CRISPR/CAS9-MEDIATED GENETIC ENGINEERING FOR DEVELOPING SALINITY-TOLERANT RICE VARIETIES FOR INDONESIAN COASTAL AGRICULTURE
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CRISPR/Cas9, Coastal Agriculture, Genetic Engineering, Rice Varieties, Salinity Tolerance
Abstract
Salinity intrusion in coastal agricultural areas has become a major constraint to rice production in Indonesia, driven by climate change, sea-level rise, and unsustainable land management practices. High soil salinity adversely affects rice growth, yield stability, and food security, particularly in coastal regions that depend heavily on rice cultivation. Conventional breeding approaches for developing salinity-tolerant rice varieties are often time-consuming and limited by genetic complexity. Advances in genome editing technologies, particularly CRISPR/Cas9, offer a precise and efficient alternative for accelerating crop improvement. The objective of this study is to develop salinity-tolerant rice varieties suitable for Indonesian coastal agriculture through CRISPR/Cas9-mediated genetic engineering targeting key genes associated with salt stress tolerance. This research employed an experimental laboratory-based design combined with controlled greenhouse evaluation. Specific salinity-responsive genes were identified and edited using the CRISPR/Cas9 system. Transgenic rice lines were generated and screened for successful gene edits using molecular analysis techniques. Edited lines were subsequently evaluated under saline and non-saline conditions to assess physiological responses, growth performance, and yield-related traits. The results demonstrate that CRISPR/Cas9-edited rice lines exhibited enhanced tolerance to saline stress, indicated by improved germination rates, higher chlorophyll content, better ion homeostasis, and increased biomass compared to non-edited controls. Several edited lines maintained stable growth and yield under moderate to high salinity levels, confirming the effectiveness of targeted gene modification. In conclusion, CRISPR/Cas9-mediated genetic engineering shows strong potential for developing salinity-tolerant rice varieties tailored to Indonesian coastal environments. This approach provides a rapid and precise strategy to enhance rice resilience, support sustainable coastal agriculture, and strengthen national food security under changing climatic conditions.
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References
Bora, B., Kauser, H., & Geed, S. R. (2025). Bioremediation strategies for xenobiotic degradation in petroleum-impacted industrial ecosystems: Practical challenges and future directions. Journal of Water Process Engineering, 70, 106877. https://doi.org/10.1016/j.jwpe.2024.106877
Chaudhary, S., Bano, K. S., Mohanty, T., Kumari, A., & Mehdi, M. M. (2025). Exploring microalgae-based biodiesel as an alternative fuel: Development, production techniques and environmental impacts. Biomass and Bioenergy, 202, 108249. https://doi.org/10.1016/j.biombioe.2025.108249
Derk, K., Nathan, S., & Jonathan, O. (2024). The Role of Biotechnology in Plant Breeding for Sustainable Agriculture in Brazil. Agriculturae Studium of Research, 1(1), 41–55. https://doi.org/10.55849/agriculturae.v1i1.172
Gill, S. S., Gill, R. K., & Sobti, R. C. (2026). Chapter 18—Clustered regularly interspaced short palindromic repeats associated protein systems in environmental biotechnology: Applications in pollution management. In R. C. Sobti, T. Kaur, H. Walia, P. Rattan, & A. Narula (Eds.), One Planet, One Health, One Future (pp. 285–310). Academic Press. https://doi.org/10.1016/B978-0-443-38325-0.00009-5
Gundlapalli, M., & Ganesan, S. (2025). Polyhydroxyalkanoates (PHAs): Key Challenges in production and sustainable strategies for cost reduction within a circular economy framework. Results in Engineering, 26, 105345. https://doi.org/10.1016/j.rineng.2025.105345
Han, J.-H., Hwang, J.-H., Shin, N.-H., Kim, S., Lee, H.-S., Kretzschmar, T., Kim, K. D., Choi, I.-R., & Chin, J. H. (2025). Chromosome-level genome assembly of IR64 near-isogenic line harboring Saltol reveals novel genomic regions associated with salinity tolerance in rice (Oryza sativa L.). Plant Physiology and Biochemistry, 229, 110669. https://doi.org/10.1016/j.plaphy.2025.110669
