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A practical approach to RNA interference for studying gene function in a refractory social insect (on a limited budget)

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Abstract

With powerful functional genomics tools, including RNA interference (RNAi), the study of gene function is moving from simpler phenotypes in model organisms to more complex traits in non-models. However, optimizing RNAi-mediated gene knockdown for a novel system can be time consuming and expensive, so researchers interested in initiating an RNAi study for functional genomics in a non-model organism will want to consider the successes and failures of RNAi in related species and similar phenotypes. Yet, sub-optimal and negative knockdown results are rarely reported alongside positive ones, so choosing the best methodological parameters can be difficult. Furthermore, social insects pose extra challenges to designing functional genomics studies, as the traits we measure are often part of the extended phenotype of a primary reproductive, emerge from the collective phenotypes of many individuals, and may be the result of a gene taking on a novel functional role in a social system. We attempt to mitigate these challenges for other social insect biologists by reporting our own successes and impediments to optimizing RNAi for the gene vitellogenin in the paper wasp Polistes fuscatus. We discuss the many factors that can affect RNAi experimental design and which parameters worked optimally for our study, as well as compile a list of working parameters from previous RNAi studies in social Hymenoptera. We highlight the difficulties of RNAi that are specific to social Hymenoptera, including the potential differences in RNA efficacy across behavioral caste, and share results on our optimized parameters as a potential roadmap for other social insect biologists.

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Acknowledgements

The authors would like to thank Jessica Riojas-Schnier and Maria Bellows for help with animal care; Ian Traniello, Amy Cash-Ahmed, and Fabio Manfredini for input on RNAi methods; Nick Howell of the Iowa State University Horticulture Research Station and Doug Sheeley of Polk County Conservation for providing space for wasp boxes; Tianna Tanasichuk for help with analyses; and the members of the Toth Lab for comments on an early version of the manuscript. This work was funded by the NSF EDGE Program Grant #1827567 awarded to ALT and MJS.

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Authors and Affiliations

  1. Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada

    A. Walton

  2. Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA

    E. Flores, A. Guinness, R. Fortune & A. L. Toth

  3. Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, USA

    M. J. Sheehan

  4. Department of Entomology, Iowa State University, Ames, IA, USA

    A. L. Toth

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  1. A. Walton
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Contributions

AW, ALT, MJS, and AG designed the research; AW and RF collected and dissected wasp samples; AW and AG performed RNAi experiments; AW and EF carried out sample processing and molecular lab work; AW analyzed the data; AW and ALT wrote the manuscript; ALT and MJS acquired funding and supervised the research.

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Correspondence to A. Walton.

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Walton, A., Flores, E., Guinness, A. et al. A practical approach to RNA interference for studying gene function in a refractory social insect (on a limited budget). Insect. Soc. 70, 213–224 (2023). https://doi.org/10.1007/s00040-023-00910-x

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