Large-scale RNAi Screen for Pest Control Targets

Nathaniel Grubbs, Ph.D.

Nathaniel Grubbs, Ph.D., Department of Entomology, North Carolina State University
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Ulrich et al (2015) have recently published an analysis of iBeetle results aimed at identifying potential targets for RNAi-based pest control.

The Holy Grail of pest control is a method that is cheap, easy to apply, and impacts only the target species, without harming the environment or the beneficial and benign insects in the area. RNA interference (RNAi) has long been thought to have the potential to serve as such a control method, primarily because of its sequence-based specificity, reducing the expression of only the target gene, and only in the target species. However, identifying targets that result in pest death after exposure to low levels of double-stranded RNA (dsRNA) can be difficult if the pest is not an established laboratory organism, and/or has few available genetic and genomic tools and resources.

iBeetle LogoTcastaneumUlrich et al. believe the iBeetle Screen may provide researchers a starting place for finding potential gene targets. The iBeetle project seeks to target all of the genes of the red flour beetle, Tribolium castaneum, with RNAi, then make the results available to the public. Thus far, ~5000 genes have been screened, so Ulrich and colleagues set about selecting genes with lethal phonotypes for further analysis to determine the most efficient targets. They initially selected 100 genes with high mortality, then narrowed the list down to 11 genes with high mortalities even at low dsRNA concentrations, creating a more realistic list for testing in non-model species.

RNAi simplified.

The authors make sure to note that there might be differences between their results via injecting dsRNA and results achieved through feeding dsRNA to target pests, but they also show that previously identified target genes for the western corn rootworm are not as efficient in Tribolium as the 11 genes identified in this paper, suggesting that the genes on their list are still likely to be more efficient than current targets.

Importantly, Ulrich et al. analyze the potential of their 11 candidate genes to impact non-target species. After comparing their dsRNA target regions to orthologous gene sequences from other species, the authors note that there is no dsRNA sequence that couldn’t potentially affect non-target species. The authors also note that there is no reliable way to predict which genes, and which regions of these genes, are likely to provide the lowest chance for off-target effects in all possible organisms. So, researchers hoping to use RNAi as a pesticide will have to work on a case-by-case basis to protect the most vulnerable non-target species.

RNAi as an insecticide.

RNAi as an insecticide.

Any researchers studying the control of insect pests, and in particular, those seeking RNAi-based methods of control, will find this paper enlightening. The genes identified by Ulrich and colleagues will be a useful starting place for identifying pesticide targets, and their off-target analysis serves as a reminder that all pest control methods carry risks, and it is our job as researchers to mitigate those risks as much as possible, while maintaining the benefits.

Ulrich, J., Dao, V., Majumdar, U., Schmitt-Engel, C., Schwirz, J. et al., 2015 Large scale RNAi screen in Tribolium reveals novel target genes for pest control and the proteasome as prime target. BMC Genomics 16: 674doi:10.1186/s12864-015-1880-y

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