Cultivating Tomorrow: Harnessing Gene Editing and Silencing for Precision Horticulture

Shubham Jain

Department of Fruit Science, ANDUAT, Ayodhya, India.

G. Ranganna

Horticultural Research Station, Vijayarai, Dr. Y.S.R. Horticultural University, 534475, Eluru, Andhra Pradesh, India.

Priyanka Shivaji Jadhav

Department of Horticulture, Mahatma Phule Krishi Vidyapeeth, Rahuri, India.

Ujjwal Shrivastava

Department of Fruit Science, Chandra Shekhar Azad University of Agriculture and Technology Kanpur, U.P (208002), India.

Ankita Sood

Department of Genetics and Plant Breeding, College of Horticulture and Forestry, Thunag, Mandi, India.

Lalu Prasad

Department of Vegetables Science, Acharya Narendra Deva University of Agriculture and Technology, Kumarganj, Ayodhya, UP, India.

Suraj Luthra

Department of Vegetables Science, Acharya Narendra Deva University of Agriculture and Technology, Kumarganj, Ayodhya, UP, India.

Anushi *

Department of Fruit Science, Chandra Shekhar Azad University of Agriculture and Technology Kanpur, U.P (208002), India.

*Author to whom correspondence should be addressed.


Precision Horticulture, propelled by gene editing and silencing technologies, emerges as a transformative approach to address the demands of sustainable and efficient crop production. Utilizing CRISPR-Cas9 and RNA interference, horticulturists can precisely modify and regulate plant genomes, ushering in a new era of tailored crops. Gene editing enables the development of crops with heightened resistance to pests, diseases, and improved adaptability. This targeted enhancement, coupled with accelerated breeding processes, results in resilient varieties that meet the challenges of evolving agricultural landscapes. Concurrently, gene silencing technologies allow for the suppression of undesirable traits, extending the shelf life of produce and minimizing post-harvest losses. Integration of these technologies into Precision Horticulture not only optimizes crop traits but also promotes sustainability by reducing reliance on chemical inputs. The approach aligns with environmental conservation, ensuring a more ecologically balanced and resource-efficient cultivation. However, responsible deployment and ethical considerations are paramount for widespread acceptance, highlighting the need for a harmonious balance between technological innovation and ethical utilization in shaping the future of horticulture.

Keywords: Gene editing, development, resistance, targeted

How to Cite

Jain , S., Ranganna, G., Jadhav , P. S., Shrivastava , U., Sood , A., Prasad , L., Luthra , S., & Anushi. (2024). Cultivating Tomorrow: Harnessing Gene Editing and Silencing for Precision Horticulture. Journal of Advances in Biology & Biotechnology, 27(1), 147–160.


Download data is not yet available.


Godfray HCJ, Beddington JR, Crute IR, Haddad L, Lawrence D, Muir JF, Pretty J, Robinson S, Thomas SM, Toulmin C. Food Security: The Challenge of Feeding 9 Billion People. Science. 2010;327:812–818.

Chen K, Wang Y, Zhang R, Zhang H, Gao C. CRISPR/Cas Genome editing and precision plant breeding in agriculture. Annu. Rev. Plant Biol. 2019;70: 667–697.

Pathak K, Gogoi B. RNA interference (RNAi): Application in crop improvement: A review. Agric. Rev. 2016:37:245–249.

Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E. A Programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science. 2012;337:816–821.

Pardo B, Gómez-González B, Aguilera A. DNA Repair in Mammalian Cells. Cell. Mol. Life Sci. 2009;66:1039–1056.

Gill RA, Scossa F, King GJ, Golicz A, Tong C, Snowdon RJ, Fernie AR.; Liu, S. On the Role of Transposable Elements in the Regulation of Gene Expression and Subgenomic Interactions in Crop Genomes. Crit. Rev. Plant Sci. 2021;40: 157–189

Mamta B, Rajam MV. RNA Interference: A Promising Approach for Crop Improvement. In Biotechnologies of Crop Improvement; Gosal, S., Wani, S., Eds.; Springer: Cham, Germany. 2018;2:41–65.

Napoli C, Lemieux C, Jorgensen R. Introduction of a Chimeric Chalcone Synthase Gene into Petunia Results in Reversible Co-Suppression of Homologous Genes in trans. Plant Cell. 1990;2:279–289.

Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature. 1998;391:806–811.

