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Brant E, Zuniga‐Soto E, Altpeter F. RNAi and genome editing of sugarcane: Progress and prospects. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2025; 121:e70048. [PMID: 40051334 PMCID: PMC11886501 DOI: 10.1111/tpj.70048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2024] [Revised: 02/01/2025] [Accepted: 02/05/2025] [Indexed: 03/09/2025]
Abstract
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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Affiliation(s)
- Eleanor Brant
- Agronomy Department, Plant Molecular and Cellular Biology Program, Genetics InstituteUniversity of Florida, IFASGainesvilleFloridaUSA
| | - Evelyn Zuniga‐Soto
- Agronomy Department, Plant Molecular and Cellular Biology Program, Genetics InstituteUniversity of Florida, IFASGainesvilleFloridaUSA
| | - Fredy Altpeter
- Agronomy Department, Plant Molecular and Cellular Biology Program, Genetics InstituteUniversity of Florida, IFASGainesvilleFloridaUSA
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2
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Belaffif MB, Brown MC, Marcial B, Baysal C, Swaminathan K. New strategies to advance plant transformation. Curr Opin Biotechnol 2025; 91:103241. [PMID: 39732097 DOI: 10.1016/j.copbio.2024.103241] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2024] [Accepted: 11/26/2024] [Indexed: 12/30/2024]
Abstract
Plants are an important source of food, energy, and bioproducts. Advances in genetics, genomics-assisted breeding, and biotechnology have facilitated the combining of desirable traits into elite cultivars. To ensure sustainable crop production in the face of climate challenges and population growth, it is essential to develop and implement techniques that increase crop yield and resilience in environments facing water scarcity, nutrient deficiencies, and other abiotic and biotic stressors. Plant transformation and genome editing are critical tools in the development of new cultivars. Here, we discuss recent advances in plant transformation technologies aimed at enhancing efficiency, throughput, and the number of transformable genotypes. These advancements include the use of morphogenic regulators, virus-mediated genetic modifications, and in planta transformation with Rhizobium rhizogenes.
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Affiliation(s)
- Mohammad B Belaffif
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806, USA; Center for Advanced Bioenergy and Bioproducts Innovation, 1206 W. Gregory Drive (IGB), Urbana, IL 61801, USA; Agria Analytica, CIBIS NINE 11th Floor, Jl.TB Simatupang No.2, Jakarta Selatan, DKI Jakarta 12560, Indonesia
| | - Morgan C Brown
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806, USA
| | - Brenda Marcial
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806, USA; Center for Advanced Bioenergy and Bioproducts Innovation, 1206 W. Gregory Drive (IGB), Urbana, IL 61801, USA; University of Alabama at Huntsville, 301 Sparkman Drive, Huntsville, AL 35899, USA
| | - Can Baysal
- Center for Advanced Bioenergy and Bioproducts Innovation, 1206 W. Gregory Drive (IGB), Urbana, IL 61801, USA; Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, MN 55108, USA
| | - Kankshita Swaminathan
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806, USA; Center for Advanced Bioenergy and Bioproducts Innovation, 1206 W. Gregory Drive (IGB), Urbana, IL 61801, USA.
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Rafiei F, Wiersma J, Scofield S, Zhang C, Alizadeh H, Mohammadi M. Facts, uncertainties, and opportunities in wheat molecular improvement. Heredity (Edinb) 2024; 133:371-380. [PMID: 39237600 PMCID: PMC11589648 DOI: 10.1038/s41437-024-00721-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 08/17/2024] [Accepted: 08/18/2024] [Indexed: 09/07/2024] Open
Abstract
The year 2020 was a landmark year for wheat. The wheat HB4 event harboring a drought-resistant gene from sunflowers, received regulatory approval and was grown commercially in Argentina, with approval for food and feed in other countries. This, indeed, is many years after the adoption of genetic modifications in other crops. The lack of consumer acceptance and resulting trade barriers halted the commercialization of the earliest events and had a chilling effect on, especially, private Research & Development (R&D) investments. As regulations for modern breeding technologies such as genome-edited cultivars are being discussed and/or adopted across the globe, we would like to propose a framework to ensure that wheat is not left behind a second time as the potential benefits far outweigh the perceived risks. In this paper, after a review of the technical challenges wheat faces with the generation of trans- and cis-genic wheat varieties, we discuss some of the factors that could help demystify the risk/reward equation and thereby the consumer's reluctance or acceptance of these techniques for future wheat improvement. The advent of next-generation sequencing is shedding light on natural gene transfer between species and the number of perturbations other accepted techniques like mutagenesis create. The transition from classic breeding techniques and embracing transgenic, cisgenic, and genome editing approaches feels inevitable for wheat improvement if we are to develop climate-resilient wheat varieties to feed a growing world population.
