Expression quantitative trait locus (eQTL) mapping with a cross between Tetranychus urticae inbred strains MR-VPi and ROS-ITi

We performed expression quantitative trait locus (eQTL) mapping between two strains of Tetranychus urticae (the two-spotted spider mite), a generalist herbivore known for its rapid evolution of acaricide resistance. For parents, we used the inbred strain MR-VPi that is highly resistant to multiple acaricides in different classes, and the inbred strain ROS-ITi that is comparatively susceptible to many acaricides. The eQTL mapping experiment was performed with F3 samples, and thousands of trans and cis eQTL were identified, including for genes in families known (or suspected) to be involved in the metabolism of xenobiotics (plant produced secondary compounds and acaricides). One trans eQTL hotspot was identified that strongly impacted the expression of many detoxification genes in different gene families. Follow up studies using derived near isogenic lines validated the trans eQTL hotspot, and RNA interference (RNAi) knockdown of tandemly duplicated genes encoding products with homology to the ligand binding domains of nuclear hormone receptor 96 genes impacted many of the same detoxification genes controlled by the hotspot. Overall design: eQTL mapping was performed using F3 mite samples, and subsequently differential gene expression analyses were performed between near isogenic lines (NILs) derived from the parents (MR-VPi and ROS-ITi) and in NILs subjected to RNAi knockdown of candidate genes (the RNAi work was performed with mites on both bean and tomato leaves; otherwise mites on bean leaves were used).