Fire ant social supergene genotyping using polymorphic indel markers

Abstract The Red Imported Fire Ant ( Solenopsis invicta ) exhibits a social polymorphism with monogyne and polygyne colonies. This social polymorphism is fully associated with two haplotype variants ( SB and Sb ) at a social supergene. Current genotyping methods are based on PCR–RFLP, multiplex PCR, or high-resolution melt PCR assays, all using primers designed on Gp-9 . However, due to occasional mutation or polymorphism, genotyping might be ineffective. Here, we developed a new supergene genotyping assay based on indel (insertion-deletion) polymorphisms outside of Gp-9 . Primers were designed for five short indels of 120–140 bp found in a 2 Mb region centered on Gp-9 . Testing of both single individuals and pooled samples showed complete consistency between the indel assays and the Gp-9 PCR–RFLP assay, thus permitting rapid genetic determination of colony social form. These new supergene genotyping assays designed outside of Gp-9 offer additional options for genotyping fire ants, including allowing experiments where Gp-9 is modified. Finally, the indel approach should be a useful and simple way to genotype supergenes in ants and other species.