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Affiliation(s)
- Fariba Rafiei
- Department of Agronomy, Purdue University, West Lafayette, IN, USA
| | - Jochum Wiersma
- Department of Agronomy and Plant Genetics, University of Minnesota, Northwest Research and Outreach Center, Crookston, MN, USA
| | - Steve Scofield
- USDA-ARS, Crop Production and Pest Control Research Unit, West Lafayette, IN, USA
| | - Cankui Zhang
- Department of Agronomy, Purdue University, West Lafayette, IN, USA
| | - Houshang Alizadeh
- Department of Agronomy & Plant Breeding, College of Agricultural and Natural Resource, University of Tehran, Karaj, Iran
| | - Mohsen Mohammadi
- Department of Agronomy, Purdue University, West Lafayette, IN, USA.
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Fontanet-Manzaneque JB, Haeghebaert J, Aesaert S, Coussens G, Pauwels L, Caño-Delgado AI. Efficient sorghum and maize transformation using a ternary vector system combined with morphogenic regulators. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 120:2076-2088. [PMID: 39527627 DOI: 10.1111/tpj.17101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Revised: 09/27/2024] [Accepted: 10/10/2024] [Indexed: 11/16/2024]
Abstract
Sorghum bicolor (sorghum) is a vital C4 monocotyledon crop cultivated in arid regions worldwide, valued for its significance in both human and animal nutrition. Despite its agricultural prominence, sorghum research has been hindered by low transformation frequency. In this study, we examined sorghum transformation using the pVS1-VIR2 ternary vector system for Agrobacterium, combined with the morphogenic genes BABY BOOM and WUSCHEL2 and selection using G418. We optimized Agrobacterium-mediated infection, targeting key parameters such as bacterial optical density, co-cultivation time, and temperature. Additionally, an excision-based transformation system enabled us to generate transgenic plants free of morphogenic regulators. The method yielded remarkable transformation frequencies, reaching up to 164.8% based on total isolated plantlets. The same combination of ternary vector, morphogenic genes and geneticin-based selection also resulted in a marked increase in transformation efficiency of the Zea mays (maize) inbred line B104. The potential for genomic editing using this approach positions it as a valuable tool for the development of sorghum and maize varieties that comply with evolving European regulations. Our work marks a significant stride in sorghum biotechnology and holds promise for addressing global food security challenges in a changing climate.
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Affiliation(s)
- Juan B Fontanet-Manzaneque
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB (Cerdanyola del Vallès), Barcelona, 08193, Spain
| | - Jari Haeghebaert
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- VIB-UGent Center for Plant Systems Biology, Ghent, 9052, Belgium
| | - Stijn Aesaert
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- VIB-UGent Center for Plant Systems Biology, Ghent, 9052, Belgium
| | - Griet Coussens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- VIB-UGent Center for Plant Systems Biology, Ghent, 9052, Belgium
| | - Laurens Pauwels
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- VIB-UGent Center for Plant Systems Biology, Ghent, 9052, Belgium
| | - Ana I Caño-Delgado
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB (Cerdanyola del Vallès), Barcelona, 08193, Spain
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Zhou Z, Yang Y, Ai G, Zhao M, Han B, Zhao C, Chen Y, Zhang Y, Pan H, Lan C, He C, Li Q, Xu J, Yan W. Overcoming genotypic dependency and bypassing immature embryos in wheat transformation by using morphogenic regulators. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1535-1538. [PMID: 38647567 DOI: 10.1007/s11427-023-2565-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 03/08/2024] [Indexed: 04/25/2024]
Affiliation(s)
- Ziru Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yawen Yang
- WIMI Biotechnology Co., Ltd., Changzhou, 213025, China
| | - Guo Ai
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Miaomiao Zhao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Baozhu Han
- WIMI Biotechnology Co., Ltd., Changzhou, 213025, China
| | - Chunjie Zhao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yiqian Chen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuwei Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hong Pan
- WIMI Biotechnology Co., Ltd., Changzhou, 213025, China
| | - Caixia Lan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chao He
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qiang Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jieting Xu
- WIMI Biotechnology Co., Ltd., Changzhou, 213025, China.
