Chloroplast SNAP Markers Reveal Cytoplasmic Genetic Diversity in Indonesian Sugar Palm (Arenga pinnata)

Sugar palm (Arenga pinnata) is widely distributed across Indonesia, yet its genetic diversity remains poorly characterized. This economically important species is valued for neera sap and young fruits. In this study, the genetic diversity of 60 Indonesian A. pinnata accessions from 15 regions was evaluated using chloroplast genome (cpDNA) SNP-based SNAP markers. The markers were developed from informative SNPs identified in complete chloroplast genomes of dwarf and tall A. pinnata types, together with one reference accession from NCBI. Haplotype network and phylogenetic analyses resolved 15 distinct haplotypes grouped into three clusters, with HAP15 identified as the most dominant lineage. Cluster III, though represented by only three accessions, occupied a distinct evolutionary position. Geographic mapping revealed that Banten and Bogor harbored the highest haplotype diversity, underscoring their importance for germplasm exploration and conservation. These findings demonstrate the effectiveness of cpDNA SNP-based SNAP markers in uncovering cytoplasmic genetic variation and provide a robust molecular basis for conservation, germplasm management, and future A. pinnata improvement programs.