Johnson N, Axtell MJ. Small RNA warfare: Exploring origins and function of trans-species microRNAs from the parasitic plant Cuscuta. Curr. Opin. Plant Biol. 2019;50: 76–81.[PubMed]

Dutta TK, Banakar P, Rao U. The status of RNAi-based transgenic research in plant nematology. Front. Microbiol. 2015;5:760.

Lunardon A, Johnson N, Hagerott E, Phifer T, Polydore S, Coruh C. Axtell MJ. Integrated annotations and analyses of small RNA–producing loci from 47 diverse plants. Genome Res. 2020;30;497–513.

Lunardon A, Kariuki SM, Axtell MJ. Expression and processing of polycistronic artificial microRNAs and trans -acting siRNAs from transiently introduced transgenes in Solanum lycopersicum and Nicotiana benthamiana. Plant J. 2021;106;1087–1104.

Yang X, Sanchez R, Kundariya H, Maher T, Dopp I, Schwegel R, Virdi K, Axtell MJ, MacKenzie SA. Segregation of an MSH1 RNAi transgene produces heritable non-genetic memory in association with methylome reprogramming. Nat. Commun. 2020;11:1–17.

Romano N, Macino G. Quelling: Transient inactivation of gene expression in Neurospora crassa by transformation with homologous sequences. Mol. Microbiol. 1992;6:3343–3353.

Wilson RC, Doudna, JA. Molecular Mechanisms of RNA Interference. Annu. Rev. Biophys. 2013;42:217–239.

Cerutti, H.; Ma, X.; Msanne, J.; Repas, T. RNA-mediated silencing in algae: Biological roles and tools for analysis of gene function. Eukaryot. Cell 2011, 10, 1164–1172.

Hammond SM, Bernstein E, Beach D, Hannon GJ. An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nat. Cell Biol. 2000;404:293–296.

Elbashir SM, Harborth J, Lendeckel W, Yalcin A, Weber K, Tuschl T. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nat. Cell Biol. 2001;411:494–498.

Ali N, Datta SK, Datta K. RNA interference in designing transgenic crops. GM Crop 2010;1:207–213.

Hammond SM. Dicing and slicing: The core machinery of the RNA interference pathway. FEBS Lett. 2005;579:5822–5829.

Hutvagner G, Simard M. Argonaute proteins: Key players in RNA silencing. Nat. Rev. Mol. Cell Biol. 2008;9: 22–32.

Redfern AD, Colley SM, Beveridge DJ, Ikeda N, Epis MR Li X, Foulds CE, Stuart LM, Barker A, Russell VJ, et al. RNA-induced silencing complex (RISC) Proteins PACT, TRBP, and Dicer are SRA binding nuclear receptor coregulators. Proc. Natl. Acad. Sci. USA 2013;110; 6536–6541.

Dash SK, Sushil KM N, MH. RNA Interference a fine tuner of gene regulation: A review. Int. J. Biotechnol. Mol. Biol. Res. 2015;6:35–39.

Zhang H, A Kolb F, Jaskiewicz L, Westhof E, Filipowicz W. Single Processing Center Models for Human Dicer and Bacterial RNase III. Cell 2004;118:57–68.

Aalto AP, E Pasquinelli A. Small non-coding RNAs mount a silent revolution in gene expression. Curr. Opin. Cell Biol. 2012;24:333–340.

Kurihara Y, Takashi Y, Watanabe Y. The interaction between DCL1 and HYL1 is important for efficient and precise processing of pri-miRNA in plant microRNA biogenesis. RNA. 2006;12: 206–212.

Kurihara Y, Watanabe Y. From The Cover: Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions. Proc. Natl. Acad. Sci. USA 2004;101:12753–12758.

Huang Y, Ji L, Huang Q, Vassylyev D, Chen X, Ma J-B. Structural insights into mechanisms of the small RNA methyltransferase HEN1. Nat. Cell Biol. 2009;461:823–827.

Li J, Yang Z, Yu B Liu J, Chen X. Methylation protects miRNAs and siRNAs from a 3′-end uridylation activity in Arabidopsis. Curr. Biol. 2005;15:1501–1507.

Guo Q, Liu, Q, ASmith N, Liang G, Wang MB. RNA silencing in plants: Mechanisms, technologies and applications in horticultural crops. Curr. Genom. 2016;17: 476–489.

