Gene editing for plant resistance to abiotic factors: a systematic review
Open accessAbstract
Agricultural crops are exposed to various abiotic stresses, such as salinity, water deficits, temperature extremes, floods, radiation, and metal toxicity. To overcome these challenges, breeding programs seek to improve methods and techniques. Gene editing by Clustered Regularly Interspaced Short Palindromic Repeats—CRISPR/Cas—is a versatile tool for editing in all layers of the central dogma with focus on the development of cultivars of plants resistant or tolerant to multiple biotic or abiotic stresses. This systematic review (SR) brings new contributions to the study of the use of CRISPR/Cas in gene editing for tolerance to abiotic stress in plants. Articles deposited in different electronic databases, using a search string and predefined inclusion and exclusion criteria, were evaluated. This SR demonstrates that the CRISPR/Cas system has been applied to several plant species to promote tolerance to the main abiotic stresses. Among the most studied crops are rice and Arabidopsis thaliana, an important staple food for the population, and a model plant in genetics/biotechnology, respectively, and more recently tomato, whose number of studies has increased since 2021. Most studies were conducted in Asia, specifically in China. The Cas9 enzyme is used in most articles, and only Cas12a is used as an additional gene editing tool in plants. Ribonucleoproteins (RNPs) have emerged as a DNA-free strategy for genome editing without exogenous DNA. This SR also identifies several genes edited by CRISPR/Cas, and it also shows that plant responses to stress factors are mediated by many complex-signaling pathways. In addition, the quality of the articles included in this SR was validated by a risk of bias analysis. The information gathered in this SR helps to understand the current state of CRISPR/Cas in the editing of genes and noncoding sequences, which plays a key role in the regulation of various biological processes and the tolerance to multiple abiotic stresses, with potential for use in plant genetic improvement programs.
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Knocking out certain genes negatively impacts root development under drought conditions, ultimately enhancing overall crop resilience to water scarcity.
“Their findings highlighted how knocking out certain genes negatively impacts root development under drought conditions, ultimately enhancing overall crop resilience to water scarcity.”
From Emerging applications of gene editing technologies for the development of climate-resilient crops (2025) · cites this paper as Nascimento et al., 2023
The Discussion (§3.4; page unavailable) reports that knocking out SlNPR1 in tomato and OsABA8ox2 in rice improved drought tolerance. It does not say those knockouts negatively affected root development or that impaired root development caused the improved tolerance. The References entry for OsERA1 instead describes increased primary root growth under nonstressed conditions. (LLM, conf=0.87)
Experimental — accuracy not yet measuredGenes that promote root development, enhance root growth, and improve water uptake have potential as targets for CRISPR/Cas9 gene editing.
“For instance, Nascimento et al. (2023) explored genes that promote root development, enhanced root growth, and improved water uptake, demonstrating their potential as targets for CRISPR/Cas9 gene editing.”
From Emerging applications of gene editing technologies for the development of climate-resilient crops (2025) · cites this paper as Nascimento et al., 2023
The References (no page available) list a CRISPR/Cas9 study of OsERA1 that reports increased primary root growth in rice under nonstressed conditions. Section 3.4 discusses genes targeted for abiotic-stress tolerance, but the copy does not show that Nascimento et al. explored genes that promote root development or improve water uptake, or that the reported root growth improved water uptake. (LLM, conf=0.78)
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Application of CRISPR/Cas9-mediated gene editing for abiotic stress management in crop plants
Kumar, M., Prusty, M. R., Pandey, M. K., Singh, P. K., Bohra, A., Guo, B. Z., & Varshney, R. K. (2023) · Frontiers in Plant Science · doi:10.3389/fpls.2023.1157678 · Cited by 245 · see citing works
“The review offers a broad and unbiased collection of relevant studies through a systematic search of databases on the application of CRISPR/Cas approach for abiotic stress tolerance (Nascimento et al., 2023).”
BackgroundCRISPR–Cas applications in agriculture and plant research
Tuncel, A., Pan, C., Clem, J. S., Liu, D., & Qi, Y. (2025) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-025-00834-3 · Cited by 139 · see citing works
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Multi-Omics Approaches Against Abiotic and Biotic Stress—A Review
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“[195] Genetic Modification Climate-smart banana development Alters genes to improve resistance to abiotic and biotic stress.”
Redesigning crop varieties to win the race between climate change and food security
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Genome editing in food and agriculture: from regulations to consumer perspectives
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“, 2023), as well as on reducing the abiotic factor effects (Santos et al., 2018; dos Santos et al., 2022; Oliveira et al., 2022; Nascimento et al., 2023).”
