Evolution of plant mutagenesis tools: a shifting paradigm from random to targeted genome editing

Mutations are the basis of all genetic variation, and classical plant breeding has exploited the power of natural mutations in the development of high-yielding varieties. Since the discovery of chemical and radiation mutagens, various mutagenesis methods have been employed effectively in molecular plant breeding to study gene functions, to identify crucial genetic mutations for conferring novel traits to plants. Here, we review the historical development and use of plant mutagenesis tools, mainly physical and chemical mutagens, PCR-based methods, T-DNA insertions, transposon insertions, RNA interference, and meganucleases. The unique feature of meganucleases such as the CRISPR/Cas system is the control of site-directed DNA changes. We highlight the recent advancements in CRISPR/Cas-based mutagenesis tools that enable various applications of genetic manipulations, including gene knock-out, gene replacement, targeted base substitutions, and nucleotide diversification of user-defined sites. In addition, we review the use of CRISPR/Cas-based mutagenesis tools in agriculture.