Huntzinger E, Izaurralde E. Gene silencing by microRNAs: Contributions of translational repression and mRNA decay. Nat. Rev. Genet. 2011;12:99–110.

Pareek M, Yogindran S, Mukherjee SK, Rajam MV. Plant MicroRNAs: Biogenesis, Functions, and Applications. In Plant Biology and Biotechnology; Springer: New Delhi, India, 2015:639–661.

Mello CC, Conte D. Revealing the world of RNA interference. Nat. Cell Biol. 2004; 431:338–342.

Bernstein E, Caudy A, Hammond SM, Hannon GJ. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nat. Cell Biol. 2001;409:363–366.

Hamilton AJ, Baulcombe DC. A species of small antisense RNA in posttranscriptional gene silencing in plants. Science. 1999; 286:950–952.

Saurabh S, Vidyarthi AS, Prasad D. RNA interference: Concept to reality in crop improvement. Planta 2014;239:543–564.

Aoki K, Moriguchi H, Yoshioka T, Okawa K, Tabara H. In vitro analyses of the production and activity of secondary small interfering RNAs in C. elegans. EMBO J. 2007;26:5007–5019.

Halic M, Moazed D. Dicer-Independent Primal RNAs Trigger RNAi and Heterochromatin Formation. Cell 2010;140:504–516.

Lee H-C, Li L, Gu W, Xue Z, Crosthwaite SK, Pertsemlidis A, Lewis Z, Freita M, Selker EU, Mello CC, et al. Diverse Pathways Generate MicroRNA-like RNAs and Dicer-Independent Small Interfering RNAs in Fungi. Mol. Cell 2010;38:803–814.

Ye R, Chen Z, Lian B, Rowley J, Xia N, Chai J, Li Y, He X-J, Wierzbicki AT, Qi Y. A Dicer-Independent Route for Biogenesis of siRNAs that Direct DNA Methylation in Arabidopsis. Mol. Cell. 2016;61:222–235.

Tester M, Langridge P. Breeding Technologies to Increase Crop Production in a Changing World. Science. 2010;327: 818–822.

Sharma VK, Basu S, Chakraborty S. RNAi mediated broad-spectrum transgenic resistance in Nicotiana benthamiana to chilli-infecting begomoviruses. Plant Cell Rep. 2015;34:1389–1399.

Rupp J, Cruz LF, Trick H, Fellers JP. RNAi-Mediated, stable resistance to Triticum mosaic virus in Wheat. Crop Sci. 2016;56:1602–1610.

Ahmed MMS, Bian S, Wang M, Zhao J, Zhang B, Liu Q, Zhang C, Tang S, Gu M, Yu H. RNAi-mediated resistance to rice black-streaked dwarf virus in transgenic rice. Transgenic Res. 2017;26: 197–207.

Hameed A, Tahir MN, Asad S, Bilal R, Van Eck J, Jander G, Mansoor S. RNAi-Mediated Simultaneous Resistance Against Three RNA Viruses in Potato. Mol. Biotechnol. 2017;59:73–83.

Yang X, Niu L, Zhang W, Yang J, Xing G, He H, Guo D, Du Q, Qian X, Yao Y, et al. RNAi-mediated SMV P3 cistron silencing confers significantly enhanced resistance to multiple Potyvirus strains and isolates in transgenic soybean. Plant Cell Rep. 2018; 37:103–114.

Kumari A, Hada A, Subramanyam K, Theboral J, Misra S, Ganapathi A, Malathi VG. RNAi-mediated resistance to yellow mosaic viruses in soybean targeting coat protein gene. Acta Physiol. Plant. 2018; 40:1–12.

Senthilraja C, Reddy MG, Rajeswaran J, Kokiladevi E, Velazhahan R. RNA interference-mediated resistance to Tobacco streak virus in transgenic peanut. Australas. Plant Pathol. 2018;47: 227–230.

Malathi P, Muzammil SA, Krishnaveni D, Balachandran S, Mangrauthia SK. Coat protein 3 of Rice tungro spherical virus is the key target gene for development of RNAi mediated tungro disease resistance in rice. Agri Gene. 2019;12:100084.

Gao L, Luo J, Ding X, Wang T, Hu T, Song P, Zhai R, Zhang H, Zhang K, Li K, et al. Soybean RNA interference lines silenced for eIF4E show broad potyvirus resistance. Mol. Plant Pathol. 2019;21; 303–317.

