Use of CRISPR Technology in Gene Editing for Tolerance to Biotic Factors in Plants: A Systematic Review

Abstract

The objective of this systematic review (SR) was to select studies on the use of gene editing by CRISPR technology related to plant resistance to biotic stresses. We sought to evaluate articles deposited in six electronic databases, using pre-defined inclusion and exclusion criteria. This SR demonstrates that countries such as China and the United States of America stand out in studies with CRISPR/Cas. Among the most studied crops are rice, tomatoes and the model plant Arabidopsis thaliana. The most cited biotic agents include the genera, Xanthomonas, Manaporthe, Pseudomonas and Phytophthora. This SR also identifies several CRISPR/Cas-edited genes and demonstrates that plant responses to stressors are mediated by many complex signaling pathways. The Cas9 enzyme is used in most articles and Cas12 and 13 are used as additional editing tools. Furthermore, the quality of the articles included in this SR was validated by a risk of bias analysis. The information collected in this SR helps to understand the state of the art of CRISPR/Cas aimed at improving resistance to diseases and pests to understand the mechanisms involved in most host-pathogen relationships. This SR shows that the CRISPR/Cas system provides a straightforward method for rapid gene targeting, providing useful information for plant breeding programs.

Keywords: CRISPR/Cas; biotic stress; pests; phytopathogens; plant diseases; plant genetic improvement.

Figure 1

A PRISMA flow diagram with the respective stages of the process of selecting studies for inclusion/exclusion in the systematic review of the CRISPR/Cas technology used to edit genes for tolerance/resistance to biotic stress in plants according to the databases [43].

Figure 2

Bibliometric indicators of the collaboration network between authors and keywords of the selected articles on CRISPR/Cas technology and biotic factors. (A) Collaborators who have published the most on CRISPR/Cas and biotic stresses in the last 12 years. (B) Keywords of the selected articles on CRISPR/Cas technology used for gene editing of tolerance/resistance to biotic stresses in plants during the extraction phase of this systematic review. Different colors for each circle indicate collaboration between groups.

Figure 3

Frequency of articles according to country of publication and crop edited by CRISPR/Cas technology for plant disease tolerance/resistance. More than one plant species per article was considered in calculating the frequency.

Figure 4

The most-studied biotic agents (bacteria, insects, oomycetes, nematodes, fungi, and viruses) in the last twelve years for resistance/tolerance to plant diseases using CRISPR/Cas technology. More than one biotic agent per article was considered in calculating frequency.

Figure 5

Explants used for the transformation of the different plant species covered in studies on gene editing via CRISPR/Cas for tolerance/resistance to biotic stress in the last 12 years. The colors of the circles represent each explant and the size of the circumference the frequency of each explant in different crops.

Figure 6

Word cloud of CRISPR/Cas edited genes in different plant species related to tolerance/resistance/susceptibility to biotic stresses.

Figure 7

Auxiliary tools and analyses used with the CRISPR/Cas technique for validation and comparison between knockout with control and/or the overexpression of mutants identified in articles on tolerance/resistance to biotic stresses in the last 12 years.

Figure 8

Frequency and word cloud of tools and software that help the CRISPR/Cas technique to search for specific target sites identified in studies on tolerance/resistance to biotic stresses in the last 12 years.

Figure 9

Frequency of articles that performed a phenotypic analysis of plants after mutation and the pathogen inoculation test.

Figure 10

Risk of bias analysis based on the following questions: “Q1: Was off-target analysis performed? Q2: Was the pathogen inoculated? Q3: Was phenotypic analysis performed after mutation in the plant? Q4: Does the article answer at least 50% of the research questions?”.