BackgroundUnlocking Plant Resilience: Metabolomic Insights into Abiotic Stress Tolerance in Crops
Głuchowska, A., Zieniuk, B., & Pawełkowicz, M. E. (2025) · Metabolites · doi:10.3390/metabo15060384 · Cited by 44 · see citing works
“By identifying genes that control key pathways related to stress tolerance, it becomes possible to precisely modify metabolite profiles to achieve desired phenotypic traits [140].”
Zhou, J., Luan, X., Liu, Y., Wang, L., Wang, J., Yang, S., Liu, S., Zhang, J., Liu, H., & Yao, D. (2023) · Plants · doi:10.3390/plants12071478 · Cited by 40 · see citing works
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“In mid-1980, editing of genes was initiated, and several crops (wheat, rice, cotton, maize, potato, tomato, and vice versa) were developed (Nascimento et al. 2023).”
CRISPR/Cas-Mediated Genome Engineering in Plants: Application and Prospectives
Mishra, S., Nayak, S., Tuteja, N., Poosapati, S., Swain, D. M., & Sahoo, R. K. (2024) · Plants · doi:10.3390/plants13141884 · Cited by 32 · see citing works
“…of the Target Gene References Drought Rice ( Oryza sativa ) ENHANCED RESPONSE TO ABA1 (OsERA1) [102] Rice ( Oryza sativa ) OsDST [98] Rice ( Oryza sativa ) PYRABACTIN RESISTANCE-LIKE 9 (OsPYL9) [99] Rice ( Oryza sativa ) SEMI-ROLLED LEAF 1 (SRL1) and SEMI-ROLLED LEAF 2 (SRL2) [9] Maize ( Zea mays )”
BackgroundRecent Advances in Tomato Gene Editing
Larriba, E., Yaroshko, О. M., & Pérez‐Pérez, J. M. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25052606 · Cited by 29 · see citing works
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“In crop breeding programs, the CRISPR/Cas system has been considered a versatile tool for editing in all layers of the central dogma with a focus on the development of plants resistant to multiple biotic and abiotic stresses [125,126].”
BackgroundSharma, N., Sharma, L., Onkarappa, D., Yogendra, K. N., Bose, J., & Sharma, R. A. (2024) · Agronomy · doi:10.3390/agronomy14010159 · Cited by 24 · see citing works
Norfaezah, J., Masani, M. Y. A., Fizree, M. D. P. M. A. A., Bahariah, B., Shaharuddin, N. A., Ho, C. L., Rasid, O. A., & Parveez, G. K. A. (2023) · Industrial Crops and Products · doi:10.1016/j.indcrop.2023.117795 · Cited by 25 · see citing works
Adane, M., & Alamnie, G. (2024) · Functional & Integrative Genomics · doi:10.1007/s10142-024-01480-2 · Cited by 23 · see citing works
“The main goal of CRISPR/Cas genome editing is to create cultivars of plants that are resistant to or tolerant of certain abiotic stressors, making it a versatile technique capable of editing across all crops (Nascimento et al. 2023 ).”
Nutritional quality of photosynthetically diverse crops under future climates
Walsh, C. A., & Lundgren, M. R. (2024) · Plants People Planet · doi:10.1002/ppp3.10544 · Cited by 12 · see citing works
CRISPR/Cas9 opens new horizon of crop improvement under stress condition
Patra, S., Chatterjee, D., Basak, S., Sen, S., & Mandal, A. (2024) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2024.130685 · Cited by 11 · see citing works
Patil, A. M., Wagh, S. G., Janvale, G. B., Pawar, B. D., & Daspute, A. A. (2024) · International Journal of Advanced Biochemistry Research · doi:10.33545/26174693.2024.v8.i3sj.885 · Cited by 8 · see citing works
Mascarenhas, M. S., Nascimento, F. D. S., Rocha, A. D. J., Ferreira, M. D. S., Oliveira, W. D. D. S., Lino, L. S. M., Mendes, T. A. D. O., Ferreira, C. F., dos Santos-Serejo, J. A., & Amorim, É. P. (2024) · Current Issues in Molecular Biology · doi:10.3390/cimb46100659 · Cited by 7 · see citing works
“These results corroborate the findings of [22] in a systematic review of gene editing using CRISPR technology to edit genes tolerant to abiotic stresses.”
