Molecular identification and phylogenetic reconstruction of sugarcane (Saccharum officinarum L.) cultivars from Indonesia based on rbcL chloroplast gene

Sugarcane (Saccharum officinarum L.) presents high genetic complexity, posing challenges in breeding efforts aimed at developing superior hybrids. This research utilizes DNA barcoding, specifically leveraging the ribulose-1,5-biphosphate carboxylase-oxygenase large subunit (rbcL) gene as a DNA barcode. This research aims to assess the effectiveness of the rbcL gene in distinguishing local sugarcane cultivars and construct a phylogenetic tree to clarify their evolutionary relationships. The rbcL gene was amplified in 19 samples collected from several regions in Indonesia through PCR methods. DNA alignment, sequencing, and analyses were conducted using Maximum Likelihood (ML) and Bayesian Inference (BI) evolutionary models. Additionally, validation was performed using genetic distance, haplotype network, and principal coordinate of analysis (PCoA). The results established successful amplification and identification of samples within the Saccharum genus. Notably, samples BKS2, BKS7, OP3, NX04, Pringu, and Kidang Kencana displayed distincy characteristic in both ML and BI analyses, substantiated by polymorphic site variations and genetic distance assessments. However, the limitations associated with the rbcL gene constrained comprehensive analysis of other local sugarcane samples, hindering precise phylogenetics placement of the other samples.