Tzean Y, Chang H-H, Tu T-C, Hou BH, Chen H-M, Chiu Y-S, Chou W-Y, Chang L, Yeh H-H. Engineering Plant Resistance to Tomato Yellow Leaf Curl Thailand Virus Using a Phloem-Specific Promoter Expressing Hairpin RNA. Mol. Plant-Microbe Interact. 2020;33:87–97.

Escobar MA, Civerolo EL, Summerfelt KR, Dandekar AM. RNAi-mediated oncogene silencing confers resistance to crown gall tumorigenesis. Proc. Natl. Acad. Sci. USA. 2001;98:13437–13442.

Katiyar-Agarwal S, Morgan R, Dahlbeck D, Borsani O, Villegas A, Zhu J-K, Staskawicz BJ, Jin H. A pathogen-inducible endogenous siRNA in plant immunity. Proc. Natl. Acad. Sci. USA. 2006;103:18002–18007.

Enrique R, Siciliano F, Favaro MA, Gerhardt N, Roeschlin R, Rigano L, Castagnaro A, Vojnov A, Sendin L, Marano MR. Novel demonstration of RNAi in citrus reveals importance of citrus callose synthase in defence against Xanthomonas citri subsp. citri. Plant Biotechnol. J. 2011; 9:394–407.

Sanju S, Siddappa S Thakur A, Shukla PK, Srivastava N, Pattanaya D, Sharma SK, Singh BP. Host-mediated gene silencing of a single effector gene from the potato pathogen Phytophthora infestans imparts partial resistance to late blight disease. Funct. Integr. Genom. 2015;15: 697–706.

Cheng W, Song X-S, Xiao-Li Q, Cao L-H, Sun K, Qiu X-L, Xu Y-B, Yang P, Huang T, Zhang J-B, et al. Host-induced gene silencing of an essential chitin synthase gene confers durable resistance to Fusarium head blight and seedling blight in wheat. Plant Biotechnol. J. 2015;13: 1335–1345.

Ghag SB, Shekhawat UKS, Ganapathi TR. Host-induced post-transcriptional hairpin RNA-mediated gene silencing of vital fungal genes confers efficient resistance against Fusarium wilt in banana. Plant Biotechnol. J. 2014;12:541–553.

Andrade CM, Tinoco MLP, Rieth AF, Maia FCO, Aragão FJL. Host-induced gene silencing in the necrotrophic fungal pathogen Sclerotinia sclerotiorum. Plant Pathol. 2016;65:626–632.

Bharti P, Jyoti P, Kapoor P, Sharma V, Shanmugam V, Yadav SK. Host-induced silencing of pathogenicity genes enhances resistance to Fusarium oxysporum wilt in tomato. Mol. Biotechnol. 2017;59:343–352.

Zhu L. Zhu J, Liu Z, Wang Z, Zhou C, Wang H. Host-induced gene silencing of rice blast fungus Magnaporthe oryzae pathogenicity genes mediated by the brome mosaic virus. Genes. 2017; 8:241.

Tiwari IM, Jesuraj A, Kamboj R, Devanna BN, Botella J, Sharma TR. Host Delivered RNAi, an efficient approach to increase rice resistance to sheath blight pathogen (Rhizoctonia solani). Sci. Rep.2017;7:1–14.

Majumdar R, Rajasekaran K, Sickler C, Lebar M, Musungu BM, Fakhoury AM, Payne GA, Geisler M, Carter-Wientjes C, Wei Q, et al. The pathogenesis-related maize seed (PRms) gene plays a role in resistance to Aspergillus flavus infection and aflatoxin contamination. Front. Plant Sci. 2017;8:1–11.

Pareek M, Rajam MV. RNAi-mediated silencing of MAP kinase signalling genes (Fmk1, Hog1, and Pbs2) in Fusarium oxysporum reduces pathogenesis on tomato plants. Fungal Biol. 2017;121:775–784.

Gilbert MK, Majumdar R, Rajasekaran K, Chen Z-Y; Wei Q; Sickler CM, Lebar MD; Cary JW, Frame BR, Wang K. RNA interference based silencing of the alpha-amylase (amy1) gene in Aspergillus flavus decreases fungal growth and aflatoxin production in maize kernels. Planta 2018;247:1465–1473.

