Genetic Structuring of the Wild Aquilaria malaccensis Population from Indonesia Inferred by trnL-trnF and trnH-psbA

Aquilaria malaccensis Lam. is known to produce high-grade agarwood, which is naturally distributed in Indonesia, and their trading has been regulated under the CITES Appendix II. This study aimed to analyze the genetic diversity of wild A. malaccensis from Indonesia. Forty-one samples of A. malaccensis were gathered from various wild populations originating from different islands, including Sumatra mainland, adjacent islands (Bintan and Lingga), West Kalimantan, and Bunguran Island—the northernmost island adjacent to West Kalimantan. Sequencing was performed using trnL-trnF and trnH-psbA. The total sequence (1417 bp) revealed six distinct haplotypes, categorized based on their phytoregion: Sumatra and its adjacent islands Bintan and Lingga, West Kalimantan, and Bunguran Island. Notably, Bunguran displayed the most distinct haplotype, featuring two unique haplotypes and one shared haplotype with the populations of Sumatra and its adjacent islands, Bintan and Lingga. The shared haplotype among Bintan, Lingga, and Bunguran with Sumatra mainland suggests a potential connection to the geographical history of these islands, which were formerly part of Sundaland. The nucleotide diversity (π) was notably low in Bunguran Island (π = 0.00215) and the West Kalimantan population (π = 0.00067), in contrast to Sumatra and its adjacent islands characterized by a nucleotide diversity of 0. Despite this low nucleotide diversity value, the phytoregional populations were genetically differentiated, with the highest differentiation between Bunguran Island and Western Borneo (F_ST = 0.83686). It is suggested that the individual trees represent each haplotype as genetic sources for ex situ conservation and cultivation.