BackgroundMethodResultAlleviating Effect of Silicon on Aluminum Toxicity in Plants
Deus, A. C. F., da Silva, A. P. R., Bertani, R. M. D. A., Soares, A. D. A. V. L., Fernandes, D. M., & Büll, L. T. (2026) · Agronomy · doi:10.3390/agronomy16040471 · Cited by 7 · see citing works
“Furthermore, this practice can enhance crop performance under abiotic stress, although its efficiency depends on continuous applications, the source used, the applied dose, and specific soil–plant interactions [116,117].”
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“The use of a genetic engineering approach to increase the resistance of agricultural plants to unfavorable environmental factors is a relevant method [1], which, however, has potential side effects [2].”
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CRISPR /Cas System for Achieving Abiotic Stress Tolerance
Younas, A., Riaz, N., Rashid, M., Tufail, A., Hyder, S., & Noreen, Z. (2024) · doi:10.1002/9781394209156.ch11 · Cited by 4 · see citing works
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“Factors like drought, salinity, extreme temperatures, and other environmental adversities can profoundly impact plant growth and development, leading to significant reductions in crop yields (Nascimento et al. 2023).”
Research hotspots and global trends in plant responses under UV-B radiation
Singh, P., & Choudhary, K. K. (2025) · Discover Plants. · doi:10.1007/s44372-025-00204-5 · Cited by 3 · see citing works
“Various studies have recently used this software for bibliometric analysis [18–20].”
Applications of CRISPR/Cas gene editing in vegetable crop disease and stress resistance
Singh, P., Markam, N. K., Shinde, S. B., Yadav, T. S., Mohanty, S. K., Prasad, M. S., Pagoch, S. S., Swain, S. K., MUSMADE, N. A., & Saikia, B. (2025) · International Journal of Advanced Biochemistry Research · doi:10.33545/26174693.2025.v9.i8sn.5290 · Cited by 3 · see citing works
Topic: boron toxicity in semi-arid crops: the overlooked metalloid in abiotic stress
Mishra, A. K., & Tiwari, S. (2026) · Physiology and Molecular Biology of Plants · doi:10.1007/s12298-026-01721-7 · Cited by 3 · see citing works
“…systems can be strategically employed to edit boron transporters (e.g., BOR1, NIP5;1) and regulatory genes to optimize B uptake, translocation, and compartmentalization, thereby reducing toxic accumulation under B-rich soils (Nascimento et al. 2023; Kumar et al. 2023; Chavhan et al. 2025).”
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Melhoramento genético de plantas para adaptabilidade às mudanças climáticas
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Unlocking crop resilience through CRISPR Cas9 mediated gene editing against environmental stressors
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“Recently, Nascimento et al. [32] emphasized the role of CRISPR/Cas as a complementary tool in modern crop breeding programs aimed at enhancing resilience to environmental stress.”
da Silva, V. L. C., Martinez, A. M., Alam, M., Noman, M., & Chalfun-Júnior, A. (2025) · Plant Gene · doi:10.1016/j.plgene.2025.100547 · Cited by 2 · see citing works
Gene Editing and Transformation Strategies for Engineering Drought‐Tolerant Legumes
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Crops exposed to extreme conditions: perspectives of gene editing to improve stress tolerance
Szabados, L., Kant, K., Rabilu, S. A., Rashid, A., & Zsigmond, L. (2026) · Plant Cell Reports · doi:10.1007/s00299-026-03891-w · Cited by 3 · see citing works
“Multiplex editing is a particularly valuable tool to engineer polygenic traits which usually determine tolerance to abiotic stresses in crops with large, polyploid genomes (Wang et al. 2018; Abdelrah-man et al. 2021; Nascimento et al. 2023; Ni et al. 2023, see Table 1).”
