Open AccessNovel real-time PCR based assays for differentiating fall armyworm strains using four single nucleotide polymorphisms
Author(s) -
Ashley E. Tessnow,
Todd M. Gilligan,
E. C. Burkness,
Caroline Placidi De Bortoli,
Juan Luís Jurat-Fuentes,
Paul Porter,
Danielle Sekula,
Gregory A. Sword
Publication year - 2021
Publication title -
peerj
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.927
H-Index - 70
ISSN - 2167-8359
DOI - 10.7717/peerj.12195
Subject(s) - biology , spodoptera , taqman , pest analysis , single nucleotide polymorphism , genetics , strain (injury) , population , fall armyworm , genotype , polymerase chain reaction , gene , botany , recombinant dna , demography , anatomy , sociology
The fall armyworm, Spodoptera frugiperda, is a polyphagous global pest with a preference for gramineous crops such as corn, sorghum and pasture grasses. This species is comprised of two morphologically identical but genetically distinct host strains known as the corn and rice strains, which can complicate pest management approaches. Two molecular markers are commonly used to differentiate between strains, however, discordance between these markers can lead to inconclusive strain identification. Here, we used double digest restriction site associated DNA sequencing to identify diagnostic single nucleotide polymorphisms (SNPs) with alleles unique to each strain. We then used these strain-specific SNPs to develop four real-time PCR based TaqMan assays to rapidly and reliably differentiate between strains and interstrain hybrids. These assays provide a new tool for differentiating between strains in field-collected samples, facilitating future studies on strain population dynamics and interstrain hybridization rates. Understanding the basic ecology of S. frugiperda strains is necessary to inform future management strategies.