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Evaluation of CRISPR/Cas12a-based DNA detection for fast pathogen diagnosis and GMO test in rice


DNA test is broadly used in diagnosis of crop disease and identification of genetic modified organism (GMO) in agriculture. However, rapid, low-cost, user-friendly, and field-deployable DNA test method is still limit. Recently, the RNA programmable nuclease of CRISPR/Cas is engineered as a new nucleic acid detection platform, but their application in plant remains to explore. In this study, we evaluated the Cas12a-based DNA detection for crop disease diagnosis and GMO test. A total of 14 crRNAs were designed to target two Magnaporthe oryzae genes and a synthetic Cry1C gene which encodes Bacillus thuringiensis δ-endotoxin and has been used to develop transgenic rice cultivar (Bt-rice) in China. Using a fluorescent reporter, targeted genes were easily detected by LbCas12a after recombinase polymerase amplification (RPA) for all crRNAs, despite that the signal strength varied 2–3-folds between different crRNAs. We further combined the filter paper-based DNA extraction and lateral flow assay (LFA) with RPA-Cas12a for DNA detection. This optimized Cas12a diagnostics method is carried at body temperature and does not require extra instrument except filter paper and LFA strip. Our data show that rice blast pathogen and Bt-rice were efficiently identified from leaf disc samples using this optimized DNA test method with highly active crRNAs. Moreover, LbCas12a exhibited variable nuclease activities on different targets; therefore, highly active crRNA is critical for successful DNA test using Cas12a and LFA. Owing to its simplicity, efficiency, and low-cost, DNA test using CRISPR/Cas12a would be easily applied in field for crop disease diagnosis and GMO administration.

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We thank Profs. Yongjun Lin and Hao Chen for providing the transgenic Bt-rice plants.


This study was supported by the National Transgenic Science and Technology program (2018ZX08010-05B), National Natural Science Foundation of China (31622047), National Key Laboratory of Crop Genetic Improvement and State Key Laboratory of Hybrid Rice. Y.Z. was also supported by the National College Student Innovative and Entrepreneurial Training Program (201810504004).

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K.X. deceived the project. YM. Z. and Y. Z. performed the experiments. YM. Z. and K.X. analyzed the data and wrote the manuscript.

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Correspondence to Kabin Xie.

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The authors declare that they have no conflict of interest.

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Zhang, Ym., Zhang, Y. & Xie, K. Evaluation of CRISPR/Cas12a-based DNA detection for fast pathogen diagnosis and GMO test in rice. Mol Breeding 40, 11 (2020).

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  • DNA test
  • CRISPR/Cas12a
  • Rice blast
  • GMO