Register      Login
Functional Plant Biology Functional Plant Biology Society
Plant function and evolutionary biology
REVIEW

Recent advances in genome editing strategies for balancing growth and defence in sugarcane (Saccharum officinarum)

Maira Tanveer https://orcid.org/0009-0007-6340-3332 A , Zain Ul Abidin A , Hussam F. Najeeb Alawadi B , Ahmad Naeem Shahzad C , Athar Mahmood https://orcid.org/0000-0003-4473-1668 D * , Bilal Ahmad Khan E , Sameer Qari F and Hesham Farouk Oraby https://orcid.org/0000-0003-4675-3297 G H *
+ Author Affiliations
- Author Affiliations

A Department of Botany, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan. Email: mairatanveeruaf@gmail.com, zainmalik8045@gmail.com

B College of Agriculture, Al-Qadisiyah University, Al-Qadisiyah, Iraq. Email: hussam.alawadi@qu.edu.iq

C Department of Agronomy, Bahauddin Zakarriya University, Multan 60650, Pakistan. Email: anaeems@gmail.com

D Department of Agronomy, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan.

E Department of Agronomy, College of Agriculture, University of Sargodha, Sargodha, Pakistan. Email: bilalahmadkhan678@gmail.com

F Department of Biology, Al-Jumum University College, Umm Al-Qura University, Makkah 21955, Saudi Arabia. Email: shqari@uqu.edu.sa

G Deanship of Scientific Research, Umm Al-Qura University, Makkah 21955, Saudi Arabia.

H Department of Crop Science, Faculty of Agriculture, Zagazig University, Zagazig 44519, Egypt.


Handling Editor: Rana Munns

Functional Plant Biology 51, FP24036 https://doi.org/10.1071/FP24036
Submitted: 7 February 2024  Accepted: 14 April 2024  Published: 2 May 2024

© 2024 The Author(s) (or their employer(s)). Published by CSIRO Publishing

Abstract

Sugarcane (Saccharum officinarum) has gained more attention worldwide in recent decades because of its importance as a bioenergy resource and in producing table sugar. However, the production capabilities of conventional varieties are being challenged by the changing climates, which struggle to meet the escalating demands of the growing global population. Genome editing has emerged as a pivotal field that offers groundbreaking solutions in agriculture and beyond. It includes inserting, removing or replacing DNA in an organism’s genome. Various approaches are employed to enhance crop yields and resilience in harsh climates. These techniques include zinc finger nuclease (ZFN), transcription activator-like effector nuclease (TALEN) and clustered regularly interspaced short palindromic repeats/associated protein (CRISPR/Cas). Among these, CRISPR/Cas is one of the most promising and rapidly advancing fields. With the help of these techniques, several crops like rice (Oryza sativa), tomato (Solanum lycopersicum), maize (Zea mays), barley (Hordeum vulgare) and sugarcane have been improved to be resistant to viral diseases. This review describes recent advances in genome editing with a particular focus on sugarcane and focuses on the advantages and limitations of these approaches while also considering the regulatory and ethical implications across different countries. It also offers insights into future prospects and the application of these approaches in agriculture.

Keywords: allelic variants, CRISPR, genomics, NHEJ, sugarcane, TALEN, transgene, zinc finger nuclease.

References

Ahmad M (2023) Plant breeding advancements with “CRISPR-Cas” genome editing technologies will assist future food security. Frontiers in Plant Science 14, 1133036.
| Crossref | Google Scholar | PubMed |

Ahmar S, Gill RA, Jung K-H, Faheem A, Qasim MU, Mubeen M, Zhou W (2020a) Conventional and molecular techniques from simple breeding to speed breeding in crop plants: recent advances and future outlook. International Journal of Molecular Sciences 21(7), 2590.
| Crossref | Google Scholar | PubMed |

Ahmar S, Saeed S, Khan MHU, Ullah Khan S, Mora-Poblete F, Kamran M, Faheem A, Maqsood A, Rauf M, Saleem S, Hong W-J, Jung K-H (2020b) A revolution toward gene-editing technology and its application to crop improvement. International Journal of Molecular Sciences 21(16), 5665.
| Crossref | Google Scholar | PubMed |

Ali A, Khan M, Sharif R, Mujtaba M, Gao S-J (2019) Sugarcane omics: an update on the current status of research and crop improvement. Plants 8(9), 344.
| Crossref | Google Scholar | PubMed |

Anderson JT, Rogers JM, Barrera LA, Bulyk ML (2020) Context and number of noncanonical repeat variable diresidues impede the design of TALE proteins with improved DNA targeting. Protein Science 29(2), 606-616.
| Crossref | Google Scholar | PubMed |

Ansari WA, Chandanshive SU, Bhatt V, Nadaf AB, Vats S, Katara JL, Sonah H, Deshmukh R (2020) Genome editing in cereals: approaches, applications and challenges. International Journal of Molecular Sciences 21(11), 4040.
| Crossref | Google Scholar | PubMed |

Anwar A, Kim J-K (2020) Transgenic breeding approaches for improving abiotic stress tolerance: recent progress and future perspectives. International Journal of Molecular Sciences 21(8), 2695.
| Crossref | Google Scholar | PubMed |

Anzalone AV, Koblan LW, Liu DR (2020) Genome editing with CRISPR–Cas nucleases, base editors, transposases and prime editors. Nature Biotechnology 38(7), 824-844.
| Crossref | Google Scholar | PubMed |

Arora R, Malik G (2021) Microbe-plant-insect interactions: a comparative dissection of interactome. In ‘Plant-pest interactions: from molecular mechanisms to chemical ecology: chemical ecology’. (Eds IK Singh, A Singh) pp. 365–398. (Springer: Singapore)

