Genetic Classification of Traditional Rice Varieties Collected from Vietnam using matK and rbcL DNA Barcode Markers

Vietnam is home to a rich collection of traditional rice (Oryza sativa L.) landraces, many of which are increasingly threatened by modern agricultural practices and genetic erosion. This study aimed to genetically classify 90 traditional Vietnamese rice varieties collected from the Northern, Central and Southern regions of Vietnam using the chloroplast DNA barcode markers matK and rbcL.

Genomic DNA from 90 rice accessions was amplified using PCR with matK and rbcL primers, followed by sequencing and polymorphism analysis. Sequence variation, including single nucleotide polymorphisms (SNPs), transitions, transversions and indels, were identified. Phylogenetic relationships were analyzed using the Tamura-Nei model and UPGMA clustering to evaluate genetic diversity and relationships among the rice varieties.

PCR amplification success rates reached 85.6% for matK and 100% for rbcL. Sequence analysis identified 11 SNPs in matK and 7 polymorphic sites in rbcL. Phylogenetic analysis grouped the rice varieties into two major clades for each marker. The matK marker provided higher resolution of intraspecific variation, distinguishing unique landraces such as Beo but bua, Nep bo and Ba la, whereas rbcL revealed generally low genetic differentiation but identified a divergent subgroup of eight genetically distinct accessions. Genetic distances ranged from 0.000-0.007 for matK and 0.000-0.004 for rbcL. These findings demonstrate that matK and rbcL are complementary molecular markers for genetic classification and varietal authentication of traditional Vietnamese rice, providing a valuable molecular basis for germplasm conservation and future rice breeding programs.