Han, Q., Ge, L., Ren, Y., & Yu, Y. (2025). Application of machine learning in soil fumigation remediation prediction and design. Journal of Environmental Chemical Engineering, 13(6), 120272. https://doi.org/10.1016/j.jece.2025.120272
Hurrah, I. M., Mohiuddin, T., Mandal, S., Kumar, V., & Gupta, A. (2025). Chapter 31—Crosstalk and interaction among salt stress tolerance pathways. In M. K. Patel, L.-S. Phan Tran, S. Pandey, & A. Mishra (Eds.), Exogenous Priming and Engineering of Plant Metabolic and Regulatory Genes (pp. 513–529). Academic Press. https://doi.org/10.1016/B978-0-443-13490-6.00031-X
Khan, N. A., Owens, L., Nuñez, M. A., & Khan, A. L. (2025). Complexity of combined abiotic stresses to crop plants. Plant Stress, 17, 100926. https://doi.org/10.1016/j.stress.2025.100926
Krishna Samal, D. P., & Sukla, L. B. (2025). Unveiling the dual potential of microalgae and seaweed biomass for sustainable biofuel production: A review. RSC Advances, 15(41), 34160–34175. https://doi.org/10.1039/d5ra04845a
Li, Z., & Li, X. (2025). Global trends and research hotspots on the improvement of saline soil: Insights from bibliometric analysis. Agricultural Water Management, 321, 109923. https://doi.org/10.1016/j.agwat.2025.109923
Luo, Z., Yu, S., Chen, J., Liu, Q., Hu, M., Yang, X., Huang, Y., & Xiao, W. (2025). Knockout of OsBURP12 enhances salt tolerance in rice seedlings. Environmental and Experimental Botany, 231, 106097. https://doi.org/10.1016/j.envexpbot.2025.106097
Maung, T. Z., Phusantisampan, T., Pichtel, J., O-Thong, S., & Meeinkuirt, W. (2025). Bioindicators of potentially toxic elements in Mangrove ecosystems. Earth-Science Reviews, 270, 105258. https://doi.org/10.1016/j.earscirev.2025.105258
Nawaz, T., Nelson, D., Fahad, S., Saud, S., Aaqil, M., Adnan, M., Saleem, A., Bibi, M., Joshi, N., Rahman, T. U., Khan, M. N. R., Khan, I., Hussain, Q., Hassan, S., & Raihan, M. J. (2025). Chapter 7—Impact of elevated CO2 and temperature on overall agricultural productivity. In S. Fahad, M. Adnan, I. Munir, R. Lal, T. Nawaz, & S. Saud (Eds.), Challenges and Solutions of Climate Impact on Agriculture (pp. 163–202). Academic Press. https://doi.org/10.1016/B978-0-443-23707-2.00007-6
Norman, R. A., Alcalde, M. C., Bron, J. E., Burke, M., Crumlish, M., Gheyas, A. A., Little, D. C., Malcorps, W., Moss, A. S., Newton, R., & Pounds, A. (2026). Global aquaculture systems. In P. Alexander (Ed.), Encyclopedia of Agriculture and Food Systems (Third Edition) (pp. 35–60). Academic Press. https://doi.org/10.1016/B978-0-443-15976-3.00103-3
Osei-Wusu, M. O., Adjei, R. R., Appiah, K. S., Ankamah-Yeboah, T., & Adusei-Fosu, K. (2025). Advanced breeding strategies for combating rice salinity stress in Ghana: A critical review and future perspective. Scientific African, 29, e02784. https://doi.org/10.1016/j.sciaf.2025.e02784
Ozal, G., Ilyasova, C., & Ilgiz, V. (2024). Post-Harvest Storage and Processing Technology in Russia: Reducing Yield Loss. Agriculturae Studium of Research, 1(1), 28–49. https://doi.org/10.55849/agriculturae.v1i1.172
Pandit, G. K., Abubakar, A. M., Mamoudou, H., Tariq, M., Abdulrazak, M., Wali, S. A., & Asif, M. (2025). Chapter 22—Molecular underpinning of plants hormonal signaling to abiotic stressors using plant chemical and synthetic biology approaches. In Z. Ulhassan, Y. Hamid, W. Zhou, D. K. Tripathi, V. P. Singh, & F. J. Corpas (Eds.), Role of Antioxidants in Abiotic Stress Management (pp. 383–393). Academic Press. https://doi.org/10.1016/B978-0-443-14139-3.00012-9
Rajput, S., Johar, P., & Salgotra, R. K. (2026). Chapter 29—Genetically engineered crops for climate resilient agriculture. In R. C. Sobti, T. Kaur, H. Walia, P. Rattan, & A. Narula (Eds.), One Planet, One Health, One Future (pp. 441–460). Academic Press. https://doi.org/10.1016/B978-0-443-38325-0.00005-8
Rehman, S. ur, Yang, J., Zhang, J., Zhang, L., Hao, X., Song, R., Chen, S., Wang, G., & Hua, L. (2025). Salt stress in wheat: A physiological and genetic perspective. Plant Stress, 16, 100832. https://doi.org/10.1016/j.stress.2025.100832