| | - Wenhao Yan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
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Sato Y, Minamikawa MF, Pratama BB, Koyama S, Kojima M, Takebayashi Y, Sakakibara H, Igawa T. Autonomous differentiation of transgenic cells requiring no external hormone application: the endogenous gene expression and phytohormone behaviors. FRONTIERS IN PLANT SCIENCE 2024; 15:1308417. [PMID: 38633452 PMCID: PMC11021773 DOI: 10.3389/fpls.2024.1308417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 03/18/2024] [Indexed: 04/19/2024]
Abstract
The ectopic overexpression of developmental regulator (DR) genes has been reported to improve the transformation in recalcitrant plant species because of the promotion of cellular differentiation during cell culture processes. In other words, the external plant growth regulator (PGR) application during the tissue and cell culture process is still required in cases utilizing DR genes for plant regeneration. Here, the effect of Arabidopsis BABY BOOM (BBM) and WUSCHEL (WUS) on the differentiation of tobacco transgenic cells was examined. We found that the SRDX fusion to WUS, when co-expressed with the BBM-VP16 fusion gene, significantly influenced the induction of autonomous differentiation under PGR-free culture conditions, with similar effects in some other plant species. Furthermore, to understand the endogenous background underlying cell differentiation toward regeneration, phytohormone and RNA-seq analyses were performed using tobacco leaf explants in which transgenic cells were autonomously differentiating. The levels of active auxins, cytokinins, abscisic acid, and inactive gibberellins increased as cell differentiation proceeded toward organogenesis. Gene Ontology terms related to phytohormones and organogenesis were identified as differentially expressed genes, in addition to those related to polysaccharide and nitrate metabolism. The qRT-PCR four selected genes as DEGs supported the RNA-seq data. This differentiation induction system and the reported phytohormone and transcript profiles provide a foundation for the development of PGR-free tissue cultures of various plant species, facilitating future biotechnological breeding.
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Affiliation(s)
- Yuka Sato
- Plant Cell Technology Laboratory, Graduate School of Horticulture, Chiba University, Matsudo, Japan
| | - Mai F. Minamikawa
- Institute for Advanced Academic Research (IAAR), Chiba University, Chiba, Japan
| | - Berbudi Bintang Pratama
- Plant Cell Technology Laboratory, Graduate School of Horticulture, Chiba University, Matsudo, Japan
| | - Shohei Koyama
- Plant Cell Technology Laboratory, Graduate School of Horticulture, Chiba University, Matsudo, Japan
| | - Mikiko Kojima
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | | | - Hitoshi Sakakibara
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Tomoko Igawa
- Plant Cell Technology Laboratory, Graduate School of Horticulture, Chiba University, Matsudo, Japan
- Plant Molecular Science Center, Chiba University, Chiba, Japan
- Research Center for Space Agriculture and Horticulture, Chiba University, Matsudo, Japan
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Zhang Y, Patankar H, Aljedaani F, Blilou I. A framework for date palm (Phoenix dactylifera L.) tissue regeneration and stable transformation. PHYSIOLOGIA PLANTARUM 2024; 176:e14189. [PMID: 38342489 DOI: 10.1111/ppl.14189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 01/04/2024] [Accepted: 01/10/2024] [Indexed: 02/13/2024]
Abstract
