Advances in Plant Genome Editing and Transformation

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: closed (28 February 2026) | Viewed by 4562

Special Issue Editor


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Guest Editor
Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
Interests: plant synthetic biology; genome editing; comparative genomics; climate change; bioenergy; photosynthesis; plant genomics
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Special Issue Information

Dear Colleagues,

The world faces pressing challenges in the security of food, energy, and environment due to climate change and population growth. Genome-editing technologies and novel plant transformation methods have revolutionized plant research by enabling precise and efficient genetic modifications. Highlighting these advances can accelerate their adoption in the genetic improvement of crops. This Special Issue explores the latest advancements in genome-editing and -transformation technologies, highlighting their transformative impact on plant science and agriculture. We invite original research articles, reviews, and perspectives that address the following topics: (1) new technologies for editing or transforming plant nuclear and organellar genomes and high-throughput transformation systems, including tissue culture-independent methods and robotic automation; (2) applications of genome editing and transformation in the genetic improvement of various crop plants; (3) technical innovations for improving transformation efficiency in recalcitrant species and addressing off-target effects to ensure precision in genome editing; (4) computational tools and data-driven approaches for optimizing genome-editing procedures (e.g., selecting the most efficient guide RNA (gRNA) sequences for CRISPR-Cas9, minimizing off-target effects, and predicting editing outcomes based on genomic features); (5) ethical considerations, public perception, and regulatory frameworks surrounding genome-edited crops, and pathways for the responsible deployment of genome-editing technologies in agriculture; and (6) future directions, such as emerging genome-editing systems and the role of artificial intelligence and automation in advancing genome editing and transformation.

Dr. Xiaohan Yang
Guest Editor

Manuscript Submission Information

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Keywords

  • genome editing
  • plant transformation
  • genetic improvement
  • CRISPR
  • artificial intelligence

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Published Papers (2 papers)

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Research

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17 pages, 5267 KB  
Article
RUBY-Mediated Visual Selection Facilitates Transgenic Screening and Red Floral Pigmentation in Petunia × hybrida
by Jian Yao, Fanzhuang Yan, Ajithan Chandrasekaran, Theint Theint Aung, Sangrim Youn, Youngtak Kim and Geung-Joo Lee
Plants 2026, 15(6), 886; https://doi.org/10.3390/plants15060886 - 12 Mar 2026
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Abstract
Visual transgenic marker systems enabling rapid and non-destructive transformant detection are crucial for efficient plant genetic transformation and selection. RUBY is a highly effective reporter system based on betalain biosynthesis; however, its application to species outside of the order Caryophyllales (i.e., species lacking [...] Read more.
Visual transgenic marker systems enabling rapid and non-destructive transformant detection are crucial for efficient plant genetic transformation and selection. RUBY is a highly effective reporter system based on betalain biosynthesis; however, its application to species outside of the order Caryophyllales (i.e., species lacking betalains) has not been established. In this study, we performed the first systematic evaluation of the RUBY system using Petunia × hybrida lines obtained via Agrobacterium-mediated gene transformation. Stable RUBY transgenic plants were obtained from an optimized transformation and organogenesis system. The transgenic lines displayed a gradient of betalain accumulation, with pigment intensity positively correlated with RUBY expression levels and metabolite contents. In a morphological analysis, there was a negative correlation between RUBY expression and corolla opening, suggesting that RUBY pigment overaccumulation is associated with altered floral development and morphology. RUBY overexpression significantly reduced expression levels of gibberellin biosynthetic genes (PhGA20ox1 and PhGA3ox1) and flowering- and senescence-related regulators (PhNF-YC2 and PhOBF1). These findings indicate that high-level betalain accumulation is associated with changes in floral development and gene expression, highlighting both the utility of the RUBY system as a visual reporter and the importance of carefully evaluating potential developmental effects under strong expression conditions. Full article
(This article belongs to the Special Issue Advances in Plant Genome Editing and Transformation)
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Review

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22 pages, 9070 KB  
Review
Woody Plant Transformation: Current Status, Challenges, and Future Perspectives
by Bal Krishna Maharjan, Md Torikul Islam, Adnan Muzaffar, Timothy J. Tschaplinski, Gerald A. Tuskan, Jin-Gui Chen and Xiaohan Yang
Plants 2025, 14(22), 3420; https://doi.org/10.3390/plants14223420 - 8 Nov 2025
Cited by 2 | Viewed by 3142
Abstract
Woody plants, comprising forest and fruit tree species, provide essential ecological and economic benefits to society. Their genetic improvement is challenging due to long generation intervals and high heterozygosity. Genetic transformation, which combines targeted DNA delivery with plant regeneration from transformed cells, offers [...] Read more.
Woody plants, comprising forest and fruit tree species, provide essential ecological and economic benefits to society. Their genetic improvement is challenging due to long generation intervals and high heterozygosity. Genetic transformation, which combines targeted DNA delivery with plant regeneration from transformed cells, offers a powerful alternative to accelerating their domestication and improvement. Agrobacterium tumefaciens, Rhizobium rhizogenes, and particle bombardment have been widely used for DNA delivery into a wide variety of explants, including leaves, stems, hypocotyls, roots, and embryos, with regeneration occurring via direct organogenesis, callus-mediated organogenesis, somatic embryogenesis, or hairy root formation. Despite successes, conventional approaches are hampered by low efficiency, genotype dependency, and a reliance on challenging tissue culture. This review provides a critical analysis of the current landscape in woody plant transformation, moving beyond a simple summary of techniques to evaluate the co-evolution of established platforms with disruptive technologies. Key advances among these include the use of developmental regulators to engineer regeneration, the rise in in planta systems to bypass tissue culture, and the imperative for DNA-free genome editing to meet regulatory and public expectations. By examining species-specific breakthroughs in key genera, including Populus, Malus, Citrus, and Pinus, this review highlights a paradigm shift from empirical optimization towards rational, predictable engineering of woody plants for a sustainable future. Full article
(This article belongs to the Special Issue Advances in Plant Genome Editing and Transformation)
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