Ashwin Narayan J, Mohan C, Esterling M, Yau Y-Y (2020) Development of transgenic sugarcane for insect resistance. In ‘Climate change, photosynthesis and advanced biofuels: the role of biotechnology in the production of value-added plant bio-products’. (Eds A Kumar, Y-Y Yau, S Ogita, R Scheibe) pp. 389–405. (Springer: Singapore)

Babu KH, Devarumath RM, Thorat AS, Nalavade VM, Saindane M, Appunu C, Suprasanna P (2021) Sugarcane transgenics: developments and opportunities. In ‘Genetically modified crops: current status, prospects and challenges, Vol. 1’. (Eds PB Kavi Kishor, MV Rajam, T Pullaiah) pp. 241–265. (Springer: Singapore)

Becker S, Boch J (2021) TALE and TALEN genome editing technologies. Gene and Genome Editing 2, 100007.
| Crossref | Google Scholar |

Bhambhani S, Kondhare KR, Giri AP (2022) Advanced genome editing strategies for manipulation of plant specialized metabolites pertaining to biofortification. Phytochemistry Reviews 21, 81-99.
| Crossref | Google Scholar |

Bhardwaj A, Nain V (2021) TALENs – an indispensable tool in the era of CRISPR: a mini review. Journal of Genetic Engineering and Biotechnology 19(1), 125.
| Crossref | Google Scholar | PubMed |

Bilichak A, Gaudet D, Laurie J (2020) Emerging genome engineering tools in crop research and breeding. In ‘Cereal genomics: methods and protocols’. (Ed. LM Vaschetto) pp. 165–181. (Springer: New York, NY, USA)

Binyameen B, Khan Z, Khan SH, Ahmad A, Munawar N, Mubarik MS, Riaz H, Ali Z, Khan AA, Qusmani AT, Abd-Elsalam KA, Qari SH (2021) Using multiplexed CRISPR/Cas9 for suppression of cotton leaf curl virus. International Journal of Molecular Sciences 22(22), 12543.
| Crossref | Google Scholar | PubMed |

Boyle EA, Becker WR, Bai HB, Chen JS, Doudna JA, Greenleaf WJ (2021) Quantification of Cas9 binding and cleavage across diverse guide sequences maps landscapes of target engagement. Science Advances 7(8), eabe5496.
| Crossref | Google Scholar |

Budeguer F, Enrique R, Perera MF, Racedo J, Castagnaro AP, Noguera AS, Welin B (2021) Genetic transformation of sugarcane, current status and future prospects. Frontiers in Plant Science 12, 768609.
| Crossref | Google Scholar | PubMed |

Cantos C, Francisco P, Trijatmiko KR, Slamet-Loedin I, Chadha-Mohanty PK (2014) Identification of “safe harbor” loci in indica rice genome by harnessing the property of zinc-finger nucleases to induce DNA damage and repair. Frontiers in Plant Science 5, 302.
| Crossref | Google Scholar |

Cao Y, Zhou H, Zhou X, Li F (2020) Control of plant viruses by CRISPR/Cas system-mediated adaptive immunity. Frontiers in Microbiology 11, 593700.
| Crossref | Google Scholar | PubMed |

Chakraborty M, Munshi SK, Islam T, Shiddiky MJA (2022) Potential transcription factors for biotic stress tolerance in sugarcane. In ‘Transcription factors for biotic stress tolerance in plants’. (Eds SH Wani, V Nataraj, GP Singh) pp. 143–174. (Springer International Publishing: Cham, Switzerland)

Char SN, Unger-Wallace E, Frame B, Briggs S, Main M, Spalding MH, Vollbrecht E, Wang K, Yang B (2019) Development and utilization of genome editing tools in maize, sorghum and rice. PhD Thesis, Department of Agronomy, Iowa State University, Ames, IA, USA.

Chen K, Wang Y, Zhang R, Zhang H, Gao C (2019) CRISPR/Cas genome editing and precision plant breeding in agriculture. Annual Review of Plant Biology 70, 667-697.
| Crossref | Google Scholar | PubMed |

Chen J-H, Chen S-T, He N-Y, Wang Q-L, Zhao Y, Gao W, Guo F-Q (2020) Nuclear-encoded synthesis of the D1 subunit of photosystem II increases photosynthetic efficiency and crop yield. Nature Plants 6(5), 570-580.
| Crossref | Google Scholar | PubMed |

Chen Q, Zhang Y, Yin H (2021) Recent advances in chemical modifications of guide RNA, mRNA and donor template for CRISPR-mediated genome editing. Advanced Drug Delivery Reviews 168, 246-258.
| Crossref | Google Scholar | PubMed |

Cheng M-H, Huang H, Dien BS, Singh V (2019) The costs of sugar production from different feedstocks and processing technologies. Biofuels, Bioproducts and Biorefining 13(3), 723-739.
| Crossref | Google Scholar |

Chojnacka-Puchta L, Sawicka D (2020) CRISPR/Cas9 gene editing in a chicken model: current approaches and applications. Journal of Applied Genetics 61(2), 221-229.
| Crossref | Google Scholar | PubMed |

Corsi GI, Qu K, Alkan F, Pan X, Luo Y, Gorodkin J (2022) CRISPR/Cas9 gRNA activity depends on free energy changes and on the target PAM context. Nature Communications 13(1), 3006.
| Crossref | Google Scholar | PubMed |

Cursi DE, Castillo RO, Tarumoto Y, Umeda M, Tippayawat A, Ponragdee W, Racedo J, Perera MF, Hoffmann HP, Carneiro MS (2022) Origin, genetic diversity, conservation, and traditional and molecular breeding approaches in sugarcane. In ‘Cash crops: genetic diversity, erosion, conservation and utilization’. (Eds PM Priyadarshan, SM Jain) pp. 83–116. (Springer International Publishing: Cham, Switzerland)

