Genetic Uniformity and Residual Divergence in Apomictic Mangosteen Garcinia mangostana L.) Revealed by RAPD Markers

Abstract

Mangosteen (Garcinia mangostana L.) is a high-value tropical fruit whose genetic improvement is constrained by obligate apomictic reproduction, which limits meiotic recombination and narrows detectable diversity. This study assessed the genetic uniformity and residual divergence among mangosteen accessions to support objective mother-tree selection and germplasm management. Twenty local accessions from Bulukumpa District, Bulukumba Regency (South Sulawesi, Indonesia), and two commercial reference genotypes (Kali Gesing and Lotan) were evaluated using five RAPD primers (OPA-01, OPA-04, OPB-01, OPB-04, and OPB-18). Genomic DNA was extracted using a modified CTAB protocol, amplified under optimized RAPD-PCR conditions, and electrophoresed on a 2% agarose gel. To ensure robustness, each primer–accession combination was amplified in duplicate; only clear, consistently reproducible bands were scored in a binary matrix (1/0), with no-template controls included to monitor for contamination. Genetic similarity was estimated using Jaccard’s coefficient and clustered using UPGMA (SAHN) in the NTSYS-pc 2.1. All primers produced clear and reproducible banding patterns, yielding two to six loci per primer. However, the polymorphism was highly limited: four primers generated exclusively monomorphic profiles, whereas primer OPA-04 produced five loci with one polymorphic locus. Overall polymorphism was ~20%, with moderate marker informativeness indicated by PIC and expected heterozygosity values of approximately 0.40 for OPA-04. Similarity coefficients were very high (0.95–1.00), reflecting a strongly homogeneous genetic structure. UPGMA clustering resolved two groups at a similarity threshold of 0.95: a major cluster containing most accessions, along with Kali Gesing and Lotan, and a minor sub-cluster comprising four accessions (MGS_9, MGS_13, MGS_17, and MGS_18) differentiated by the single polymorphic locus. These findings confirm an extremely narrow genetic base consistent with apomictic reproduction, while highlighting a small set of relatively distinct accessions that may be prioritized for conservation and evidence-based parent selection in mangosteen improvement programs.