A Review on Crispr-Cas: A Savior for Climate-Threatened Rice
Published: 2023-10-09
Page: 179-190
Issue: 2023 - Volume 6 [Issue 2]
Muaz Bin Khalid
*
Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan.
Muhammad Haris
Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan.
Muhammad Arslan
Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan.
Fajar Raheem
Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan.
Adnan Shoukat
Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan.
Muhammad Faizan
Department of Biochemistry, University of Agriculture Faisalabad, Pakistan.
Amina
Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan.
Eza Fatima
Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan.
Zubair Zaheer
Institute of Horticultural Sciences, University of Agriculture Faisalabad, Pakistan.
Ali Hassan
Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan.
Usama Waheed
Department of Plant breeding and genetics, University of Agriculture Faisalabad, Pakistan.
*Author to whom correspondence should be addressed.
Abstract
The productivity of agriculture has been greatly impacted by climate change, especially rice production, several biotic and abiotic stressors, including heat, salt, drought, heavy metals, rice blast, and bacterial blight, can severely reduce rice yields and jeopardize global food security. Numerous strategies have been employed in this regard to cultivate rice varieties that may be able to adapt to changing climate conditions. Nowadays, crop development has undergone a revolution thanks to gene editing (GE) technologies. As one of the most useful, dependable, affordable, and labor-efficient GE technologies available, the CRISPR/Cas (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein) system has gained favor among plant researchers, notably rice breeders and geneticists. Since 2013 (the year the technique was first deployed in rice), CRISPR/Cas-based GE technologies have been employed to develop a variety of trait-specific climate-resilient rice lines. Several studies that have already been released attest to the effective use of GE technologies for rice development. However, this review's primary objective is to provide a succinct, thoroughly researched summary of the most current studies (starting in 2020) on the application of GE tools—particularly CRISPR-based systems for the production of CRISPR rice—to address the serious global climate change dilemma.
Keywords: Climate resilience, Oryza sativa L., gene editing, CRISPR-Cas system, food security
How to Cite
Downloads
References
Krishnan P, et al., High-temperature effects on rice growth, yield, and grain quality. Advances in agronomy. 2011;111:87-206.
Li C, et al., Computational tools and resources for CRISPR/Cas genome editing. Genomics, proteomics & bioinformatics; 2022.
Li M, Huo YX, Guo S. CRISPR-mediated base editing: from precise point mutation to genome-wide engineering in nonmodel microbes. Biology. 2022;11(4):571.
Tao J, Bauer DE, Chiarle R. Assessing and advancing the safety of CRISPR-Cas tools: from DNA to RNA editing. Nature Communications. 2023;14(1):212.
Xie Z, et al., Genome editing in the edible fungus Poria cocos using CRISPR-Cas9 system integrating genome-wide off-target prediction and detection. Frontiers in Microbiology. 2022;13: 966231.
Liu H, et al., CRISPR/Cas9 technology and its utility for crop improvement. International Journal of Molecular Sciences .2022;23(18):10442.
Wang W, et al., A new gain-of-function OsGS2/GRF4 allele generated by CRISPR/Cas9 genome editing increases rice grain size and yield. The Crop Journal. 2022;10(4):1207-1212.
Balakrishnan M, et al., Computational tools and scientometrics for CRISPR-based genome editing. Journal of Plant Biochemistry and Biotechnology .2023:1-10.
Naim F, et al., Are the current gRNA ranking prediction algorithms useful for genome editing in plants? PLoS One. 2020;15(1):e0227994.
Uniyal AP, et al., An overview of designing and selection of sgRNAs for precise genome editing by the CRISPR-Cas9 system in plants. 3 Biotech. 2019;9(6):223.
Manghwar H, et al., CRISPR/Cas systems in genome editing: methodologies and tools for sgRNA design, off‐target evaluation, and strategies to mitigate off‐target effects. Advanced science. 2020;7(6):1902312.
Wang Y, et al., Data comparison and software design for easy selection and application of CRISPR-based genome editing systems in plants. Genomics, Proteomics & Bioinformatics. 2021;19(6):937-948.
Biswas S, et al., Optimization of protoplast isolation and transformation for a pilot study of genome editing in peanut by targeting the allergen gene Ara h 2. International Journal of Molecular Sciences. 2022;23(2):837.
Cram D, et al., WheatCRISPR: a web-based guide RNA design tool for CRISPR/Cas9-mediated genome editing in wheat. BMC Plant Biology. 2019;19:1-8.
Kim D, et al., New Genomic Techniques and Intellectual Property Law: Challenges and Solutions for the Plant Breeding Sector. Max Planck Institute for Innovation & Competition Research Paper. 2023:23-16.
