BACKGROUND/OBJECTIVES: The genus comprises approximately 70 species with high genetic diversity, among which is the most economically significant. Despite numerous studies on the genetic characterizations of , selecting optimal chloroplast DNA barcoding regions for intraspecific differentiation remains unresolved. Most studies have focused on nuclear markers (SSRs, SNPs) or widely used chloroplast loci (e.g., , ), which have shown limited resolution at the subspecies level. In this study, the complete chloroplast genomes of 34 accessions from different varieties and hybrids (, , , and ) were analyzed to identify the key genomic regions for DNA barcoding.

METHODS

Using bioinformatics tools, we assessed the genome structure, nucleotide variability, microsatellites, codon usage bias, and phylogenetic relationships among the investigated varieties.

RESULTS

The chloroplast genomes displayed a quadripartite structure, with lengths ranging from 160,906 to 160,929 bp and a guanine-cytosine (GC) content of ~37.4%. Phylogenetic analysis revealed an unusual position for VV-5 vini and VVVL-3 lab, suggesting potential taxonomic misclassification or hybridization effects. A single locus showed low discrimination power, but the concatenation of five loci (, , , , and ) exhibited significantly improved resolution (44.11% K2P), surpassing traditional markers.

CONCLUSIONS

This study addresses the gap in the literature regarding the use of concatenated chloroplast loci for subspecies research; the results validate these markers across a broader range of accessions and integrate nuclear and mitochondrial data to achieve a more comprehensive understanding of the evolutionary history and genetic diversity of .