DNA barcoding of geographical indication tagged Byadagi chilli and its cultivars using ITS2, matK and rbcL coding sequences.

Background: Byadagi chilli, a Geographical Indication (GI)-tagged chilli variety known for its special aroma and bright red colour, was accorded the GI tag in February 2011 with the GI number 129. The two traditional varieties of Byadagi chilli, namely: Dabbi and Kaddi, are the GI-tagged varieties. In this study, GI-tagged Byadagi Dabbi, Byadagi Kaddi and other cultivars of Byadagi chilli, such as Byadagi Lali (BL), Byadagi HPH 2043 (B2), Byadagi BSS 355 (B3) and another popular GI-tagged chilli variety, Guntur Sannam, were analysed to assess their inter-relationships. Due to the high market value and demand, it is important to identify and differentiate the original variety of Byadagi chilli and its associated cultivars from the other chilli cultivars, which are sold under the name of Byadagi chilli. In this study, molecular assessment by DNA barcoding was performed to establish the identity of authentic Byadagi chilli varieties.

Methods And Results: Five samples of Byadagi chilli and another GI-tagged chilli variety, Guntur Sannam, were analysed using three DNA barcodes: ITS2, matK and rbcL. The PCR products were sequenced, nucleotide BLAST was performed and ITS2 showed 97.7% identity, matK 99.1%, and rbcL 99.19% with Capsicum annuum at the genus and species levels. Phylogenetic analysis of the DNA sequences of all the six chilli samples was performed using ClustalW multiple sequence alignment in MEGA11. The genetic distance between the six samples was calculated using the maximum likelihood approach.

Conclusions: This study distinctly demonstrates that the chloroplast DNA barcodes matK and rbcL, along with the nuclear DNA barcode, ITS2, can be used for accurate identification of Byadagi chilli cultivars. This study offers significant molecular identification and establishes a robust barcoding foundation for Byadagi chilli. The phylogenetic trees generated from the barcode sequences clearly indicated the relationships among the selected cultivars.