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

Ashley E. Tessnow, Todd M. Gilligan, Eric Burkness, Caroline Placidi de Bortoli, Juan Luis Jurat-Fuentes, Patrick Porter, Danielle Sekula, Gregory A. Sword

Research output: Contribution to journalArticlepeer-review

2 Scopus citations

Abstract

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.

Original languageEnglish (US)
Article numbere12195
JournalPeerJ
Volume9
DOIs
StatePublished - Sep 24 2021

Bibliographical note

Funding Information:
This work was supported by the following: Agricultural and Food Research Initiative - Education and Workforce Development (award no. 2020-67034-31748) from the USDA National Institute of Food and Agriculture; Agricultural and Food Research Initiative (award no. 2021-67013-33566) from the USDA National Institute of Food and Agriculture; Agriculture and Food Research Initiative Foundational Program competitive grant (award no. 2018–67013-27820); Hatch Multistate NC-246 from the US Department of Agriculture National Institute of Food and Agriculture; and USDA-APHIS Cooperative Agreement (#AP19PPQS&T00C071). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Publisher Copyright:
Copyright 2021 Tessnow et al.

Keywords

  • Diagnostic assay
  • Fall armyworm
  • Genetic strains
  • Real-time PCR
  • Spodoptera frugiperda
  • TaqMan

PubMed: MeSH publication types

  • Journal Article

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