Toward Transgene-Free Transposon-Mediated Biological Mutagenesis for Plant Breeding

Abstract

Genetic diversity is a key factor for plant breeding. The birth of novel genic and genomic variants is also crucial for plant adaptation in nature. Therefore, the genomes of almost all living organisms possess natural mutagenic mechanisms. Transposable elements (TEs) are a major mutagenic force driving genetic diversity in wild plants and modern crops. The relatively rare TE transposition activity during the thousand-year crop domestication process has led to the phenotypic diversity of many cultivated species. The utilization of TE mutagenesis by artificial and transient acceleration of their activity in a controlled mode is an attractive foundation for a novel type of mutagenesis called TE-mediated biological mutagenesis. Here, I focus on TEs as mutagenic sources for plant breeding and discuss existing and emerging transgene-free approaches for TE activation in plants. Furthermore, I also review the non-randomness of TE insertions in a plant genome and the molecular and epigenetic factors involved in shaping TE insertion preferences. Additionally, I discuss the molecular mechanisms that prevent TE transpositions in germline plant cells (e.g., meiocytes, pollen, egg and embryo cells, and shoot apical meristem), thereby reducing the chances of TE insertion inheritance. Knowledge of these mechanisms can expand the TE activation toolbox using novel gene targeting approaches. Finally, the challenges and future perspectives of plant populations with induced novel TE insertions (iTE plant collections) are discussed.

Keywords: RNA-dependent DNA methylation; gene silencing; mutagenesis; plants; transposons.

Figure 1

Approaches for TE-mediated biological mutagenesis: application of various stress factors (‘genomic shock’) such as crossing with plant lines possessing hyperactive TEs (e.g., Mutator lines of maize) or plant tissue culture (e.g., activation of Tos17 TE of rice); TEgenesis^® (application of stress (e.g., heat stress) to the plants grown on medium containing zebularine (cytidine analog) and alpha-amanitin (a PolII inhibitor)); and new perspective tools (e.g., CRISPRi and VIGS) for transient knock-down of genes involved in RdDM pathway.

Figure 2

Transposon silencing in germline cells, gametes, or embryos (GGE cells) via small RNA movement (sRNA) from nurse somatic cells. (A) TE silencing in meiocytes in anthers and in egg cells in ovules via tapetum-derived sRNAs and central cell/synergid cells (SC) sRNA, respectively. AC—antipodal cells. (B) TE silencing in the generative cell of pollen via sRNAs produced by miRNA and RdDM. The figures were generated using BioRender (https://biorender.com/, accessed on 3 June 2023). (C) TE silencing via sRNAs movement from endosperm to embryo in a seed; (D) easiRNA-mediated TE silencing in the shoot apical meristem (SAM).

Figure 3

Overview of TE-mediated biological mutagenesis. (A) TE activation in the germline cells using different approaches. (B) Development of iTE collections (collections of plant lines with novel TE insertions) and (C) their applications in research and plant breeding.