The date palm is a resilient, socioeconomically valuable desert fruit tree renowned for its heat, drought, and salinity tolerance. Date palm fruits are rich in nutrients and antioxidants, and their beneficial health properties can mitigate current and future food security challenges. However, it is challenging to improve date palm production through conventional breeding methods due to its slow growth. Date palm seeds do not produce true-to-type progeny, and commercial propagation relies on direct organogenesis from maternal tissue. Consequently, numerous economically important and valuable cultivars are lost due to tissue recalcitrance and challenges in inducing cell dedifferentiation and regeneration. Moreover, genetic engineering of date palms is currently impossible due to the lack of a stable genetic transformation protocol. This hampers the development of genetic resources in date palms. This study established a tissue culture pipeline and a genetic transformation protocol for various commercially important date palm cultivars. We used the non-invasive visual reporter RUBY and four morphogenic regulators to validate and improve date palm transformation potential. We found that the date palm BABY-BOOM (PdBBM) and the WOUND INDUCED DEDIFFERENTIATION (PdWIND1) enhanced transformation efficacy. We show that PdBBM can induce embryogenesis in hormone-free media and regenerate roots and shoots in recalcitrant varieties. On the other hand, PdWIND1 maintained embryogenic cells in their undifferentiated state. Our study provides a foundation for genetically improving date palms and a potential solution for preserving economically valuable varieties.
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Affiliation(s)
- Yasha Zhang
- BESE Division, Plant Cell and Developmental Biology, Center for Desert and Agriculture, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Himanshu Patankar
- BESE Division, Plant Cell and Developmental Biology, Center for Desert and Agriculture, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Fatima Aljedaani
- BESE Division, Plant Cell and Developmental Biology, Center for Desert and Agriculture, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Ikram Blilou
- BESE Division, Plant Cell and Developmental Biology, Center for Desert and Agriculture, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
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Lopos LC, Bykova NV, Robinson J, Brown S, Ward K, Bilichak A. Diversity of transgene integration and gene-editing events in wheat ( Triticum aestivum L.) transgenic plants generated using Agrobacterium-mediated transformation. Front Genome Ed 2023; 5:1265103. [PMID: 38192430 PMCID: PMC10773716 DOI: 10.3389/fgeed.2023.1265103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 11/10/2023] [Indexed: 01/10/2024] Open
Abstract
Improvement in agronomic traits in crops through gene editing (GE) relies on efficient transformation protocols for delivering the CRISPR/Cas9-coded transgenes. Recently, a few embryogenesis-related genes have been described, the co-delivery of which significantly increases the transformation efficiency with reduced genotype-dependency. Here, we characterized the transgenic and GE events in wheat (cv. Fielder) when transformed with GROWTH-REGULATING FACTOR 4 (GRF4) and its cofactor GRF-INTERACTING FACTOR 1 (GIF1) chimeric gene. Transformation efficiency in our experiments ranged from 22% to 68%, and the editing events were faithfully propagated into the following generation. Both low- and high-copy-number integration events were recovered in the T0 population with various levels of integrity of the left and right T-DNA borders. We also generated a population of wheat plants with 10 different gRNAs targeting 30 loci in the genome. A comparison of the epigenetic profiles at the target sites and editing efficiency revealed a significant positive correlation between chromatin accessibility and mutagenesis rate. Overall, the preliminary screening of transgene quality and GE events in the T0 population of plants regenerated through the co-delivery of GRF-GIF can allow for the propagation of the best candidates for further phenotypic analysis.
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Affiliation(s)
| | | | | | | | | | - Andriy Bilichak
- Agriculture and Agri-Food Canada, Morden Research and Development Centre, Morden, MB, Canada
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Harwood W. Breaking transformation barriers. NATURE PLANTS 2023; 9:854-855. [PMID: 37193774 DOI: 10.1038/s41477-023-01420-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Affiliation(s)
- Wendy Harwood
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK.
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