Das R, Shelke RG, Rangan L, Mitra S (2018) Estimation of nuclear genome size and characterization of Ty1-copia like LTR retrotransposon in Mesua ferrea L. Journal of Plant Biochemistry and Biotechnology 27, 478-487.
| Crossref | Google Scholar |

Das D, Singha DL, Paswan RR, Chowdhury N, Sharma M, Reddy PS, Chikkaputtaiah C (2022) Recent advancements in CRISPR/Cas technology for accelerated crop improvement. Planta 255(5), 109.
| Crossref | Google Scholar | PubMed |

de Moraes Barbosa A, Rebes Zilliani R, Tiritan CS, Maia Souza G, de Almeida Silva M (2021) Energy conversion efficiency in sugarcane cultivars as a function of production environments in Brazil. Renewable and Sustainable Energy Reviews 150, 111500.
| Crossref | Google Scholar |

Deomano E, Jackson P, Wei X, Aitken K, Kota R, Pérez-Rodríguez P (2020) Genomic prediction of sugar content and cane yield in sugar cane clones in different stages of selection in a breeding program, with and without pedigree information. Molecular Breeding 40, 38.
| Crossref | Google Scholar |

Dessoky ES, Ismail RM, Elarabi NI, Abdelhadi AA, Abdallah NA (2021) Improvement of sugarcane for borer resistance using Agrobacterium mediated transformation of cry1Ac gene. GM Crops & Food 12(1), 47-56.
| Crossref | Google Scholar | PubMed |

Dinesh Babu KS, Janakiraman V, Palaniswamy H, Kasirajan L, Gomathi R, Ramkumar TR (2022) A short review on sugarcane: its domestication, molecular manipulations and future perspectives. Genetic Resources and Crop Evolution 69(8), 2623-2643.
| Crossref | Google Scholar | PubMed |

Duensing N, Sprink T, Parrott WA, Fedorova M, Lema MA, Wolt JD, Bartsch D (2018) Novel features and considerations for ERA and regulation of crops produced by genome editing. Frontiers in Bioengineering and Biotechnology 6, 79.
| Crossref | Google Scholar | PubMed |

Edmondson C, Zhou Q, Liu X (2021) Analysis of conventional and alternative CRISPR/Cas9 genome editing to enhance a single-base pair knock-in mutation. BMC Biotechnology 21, 45.
| Crossref | Google Scholar |

Eid A, Mohan C, Sanchez S, Wang D, Altpeter F (2021) Multiallelic, targeted mutagenesis of magnesium chelatase with CRISPR/Cas9 provides a rapidly scorable phenotype in highly polyploid sugarcane. Frontiers in Genome Editing 3, 654996.
| Crossref | Google Scholar | PubMed |

Franco-Duran J, Crossa J, Chen J, Hearne SJ (2019) The impact of sample selection strategies on genetic diversity and representativeness in germplasm bank collections. BMC Plant Biology 19(1), 520.
| Crossref | Google Scholar |

Fukase E, Martin W (2020) Economic growth, convergence, and world food demand and supply. World Development 132, 104954.
| Crossref | Google Scholar |

Gabol WA, Ahmed A, Bux H, Ahmed K, Mahar A, Laghari S (2012) Genetically modified organisms (GMOs) in Pakistan. African Journal of Biotechnology 11(12), 2807-2813.
| Crossref | Google Scholar |

Garcia Tavares R, Lakshmanan P, Peiter E, O’Connell A, Caldana C, Vicentini R, Soares JS, Menossi M (2018) ScGAI is a key regulator of culm development in sugarcane. Journal of Experimental Botany 69(16), 3823-3837.
| Crossref | Google Scholar | PubMed |

Guha TK, Wai A, Hausner G (2017) Programmable genome editing tools and their regulation for efficient genome engineering. Computational and Structural Biotechnology Journal 15, 146-160.
| Crossref | Google Scholar | PubMed |

Gupta S, Kumar A, Patel R, Kumar V (2021) Genetically modified crop regulations: scope and opportunity using the CRISPR-Cas9 genome editing approach. Molecular Biology Reports 48(5), 4851-4863.
| Crossref | Google Scholar | PubMed |

Haq AU, Lone ML, Farooq S, Parveen S, Altaf F, Tahir I (2022) The use of genomics and precise breeding to genetically improve the traits of agriculturally important organisms. In ‘Sustainable agriculture: technical progressions and transitions’. (Ed. SA Bandh) pp. 173–187. (Springer International Publishing: Cham, Switzerland)

Haun W, Coffman A, Clasen BM, Demorest ZL, Lowy A, Ray E, Retterath A, Stoddard T, Juillerat A, Cedrone F, Mathis L, Voytas DF, Zhang F (2014) Improved soybean oil quality by targeted mutagenesis of the fatty acid desaturase 2 gene family. Plant Biotechnology Journal 12(7), 934-940.
| Crossref | Google Scholar | PubMed |

Heddleson RA, Kodali DR (2022) Chapter 7 – High-oleic oils: future developments and technologies. In ‘High oleic oils’. (Ed. FJ Flider) pp. 143–188. (AOCS Press)

Holkar SK, Balasubramaniam P, Kumar A, Kadirvel N, Shingote PR, Chhabra ML, Kumar S, Kumar P, Viswanathan R, Jain RK, Pathak AD (2020) Present status and future management strategies for Sugarcane yellow leaf virus: a major constraint to the global sugarcane production. The Plant Pathology Journal 36(6), 536-557.
| Crossref | Google Scholar | PubMed |

Huang J, Khan MT, Perecin D, Coelho ST, Zhang M (2020) Sugarcane for bioethanol production: potential of bagasse in Chinese perspective. Renewable and Sustainable Energy Reviews 133, 110296.
| Crossref | Google Scholar |

