Novel genetic basis of resistance to Bt toxin Cry1Ac in Helicoverpa zea

Crops genetically engineered to produce insecticidal proteins from the bacterium Bacillus thuringiensis (Bt) have advanced pest management, but their benefits are diminished when pests evolve resistance. Elucidating the genetic basis of pest resistance to Bt toxins can improve resistance monitoring, resistance management, and design of new insecticides. Here, we investigated the genetic basis of resistance to Bt toxin Cry1Ac in the lepidopteran Helicoverpa zea, one of the most damaging crop pests in the United States. To facilitate this research, we built the first chromosome-level genome assembly for this species. Using a genome-wide association study, fine-scale mapping, and RNA-seq, we identified a 250kb QTL on chromosome 13 that was strongly associated with resistance in a strain of H. zea that had been selected for resistance in the field and lab. This QTL contains no genes with a previously reported role in resistance or susceptibility to Bt toxins. However, within this QTL, we discovered a premature stop codon in a kinesin gene. We hypothesize that this mutation contributes to resistance. The results indicate the mutation on chromosome 13 was necessary but not sufficient for resistance, and therefore conclude that mutations in more than one gene contributed to resistance. Moreover, we found no changes in gene sequence or expression consistently associated with resistance for 11 genes previously implicated in lepidopteran resistance to Cry1Ac. Thus, the results reveal a novel and polygenic basis of resistance and extend the list of genes contributing to pest resistance to Bt toxins.