RNAi and genome editing of sugarcane: Progress and prospects

Brant, Eleanor; Zuniga‐Soto, Evelyn; Altpeter, Fredy

doi:10.1111/tpj.70048

RNAi and genome editing of sugarcane: Progress and prospects

Journal Article · Fri Mar 07 00:00:00 EST 2025 · The Plant Journal

DOI:https://doi.org/10.1111/tpj.70048· OSTI ID:2549515

Brant, Eleanor ^[1]; Zuniga‐Soto, Evelyn ^[1]; ^[1]

Agronomy Department, Plant Molecular and Cellular Biology Program, Genetics Institute University of Florida, IFAS Gainesville Florida USA

SUMMARY

Sugarcane, which provides 80% of global table sugar and 40% of biofuel, presents unique breeding challenges due to its highly polyploid, heterozygous, and frequently aneuploid genome. Significant progress has been made in developing genetic resources, including the recently completed reference genome of the sugarcane cultivar R570 and pan‐genomic resources from sorghum, a closely related diploid species. Biotechnological approaches including RNA interference (RNAi), overexpression of transgenes, and gene editing technologies offer promising avenues for accelerating sugarcane improvement. These methods have successfully targeted genes involved in important traits such as sucrose accumulation, lignin biosynthesis, biomass oil accumulation, and stress response. One of the main transformation methods—biolistic gene transfer or Agrobacterium ‐mediated transformation—coupled with efficient tissue culture protocols, is typically used for implementing these biotechnology approaches. Emerging technologies show promise for overcoming current limitations. The use of morphogenic genes can help address genotype constraints and improve transformation efficiency. Tissue culture‐free technologies, such as spray‐induced gene silencing, virus‐induced gene silencing, or virus‐induced gene editing, offer potential for accelerating functional genomics studies. Additionally, novel approaches including base and prime editing, orthogonal synthetic transcription factors, and synthetic directed evolution present opportunities for enhancing sugarcane traits. These advances collectively aim to improve sugarcane's efficiency as a crop for both sugar and biofuel production. This review aims to discuss the progress made in sugarcane methodologies, with a focus on RNAi and gene editing approaches, how RNAi can be used to inform functional gene targets, and future improvements and applications.

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Sponsoring Organization:: USDOE

Grant/Contract Number:: SC0018420

OSTI ID:: 2549515

Alternate ID(s):: OSTI ID: 2554100

Journal Information:: The Plant Journal, Journal Name: The Plant Journal Journal Issue: 5 Vol. 121; ISSN 0960-7412

