Phylogenetic and Genetic Variation of Sugarcane (Saccharum spp.) from Island of Java, Indonesia based on trnK Chloroplast Gene

Sugarcane (Saccharum officinarum L.) belongs to the Poaceae family, which is the largest family in the Poales order. Sugarcane plays a crucial role as the primary ingredient in the production of sweeteners such as sugar on a large scale. The sugarcane plants extensively cultivated in Indonesia are hybrids resulting from the crossbreeding of Saccharum officinarum with Saccharum spontaneum. Phylogenetic analysis and genetic diversity of sugarcane cultivars have been proposed to identify specific potential groups and to optimize hybridization procedures and selection to evaluate superior genotypes. This study aims to determine the genetic and phylogenetic diversity of S. officinarum based on the DNA barcoding molecular approach using the trnK gene. In this research, the trnK gene was amplified through PCR method on five S. officinarum cultivars originating from Java Island. The amplified results were then sequenced and aligned using MegaX software. Ambiguous DNA nucleotides were manually edited using GeneStudio software. Genetic variations including the number of haplotypes (h), haplotype diversity (Hd), number of polymorphic sites, and number of parsimony sites were analyzed using DnaSP software and confirmed using GenAIEx 6 software. The phylogenetic tree was reconstructed using the Maximum-Likelihood (ML) method. The sugarcane cultivars POJ, JR03, Pringu, KK, and NX04 showed trnK gene amplification with a 252bp fragment and formed a single clade in phylogenetic analysis (ML bootstrap value of 100; BI posterior probability of 1). Haplotype analysis revealed they do not belong to the same group. Indonesian sugarcane has distinct trnK genetic flow compared to those in Japan, China, South Africa, Brazil, and Australia. © 2024, Unique Scientific Publishers. All rights reserved.