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Journal of Integrative Agriculture  2022, Vol. 21 Issue (1): 170-177    DOI: 10.1016/S2095-3119(20)63394-9
Plant Protection Advanced Online Publication | Current Issue | Archive | Adv Search |
Using transcriptome Shannon entropy to evaluate the off-target effects and safety of insecticidal siRNAs
MA Wei-hua1, WU Tong1, 2, ZHANG Zan3, LI Hang3, SITU Gong-ming3, YIN Chuan-lin2, YE Xin-hai2, CHEN Meng-yao2, ZHAO Xian-xin2, HE Kang2, LI Fei2 
1 College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, P.R.China
2 State Key Laboratory of Rice Biology/Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests/Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, P.R.China
3 College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, P.R.China
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Abstract  A recent breakthrough in agricultural biotechnology is the introduction of RNAi-mediated strategies in pest control.  However, the off-target effects of RNAi pest control are still not fully understood.  Here, we studied the off-target effects of two insecticidal siRNAs in both target and non-target insects.  The results revealed that off-target effects of insecticidal siRNAs occur widely in both target and non-target insects.  We classified the expression-changed genes according to their homology to the siRNA-targeted gene, related KEGG pathways with the siRNA-targeted gene and continuous matches with siRNAs.  Surprisingly, the unintended significant changes in gene expression levels did not strictly match with the number of contiguous nucleotides in the siRNAs.  As expected, the expression of small portions of the homologous and KEGG-related genes were significantly changed.  We calculated the Shannon entropy of the transcriptome profile of the insects after injecting them with insecticidal siRNAs.  Though hundreds of genes were affected in their expression levels post siRNA-treatment, the Shannon entropy of the transcriptome remained unchanged, suggesting that the transcriptome expression was balanced.  Our results provide evidence that siRNAs cross-reacted with individual genes in non-target species, but did not have significant effects on the integrity of the transcriptome profiles in either target or non-target species on a genomic scale.  The metric we proposed can be used to estimate the off-target effects of insecticidal siRNAs, which might be useful for evaluating the safety of RNAi in pest control.  
Keywords:  RNAi       off-target effect        transcriptome entropy        non-target organisms        RNAi-mediated pest management  
Received: 12 June 2020   Accepted: 08 August 2020
Fund: This work was funded by grants from the National Science and Technology Major Project of China (2016ZX08011002).  We also thank the DBMediting Company for professional English language editing services.  
About author:  MA Wei-hua, E-mail:; Correspondence LI Fei, E-mail:

Cite this article: 

MA Wei-hua, WU Tong, ZHANG Zan, LI Hang, SITU Gong-ming, YIN Chuan-lin, YE Xin-hai, CHEN Meng-yao, ZHAO Xian-xin, HE Kang, LI Fei . 2022. Using transcriptome Shannon entropy to evaluate the off-target effects and safety of insecticidal siRNAs. Journal of Integrative Agriculture, 21(1): 170-177.

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