Abstract
Site-directed nucleases (SDNs) used for targeted genome editing are powerful new tools to introduce precise genetic changes into plants. Like traditional approaches, such as conventional crossing and induced mutagenesis, genome editing aims to improve crop yield and nutrition. Next-generation sequencing studies demonstrate that across their genomes, populations of crop species typically carry millions of single nucleotide polymorphisms and many copy number and structural variants. Spontaneous mutations occur at rates of ∼10-8 to 10-9 per site per generation, while variation induced by chemical treatment or ionizing radiation results in higher mutation rates. In the context of SDNs, an off-target change or edit is an unintended, nonspecific mutation occurring at a site with sequence similarity to the targeted edit region. SDN-mediated off-target changes can contribute to a small number of additional genetic variants compared to those that occur naturally in breeding populations or are introduced by induced-mutagenesis methods. Recent studies show that using computational algorithms to design genome editing reagents can mitigate off-target edits in plants. Finally, crops are subject to strong selection to eliminate off-type plants through well-established multigenerational breeding, selection, and commercial variety development practices. Within this context, off-target edits in crops present no new safety concerns compared to other breeding practices. The current generation of genome editing technologies is already proving useful to develop new plant varieties with consumer and farmer benefits. Genome editing will likely undergo improved editing specificity along with new developments in SDN delivery and increasing genomic characterization, further improving reagent design and application.
Highlights
Plant Genetic Variability Genetic differences between individuals are the basis of adaptation and evolution
This study suggests that, as new protein motifs and editing strategies are developed, the intended activity and potential for off-target activity should be evaluated
The identification of high background mutation rates for C-to-T base editor enzymes (Jin et al, 2019) suggests the need for careful screening of the effects of new approaches. These results suggest that whole genome resequencing (WGRS) is best applied to new approaches and may not be necessary for routine application of site-directed nuclease (SDN), as unintended activity will generally be predictable by computational algorithms that allow for the optimal design of guide RNA (gRNA) (Tang et al, 2018; Lee et al, 2019; Young et al, 2019)
Summary
Plant Genetic Variability Genetic differences between individuals are the basis of adaptation and evolution. Modern plant breeding is a more directed process than the crop improvement that occurred through the history and pre-history of most cultivated species, but it continues to involve lengthy development cycles. Progress in our understanding of the genetic basis of traits and refined approaches to select superior progeny have contributed to increased yield for most major crops. Crop yields have increased by greater than one percent each year for much of the past century (Xu et al, 2017) Technological innovations, including those that increased our understanding of nucleic acid sequence and function, have contributed to this progress. The relatively recent introduction of genome editing, which permits targeted genetic changes, is part of a continuum of development of plant breeding techniques (Lusser et al., 2012). Its primary appeal is that, in contrast to established mutagenesis techniques, changes can be targeted to desired genes
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