Characterization of Long Non-Coding RNAs in the Bollworm, Helicoverpa zea, and Their Possible Role in Cry1Ac-Resistance

Simple Summary Multiple caterpillar pest species have become resistant to transgenic crops. These crops were originally engineered to make a bacteria protein that would kill the caterpillar when the insect eats the plant. This project focused on comparing gene expression patterns in a bollworm caterpillar resistant strain compared to a susceptible bollworm strain. Expression differences were found in long non-coding RNAs, sequences that do not make proteins but can regulate making proteins. There were increased and decreased levels of different long non-coding RNAs in the resistant strain. Proximity relationships of these non-coding RNAs to protein coding-genes that have functions known to cause resistance were also found. Proximity is one way long non-coding RNA regulates the making of proteins and could be a mechanism of how these insects became resistant. The potential of using these discoveries in managing insect pest resistance levels in the field is discussed. Multiple insect pest species have developed field resistance to Bt-transgenic crops. There has been a significant amount of research on protein-coding genes that contribute to resistance, such as the up-regulation of protease activity or altered receptors. However, our understanding of the role of non-protein-coding mechanisms in Bt-resistance is minimal, as is also the case for resistance to chemical pesticides. To address this problem relative to Bt, RNA-seq was used to examine statistically significant, differential gene expression between a Cry1Ac-resistant (similar to 100-fold resistant) and Cry1Ac-susceptible strain of Helicoverpa zea, a prevalent caterpillar pest in the USA. Significant differential expression of putative long non-coding RNAs (lncRNAs) was found in the Cry1Ac-resistant strain (58 up- and 24 down-regulated gene transcripts with an additional 10 found only in resistant and four only in susceptible caterpillars). These lncRNAs were examined as potential pseudogenes and for their genomic proximity to coding genes, both of which can be indicative of regulatory relationships between a lncRNA and coding gene expression. A possible pseudogenic lncRNA was found with similarities to a cadherin. In addition, putative lncRNAs were found significantly proximal to a serine protease, ABC transporter, and CYP coding genes, potentially involved in the mechanism of Bt and/or chemical insecticide resistance. Characterization of non-coding genetic mechanisms in Helicoverpa zea will improve the understanding of the genomic evolution of insect resistance, improve the identification of specific regulators of coding genes in general (some of which could be important in resistance), and is the first step for potentially targeting these regulators for pest control and resistance management (using molecular approaches, such as RNAi and others).