Hussain N (2023) Predicting forecast of sugarcane production in Pakistan. Sugar Tech 25(3), 681-690.
| Crossref | Google Scholar |

Iqbal A, Qiang D, Zhun W, Xiangru W, Huiping G, Hengheng Z, Nianchang P, Xiling Z, Meizhen S (2020) Growth and nitrogen metabolism are associated with nitrogen-use efficiency in cotton genotypes. Plant Physiology and Biochemistry 149, 61-74.
| Crossref | Google Scholar | PubMed |

Iqbal A, Khan RS, Khan MA, Gul K, Jalil F, Shah DA, Rahman H, Ahmed T (2021) Genetic engineering approaches for enhanced insect pest resistance in sugarcane. Molecular Biotechnology 63(7), 557-568.
| Crossref | Google Scholar | PubMed |

Islam MS, McCord P, Read QD, Qin L, Lipka AE, Sood S, Todd J, Olatoye M (2022) Accuracy of genomic prediction of yield and sugar traits in Saccharum spp. hybrids. Agriculture 12(9), 1436.
| Crossref | Google Scholar |

Jogam P, Sandhya D, Alok A, Peddaboina V, Singh SP, Abbagani S, Zhang B, Allini VR (2023) Editing of TOM1 gene in tobacco using CRISPR/Cas9 confers resistance to Tobacco mosaic virus. Molecular Biology Reports 50(6), 5165-5176.
| Crossref | Google Scholar | PubMed |

Jung JH, Altpeter F (2016) TALEN mediated targeted mutagenesis of the caffeic acid O-methyltransferase in highly polyploid sugarcane improves cell wall composition for production of bioethanol. Plant Molecular Biology 92, 131-142.
| Crossref | Google Scholar | PubMed |

Karlson CKS, Mohd-Noor SN, Nolte N, Tan BC (2021) CRISPR/dCas9-based systems: mechanisms and applications in plant sciences. Plants 10(10), 2055.
| Crossref | Google Scholar | PubMed |

Khan MS (2023) Introductory Chapter: integrative technologies for sustainable plant improvement. In ‘Tropical plant species and technological interventions for improvement’. (Ed. K Muhammad Sarwar) pp. 1–11. (IntechOpen: Rijeka, Croatia)

Khan MT, Khan IA, Yasmeen S (2019) Genetically modified sugarcane for biofuels production: status and perspectives of conventional transgenic approaches, RNA interference, and genome editing for improving sugarcane for biofuels. In ‘Sugarcane biofuels: status, potential, and prospects of the sweet crop to fuel the world’. (Eds MT Khan, IA Khan) pp. 67–96. (Springer International Publishing: Cham, Switzerland)

Khan ZA, Kumar R, Dasgupta I (2022) CRISPR/Cas-mediated resistance against viruses in plants. International Journal of Molecular Sciences 23(4), 2303.
| Crossref | Google Scholar | PubMed |

Khojasteh M, Shah SMA, Haq F, Xu X, Taghavi SM, Osdaghi E, Chen G (2020) Transcription activator-like effectors diversity in Iranian strains of Xanthomonas translucens. Phytopathology 110(4), 758-767.
| Crossref | Google Scholar | PubMed |

Koerniati S, Sukmadjaja D, Samudra IM (2020) C synthetic gene of CryIAb-CryIAc fusion to generate resistant sugarcane to shoot or stem borer. IOP Conference Series: Earth and Environmental Science 418(1), 012069.
| Crossref | Google Scholar |

Kumar K, Gambhir G, Dass A, Tripathi AK, Singh A, Jha AK, Yadava P, Choudhary M, Rakshit S (2020) Genetically modified crops: current status and future prospects. Planta 251, 91.
| Crossref | Google Scholar |

Kurita T, Iwai M, Moroi K, Okazaki K, Nomura S, Saito F, Maeda S, Takami A, Sakamoto A, Ohta H, Sakuma T, Yamamoto T (2022) Genome editing with removable TALEN vectors harboring a yeast centromere and autonomous replication sequence in oleaginous microalga. Scientific Reports 12(1), 2480.
| Crossref | Google Scholar | PubMed |

Lassoued R, Macall DM, Smyth SJ, Phillips PWB, Hesseln H (2019) Risk and safety considerations of genome edited crops: expert opinion. Current Research in Biotechnology 1, 11-21.
| Crossref | Google Scholar |

Lebedev VG, Popova AA, Shestibratov KA (2021) Genetic engineering and genome editing for improving nitrogen use efficiency in plants. Cells 10(12), 3303.
| Crossref | Google Scholar | PubMed |

Li J, Kong D, Ke Y, Zeng W, Miki D (2024) Application of multiple sgRNAs boosts efficiency of CRISPR/Cas9-mediated gene targeting in Arabidopsis. BMC Biology 22(1), 6.
| Crossref | Google Scholar | PubMed |

Liang Z, Zhang K, Chen K, Gao C (2014) Targeted mutagenesis in Zea mays using TALENs and the CRISPR/Cas system. Journal of Genetics and Genomics 41(2), 63-68.
| Crossref | Google Scholar | PubMed |

Liu S, An Y, Tong W, Qin X, Samarina L, Guo R, Xia X, Wei C (2019) Characterization of genome-wide genetic variations between two varieties of tea plant (Camellia sinensis) and development of InDel markers for genetic research. BMC Genomics 20(1), 935.
| Crossref | Google Scholar |

Lor VS, Starker CG, Voytas DF, Weiss D, Olszewski NE (2014) Targeted mutagenesis of the tomato PROCERA gene using transcription activator-like effector nucleases. Plant Physiology 166(3), 1288-1291.
| Crossref | Google Scholar | PubMed |

