Genome editing for healthy crops: traits, tools and impacts

Abstract

Crop cultivars in commercial use have often been selected because they show high levels of resistance to pathogens. However, widespread cultivation of these crops for many years in the environments favorable to a pathogen requires durable forms of resistance to maintain "healthy crops". Breeding of new varieties tolerant/resistant to biotic stresses by incorporating genetic components related to durable resistance, developing new breeding methods and new active molecules, and improving the Integrated Pest Management strategies have been of great value, but their effectiveness is being challenged by the newly emerging diseases and the rapid change of pathogens due to climatic changes. Genome editing has provided new tools and methods to characterize defense-related genes in crops and improve crop resilience to disease pathogens providing improved food security and future sustainable agricultural systems. In this review, we discuss the principal traits, tools and impacts of utilizing genome editing techniques for achieving of durable resilience and a "healthy plants" concept.

Keywords: CRISPR; crop improvement; crops; durable resistance; fungal, bacterial and virus infections; parasitic weeds; pathogens; resilience.

Figure 1

The activation of the plant innate immune system requires tree steps; immune recognition, signal integration and defense response. Plants use numerous cell surface and intracellular immune receptors to recognize microorganism/host-derived molecular patterns (MAMPs and DAMPs), or apoplastic/avirulance effectors (AE). Cell surface pattern recognition receptors (PRRs) bind to MAMPs or DAMPs or AE directly through their extracellular domain while NOD- like receptors (NLRs) recognize effectors delivered inside host cells by directly binding effectors or sensing modulation of effector host targets. PRR- mediated recognition of MAMPs or DAMPs elicits pattern- triggered immunity (PTI), and NLR- mediated pathways trigger effector-triggered immunity (ETI). Activation of immune receptors subsequently initiates the second phase of immune system. In this phase, various immune signaling events such as calcium fluxes, activation of mitogen- activated protein kinase (MAPK) cascades, alteration of host transcription and phytohormone signaling trigger the defense response in each cellular compartment in plants. Hormone- dependent response generally activates a large set of plant defense-related genes against biotrophs. For instance, hormone accumulation in plants triggers hypersensitive response (HR) which cause rapid local death of the infected and surrounding cells to restrict the spread of pathogens to other parts of the plant. Accumulation of hormones and pathogenesis-related proteins in the plants can also induce long-lasting protection against a broad spectrum of pathogens, called systemic acquired resistance (SAR). In this resistance, putative SAR signal molecules move from the infected systemic organs to non-infected distant parts of the plant where it make more resistance to pathogens prior to infection. Induced Systemic Resistance (ISR) is another defense response increasing physical or chemical barriers of the host plant against pathogens rather than direct killing or inhibiting the invading pathogen. RNA interference (RNAi) is the last plant resistance mechanism activated during the viral infection.

Figure 2

Theoretical and already tested CRISPR/Cas applications to increase plant resistance toward pathogens. CRISPR/Cas9 can be used to disrupt plant susceptibility (S) genes (such as Eukaryotic translation initiation factor 4E (elf4E)) by targeting coding regions to knock out these genes, or to alter sequences of promoter regions, precluding pathogen effector binding to the promoter and thus disrupting plant susceptibility. In addition, Dead Cas9-based CRISPR systems could be used to overexpression of resistance genes or suppression of S genes. CRISPR-mediated homology-directed repair (HDR) can be used to introduce resistance (R) genes against pathogens in cases where the plant-pathogen interaction (and S genes) is not well studied. To develop pathogen resistance without disrupting or replacing whole genes, CRISPR based base-edition technology can be used to achieve specific mutations (biomimicking) in genes to turn them into resistant genes against pathogens of interest. The native function of CRISPR can be also mimicked directly to target and interfere with the genomes of pathogens of interest without affecting plant genome. For example, CRISPR can interfere with DNA genomes of viruses through DNA-targeting gRNA/Cas9 systems or it can disrupt pathogen’s RNA genomes through RNA-targeting gRNA/Cas13a systems. Loss of function in S genes.