Muñoz CF, et al., Genetic engineering of microalgae for enhanced lipid production. Biotechnology advances. 2021;52:107836.
Lopes FSdS, The bioethics of genome editing in livestock; 2021.
Kim TH, Lee SW. Therapeutic Application of Genome Editing Technologies in Viral Diseases. International Journal of Molecular Sciences .2022;23(10):5399.
Chakraborty K, et al., Rice with SUB1 QTL possesses greater initial leaf gas film thickness leading to delayed perception of submergence stress. Annals of Botany. 2021;127(2):251-265.
Kuroha T. Ashikari M. Molecular mechanisms and future improvement of submergence tolerance in rice. Molecular Breeding. 2020;40(4):41.
Shaheen N, et al., CRISPR-Cas System, a Possible “Savior” of Rice Threatened by Climate Change: An Updated Review. Rice. 2023;16(1):39.
Ahmad S, et al., CRISPR/Cas9 for development of disease resistance in plants: recent progress, limitations and future prospects. Briefings in Functional Genomics. 2020;19(1):26-39.
Alam MS, et al., Loss-of-function mutations of OsbHLH044 transcription factor lead to salinity sensitivity and a greater chalkiness in rice (Oryza sativa L.). Plant Physiology and Biochemistry. 2022;193:110-123.
Rao MJ, Wang L. CRISPR/Cas9 technology for improving agronomic traits and future prospective in agriculture. Planta. 2021;254:1-16.
Bohra A, et al., Reap the crop wild relatives for breeding future crops. Trends in Biotechnology. 2022;40(4):412-431.
Zhu H, C Li, Gao C. Applications of CRISPR–Cas in agriculture and plant biotechnology. Nature Reviews Molecular Cell Biology .2020;21(11):661-677.
Yadav RK, et al., Genome Editing and Improvement of Abiotic Stress Tolerance in Crop Plants. Life. 2023;13(7):1456.
Matres JM, et al., Genome editing in cereal crops: an overview. Transgenic research .2021;30: 461-498.
Hua K, et al., Perspectives on the application of genome-editing technologies in crop breeding. Molecular Plant. 2019;12(8):1047-1059.
Ariga H, Toki S, Ishibashi K. Potato virus X vector-mediated DNA-free genome editing in plants. Plant and Cell Physiology. 2020;61(11):1946-1953.
Miladinovic D, et al., Targeted plant improvement through genome editing: from laboratory to field. Plant cell reports. 2021;40:935-951.
Xu J, Hua K, Lang Z. Genome editing for horticultural crop improvement. Horticulture research. 2019;6.
Hameed A, et al., Effects of salinity stress on chloroplast structure and function. Cells .2021; 10(8):2023.
Zhang Z, et al., Exogenous melatonin promotes the salt tolerance by removing active oxygen and maintaining ion balance in wheat (Triticum aestivum L.). Frontiers in Plant Science. 2022; 12:787062.
Rahman MA, et al., Regulation of Na+/H+ exchangers, Na+/K+ transporters, and lignin biosynthesis genes, along with lignin accumulation, sodium extrusion, and antioxidant defense, confers salt tolerance in alfalfa. Frontiers in Plant Science. 2022;13:1041764.
Zhou‐Tsang A, et al., Grapevine salt tolerance. Australian Journal of Grape and Wine Research .2021;27(2):149-168.
Zhu J, et al., Understanding mechanisms of salinity tolerance in barley by proteomic and biochemical analysis of near-isogenic lines. International Journal of Molecular Sciences. 2020;21(4):1516.
Abbasi-Vineh MA, Sabet MS, Karimzadeh G. Identification and functional analysis of two purple acid phosphatases AtPAP17 and AtPAP26 involved in salt tolerance in Arabidopsis thaliana plant. Frontiers in Plant Science. 2021;11:2326.
Khan W, et al., Insights concerning advancing the agroecological sustainability of salinity tolerance through proteomics profiling of hexaploid wheat (Triticum aestivum L.). South African Journal of Botany. 2023;158:142-148.
Solis CA, et al., Back to the wild: on a quest for donors toward salinity tolerant rice. Frontiers in Plant Science .2020;11:323.
Ullah A, et al., Exogenous γ-aminobutyric acid (GABA) mitigated salinity-induced impairments in mungbean plants by regulating their nitrogen metabolism and antioxidant potential. Frontiers in Plant Science. 2023;13:1081188.
Yousefirad S, et al., The RNA-seq transcriptomic analysis reveals genes mediating salt tolerance through rapid triggering of ion transporters in a mutant barley. Plos one, 2020;15(3): e0229513.
Plasencia FA, et al., The Ca2+ sensor calcineurin b–like protein 10 in plants: emerging new crucial roles for plant abiotic stress tolerance. Frontiers in Plant Science .2021;11:599944.