Mahadevaiah C, Appunu C, Aitken K, Suresha GS, Vignesh P, Mahadeva Swamy HK, Valarmathi R, Hemaprabha G, Alagarasan G, Ram B (2021) Genomic selection in sugarcane: current status and future prospects. Frontiers in Plant Science 12, 708233.
| Crossref | Google Scholar | PubMed |

Mahas A, Mahfouz M (2018) Engineering virus resistance via CRISPR–Cas systems. Current Opinion in Virology 32, 1-8.
| Crossref | Google Scholar | PubMed |

Mbambalala N, Panda SK, van der Vyver C (2021) Overexpression of AtBBX29 improves drought tolerance by maintaining photosynthesis and enhancing the antioxidant and osmolyte capacity of sugarcane plants. Plant Molecular Biology Reporter 39, 419-433.
| Crossref | Google Scholar |

Meena MR, Appunu C, Arun Kumar R, Manimekalai R, Vasantha S, Krishnappa G, Kumar R, Pandey SK, Hemaprabha G (2022) Recent advances in sugarcane genomics, physiology, and phenomics for superior agronomic traits. Frontiers in Genetics 13, 854936.
| Crossref | Google Scholar | PubMed |

Mirajkar SJ, Devarumath RM, Nikam AA, Sushir KV, Babu H, Suprasanna P (2019) Sugarcane (Saccharum spp.): breeding and genomics. In ‘Advances in plant breeding strategies: industrial and food crops, Vol. 6’. (Eds JM Al-Khayri, SM Jain, DV Johnson) pp. 363–406. (Springer International Publishing: Cham, Switzerland)

Mohan C (2016) Genome editing in sugarcane: challenges ahead. Frontiers in Plant Science 7, 1542.
| Crossref | Google Scholar | PubMed |

Mohan C, Easterling M, Yau Y-Y (2022) Gene editing technologies for sugarcane improvement: opportunities and limitations. Sugar Tech 24, 369-385.
| Crossref | Google Scholar | PubMed |

Munawar N, Ahsan K, Ahmad A (2024) Chapter 18 – CRISPR-edited plants’ social, ethical, policy, and governance issues. In ‘Global regulatory outlook for CRISPRized plants’. (Eds KA Abd-Elsalam, A Ahmad) pp. 367–396. (Academic Press)

Namo FM, Belachew GT (2021) Genome editing technologies for crop improvement: current status and future prospective. Plant Cell Biotechnology and Molecular Biology 22, 1-19.
| Google Scholar |

Nidhi S, Anand U, Oleksak P, Tripathi P, Lal JA, Thomas G, Kuca K, Tripathi V (2021) Novel CRISPR–Cas systems: an updated review of the current achievements, applications, and future research perspectives. International Journal of Molecular Sciences 22(7), 3327.
| Crossref | Google Scholar | PubMed |

Oliveira GK, Soares NR, Costa ZP, Almeida CB, Machado RM, Mesquita AT, Carneiro MS, Forni-Martins ER, Mondin M, Vieira MLC (2023) Meiotic abnormalities in sugarcane (Saccharum spp.) and parental species: evidence for peri- and paracentric inversions. Annals of Applied Biology 183(3), 271-286.
| Crossref | Google Scholar |

Olusola LO, Oluwadurotimi SA, Margaret IO, Onyemaechi HO, Oluwakemi B, Olubunmi MA, Ayodele AS, Jacob OP, Olawole OO (2021) Impact and management of diseases of Solanum tuberosum. In ‘Solanum tuberosum: a promising crop for starvation problem’. (Eds Y Mustafa, O Yasin) pp. 1–19. (IntechOpen: Rijeka, Croatia)

Oz MT, Altpeter A, Karan R, Merotto A, Altpeter F (2021) CRISPR/Cas9-mediated multi-allelic gene targeting in sugarcane confers herbicide tolerance. Frontiers in Genome Editing 3, 673566.
| Crossref | Google Scholar | PubMed |

Parvaiz A, Mustafa G, Khan MS, Ali MA (2021) Over-expression of endogenous SUGARWIN genes exalted tolerance against Colletotrichum infection in sugarcane. Plants 10(5), 869.
| Crossref | Google Scholar | PubMed |

Parvaiz A, Joyia FA, Saeed M, Azwar M, Khan MS, Mustafa G (2022) Defense-related proteins in sugarcane and their role in disease resistance: molecular advancements and beyond. In ‘Agro-industrial perspectives on sugarcane production under environmental stress’. (Eds KK Verma, X-P Song, VD Rajput, S Solomon, Y-R Li, GP Rao) pp. 171–192. (Springer Nature: Singapore)

Petersen B (2017) Basics of genome editing technology and its application in livestock species. Reproduction in Domestic Animals 52, 4-13.
| Crossref | Google Scholar | PubMed |

Platani M, Sokefun O, Bassil E, Apidianakis Y (2023) Genetic engineering and genome editing in plants, animals and humans: facts and myths. Gene 856, 147141.
| Crossref | Google Scholar | PubMed |

Putra LK, Kristini A, Jati WW (2023) Viral diseases of sugarcane in Indonesia: occurrence notes, pathogenic characteristics and management strategies. AIP Conference Proceedings 2583(1), 020038.
| Crossref | Google Scholar |

Raina A, Sahu PK, Laskar RA, Rajora N, Sao R, Khan S, Ganai RA (2021) Mechanisms of genome maintenance in plants: playing it safe with breaks and bumps. Frontiers in Genetics 12, 675686.
| Crossref | Google Scholar | PubMed |

Rajput R, Naik J, Misra P, Trivedi PK, Pandey A (2023) Gene pyramiding in transgenic plant development: approaches and challenges. Journal of Plant Growth Regulation 42(10), 6038-6056.
| Crossref | Google Scholar |

Rana S, Aggarwal PR, Shukla V, Giri U, Verma S, Muthamilarasan M (2022) Genome editing and designer crops for the future. In ‘Plant gene silencing: methods and protocols’. (Eds KS Mysore, M Senthil-Kumar) pp. 37–69. (Springer: New York, NY, USA)