Advances in Plant Phenotyping for Enhanced Salt Tolerance
Adeboye, K. A., Oyetunde, O. A., Bamisaye, V. J., & Idehen, E. O. (2024) · CABI eBooks · doi:10.1079/9781800623033.0009 · Cited by 2 · see citing works
Research Progress of CRISPR Technology in Plant Abiotic Stress
Xiang, M. (2025) · Theoretical and Natural Science · doi:10.54254/2753-8818/2024.ka19746 · Cited by 1 · see citing works
Genome Editing in Banana: Tools, Techniques, and Challenges
Tripathi, J. N., Muiruri, S., Waweru, D. N., & Tripathi, L. (2025) · Springer eBooks · doi:10.1007/978-981-95-0309-4_3 · Cited by 1 · see citing works
Polyamines for boosting plant stress tolerance
Eman, I., Akram, A., Malik, M., Amjad, K., Hameed, M., Khan, Z., & Shah, T. (2026) · Elsevier eBooks · doi:10.1016/b978-0-443-45576-6.00011-x · Cited by 1 · see citing works
Hina, A., Abbasi, A., Chaudhry, A., Sanaullah, T., Arshad, M., Sarwar, H. M., Sarfaraz, S., Karikari, B., & Kavhiza, N. J. (2026) · Frontiers in Plant Science · doi:10.3389/fpls.2026.1865665 · Cited by 1 · see citing works
Genome engineering in maize using CRISPR/CAS9 system
Rafique, K., Gul, A., Ahmad, N., & Mushtaq, N. (2024) · Elsevier eBooks · doi:10.1016/b978-0-443-26614-0.00002-3 · Cited by 1 · see citing works
Genome editing for value addition in medicinal plants
Pandey, A. K. (2024) · Elsevier eBooks · doi:10.1016/b978-0-443-22264-1.00019-0 · Cited by 1 · see citing works
Genome Editing: A Novel Breeding Strategy for Enhanced Stress Tolerance and Quality in Oilseed Crops
Achary, V. M. M., Hearne, S., & Bandyopadhyay, A. (2025) · Springer eBooks · doi:10.1007/978-981-97-7744-0_9 · Cited by 1 · see citing works
Fatima, S., Zafar, Z., Ahad, A., Gul, A., & Bux, H. (2024) · Elsevier eBooks · doi:10.1016/b978-0-443-26614-0.00005-9
Silva, V., Matinez, A. M., Vincente, M. A., Alam, M., Noman, M., & Chalfun-Júnior, A. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.12.26.630382
Bolívar-González, A., Tapia-Fernández, A., Chaverri-Echandi, P., & Gatica-Arias, A. (2025) · Plant Cell Tissue and Organ Culture (PCTOC) · doi:10.1007/s11240-025-03013-6
“At the same time, CRISPR/Cas9 and other gene-editing technologies allow for precise regulation of gene expression, ensuring stable and durable resistance (Marraccini 2020; Nascimento et al. 2023 ).”
CRISPR plants against oxidative stress: Methods and applications
Ghosal, K. (2025) · Elsevier eBooks · doi:10.1016/b978-0-443-24135-2.00013-x
CRISPR plants against heavy metal and metalloid stresses: Methods and applications
Sanjay, S., Banadka, A., Barwad, A., Mamtha, R. S., Ramakrishnan, R., Meghana, U., Kavyashree, A., Al-Khayri, J. M., & Nagella, P. (2025) · Elsevier eBooks · doi:10.1016/b978-0-443-24135-2.00014-1
Genomic Resources and Their Role in Camellia Breeding Strategies
Huang, J., Zhao, M., & Huang, X. (2024) · Plant Gene and Trait · doi:10.5376/pgt.2024.15.0021
Liang, K. (2024) · Tree Genetics and Molecular Breeding · doi:10.5376/tgmb.2024.14.0007
Integrating Advanced Metabolomics with Plant Functional Genomics
Shaikh, A., Toppo, V., Al-Khayri, J. M., & Nagella, P. (2025) · CABI biotechnology series. · doi:10.1079/9781800626911.0017
Kaur, S., Chopra, S., Kumar, V., & Guleria, P. (2025) · Elsevier eBooks · doi:10.1016/b978-0-443-23818-5.00009-0
Ansarì, M. S., Khan, A. A., & Ulhassan, Z. (2025) · Elsevier eBooks · doi:10.1016/b978-0-443-14139-3.00007-5
Dissecting Stress-tolerant Traits of CRISPR-edited Crops by High-throughput Omics Technologies
Kumari, R., Pandey, E., Faizan, S., Bushra, S., Hussain, A., Verma, P., & Akhtar, M. S. (2025) · CABI biotechnology series. · doi:10.1079/9781800627307.0016
Joe, A. D., Liu, R., Luo, X., Liu, M., Syed, R., Aslam, F., Barclay, C. A. G., & Zheng, Z. (2025) · Journal of Plant Growth Regulation · doi:10.1007/s00344-025-11942-x
Stress Resilience in Tuber Crops: A Closer View on Genome Editing and Molecular Approaches
Rajendran, P., Saravanan, K., Jagadhesan, B., Ramesh, R., Bharathi, D., Suriyakumar, P., Sharma, N., Yele, Y., Marate, A., Prasad, N., et al. (2025) · Journal of Plant Growth Regulation · doi:10.1007/s00344-025-11936-9
Does Modern Plant Breeding Techniques Increase Crop Stability Performance?