Yoshioka M, Adachi A, Sato Y, Doke N, Kondo T, Yoshioka H. RNAi of the sesquiterpene cyclase gene for phytoalexin production impairs pre- and post-invasive resistance to potato blight pathogens. Mol. Plant Pathol. 2019;20: 907–922.

Wang L, Wang H, He S, Meng F, Zhang C, Fan S, Wu J, Zhang S, Xu P. GmSnRK1. 1, a sucrose nonfermenting-1 (SNF1)-Related Protein Kinase, Promotes Soybean Resistance to Phytophthora sojae. Front. Plant Sci. 2019;10:996.

Singh N, Mukherjee SK, Rajam MV. Silencing of the ornithine decarboxylase gene of Fusarium oxysporum f. sp. lycopersici by host-induced RNAi confers resistance to Fusarium wilt in tomato. Plant Mol. Biol. Rep. 2020;38:419–429.

Mamta Reddy, KRK, Rajam MV. Targeting chitinase gene of Helicoverpa armigera by host-induced RNA interference confers insect resistance in tobacco and tomato. Plant Mol. Biol. 2016;90:281–292.

Malik HJ, Raza A, Amin I, Scheffler JA, Scheffler BE, Brown JK, Mansoor S. RNAi-mediated mortality of the whitefly through transgenic expression of double- stranded RNA homologous to acetylcholinesterase and ecdysone receptor in tobacco plants. Sci. Rep. 2016, 6, 1–11.

Ibrahim AB, Monteiro TR, Cabral G, Aragão FJL. RNAi-mediated resistance to whitefly (Bemisia tabaci) in genetically engineered lettuce (Lactuca sativa). Transgenic Res. 2017;26:613–624.

Bhatia, V.; Bhattacharya, R. Host-mediated RNA interference targeting a cuticular protein gene impaired fecundity in the green peach aphid Myzus persicae. Pest Manag. Sci. 2018;74:2059–2068.

Shin YH, Lee SH, Park, Y-D. Development of mite (Tetranychus urticae)-resistant transgenic Chinese cabbage using plant-mediated RNA interference. Hortic. Environ. Biotechnol. 2020;61:305–315.

Dutta TK, Papolu PK, Banakar P, Choudhary D, Sirohi A, Rao U. Tomato transgenic plants expressing hairpin construct of a nematode protease gene conferred enhanced resistance to root-knot nematodes. Front. Microbiol. 2015, 6, 260.

Li Ym, Wang K, Lu Q, Du J, Wang Z, Wang D, Sun B, Li H. Transgenic Nicotiana benthamiana plants expressing a hairpin RNAi construct of a nematode Rs-cps gene exhibit enhanced resistance to Radopholus similis. Sci. Rep. 2017;7:1–11.

Chukwurah PN, Poku SA, Yokoyama A, Fukuda H, Shishido M, Nakamura I. Expression of Meloidogyne incognita PolA1 hairpin RNA reduced nematode multiplication in transgenic tomato. Plant Biotechnol. Rep. 2019;13: 591–601.

Hu Y, You J, Li C, Pan F, Wang C. The Heterodera glycines effector Hg16B09 is required for nematode parasitism and suppresses plant defense response. Plant Sci. 2019;289:110271.

Tian B, Li J, Vodkin LO, Todd TC, Finer JJ, Trick HN. Host-derived gene silencing of parasite fitness genes improves resistance to soybean cyst nematodes in stable transgenic soybean. Theor. Appl. Genet. 2019;132:2651–2662.

Joshi I, Kumar A, Kohli D, Singh AK, Sirohi A, Subramaniam K, Chaudhury A, Jain PK. Conferring root-knot nematode resistance via host-delivered RNAi-mediated silencing of four Mi-msp genes in Arabidopsis. Plant Sci. 2020, 298, 110592.

Shi Y, Liu, P, Xia Y, Wei P, Li W, Zhang W, Chen, X, Cao, P, Xu Y, Jin L, et al. Downregulation of the lycopene e-cyclase gene confers tolerance to salt and drought stress in Nicotiana tabacum. Acta Physiol. Plant 2015;37:1–15.

Rajput M, Choudhary K, Kumar M, Vivekanand V, Chawade A, Ortiz R, Pareek N. RNA interference and CRISPR/Cas gene editing for crop improvement: Paradigm shift towards sustainable agriculture. Plants. 2021;10 (9):1914.