The Capsicum genus comprises several species that are closely related to each other in terms of morphology. This usually leads to species misidentification when relying solely on their physical traits. Due to this, it becomes necessary to develop a method that will authenticate and identify the species, for which the present study was conducted to develop barcodes for Capsicum frutescens utilizing five different genetic loci (matK, ITS, trnH- psbA, rpoB, and rbcL) and comparing it with other Capsicum species. The present study evaluates the delimiting effect of these barcodes in effectively identifying C. frutescens and distinguishing between the three Capsicum species (annuum, frutescens, and chinense). It will be a unique study that will develop barcoding data using five genetic markers for C. frutescens. After analysis, it was found that the combination of rbcL + ITS proved to be a good barcode to differentiate between the three morphologically similar sisters Capsicum species, while matK, rbcL, and rpoB genetic loci were suitable for identifying C. frutescens. The present work will be a strong base, on which molecular identification of C. frutescens can be performed, and it will also aid in differentiating the morphologically closely resembling “annuum-frutescens -chinense” group.
Key words: frutescens, DNA barcode, rbcL, matK, phylogenetic
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