Causes and consequences of experimental variation in Nicotiana benthamiana transient expression

Tang, S. N.; Szarzanowicz, M.; Lanctot, A.; Sirirungruang, S.; Kirkpatrick, L. D.; Drako, K.; Alamos, S.; Cheng, A.; Waldburger, L. M.; Liu, S.; Thompson, M.; Shih, P.

doi:10.1101/2025.06.12.659391

bioRxiv · 10.1101/2025.06.12.659391

Causes and consequences of experimental variation in Nicotiana benthamiana transient expression

Tang, S. N.·Szarzanowicz, M.·Lanctot, A.·Sirirungruang, S.·Kirkpatrick, L. D.·Drako, K.·Alamos, S.·Cheng, A.·Waldburger, L. M.·Liu, S.·Thompson, M.·Shih, P.

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Abstract

Infiltration of Agrobacterium tumefaciens into Nicotiana benthamiana has become a foundational technique in plant biology, enabling efficient delivery of transgenes in planta with technical ease, robust signal, and relatively high throughput. Despite transient expressions prevalence in disciplines such as synthetic biology, little work has been done to describe and address the variability inherent in this system, a concern for experiments that rely on highly quantitative readouts. In a comprehensive analysis of N. benthamiana agroinfiltration experiments, we model sources of variability that affect transient expression. Our findings emphasize the need to validate normalization methods under the specific conditions of each study, as distinct normalization schemes do not always reduce variation either within or between experiments. Using a dataset of 1,915 plants collected over three years, we develop a model of variation in N. benthamiana transient expression, using power analysis to determine the number of individual plants required for a given effect size. Drawing on our longitudinal data, these findings inform practical guidelines for minimizing variability through strategic experimental design and power analysis, providing a foundation for more robust and reproducible use of N. benthamiana in quantitative plant biology and synthetic biology applications.

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Tang, S. N., Szarzanowicz, M., Lanctot, A., Sirirungruang, S., Kirkpatrick, L. D., Drako, K., Alamos, S., Cheng, A., Waldburger, L. M., Liu, S., Thompson, M., Shih, P.. 2025-06-16. Causes and consequences of experimental variation in Nicotiana benthamiana transient expression. https://doi.org/10.1101/2025.06.12.659391

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