)

Summary

Introduction

Crop genebanks provide research materials (plant germplasm) that are essential for the study of crop domestication/evolution, as well as for crop improvement, archeological, ecological, botanical, etc. research worldwide [1]. Plant materials examined and their genebank inventory numbers [Plant Introduction (PI) or GRIF] included representative examples of the five cultivated Capsicum species ; C. annuum var. Additional plant materials (Group II) were examined in order to further evaluate variability both within and among members of the C. annuum complex and to validate the efficacy of markers identified in Group I in differentiating species.

Results

Conclusion