Publisher:: Wiley-BlackwellCopyright Statement

Country of Publication:: United Kingdom

Language:: English

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Efficiency, Specificity and Temperature Sensitivity of Cas9 and Cas12a RNPs for DNA-free Genome Editing in Plants Banakar, Raviraj; Schubert, Mollie; Kurgan, Gavin Frontiers in Genome Editing, Vol. 3 https://doi.org/10.3389/fgeed.2021.760820	journal	January 2022
Comparison of genotyping assays for detection of targeted CRISPR/Cas mutagenesis in highly polyploid sugarcane Brant, Eleanor J.; May, David; Eid, Ayman Frontiers in Genome Editing, Vol. 6 https://doi.org/10.3389/fgeed.2024.1505844	journal	December 2024
DNA damage and repair in plants – from models to crops Manova, Vasilissa; Gruszka, Damian Frontiers in Plant Science, Vol. 6 https://doi.org/10.3389/fpls.2015.00885	journal	October 2015
Plant Small Non-coding RNAs and Their Roles in Biotic Stresses Brant, Eleanor J.; Budak, Hikmet Frontiers in Plant Science, Vol. 9 https://doi.org/10.3389/fpls.2018.01038	journal	July 2018
The Plant DNA Damage Response: Signaling Pathways Leading to Growth Inhibition and Putative Role in Response to Stress Conditions Nisa, Maher-Un; Huang, Ying; Benhamed, Moussa Frontiers in Plant Science, Vol. 10 https://doi.org/10.3389/fpls.2019.00653	journal	May 2019
Genome Edited Crops Touch the Market: A View on the Global Development and Regulatory Environment Menz, Jochen; Modrzejewski, Dominik; Hartung, Frank Frontiers in Plant Science, Vol. 11 https://doi.org/10.3389/fpls.2020.586027	journal	October 2020
RNA Viral Vectors for Accelerating Plant Synthetic Biology Khakhar, Arjun; Voytas, Daniel F. Frontiers in Plant Science, Vol. 12 https://doi.org/10.3389/fpls.2021.668580	journal	June 2021
Genetic Transformation of Sugarcane, Current Status and Future Prospects Budeguer, Florencia; Enrique, Ramón; Perera, María Francisca Frontiers in Plant Science, Vol. 12 https://doi.org/10.3389/fpls.2021.768609	journal	November 2021
Genetic Transformation of Recalcitrant Upland Switchgrass Using Morphogenic Genes Xu, Nuoya; Kang, Minjeong; Zobrist, Jacob D. Frontiers in Plant Science, Vol. 12 https://doi.org/10.3389/fpls.2021.781565	journal	February 2022
New Insights Into Tissue Culture Plant-Regeneration Mechanisms Long, Yun; Yang, Yun; Pan, Guangtang Frontiers in Plant Science, Vol. 13 https://doi.org/10.3389/fpls.2022.926752	journal	June 2022
U.S. EPA oversight of pesticide traits in genetically modified plants and recent biotechnology innovation efforts Mendelsohn, Michael; Pierce, Amanda A.; Striegel, Wiebke Frontiers in Plant Science, Vol. 14 https://doi.org/10.3389/fpls.2023.1126006	journal	February 2023
Rapid and highly efficient morphogenic gene-mediated hexaploid wheat transformation Johnson, Kari; Cao Chu, Uyen; Anthony, Geny Frontiers in Plant Science, Vol. 14 https://doi.org/10.3389/fpls.2023.1151762	journal	March 2023
CRISPR technology towards genome editing of the perennial and semi-perennial crops citrus, coffee and sugarcane Prado, Guilherme Souza; Rocha, Dhiôvanna Corrêia; Santos, Lucas Nascimento dos Frontiers in Plant Science, Vol. 14 https://doi.org/10.3389/fpls.2023.1331258	journal	January 2024
Enhancing Agrobacterium-mediated plant transformation efficiency through improved ternary vector systems and auxotrophic strains Aliu, Ephraim; Ji, Qing; Wlazlo, Anna Frontiers in Plant Science, Vol. 15 https://doi.org/10.3389/fpls.2024.1429353	journal	July 2024
Synthetic directed evolution for targeted engineering of plant traits Kababji, Ahad Moussa; Butt, Haroon; Mahfouz, Magdy Frontiers in Plant Science, Vol. 15 https://doi.org/10.3389/fpls.2024.1449579	journal	September 2024
Transgene-Free Genome Editing for Biotic and Abiotic Stress Resistance in Sugarcane: Prospects and Challenges Surya Krishna, Sakthivel; Harish Chandar, S. R.; Ravi, Maruthachalam Agronomy, Vol. 13, Issue 4 https://doi.org/10.3390/agronomy13041000	journal	March 2023
A Review of the Diverse Genes and Molecules Involved in Sucrose Metabolism and Innovative Approaches to Improve Sucrose Content in Sugarcane Khan, Qaisar; Qin, Ying; Guo, Dao-Jun Agronomy, Vol. 13, Issue 12 https://doi.org/10.3390/agronomy13122957	journal	November 2023
RNAi as a Foliar Spray: Efficiency and Challenges to Field Applications Hoang, Bao Tram L.; Fletcher, Stephen J.; Brosnan, Christopher A. International Journal of Molecular Sciences, Vol. 23, Issue 12 https://doi.org/10.3390/ijms23126639	journal	June 2022
Antisense Transcription in Plants: A Systematic Review and an Update on cis-NATs of Sugarcane Santini, Luciane; Yoshida, Leonardo; de Oliveira, Kaique Dias International Journal of Molecular Sciences, Vol. 23, Issue 19 https://doi.org/10.3390/ijms231911603	journal	October 2022
RNA Interference Past and Future Applications in Plants Koeppe, Sarah; Kawchuk, Lawrence; Kalischuk, Melanie International Journal of Molecular Sciences, Vol. 24, Issue 11 https://doi.org/10.3390/ijms24119755	journal	June 2023
Establishment of an Efficient Sugarcane Transformation System via Herbicide-Resistant CP4-EPSPS Gene Selection Wang, Wenzhi; Javed, Talha; Shen, Linbo Plants, Vol. 13, Issue 6 https://doi.org/10.3390/plants13060852	journal	March 2024
Genetic Engineering for Enhancing Sugarcane Tolerance to Biotic and Abiotic Stresses Kumar, Tanweer; Wang, Jun-Gang; Xu, Chao-Hua Plants, Vol. 13, Issue 13 https://doi.org/10.3390/plants13131739	journal	June 2024
Interactive Role of Silicon and Plant–Rhizobacteria Mitigating Abiotic Stresses: A New Approach for Sustainable Agriculture and Climate Change Verma, Krishan K.; Song, Xiu-Peng; Li, Dong-Mei Plants, Vol. 9, Issue 9 https://doi.org/10.3390/plants9091055	journal	August 2020
Establishment of an in vitro regeneration system for genetic transformation of selected sugarcane genotypes Ijaz, S.; Rana, I. A.; Khan, I. A. Genetics and Molecular Research, Vol. 11, Issue 1 https://doi.org/10.4238/2012.March.6.4	journal	January 2012
Molecular Mechanisms and Biological Functions of siRNA No authors listed International Journal of Biomedical Science, Vol. 13, Issue 2 https://doi.org/10.59566/IJBS.2017.13048	journal	June 2017

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