Rao GP, Alvarez E, Yadav A (2018) Phytoplasma diseases of industrial crops. In ‘Phytoplasmas: plant pathogenic bacteria – I: characterisation and epidemiology of phytoplasma – associated diseases’. (Eds GP Rao, A Bertaccini, N Fiore, LW Liefting) pp. 91–121. (Springer: Singapore)

Rasheed A, Gill RA, Hassan MU, Mahmood A, Qari S, Zaman QU, Ilyas M, Aamer M, Batool M, Li H, Wu Z (2021) A critical review: recent advancements in the use of CRISPR/Cas9 technology to enhance crops and alleviate global food crises. Current Issues in Molecular Biology 43(3), 1950-1976.
| Crossref | Google Scholar | PubMed |

Raza G, Ali K, Ashraf MY, Mansoor S, Javid M, Asad S (2016) Overexpression of an H+-PPase gene from Arabidopsis in sugarcane improvesdrought tolerance, plant growth, and photosynthetic responses. Turkish Journal of Biology 40(1), 109-119.
| Crossref | Google Scholar |

Razzaq MK, Aleem M, Mansoor S, Khan MA, Rauf S, Iqbal S, Siddique KHM (2021) Omics and CRISPR-Cas9 approaches for molecular insight, functional gene analysis, and stress tolerance development in crops. International Journal of Molecular Sciences 22(3), 1292.
| Crossref | Google Scholar | PubMed |

Riaz A, Karamat U, Tabusam J, Manan A, Buttar SU, Shafqat K (2018) Benefits of genetically modified crops, Biosafety concerns and related risks; a South Asian perspective. Nature and Science 16(9), 87-93.
| Crossref | Google Scholar |

Ricroch A (2019) Global developments of genome editing in agriculture. Transgenic Research 28, 45-52.
| Crossref | Google Scholar | PubMed |

Rivero RM, Mittler R, Blumwald E, Zandalinas SI (2022) Developing climate-resilient crops: improving plant tolerance to stress combination. The Plant Journal 109(2), 373-389.
| Crossref | Google Scholar | PubMed |

Romay G, Bragard C (2017) Antiviral defenses in plants through genome editing. Frontiers in Microbiology 8, 47.
| Crossref | Google Scholar | PubMed |

Rout GR, Swain R, Sahoo DP (2023) Journey of genetically modified crops: status and prospects. Magna Scientia Advanced Research and Reviews 7, 103-128.
| Crossref | Google Scholar |

Rozas P, Kessi-Pérez EI, Martínez C (2022) Genetically modified organisms: adapting regulatory frameworks for evolving genome editing technologies. Biological Research 55, 31.
| Crossref | Google Scholar |

Saini P, Saini P, Kaur JJ, Francies RM, Gani M, Rajendra AA, Negi N, Jagtap A, Kadam A, Singh C, Chauhan SS (2020) Molecular approaches for harvesting natural diversity for crop improvement. In ‘Rediscovery of genetic and genomic resources for future food security’. (Eds RK Salgotra, SM Zargar) pp. 67–169. (Springer: Singapore)

Salava H, Thula S, Mohan V, Kumar R, Maghuly F (2021) Application of genome editing in tomato breeding: mechanisms, advances, and prospects. International Journal of Molecular Sciences 22(2), 682.
| Crossref | Google Scholar | PubMed |

Sanagala R, Moola AK, Bollipo Diana RK (2017) A review on advanced methods in plant gene targeting. Journal of Genetic Engineering and Biotechnology 15(2), 317-321.
| Crossref | Google Scholar | PubMed |

Sanches GM, Bordonal RdO, Magalhães PSG, Otto R, Chagas MF, Cardoso TdF, Luciano ACdS (2023) Towards greater sustainability of sugarcane production by precision agriculture to meet ethanol demands in south-central Brazil based on a life cycle assessment. Biosystems Engineering 229, 57-68.
| Crossref | Google Scholar |

Sanghera GS, Malhotra PK (2018) Engineering sugarcane (Saccharum spp) for disease resistance: recent approaches. Research & Reviews in Biotechnology and Biosciences 5(1), 15-28.
| Google Scholar |

Shan Q, Wang Y, Chen K, Liang Z, Li J, Zhang Y, Zhang K, Liu J, Voytas DF, Zheng X, Zhang Y, Gao C (2013) Rapid and efficient gene modification in rice and Brachypodium using TALENs. Molecular Plant 6(4), 1365-1368.
| Crossref | Google Scholar | PubMed |

Shankar S, Sreekumar A, Prasad D, Das AV, Pillai MR (2018) Genome editing of oncogenes with ZFNs and TALENs: caveats in nuclease design. Cancer Cell International 18(1), 169.
| Crossref | Google Scholar |

Sharma D, Singh S, Sharma SK, Singh R (2023) ‘Smart plant breeding for field crops in post-genomics era.’ (Springer Nature)

Shrivastava AK, Pathak AD, Misra V, Srivastava S, Swapna M, Shukla SP (2017) Sugarcane crop: its tolerance towards abiotic stresses. In ‘Abiotic stress management for resilient agriculture’. (Eds PS Minhas, J Rane, RK Pasala) pp. 375–397. (Springer: Singapore)

Singh P, Singh SN, Tiwari AK, Pathak SK, Singh AK, Srivastava S, Mohan N (2019) Integration of sugarcane production technologies for enhanced cane and sugar productivity targeting to increase farmers’ income: strategies and prospects. 3 Biotech 9, 48.
| Crossref | Google Scholar |

Song W, Shao H, Zheng A, Zhao L, Xu Y (2023) Advances in roles of salicylic acid in plant tolerance responses to biotic and abiotic stresses. Plants 12(19), 3475.
| Crossref | Google Scholar | PubMed |

