CRISPR-Cas-Led Revolution in Diagnosis and Management of Emerging Plant Viruses: New Avenues Toward Food and Nutritional Security

Abstract

Plant viruses pose a serious threat to agricultural production systems worldwide. The world's population is expected to reach the 10-billion mark by 2057. Under the scenario of declining cultivable land and challenges posed by rapidly emerging and re-emerging plant pathogens, conventional strategies could not accomplish the target of keeping pace with increasing global food demand. Gene-editing techniques have recently come up as promising options to enable precise changes in genomes with greater efficiency to achieve the target of higher crop productivity. Of genome engineering tools, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) proteins have gained much popularity, owing to their simplicity, reproducibility, and applicability in a wide range of species. Also, the application of different Cas proteins, such as Cas12a, Cas13a, and Cas9 nucleases, has enabled the development of more robust strategies for the engineering of antiviral mechanisms in many plant species. Recent studies have revealed the use of various CRISPR-Cas systems to either directly target a viral gene or modify a host genome to develop viral resistance in plants. This review provides a comprehensive record of the use of the CRISPR-Cas system in the development of antiviral resistance in plants and discusses its applications in the overall enhancement of productivity and nutritional landscape of cultivated plant species. Furthermore, the utility of this technique for the detection of various plant viruses could enable affordable and precise in-field or on-site detection. The futuristic potential of CRISPR-Cas technologies and possible challenges with their use and application are highlighted. Finally, the future of CRISPR-Cas in sustainable management of viral diseases, and its practical utility and regulatory guidelines in different parts of the globe are discussed systematically.

Current and emerging trends in techniques for plant pathogen detection

“…Although until now CRISPR-Cas-based assays are predominantly developed for use in medical diagnostics, recent studies demonstrated the proof-of-concept of CRISPR-Cas-based assays in detection of plant pathogens as well ( Sharma et al., 2021 ; Karmakar et al., 2022 ). For instance, Aman et al.…”

Applicability of Smart Tools in Vegetable Disease Diagnostics

“…Other studies have shown that it is possible to efficiently combine lateral flow chemistry and CRISPR diagnostics. Based on this idea, there is a possibility of introducing rapid, reliable, specific, and cheap diagnostic kits in the near future [84,85]. In-field applicable and sensitive tools for the vegetable sector may be also appear in the near future [86].…”

Wheat Biofortification: Utilizing Natural Genetic Diversity, Genome-Wide Association Mapping, Genomic Selection, and Genome Editing Technologies

“…Since wheat carries a complex hexaploid genome, CRISPR/Cas9—mediated wheat geminiviral based DNA replicons, delivering RNPs by biolistic method and multiplex editing has proved to be a more appropriate method of genome editing ( 102 , 103 ). The TALEN and CRISPR/Cas9 systems have already demonstrated their utility for generating abiotic and biotic stress-resistant engineered wheat plants ( 37 ). For instance, the mildew resistance locus O ( TaMLO ) gene was edited by CRISPR/Cas9 and TALEN through PEG-mediated protoplast fusion method ( 39 , 104 ), to achieve resistance to the fungal pathogen.…”

“…Further, in recent years, genome-wide association study (GWAS), which uses diverse germplasm lines or multiparent populations, has developed as a powerful tool for high-resolution trait mapping in crops and can be used to map nutritional quality traits using diverse association panels constituted from landraces, synthetics and wild species (34)(35)(36). Furthermore, recently, genome editing technologies, including prime editing and base editing have become promising targeted mutagenesis tools for crop improvement (37,38). The first report of gene editing in wheat was the development of the targeted knockout for the Mlo gene that confers resistance against powdery mildew pathogen, Blumeria graminis f.sp.…”