Integrating CRISPR-Cas and Next Generation Sequencing in Plant Virology

Abstract

Plant pathology has been revolutionized by the emergence and intervention of next-generation sequencing technologies (NGS) which provide a fast, cost-effective, and reliable diagnostic for any class of pathogens. NGS has made tremendous advancements in the area of research and diagnostics of plant infecting viromes and has bridged plant virology with other advanced research fields like genome editing technologies. NGS in a broader perspective holds the potential for plant health improvement by diagnosing and mitigating the new or unusual symptoms caused by novel/unidentified viruses. CRISPR-based genome editing technologies can enable rapid engineering of efficient viral/viroid resistance by directly targeting specific nucleotide sites of plant viruses and viroids. Critical genes such as eIf (iso) 4E or eIF4E have been targeted via the CRISPR platform to produce plants resistant to single-stranded RNA (ssRNA) viruses. CRISPR/Cas-based multi-target DNA or RNA tests can be used for rapid and accurate diagnostic assays for plant viruses and viroids. Integrating NGS with CRISPR-based genome editing technologies may lead to a paradigm shift in combating deadly disease-causing plant viruses/viroids at the genomic level. Furthermore, the newly discovered CRISPR/Cas13 system has unprecedented potential in plant viroid diagnostics and interference. In this review, we have highlighted the application and importance of sequencing technologies on covering the viral genomes for precise modulations. This review also provides a snapshot vision of emerging developments in NGS technologies for the characterization of plant viruses and their potential utilities, advantages, and limitations in plant viral diagnostics. Furthermore, some of the notable advances like novel virus-inducible CRISPR/Cas9 system that confers virus resistance with no off-target effects have been discussed.

Multidimensional Role of Silicon to Activate Resilient Plant Growth and to Mitigate Abiotic Stress

“…All these reports strongly suggest that genetic engineering technology speeds up the development of stress-resilient crop plants for food and nutritional security. The last few decades have witnessed shifting research on genome-editing technologies, such as ZFN, TALEN, and CRISPR/Cas systems, for higher accuracy and precision to develop desired crop plants with tolerance to different abiotic stressors ( Mushtaq et al, 2021 ; Pandita, 2021 ). For instance, Li et al (2019) employed CRISPR/Cas9 to mediate mutagenesis of SlNPR1 to enhance drought tolerance in tomatoes.…”

Recent developments in multi-omics and breeding strategies for abiotic stress tolerance in maize (Zea mays L.)

“…Some of the wellknown genome editing tools are ZFNs (zinc-finger nucleases), TALENs (transcription activator-like effector nucleases), and clustered CRISPR (regularly interspaced short palindromic repeats)/Cas systems (Miller et al, 1985;Jinek et al, 2012;Joung and Sander, 2013). These tools use common sequence-specific nucleases to identify specific DNA sequences in the genome and generate desired double-stranded breaks (DSBs) (Mushtaq et al, 2021). ZFNs have been used to modify various crop plants, including maize.…”

New Hope for Genome Editing in Cultivated Grasses: CRISPR Variants and Application

“…It has been possible with CRISPR-Cas -based genome editing to engineer crops resistant to bacterial, fungal, and viral diseases as well as oomycetes. For instance, rice, wheat, maize, and barley have seen great success in the ability to increasing resistance to powdery mildews, bacterial blights, and blast diseases ( Chen et al, 2019 ; Mushtaq et al, 2021 ; Ali et al, 2022 ). A study conducted by Wang et al (2014) developed a powdery mildew resistant wheat by disrupting the TAMLOA1 , TAMLOA2 , and TAMLOA3 genes in the wheat genome using the CRISPR-Cas 9 system.…”