Efficient pathogen diagnostics and genotyping methods enable effective disease management and breeding, improve crop productivity and ensure food security. However, current germplasm selection and pathogen detection techniques are laborious, time-consuming, expensive and not easy to mass-scale application in the field. Here, we optimized a field-deployable lateral flow assay, Bio-SCAN, as a highly sensitive tool to precisely identify elite germplasm and detect mutations, transgenes and phytopathogens in <1 h, starting from sample isolation to result output using lateral flow strips. As a proof of concept, we genotyped various wheat germplasms for the Lr34 and Lr67 alleles conferring broad-spectrum resistance to stripe rust, confirmed the presence of synthetically produced herbicide-resistant alleles in the rice genome and screened for the presence of transgenic elements in the genome of transgenic tobacco and rice plants with 100% specificity. We also successfully applied this new assay to the detection of phytopathogens, including viruses and bacterial pathogens in Nicotiana benthamiana, and two destructive fungal pathogens (Puccinia striiformis f. sp. tritici and Magnaporthe oryzae Triticum) in wheat. Our results illustrate the power of Bio-SCAN in crop breeding, genetic engineering and pathogen diagnostics to enhance food security. The high sensitivity, simplicity, versatility and in-field deployability make the Bio-SCAN as an attractive molecular diagnostic tool for diverse applications in agriculture.
Bibliographical noteFunding Information:
This work was supported, in part, by BAS/1/1035-01-01 grant from the KAUST to MM. TI received partial funding through the OFANS project of the Krishi Gobeshona Foundation of Bangladesh. We would like to thank professor Simon Krattinger and his team at the Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia, for providing the Lr34 referenced wheat germplasm. We would like to thank Nur Uddin Mahmud of the Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh, for assistance in extracting DNA from wheat blast fungus, Magnaporthe oryzae Triticum isolates. We would like to thank Dr. Haroon Butt at the Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia, for providing the SGR3, SGR5 and OsmALS rice lines. We would like to thank Dr Nasir Saeed, Wheat Biotechnology Lab, NIBGE, Pakistan for providing wheat landraces and genomic DNA samples. We also thank members of the genome engineering and synthetic biology laboratory for insightful discussions and technical support.
This work was supported, in part, by BAS/1/1035‐01‐01 grant from the KAUST to MM. TI received partial funding through the OFANS project of the Krishi Gobeshona Foundation of Bangladesh.
© 2022 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.
- CRISPR/dCas9 and dCas9
- lateral flow assay
- nucleic acid detection
ASJC Scopus subject areas
- Agronomy and Crop Science
- Plant Science