Rogger, T., Jonathan, H., & Lindsey, K. (2024). Smart Fertilization Technology for Agricultural Efficiency in Canada. Agriculturae Studium of Research, 1(1), 56–70. https://doi.org/10.55849/agriculturae.v1i1.172
Rohilla, M., Mazumder, A., Chakraborty, K., Chowdhury, D., Prakash, N., & Mondal, T. K. (2025). The private life of deepwater rice: Unravelling exclusive features and unexplored mechanisms. Plant Stress, 17, 100910. https://doi.org/10.1016/j.stress.2025.100910
Selwal, N., Sultana, H., Rahayu, F., Hariyono, B., Riajaya, P. D., Kadarwati, F. T., Herwati, A., Latifah, E., Indriani, F. C., Saeri, M., Dar, M. A., Chopra, C., Abass, K. S., & Wani, A. K. (2025). Emerging technologies in biomass conversion: Bioengineering and nanocatalysts to AI-driven process optimization. Biomass and Bioenergy, 200, 108054. https://doi.org/10.1016/j.biombioe.2025.108054
Sharma, S., Malik, V., Singh, D., Anuja, Rani, S., Kiran, K., Priyanka, Sharma, P., Kapoor, D., & Husen, A. (2025). Chapter 1—Current understanding of antioxidants and plant productivity: An overview. In A. Husen (Ed.), Role of Antioxidants in Mitigating Plant Stress (pp. 1–35). Academic Press. https://doi.org/10.1016/B978-0-443-26799-4.00010-4
Shukla, S., Chaudhary, K., Aahana, Phutela, S., Bhutani, R., & Shukla, S. K. (2025). 18—Smart crop varieties and Precision agriculture: A way ahead for climate-resilient sustainable agriculture. In A. Kumar, O. O. Babalola, J. S. Panwar, & G. Santoyo (Eds.), Climate Change and Agricultural Ecosystems (Second Edition) (pp. 435–466). Woodhead Publishing. https://doi.org/10.1016/B978-0-443-26520-4.00027-5
Simarmata, T., Hibatullah, F. H., Khumairah, F. H., Irwandhi, Ambarita, D. D. M., Nurbaity, A., Herdiyantoro, D., & Kamaluddin, N. N. (2025). Advancing climate-resilient rhizomicrobiome engineering for enhancing productivity and sustainability of strategic crop farming in Indonesia’s problematic soils. Environmental and Sustainability Indicators, 27, 100821. https://doi.org/10.1016/j.indic.2025.100821
Sinha, D., Majgaonkar, A., Kazi, Z., Chatterjee, S., Paul, I., Paulchoudhury, A., & Das, S. (2025). Chapter 13—Pangenomics for developing heavy metal stress-tolerant plants. In J.-T. Chen (Ed.), Plant Pangenomes and Pangenomics (pp. 255–286). Academic Press. https://doi.org/10.1016/B978-0-443-26791-8.00013-3
Tiozon, R. Jr. N., Zhang, C., Kim, S.-R., Liu, Q., Fernie, A. R., & Sreenivasulu, N. (2025). Unlocking the potential of wild rice to bring missing nutrition to elite grains. Plant Communications, 6(6), 101344. https://doi.org/10.1016/j.xplc.2025.101344
Xiong, M., Wang, C., Liang, X., Yu, J., Liu, T., Peng, B., Du, X., Yang, T., Feng, G., Liu, Q., & Li, Q. (2025). Multi-omics approach reveals the contribution of brassinosteroids to salt tolerance for seed germination in rice. Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.08.008
Xu, C., Li, H., Chen, M., Zhao, N., Yan, B., Liu, Y., Zhang, H., & Zheng, H. (2025). Comprehensive analysis of MAPK cascade genes in mollusks and their expression patterns in noble scallop Chlamys nobilis under low temperature stress. Aquaculture, 609, 742830. https://doi.org/10.1016/j.aquaculture.2025.742830
Xu, Z., Wang, Z., Zheng, Y., Gao, H., Shen, Q., & Zhang, G. (2025). Sea barley: Evolutionary insights and potential for crop improvement. Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.10.010
Yuan, J., Cao, H., Qin, W., Yang, S., Zhang, D., Zhu, L., Song, H., & Zhang, Q. (2025). Genomic and modern biotechnological strategies for enhancing salt tolerance in crops. New Crops, 2, 100057. https://doi.org/10.1016/j.ncrops.2024.100057
Zhang, T., Jin, M., Ding, Y., Wang, C., Wang, K., Qi, Q., Cui, Y., Guo, L., Liu, X., & Zhang, H. (2026). Research on the regulation mechanism of salt tolerance in wheat. Plant Stress, 19, 101172. https://doi.org/10.1016/j.stress.2025.101172
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Copyright (c) 2025 James Scott, Sarah Williams, David Martin
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