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, which has 31 chromosomes containing 375 Mb and 15,482 predicted proteins. Using a genome-wide association study, fine-scale mapping, and RNA-seq, we identified a 250-kb quantitative trait locus (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. The mutation in this QTL contributed to but was not sufficient for resistance, which implies alleles in more than one gene contributed to resistance. This QTL contains no genes with a previously reported role in resistance or susceptibility to Bt toxins. However, in resistant insects, this QTL has a premature stop codon in a kinesin gene which is a primary candidate as a mutation contributing to resistance. 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.

Transgenic crops producing insecticidal proteins from the bacterium Bacillus thuringiensis (Bt) control some important insect pests. However, evolution of resistance by pests reduces the efficacy of Bt crops. Here we review resistance to Bt cotton in the pink bollworm, Pectinophora gossypiella, one of the world’s most damaging pests of cotton. Field outcomes with Bt cotton and pink bollworm during the past quarter century differ markedly among the world’s top three cotton-producing countries: practical resistance in India, sustained susceptibility in China, and eradication of this invasive lepidopteran pest from the United States achieved with Bt cotton and other tactics. We compared the molecular genetic basis of pink bollworm resistance between lab-selected strains from the U.S. and China and field-selected populations from India for two Bt proteins (Cry1Ac and Cry2Ab) produced in widely adopted Bt cotton. Both lab- and field-selected resistance are associated with mutations affecting the cadherin protein PgCad1 for Cry1Ac and the ATP-binding cassette transporter protein PgABCA2 for Cry2Ab. The results imply lab selection is useful for identifying genes important in field-evolved resistance to Bt crops, but not necessarily the specific mutations in those genes. The results also suggest that differences in management practices, rather than genetic constraints, caused the strikingly different outcomes among countries.

During the messenger RNA (mRNA) maturation process, RNA polyadenylation is a key step, and is coupled to the termination of transcription. Various cis-acting elements near the cleavage site and their binding factors would affect the process of polyadenylation, and AAUAAA, a highly conserved hexamer, was the most important polyadenylation signal (PAS). PAS usage is one of the critical modification determinants targeted at mRNA post-transcription. The full-length transcriptome has recently generated a massive amount of sequencing data, revealing poly(A) variation and alternative polyadenylation (APA) in Spodoptera frugiperda. We identified 50,616 polyadenylation signals in Spodoptera frugiperda via analysis of full-length transcriptome combined with expression Sequence Tags Technology (EST). The polyadenylation signal usage in Spodoptera frugiperda is conserved, and it is similar to that of flies and other animals. AAUAAA and AUUAAA are the most highly conserved polyadenylation signals of all polyadenylation signals we identified. Additionally, we found the U/GU-rich downstream sequence element (DSE) in the cleavage site. These results demonstrate that APA in Spodoptera frugiperda plays a significant role in root growth and development. This is the first polyadenylation signal usage analysis in agricultural pests, which can deepen our understanding of Spodoptera frugiperda and provide a theoretical basis for pest control.

Flavone is widely found in plants and plays an important role in plant defense against pests. Many pests, such as Helicoverpa armigera, use flavone as a cue to upregulate counter-defense genes for detoxification of flavone. Yet the spectrum of the flavone-inducible genes and their linked cis-regulatory elements remains unclear. In this study, 48 differentially expressed genes (DEGs) were found by RNA-seq. These DEGs were mainly concentrated in the retinol metabolism and drug metabolism-cytochrome P450 pathways. Further in silico analysis of the promoter regions of 24 upregulated genes predicted two motifs through MEME and five previously characterized cis-elements including CRE, TRE, EcRE, XRE-AhR and ARE. Functional analysis of the two predicted motifs and two different versions of ARE (named ARE1 and ARE2) in the promoter region of the flavone-inducible carboxylesterase gene CCE001j verified that the two motifs and ARE2 are not responsible for flavone induction of H. armigera counter-defense genes, whereas ARE1 is a new xenobiotic response element to flavone (XRE-Fla) and plays a decisive role in flavone induction of CCE001j. This study is of great significance for further understanding the antagonistic interaction between plants and herbivorous insects.