Using targeted sequencing and TaqMan approaches to detect acaricide (bifenthrin, bifenazate, and etoxazole) resistance associated SNPs in Tetranychus urticae collected from peppermint fields and hop yards

Abstract

Tetranychus urticae (Koch) is an economically important pest of many agricultural commodities world-wide. Multiple acaricides, including bifenazate, bifenthrin, and extoxazole, are currently registered to control T. urticae. However, populations of T. urticae in many different growing regions have developed acaricide resistance through multiple mechanisms. Within T. urticae, single nucleotide polymorphisms (SNPs) have been documented in different genes which are associated with acaricide resistance phenotypes. The detection of these mutations through TaqMan qPCR has been suggested as a practical, quick, and reliable tool to inform agricultural producers of acaricide resistance phenotypes present within their fields and have potential utility for making appropriate acaricide application and integrated pest management decisions. Within this investigation we examined the use of a TaqMan qPCR-based approach to determine genotypes which have been previously associated with acaricide resistance in field-collected populations of T. urticae from peppermint fields and hop yards in the Pacific Northwest of the United States and confirmed the results with a multiplex targeted sequencing. The results suggest that a TaqMan qPCR approach accurately genotypes T. urticae populations for SNPs that have been linked to Bifenazate, Bifenthrin, and Etoxazole resistance. The results also demonstrated that different populations of mites in Washington and Idaho displayed varying frequencies of the examined SNPs. While we were able to detect the SNPs associated with the examined acaricides, the mutation G126S was not an appropriate or accurate indicator for bifenazate resistance.

Agrigenomic Diversity Unleashed: Current Single Nucleotide Polymorphism Genotyping Methods for the Agricultural Sciences

“…In the study, the authors were able to accurately genotype Bifenazate, Bifenthrin, and Etoxazole resistance in the mites [25]. However, they note that certain populations of T. urticae had varying diversity of the SNPs, relative to these resistances [25]. They also note that one of the selected SNPs (G126S, a potential indicator of bifenazate resistance) was not an accurate identifier of resistance [25].…”

“…One of the most common methods of SNP genotyping with qPCR is the TaqMan method [16,24]. This method remains one of the most commonly used in genotyping today [25][26][27]. This method is ideal for genotyping known polymorphisms that are allele specific in a given genome.…”

“…For example, the reaction mastermix solutions for KASP and TaqMan genotyping are different [16]. Additional example cases include Shumate et al (2023), where the TaqMan method was applied to identify acaricide resistance in Tetranychus urticae [25]. In the study, the authors were able to accurately genotype Bifenazate, Bifenthrin, and Etoxazole resistance in the mites [25].…”

“…Additional example cases include Shumate et al (2023), where the TaqMan method was applied to identify acaricide resistance in Tetranychus urticae [25]. In the study, the authors were able to accurately genotype Bifenazate, Bifenthrin, and Etoxazole resistance in the mites [25]. However, they note that certain populations of T. urticae had varying diversity of the SNPs, relative to these resistances [25].…”

“…However, they note that certain populations of T. urticae had varying diversity of the SNPs, relative to these resistances [25]. They also note that one of the selected SNPs (G126S, a potential indicator of bifenazate resistance) was not an accurate identifier of resistance [25]. This outlines the importance of SNP selection in assay design, as not all SNPs will be relative to a research question or ubiquitous in a species.…”