New traits in crops produced by genome editing techniques based on deletions
Open accessAbstract
One of the most promising New Plant Breeding Techniques is genome editing (also called gene editing) with the help of a programmable site-directed nuclease (SDN). In this review, we focus on SDN-1, which is the generation of small deletions or insertions (indels) at a precisely defined location in the genome with zinc finger nucleases (ZFN), TALENs, or CRISPR-Cas9. The programmable nuclease is used to induce a double-strand break in the DNA, while the repair is left to the plant cell itself, and mistakes are introduced, while the cell is repairing the double-strand break using the relatively error-prone NHEJ pathway. From a biological point of view, it could be considered as a form of targeted mutagenesis. We first discuss improvements and new technical variants for SDN-1, in particular employing CRISPR-Cas, and subsequently explore the effectiveness of targeted deletions that eliminate the function of a gene, as an approach to generate novel traits useful for improving agricultural sustainability, including disease resistances. We compare them with examples of deletions that resulted in novel functionality as known from crop domestication and classical mutation breeding (both using radiation and chemical mutagens). Finally, we touch upon regulatory and access and benefit sharing issues regarding the plants produced.
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SDN3 mutants use a repair template with homologous regions of at least 500 base pairs flanking the DSB, enabling the insertion of new sequences, similar to transgenic or cisgenic approaches.
“SDN3 mutants use a repair template with homologous regions of at least 500 base pairs flanking the DSB, enabling the insertion of new sequences, similar to transgenic or cisgenic approaches.”
From Emerging applications of gene editing technologies for the development of climate-resilient crops (2025) · cites this paper as Van de Wiel et al., 2017
The Introduction (page not provided) says SDN-3 uses a longer repair template that can insert native or foreign sequences at a targeted location, and compares it with genetic transformation. It does not specify homologous regions flanking the break or a minimum length of 500 base pairs. (LLM, conf=0.87)
Experimental — accuracy not yet measuredSDN3 applications in plants face challenges due to the low efficiency of homologous recombination, making them complex and less efficient.
“Nonetheless, SDN3 applications in plants face challenges due to the low efficiency of homologous recombination (HDR), making them complex and less efficient (Verma et al., 2020; Podevin et al., 2013; Van de Wiel et al., 2017).”
From Emerging applications of gene editing technologies for the development of climate-resilient crops (2025) · cites this paper as Van de Wiel et al., 2017
The Introduction says SDN-3 uses the same HDR-based repair approach described for SDN-2 and that HDR is “a relatively difficult to control mechanism.” This supports the claim that SDN-3 faces a technical challenge, but the paper does not specifically attribute that challenge to low homologous-recombination efficiency or state that SDN-3 applications are less efficient. No page number is available in our copy. (LLM, conf=0.82)
Experimental — accuracy not yet measured
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Self-citation
- Authors
- van de Wiel, C. C. M., Schaart, J. G., Lotz, L. A. P., & Smulders, M. J. M.
- Affiliations
- Wageningen University & Research (NL)
- Corresponding author
- Smulders, M. J. M.
- Venue
- Plant Biotechnology Reports
- Published
- 2017-02
- Volume
- 11
- Issue
- 1
- Pages
- 1-8
- ISSN
- 1863-5466 (ISSN-L)
- 1863-5474
- PMC
- PMC5360818
- OpenAlex
- W2587919670
- Cited by
- 80
- References
- 77
- Citations by year
- 2026: 2 · 2025: 8 · 2024: 4 · 2023: 6 · 2022: 9 · 2021: 13 · 2020: 9 · 2019: 11 · 2018: 16 · 2017: 2
- FWCI
- 0.97
- Type
- journal article
- Language
- en
- Update notices
- correction (2018-09-27)
- Open access
- hybrid
- doi.org
- Locations
- Plant Biotechnology Reports (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Socio-Environmental Systems Modeling (acceptedVersion, cc-by)
- Data Archiving and Networked Services (DANS) (submittedVersion, cc-by)
- Funders
- Ministry of Economic Affairs, The Netherlands (BO-20-003-006)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Genetic and Mutation Studies
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Genetically Modified Organisms Research
- Keywords
- genome editing, new plant breeding techniques, CRISPR/Cas9, zinc finger nucleases, TALEN, indels, targeted deletion, non-homologous end joining, targeted mutagenesis, disease resistance, crop domestication, mutation breeding, regulatory challenges, access and benefit sharing, crop improvement
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