Novel real-time PCR based assays for differentiating fall armyworm strains using four single nucleotide polymorphisms

The fall armyworm, Spodoptera frugiperda, is a polyphagous global pest with preference for gramineous crops such as corn, sorghum and pasture grasses. This species comprised of two morphologically identical but genetically distinct host strains known the corn rice strains, which can complicate management approaches. Two molecular markers are commonly used to differentiate between however, discordance these lead inconclusive strain identification. Here, we double digest restriction site associated DNA sequencing identify diagnostic single nucleotide polymorphisms (SNPs) alleles unique each strain. We then strain-specific SNPs develop four real-time PCR based TaqMan assays rapidly reliably interstrain hybrids. These provide new tool differentiating in field-collected samples, facilitating future studies on population dynamics hybridization rates. Understanding basic ecology S. frugiperda necessary inform strategies.