Sufyan M, Daraz U, Hyder S, Zulfiqar U, Iqbal R, Eldin SM, Rafiq F, Mahmood N, Shahzad K, Uzair M, Fiaz S, Ali I (2023) An overview of genome engineering in plants, including its scope, technologies, progress and grand challenges. Functional & Integrative Genomics 23(2), 119.
| Crossref | Google Scholar | PubMed |

Surabhi GK, Badajena B, Sahoo SK (2019) Genome editing and abiotic stress tolerance in crop plants. In ‘Recent approaches in omics for plant resilience to climate change’. (Ed. SH Wani) pp. 35–56. (Springer International Publishing: Cham, Switzerland)

Surya Krishna S, Viswanathan R, Valarmathi R, Lakshmi K, Appunu C (2023a) CRISPR/Cas-mediated genome editing approach for improving virus resistance in sugarcane. Sugar Tech 25, 735-750.
| Crossref | Google Scholar |

Surya Krishna S, Harish Chandar SR, Ravi M, Valarmathi R, Lakshmi K, Prathima PT, Manimekalai R, Viswanathan R, Hemaprabha G, Appunu C (2023b) Transgene-free genome editing for biotic and abiotic stress resistance in sugarcane: prospects and challenges. Agronomy 13(4), 1000.
| Crossref | Google Scholar |

Talakayala A, Katta S, Garladinne M (2020) Genetic engineering of crops for insect resistance: an overview. Journal of Biosciences 45(1), 114.
| Crossref | Google Scholar |

Tashkandi M, Ali Z, Aljedaani F, Shami A, Mahfouz MM (2018) Engineering resistance against Tomato yellow leaf curl virus via the CRISPR/Cas9 system in tomato. Plant Signaling & Behavior 13(10), e1525996.
| Crossref | Google Scholar | PubMed |

Thomas L, Singh I (2020) Microbe-mediated biotic stress signaling and resistance mechanisms in plants. In ‘Plant stress biology: strategies and trends’. (Eds B Giri, MP Sharma) pp. 297–334. (Springer: Singapore)

Thurtle-Schmidt DM, Lo T-W (2018) Molecular biology at the cutting edge: a review on CRISPR/CAS9 gene editing for undergraduates. Biochemistry and Molecular Biology Education 46(2), 195-205.
| Crossref | Google Scholar | PubMed |

Thuy NP, Loc HT, Chakravarthy A (2022) Application of genetic engineering technologies to manage crop pests and diseases in Vietnam. In ‘Genetic methods and tools for managing crop pests’. (Ed. AK Chakravarthy) pp. 253–284. (Springer)

Tiwari JK, Buckseth T, Singh RK, Kumar M, Kant S (2020) Prospects of improving nitrogen use efficiency in potato: lessons from transgenics to genome editing strategies in plants. Frontiers in Plant Science 11, 597481.
| Crossref | Google Scholar | PubMed |

Tiwari JK, A. J, Tuteja N, Khurana SMP (2022) Genome editing (CRISPR-Cas)-mediated virus resistance in potato (Solanum tuberosum L.). Molecular Biology Reports 49(12), 12109-12119.
| Crossref | Google Scholar | PubMed |

Touzdjian Pinheiro Kohlrausch Távora F, de Assis dos Santos Diniz F, de Moraes Rêgo-Machado C, Chagas Freitas N, Barbosa Monteiro Arraes F, Chumbinho de Andrade E, Furtado LL, Osiro KO, Lima de Sousa N, Cardoso TB, Márcia Mertz Henning L, Abrão de Oliveira Molinari P, Feingold SE, Hunter WB, Fátima Grossi de Sá M, Kobayashi AK, Lima Nepomuceno A, Santiago TR, Correa Molinari HB (2022) CRISPR/Cas- and topical RNAi-based technologies for crop management and improvement: reviewing the risk assessment and challenges towards a more sustainable agriculture. Frontiers in Bioengineering and Biotechnology 10, 913728.
| Crossref | Google Scholar |

Tripathy SK (2022) Genomics-assisted precision breeding for drought tolerance in sugarcane. In ‘Omics approaches for sugarcane crop improvement’. (Ed. RK Gaur) pp. 131–162. (CRC Press)

Tussipkan D, Manabayeva SA (2021) Employing CRISPR/Cas technology for the improvement of potato and other tuber crops. Frontiers in Plant Science 12, 747476.
| Crossref | Google Scholar | PubMed |

Tyagi S, Kumar R, Das A, Won SY, Shukla P (2020) CRISPR-Cas9 system: a genome-editing tool with endless possibilities. Journal of Biotechnology 319, 36-53.
| Crossref | Google Scholar | PubMed |

Tyagi S, Kumar R, Kumar V, Won SY, Shukla P (2021) Engineering disease resistant plants through CRISPR-Cas9 technology. GM Crops & Food 12(1), 125-144.
| Crossref | Google Scholar | PubMed |

Vats S, Kumawat S, Kumar V, Patil GB, Joshi T, Sonah H, Sharma TR, Deshmukh R (2019) Genome editing in plants: exploration of technological advancements and challenges. Cells 8(11), 1386.
| Crossref | Google Scholar | PubMed |

Venezia M, Creasey Krainer KM (2021) Current advancements and limitations of gene editing in orphan crops. Frontiers in Plant Science 12, 742932.
| Crossref | Google Scholar | PubMed |

Visarada KBRS, Meena K, Aruna C, Srujana S, Saikishore N, Seetharama N (2009) Transgenic breeding: perspectives and prospects. Crop Science 49(5), 1555-1563.
| Crossref | Google Scholar |

