Transgene-free genome editing and RNAi ectopic application in fruit trees: Potential and limitations

Abstract

For the past fifteen years, significant research advances in sequencing technology have led to a substantial increase in fruit tree genomic resources and databases with a massive number of OMICS datasets (transcriptomic, proteomics, metabolomics), helping to find associations between gene(s) and performance traits. Meanwhile, new technology tools have emerged for gain- and loss-of-function studies, specifically in gene silencing and developing tractable plant models for genetic transformation. Additionally, innovative and adapted transformation protocols have optimized genetic engineering in most fruit trees. The recent explosion of new gene-editing tools allows for broadening opportunities for functional studies in fruit trees. Yet, the fruit tree research community has not fully embraced these new technologies to provide large-scale genome characterizations as in cereals and other staple food crops. Instead, recent research efforts in the fruit trees appear to focus on two primary translational tools: transgene-free gene editing via Ribonucleoprotein (RNP) delivery and the ectopic application of RNA-based products in the field for crop protection. The inherent nature of the propagation system and the long juvenile phase of most fruit trees are significant justifications for the first technology. The second approach might have the public favor regarding sustainability and an eco-friendlier environment for a crop production system that could potentially replace the use of chemicals. Regardless of their potential, both technologies still depend on the foundational knowledge of gene-to-trait relationships generated from basic genetic studies. Therefore, we will discuss the status of gene silencing and DNA-based gene editing techniques for functional studies in fruit trees followed by the potential and limitations of their translational tools (RNP delivery and RNA-based products) in the context of crop production.

Keywords: RNA-based ectopic application; RNP delivery; fruit trees; gene silencing and editing; genetic tools.

Figure 1

Examples of recently developed and validated genetic tools in plants for RNAi-silencing and DNA-based gene editing based on figures from previously published figures: (1) (Carbonell, 2019), (2) (Cisneros and Carbonell, 2020), (3) (Lowder et al., 2016), (4) (Zhong et al., 2020), (5) (Hassan et al., 2020).

Figure 2

Significant milestones achieved for RNA-based ectopic application. [1, 2]: Wang et al., 2014; Schwartz et al., 2020, [3-5]: Mitter et al., 2017, Zhang et al., 2019a, Demirer et al., 2020, [6-8]: Ahmed et al., 2020, Bennett et al., 2020, Sciabola et al., 2021, [9]: Delgado-Martín et al., 2022.