Development and characterization of polymorphic microsatellite markers for Macrotermes carbonarius (Blattodea: Termitidae)

Macrotermes carbonarius is a fungus-growing termite widely distributed in Southeast Asia and is ecologically important in both natural and urban environments. In Malaysia, this species may act as a secondary pests following the suppression of primary termite infestations, making an understanding of colony structure and spatial connectivity particularly relevant. Microsatellite markers are widely used for such population-level studies; however, the performance and informativeness of loci developed for related taxa remain uncertain for M. carbonarius. In this study, genome-derived microsatellite markers were developed using Illumina-based next-generation sequencing. Seven loci showing strong amplification and high polymorphism were validated across 60 individuals from 6 locations in Penang, Malaysia. The number of alleles per locus ranged from 9 to 13, with expected heterozygosity (HE) values ranging from 0.751 to 0.888. All loci exhibited high polymorphic information content (PIC = 0.707 to 0.869), indicating their suitability for genetic studies. Population genetic analyses revealed high population differentiation (FST = 0.282 to 0.424), suggesting limited gene flow and substantial genetic structuring among colonies. The consistently high inbreeding coefficient (FIS = 1) reflects the species’ eusocial reproductive system, where colony members are closely related. These developed markers provide valuable molecular tools for examining genetic diversity, colony organization, and population connectivity in M. carbonarius.