Ćeran, M., Đorđević, V., Miladinović, J., Miladinović, D., Trkulja, D., Radanović, A., & Kondić‐Špika, A. (2026) · Springer eBooks · doi:10.1007/978-981-95-5664-9_5
Physiological, Biochemical and Molecular Responses of Plants Under Abiotic and Biotic Stresses
Ibrahimov, A., Eren, B., Alptekın, H., Rahimova, S., Tan, U., Gören, H. K., Başar, Y., Tülek, A., Gürbüz, R., Alaserhat, İ., et al. (2026) · Springer eBooks · doi:10.1007/978-3-032-24219-8_2
Atimango, A. O., Kalule, S., Senyange, B., Verbeke, W., & de Steur, H. (2026) · GM crops & food · doi:10.1080/21645698.2026.2698267
“…the technology for its potential in improving crop yield, enhancing resilience to climate change (e.g. high temperatures and water scarcity), 22,23 boosting resistance to biotic stresses such as pests, diseases and weeds, 24 leading to reduced chemical use in the agrifood system, and…”
Tocopherol: Enhancing Plant Tolerance to Stress
Dikilitaş, M., Baran, B., Arslan, B., & Latef, A. A. H. A. (2026) · Sustainability Sciences in Asia and Africa · doi:10.1007/978-981-95-8593-9_7
CRISPR-Cas systems for enhancing chilling tolerance in rice: recent advances and future prospects
Zaman, M. S., Azeem, A., Nouman, A., Khalid, A., Ghafoor, S., Haq, M. Z. U., Aslam, M. T., & EL-BELTAGI, H. S. (2026) · Biologia Futura · doi:10.1007/s42977-026-00326-1
The Role of Gene Editing in Sustainable Agriculture
Das, N., Kumar, A., Rohit, K. C., & Sachan, S. (2026) · IGI Global eBooks · doi:10.4018/979-8-2600-3575-7.ch006
The role of constructed wetland plants in the treatment of emerging contaminants: A review
Wang, M., Xu, H., Li, G., Huang, L., Li, Y., & Fang, Y. (2026) · Journal of Water Process Engineering · doi:10.1016/j.jwpe.2026.110901
Figueroa‐Varela, P. A., Góngora, C. E., Martínez, C. P., Ortíz, A., Navarro-Escalante, L., Acuña, R., & Villanueva-Mejía, D. F. (2026) · Horticulturae · doi:10.3390/horticulturae12091150
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- Authors
- Nascimento, F. D. S., Rocha, A. D. J., Soares, J. M. D. S., Mascarenhas, M. S., Ferreira, M. D. S., Morais Lino, L. S., Ramos, A. P. D. S., Diniz, L. E. C., Mendes, T. A. D. O., Ferreira, C. F., Santos-Serejo, J. A. D., & Amorim, E. P.
- Affiliations
- Universidade Estadual de Feira de Santana (BR)
- Embrapa Mandioca e Fruticultura, Cruz das Almas 44380-000, BA, Brazil
- Embrapa (BR)
- Embrapa Soja, Londrina 86000-000, PR, Brazil
- Universidade Federal de Viçosa (BR)
- ORCID
- Nascimento, Fernanda dos Santos
- Rocha, Anelita de Jesus
- Soares, Julianna Matos da Silva
- Mascarenhas, Marcelly Santana
- Ferreira, Mileide dos Santos
- Morais Lino, Lucymeire Souza
- Ramos, Andresa Priscila de Souza
- Diniz, Leandro Eugenio Cardamone
- Mendes, Tiago Antônio de Oliveira
- Ferreira, Claudia Fortes
- Santos-Serejo, Janay Almeida dos
- Amorim, Edson Perito
- Venue
- Plants
- Publisher
- MDPI AG
- Published
- 2023-01-09
- Volume
- 12
- Issue
- 2
- Pages
- 305
- ISSN
- 2223-7747 (ISSN-L)
- PMC
- PMC9860801
- OpenAlex
- W4313889986
- Cited by
- 71
- References
- 262
- Citations by year
- 2026: 18 · 2025: 25 · 2024: 22 · 2023: 6
- FWCI
- 1.88
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Plants (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- IITA/The Bill and Melinda Gates Foundation (OPP1093845)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Stress Responses and Tolerance
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Genetically Modified Organisms Research
- Keywords
- CRISPR gene editing, abiotic stress tolerance, plant stress tolerance, salt stress, drought stress, temperature extremes, flooding stress, metal toxicity, rice, Arabidopsis thaliana, tomato, Cas9, CRISPR/Cas12a, stress signaling pathways, plant genetic improvement
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