Wada N, Ueta R, Osakabe Y, Osakabe K (2020) Precision genome editing in plants: state-of-the-art in CRISPR/Cas9-based genome engineering. BMC Plant Biology 20, 234.
| Crossref | Google Scholar |

Wang Y, Cheng X, Shan Q, Zhang Y, Liu J, Gao C, Qiu J-L (2014) Simultaneous editing of three homoeoalleles in hexaploid bread wheat confers heritable resistance to powdery mildew. Nature Biotechnology 32(9), 947-951.
| Crossref | Google Scholar | PubMed |

Wang C, Qu Y, Cheng JKW, Hughes NW, Zhang Q, Wang M, Cong L (2022) dCas9-based gene editing for cleavage-free genomic knock-in of long sequences. Nature Cell Biology 24(2), 268-278.
| Crossref | Google Scholar | PubMed |

Weeks DP, Spalding MH, Yang B (2016) Use of designer nucleases for targeted gene and genome editing in plants. Plant Biotechnology Journal 14(2), 483-495.
| Crossref | Google Scholar | PubMed |

Wei T, Cheng Q, Min Y-L, Olson EN, Siegwart DJ (2020) Systemic nanoparticle delivery of CRISPR-Cas9 ribonucleoproteins for effective tissue specific genome editing. Nature Communications 11(1), 3232.
| Crossref | Google Scholar | PubMed |

Wendt T, Holm PB, Starker CG, Christian M, Voytas DF, Brinch-Pedersen H, Holme IB (2013) TAL effector nucleases induce mutations at a pre-selected location in the genome of primary barley transformants. Plant Molecular Biology 83, 279-285.
| Crossref | Google Scholar | PubMed |

Wiangwiset K, Dermail A, Piwpuan N, Songsri P, Jongrungklang N (2023) Diversity and heterosis of leaf anatomical traits in backcross 1 (BC1) derived from interspecific hybridization between commercial cane (Saccharum spp. Hybrid) and wild type (S. spontaneum). Agronomy 13(10), 2457.
| Crossref | Google Scholar |

Wu T, Liu C, Zou S, Lyu R, Yang B, Yan H, Zhao M, Tang W (2023) An engineered hypercompact CRISPR-Cas12f system with boosted gene-editing activity. Nature Chemical Biology 19(11), 1384-1393.
| Crossref | Google Scholar | PubMed |

Xia X, Cheng X, Li R, Yao J, Li Z, Cheng Y (2021) Advances in application of genome editing in tomato and recent development of genome editing technology. Theoretical and Applied Genetics 134(9), 2727-2747.
| Crossref | Google Scholar | PubMed |

Xu R, Yang Y, Qin R, Li H, Qiu C, Li L, Wei P, Yang J (2016) Rapid improvement of grain weight via highly efficient CRISPR/Cas9-mediated multiplex genome editing in rice. Journal of Genetics and Genomics 43(8), 529-532.
| Crossref | Google Scholar | PubMed |

Yang Y, Zhou H (2024) Chapter 14 – Regulatory overview of genome-edited plants in Asian countries. In ‘Global regulatory outlook for CRISPRized plants’. (Eds KA Abd-Elsalam, A Ahmad) pp. 293–318. (Academic Press: Massachusetts, USA)

Yang H, Ren S, Yu S, Pan H, Li T, Ge S, Zhang J, Xia N (2020) Methods favoring homology-directed repair choice in response to CRISPR/Cas9 induced-double strand breaks. International Journal of Molecular Sciences 21(18), 6461.
| Crossref | Google Scholar | PubMed |

Yin K, Qiu J-L (2019) Genome editing for plant disease resistance: applications and perspectives. Philosophical Transactions of the Royal Society B: Biological Sciences 374(1767), 20180322.
| Crossref | Google Scholar |

Yugander A, Sundaram RM, Ladhalakshmi D, Hajira SK, Prakasam V, Prasad MS, Sheshu Madhav M, Ravindra Babu V, Laha GS (2017) Virulence profiling of Xanthomonas oryzae pv. oryzae isolates, causing bacterial blight of rice in India. European Journal of Plant Pathology 149, 171-191.
| Crossref | Google Scholar |

Zhang Y, Zhang F, Li X, Baller JA, Qi Y, Starker CG, Bogdanove AJ, Voytas DF (2013) Transcription activator-like effector nucleases enable efficient plant genome engineering. Plant Physiology 161(1), 20-27.
| Crossref | Google Scholar | PubMed |

Zhang Y, Liang Z, Zong Y, Wang Y, Liu J, Chen K, Qiu J-L, Gao C (2016) Efficient and transgene-free genome editing in wheat through transient expression of CRISPR/Cas9 DNA or RNA. Nature Communications 7(1), 12617.
| Crossref | Google Scholar |

Zhang K, Raboanatahiry N, Zhu B, Li M (2017) Progress in genome editing technology and its application in plants. Frontiers in Plant science 8, 177.
| Google Scholar | PubMed |

Zhang Y, Massel K, Godwin ID, Gao C (2018) Applications and potential of genome editing in crop improvement. Genome Biology 19, 210.
| Crossref | Google Scholar |

Zhang Q, Qi Y, Pan H, Tang H, Wang G, Hua X, Wang Y, Lin L, Li Z, Li Y, et al. (2022) Genomic insights into the recent chromosome reduction of autopolyploid sugarcane Saccharum spontaneum. Nature Genetics 54(6), 885-896.
| Crossref | Google Scholar | PubMed |

Zhao M, Zhou Y, Su L, Li G, Huang Z, Huang D, Wu W, Zhao Y (2022) Expression of Pinellia pedatisecta agglutinin PPA gene in transgenic sugarcane led to stomata patterning change and resistance to sugarcane woolly aphid, Ceratovacuna lanigera Zehntner. International Journal of Molecular Sciences 23(13), 7195.
| Crossref | Google Scholar | PubMed |