Improving Bt resistance risk assessment and management through genomic monitoring

The US government views the insecticidal properties of Bacillus thuringiensis (Bt) as a “public good”, and mandates that Bt be used in a manner that reduces the risk of insect pests evolving resistance. Both the US-EPA and USDA have concluded that monitoring for resistance could improve agricultural management practices aimed at decreasing resistance risk. Yet a lack of unbiased, standardized monitoring tools has made it challenging to identify field-collected pest populations with heritable Bt resistance mechanisms prior to crop failure. To address this need, we developed a Double-Digest Restriction-site Associated DNA Sequencing (ddRAD-seq) monitoring approach capable of detecting allele frequency changes throughout the insect genome. Using this genomic approach, we scanned the genomes of archived Heliothis virescens and Helicoverpa zea specimens from 1997 through 2012 and discovered a number of genomic regions that have changed over time, likely in response to Bt selection. In some cases, these genomic regions were located near to previously described Bt resistance genes. In other cases, new candidate genes appeared to be evolving in response to selection by Bt crops.  Ultimately, our work will confirm whether the evolution of insect resistance to Bt-expressing crops can be predicted by quantifying patterns of genomic change over time.