Structural aspects of DNA repair and recombination in crop improvement
Open accessAbstract
The adverse effects of global climate change combined with an exponentially increasing human population have put substantial constraints on agriculture, accelerating efforts towards ensuring food security for a sustainable future. Conventional plant breeding and modern technologies have led to the creation of plants with better traits and higher productivity. Most crop improvement approaches (conventional breeding, genome modification, and gene editing) primarily rely on DNA repair and recombination (DRR). Studying plant DRR can provide insights into designing new strategies or improvising the present techniques for crop improvement. Even though plants have evolved specialized DRR mechanisms compared to other eukaryotes, most of our insights about plant-DRRs remain rooted in studies conducted in animals. DRR mechanisms in plants include direct repair, nucleotide excision repair (NER), base excision repair (BER), mismatch repair (MMR), non-homologous end joining (NHEJ) and homologous recombination (HR). Although each DRR pathway acts on specific DNA damage, there is crosstalk between these. Considering the importance of DRR pathways as a tool in crop improvement, this review focuses on a general description of each DRR pathway, emphasizing on the structural aspects of key DRR proteins. The review highlights the gaps in our understanding and the importance of studying plant DRR in the context of crop improvement.
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SDN2 is limited for larger insertions due to its reliance on microhomology-mediated end joining.
“However, SDN2 is limited for larger insertions due to its reliance on microhomology-mediated end joining (Verma et al., 2020).”
From Emerging applications of gene editing technologies for the development of climate-resilient crops (2025) · cites this paper as Verma et al., 2020
In “Modification of Genome Editing Techniques” (page not supplied), the paper says SDN2 relies on homologous recombination, not microhomology-mediated end joining, and identifies low homologous-recombination frequency as its main limitation. The “DSB Repair” section discusses microhomology-mediated end joining as a separate repair pathway. (LLM, conf=0.93)
Checked by a reasoning model — may be wrong.
Experimental — accuracy not yet measuredSDN3 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 Verma et al., 2020
The “Modification of Genome Editing Techniques” section (page unavailable) says SDN3 repairs double-strand breaks through homologous recombination and uses donor DNA that often contains an insert as large as a transgene. It does not specify homologous regions of at least 500 base pairs flanking the break or describe SDN3 as similar to cisgenic approaches. (LLM, conf=0.86)
Experimental — accuracy not yet measuredSDN2 mutants utilize a repair template to modify one or a few bases at a DSB site, yielding outcomes that mimic natural mutations and can be achieved with traditional breeding.
“SDN2 mutants, on the other hand, utilize a repair template to modify one or a few bases at a DSB site, yielding outcomes that mimic natural mutations and can be achieved with traditional breeding.”
From Emerging applications of gene editing technologies for the development of climate-resilient crops (2025) · cites this paper as Verma et al., 2020
The “Modification of Genome Editing Techniques” section (page not provided) says SDN2 uses an externally supplied donor DNA template to repair a double-strand break and modify a predetermined site. It does not specify that SDN2 changes only one or a few bases, or say that its outcomes mimic natural mutations or can be achieved through traditional breeding. (LLM, conf=0.86)
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 Verma et al., 2020
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Endonuclease activities of MutLα and its homologs in DNA mismatch repair
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Manipulation of crossover frequency and distribution for plant breeding
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Flagged first, then by citations
1 of the 307 references couldn’t be matched to a known paper.
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An Outlook on Global Regulatory Landscape for Genome-Edited Crops
Ahmad, A., Munawar, N., Khan, Z., Qumsani, A. T., Khan, S. H., Jamil, A., Ashraf, S., Ghouri, M. Z., Aslam, S., Mubarik, M. S., et al. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms222111753 · Cited by 137 · see citing works
Stress Management in Plants: Examining Provisional and Unique Dose-Dependent Responses
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How Do Plants Cope with DNA Damage? A Concise Review on the DDR Pathway in Plants
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“Nonetheless, SDN3 applications in plants face challenges due to the low ef fi ciency of homologous recombination (HDR), making them complex and less ef fi cient (Verma et al., 2020; Podevin et al., 2013; Van de Wiel et al., 2017).”
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Helicase: A genetic tool for providing stress tolerance in plants
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Comparative Transcriptomics for Pepper (Capsicum annuum L.) under Cold Stress and after Rewarming
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Enhancing the quality of staple food crops through CRISPR/Cas-mediated site-directed mutagenesis
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MSH7 confers quantitative variation in pollen fertility and boosts grain yield in maize
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Erasing Methylation Marks on DNA by Plant-Specific DEMETER Family DNA Glycosylases
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CRISPR‐Cas9 and beyond: identifying target genes for developing disease‐resistant plants
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CRISPR-Cas9 system: a possible “Savior” of scented Katarni rice
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Establishment of an Efficient Protoplast-Based Base Editing Platform in Lettuce
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Recent developments in ultraviolet-induced deoxyribonucleic acid damage and repair in higher plants
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- Authors
- Verma, P., Tandon, R., Yadav, G., & Gaur, V.
- Affiliations
- National Institute of Plant Genome Research (IN)
- Corresponding author
- Gaur, Vineet
- Venue
- Frontiers in Genetics
- Publisher
- Frontiers Media SA
- Published
- 2020-09-11
- Volume
- 11
- Pages
- 574549-574549
- ISSN
- 1664-8021 (ISSN-L)
- PMC
- PMC7516265
- OpenAlex
- W3085544283
- Cited by
- 29
- References
- 307
- Citations by year
- 2026: 4 · 2025: 4 · 2024: 6 · 2023: 6 · 2022: 3 · 2021: 6
- FWCI
- 0.36
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Frontiers in Genetics (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Department of Biotechnology, Ministry of Science and Technology, India
- Biotechnology and Biological Sciences Research Council (BB/P027970/1)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Molecular Biology Research
- Keywords
- DNA repair, DNA recombination, crop improvement, nucleotide excision repair, base excision repair, DNA mismatch repair, non-homologous end joining, homologous recombination, direct repair, DNA repair proteins, genome editing, genome modification, food security
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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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