RNA sequencing uncovers acaricide resistance mechanisms in Tetranychus urticae on hops

Hops (Humulus lupulus) are used to impart flavor and preservative attributes to beer. The Pacific Northwest region (PNW) contributes approximately 99% of the total hops production in the USA. However, hot and dry conditions in PNW create a conducive environment for the proliferation of two-spotted spider mite (TSSM), Tetranychus urticae. TSSM management on hops heavily depends on the use of acaricides. However, TSSM has been reported to develop resistance to numerous classes of acaricides, posing a significant challenge to its effective management. Here, we performed RNA sequencing (RNA-seq) to understand the molecular mechanisms underpinning acaricide resistance in hops TSSM populations. A sample of the susceptible TSSM population was collected from a hops field from Prosser, WA, and subjected to selection pressure against two acaricides, abamectin, and bifenthrin to generate acaricide-resistant populations. Gene ontology enrichment analysis revealed a number of differential expressed genes in the resistant TSSM populations when compared with the susceptible one. The upregulated genes in the resistant populations were associated with metabolic processes, including genes encoding cytochrome P450s, glutathione S-transferases, carboxylesterases, lipocalin, and peptidases. While downregulated genes were predominately associated with chitin metabolism. Additionally, RNA-seq reads were leveraged to identify mutations within the coding region. Functionally important mutations in detoxification genes that may facilitate acaricide resistance in TSSM were detected. These findings can aid in developing molecular tools to detect and monitor acaricide resistance in the field, enabling better planning for the effective use of acaricides to break or slow down resistance buildup.