Precise in-field molecular diagnostics of crop diseases by smartphone-based mutation-resolved pathogenic RNA analysis

• Published in: Nature communications 2023-07, Vol.14 (1), p.4327-13, Article 4327
• Main Authors: Zhang, Ting, Zeng, Qingdong, Ji, Fan, Wu, Honghong, Ledesma-Amaro, Rodrigo, Wei, Qingshan, Yang, Hao, Xia, Xuhan, Ren, Yao, Mu, Keqing, He, Qiang, Kang, Zhensheng, Deng, Ruijie
• Format: Article
• Language: English
• Subjects: 38/22; 38/23; 38/77; 38/90; 631/1647/2234; 631/449/2169/2674; 631/61/350/59; 639/638/11/872; Amplification; Basidiomycota - genetics; Catalysis; Colorimetry; Crop diseases; Crop yield; Crops; Diagnostic software; Fungi - genetics; Fungicides; Humanities and Social Sciences; Metal ions; multidisciplinary; Multiplexing; Mutation; Needles; Nucleic Acid Amplification Techniques - methods; Nucleic acids; Pathogens; Pathology, Molecular; Pesticide application; Pesticide use reduction; Pesticides; Plant diseases; Point mutation; Ribonucleic acid; RNA; Science; Science (multidisciplinary); Smartphone; Smartphones; Stripe rust; Urease; Wheat
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-023-39952-x

Molecular diagnostics for crop diseases can guide the precise application of pesticides, thereby reducing pesticide usage while improving crop yield, but tools are lacking. Here, we report an in-field molecular diagnostic tool that uses a cheap colorimetric paper and a smartphone, allowing multiplexed, low-cost, rapid detection of crop pathogens. Rapid nucleic acid amplification-free detection of pathogenic RNA is achieved by combining toehold-mediated strand displacement with a metal ion-mediated urease catalysis reaction. We demonstrate multiplexed detection of six wheat pathogenic fungi and an early detection of wheat stripe rust. When coupled with a microneedle for rapid nucleic acid extraction and a smartphone app for results analysis, the sample-to-result test can be completed in ~10 min in the field. Importantly, by detecting fungal RNA and mutations, the approach allows to distinguish viable and dead pathogens and to sensitively identify mutation-carrying fungicide-resistant isolates, providing fundamental information for precision crop disease management. On-site crop disease diagnostics is critical for precise application of pesticides. Here, the authors report an in-field molecular diagnostic tool for wheat pathogens using a nucleic acid amplification-free, gene mutation-resolved and smartphone-integrated genetic assay.