Su N, et al., GABA operates upstream of H+-ATPase and improves salinity tolerance in Arabidopsis by enabling cytosolic K+ retention and Na+ exclusion. Journal of Experimental Botany. 2019;70(21):6349-6361.
Cho KH, et al., Novel QTL identification and candidate gene analysis for enhancing salt tolerance in soybean (Glycine max (L.) Merr.). Plant Science. 2021;313:111085.
Gao Q, et al., OsJRL40, a Jacalin-Related Lectin Gene, Promotes Salt Stress Tolerance in Rice. International Journal of Molecular Sciences .2023;24(8):7441.
Maryum Z, et al., An overview of salinity stress, mechanism of salinity tolerance and strategies for its management in cotton. Frontiers in Plant Science .2022;13:907937.
Joshi S, et al., Ion transporters and their regulatory signal transduction mechanisms for salinity tolerance in plants. Physiologia Plantarum. 2022;174(3):e13702.
Fan D, Smith DL. Mucilaginibacter sp. K improves growth and induces salt tolerance in nonhost plants via multilevel mechanisms. Frontiers in Plant Science. 2022;13:938697.
Choudhary S, et al., Cellular responses, osmotic adjustments, and role of osmolytes in providing salt stress resilience in higher plants: Polyamines and nitric oxide crosstalk. Journal of Plant Growth Regulation. 2023;42(2):539-553.
Elhindi KM, Almana FA, Al-Yafrsi MA. Role of Humic Acid on Inducing Salt Tolerance of Ivy Geranium (Pelargonium peltatum L.) Plants. Horticulturae. 2023;9(9):1012.
Ashraf M, Munns R. Evolution of approaches to increase the salt tolerance of crops. Critical Reviews in Plant Sciences. 2022;41(2):128-160.
Athar HuR, et al., Salt stress proteins in plants: An overview. Frontiers in Plant Science. 2022; 13:999058.
Kim TH, Kim SM. Identification of Candidate Genes for Salt Tolerance at the Seedling Stage Using Integrated Genome-Wide Association Study and Transcriptome Analysis in Rice. Plants. 2023;12(6):1401.
Mostofa MG, et al., Potassium in plant physiological adaptation to abiotic stresses. Plant Physiology and Biochemistry; 2022.
Nagarajan S, Varatharajan N, Gandhimeyyan RV. Understanding the responses, mechanism and development of salinity stress tolerant cultivars in Rice. Integrative advances in rice research. 2022:91.
Naz T, et al., Carbohydrate partitioning, growth and ionic compartmentalisation of wheat grown under boron toxic and salt degraded land. Agronomy. 2022;12(3):740.
Wang T, et al., Salt tolerance in Brassicaceae crops: physiological responses and molecular mechanisms. Functional Plant Biology; 2023.
Rengel Z, Plant responses to soil-borne ion toxicities, in Marschner's Mineral Nutrition of Plants. 2023;665-722.
Faried HN, et al., Assessing salt tolerance induction in potato by salicylic acid using morpho-physio-biochemical, ionic, and yield indices. Potato Research. 2022;65(3):677-691.
Zhou T, et al., A key role of pectin demethylation-mediated cell wall Na+ retention in regulating differential salt stress resistance in allotetraploid rapeseed genotypes. bioRxiv. 2023;09. 09. 556983.
Saxena B, et al., Insights into the molecular aspects of salt stress tolerance in mycorrhizal plants. World Journal of Microbiology and Biotechnology. 2022; 38(12):253.
Lopes M, et al., Towards the Sustainable Exploitation of Salt-Tolerant Plants: Nutritional Characterisation, Phenolics Composition, and Potential Contaminants Analysis of Salicornia ramosissima and Sarcocornia perennis alpini. Molecules. 2023;28(6):2726.
Farooq M, et al., Effect of different salts on nutrients uptake, gene expression, antioxidant, and growth pattern of selected rice genotypes. Frontiers in Plant Science. 2022;13:895282.
dos Santos TB, et al., Physiological responses to drought, salinity, and heat stress in plants: a review. Stresses. 2022;2(1):113-135.
Ji H, et al., Regulation of salt tolerance in the roots of Zea mays by L-histidine through transcriptome analysis. Frontiers in Plant Science. 2022;13:1049954.
Zhu J, et al., Potassium application increases cotton (Gossypium hirsutum L.) fiber length by improving K+/Na+ homeostasis and potassium transport capacity in the boll-leaf system under moderate salinity. Agronomy. 2022;12(12):2962.
Yuan Y, et al., Chaetomium globosum D5 confers salinity tolerance on Paeonia lactiflora Pall. Journal of Plant Physiology. 2023;280:153878.