Rokhana Faizah, Turhadi Turhadi, Delvi Maretta, Sri Wening, Yogesh K. Ahlawat, Ajaya K. Biswal
Ganoderma boninense causes basal stem rot, which significantly reduces oil palm productivity. Understanding the genetic basis of resistance is critical for developing successful breeding techniques. The laccase-24 (EgLCC24) gene plays a pointed role in lignin polymerization and cell wall formation in oil palm (Elaeis guineensis), potentially contributing to structural defences against G. boninense. Single nucleotide amplified polymorphism (SNAP), amplification refractory mutation system PCR (ARMS-PCR), and insertion site-based polymorphism (ISBP) markers were used in this study. These markers were used to evaluate population structure and genetic variation across oil palm genotypes with different levels of G. boninense resistance based on the EgLCC24 gene. Multivariate analysis employing principal coordinate analysis (PCoA) indicated considerable genetic differentiation between resistant and susceptible genotypes, which was compatible with population structure inference. Differential marker polymorphism also contributed to the observed separation, showing coordinated genetic changes related to resistance status. These findings shed light on the genetic architecture of G. boninense resistance and show the effectiveness of multivariate marker-based techniques in resistance-oriented oil palm breeding programs. Using ISBP, SNAP, and ARMS-PCR markers combined with multivariate and clustering analyses, it was demonstrated structured genetic variation between oil palm genotypes contrasting in resistance to G . boninense . Principal coordinate analysis and population structure inference consistently revealed resistance with associated genetic clustering, highlighting coordinated genomic differences underlying resistance phenotypes. Population structure analysis (ΔK = 2) further confirmed clear genetic separation between resistant and susceptible groups, supporting the potential application of EgLCC24 gene-based markers. © 2026 Elsevier Ltd.
Laboratory of Plant Molecular Biology, Agriculture Faculty, IPB University, Bogor, Indonesia; Laboratory of Molecular Biology, Indonesian Oil Palm Research Institute, Medan-Bogor, Indonesia; PT Indonesian Research Institute for Estate Crops (Ltd.), a subsidiary of Nusantara Holding Company, Bogor, Indonesia; Department of Biology, Brawijaya University, Malang, Indonesia; Research Center for Applied Botany, National Research and Innovation Agency Republic of Indonesia, Jakarta, Indonesia; Allied Health Sciences, Datta Meghe Institute of Higher Education and Research, Maharashtra, Wardha, India; Department of Life Sciences, Faculty of Allied Health Sciences, SGT University, Haryana, Gurugram, 122505, India; Department of Biochemistry and Molecular Biology, University of Georgia, Athens, 30602, GA, United States; Complex Carbohydrate Research Center, University of Georgia, Athens, 30602, GA, United States
