INTEGRATING SSRS AND GENOME-WIDE SNPS TO ASSESS GENETIC DIVERSITY AND POPULATION STRUCTURE OF RUBROSHOREA LEPROSUL FOR CONSERVATION

Abstract

Assessing genetic diversity and population structure with multiple marker systems provides critical insights for the conservation and sustainable management of tropical tree species. We applied simple sequence repeats (SSRs) and genome-wide single nucleotide polymorphisms (SNPs) to characterise genetic variation in Rubroshorea leprosula, a widely distributed dipterocarp in Southeast Asia. SSRs revealed higher allelic richness and heterozygosity, consistent with their multi-allelic nature and high mutation rates, whereas SNPs produced more conservative but genome-wide estimates of diversity. SNP analyses indicated consistently negative inbreeding coefficients and relatively high nucleotide diversity (π = 0.008–0.010), suggesting substantial standing variation and strong adaptive potential. Population differentiation indicates a higher value with SSRs (F_ST = 0.061) than with SNPs (F_ST = 0.027), reflecting the ability of SSRs to detect finer-scale versus the genome-wide connectivity captured by SNPs. Both marker systems consistently identified two major genetic clusters aligned with a north–south division across Peninsular Malaysia, with admixture indicating historical or ongoing gene flow. A localised inbreeding signal was detected in the Belum–Temenggor complex, highlighting populations at elevated risk under fragmentation. Together, these results demonstrate the complementary strengths of SSRs for detecting rare alleles and local differentiation, and SNPs for capturing broad genomic patterns. Integrating both marker systems strengthens conservation planning by informing strategies for maintaining connectivity, and guiding conservation effort to safeguard the adaptive capacity and genetic potential of R. leprosula.