Assessing the Utility of Partial Chloroplast matK Sequences for DNA Barcoding of Indonesian Grapevine (Vitis vinifera L.) Cultivar from Magelang, Central Java

Abstract

Grapevine (Vitis vinifera) is an important fruit crop in Indonesia, but its local cultivars remain poorly characterized at the molecular level. This study evaluated the utility of a partial chloroplast maturase K (matK) gene for preliminary DNA barcoding of nine grapevine samples from Magelang, Indonesia. DNA was extracted and amplified using conventional PCR, but only five samples yielded usable matK sequences. Phylogenetic and Automatic Barcode Gap Discovery (ABGD) analyses showed that the 131 bp matK fragment was highly conserved, with no nucleotide variation among the Indonesian samples. The sequences formed a single clade, while ABGD detected no clear barcode gap or cultivar differentiation. These findings indicate that the short partial matK fragment has limited utility for discriminating Indonesian grapevine cultivars. Future studies should use longer or multiple barcode regions and higher-resolution molecular markers to improve cultivar identification and genetic characterization.