Unlocking genetic diversity: A-to-K base editing achieves new milestones
image: Heritable and efficient A-to-K editing induced by AKBEs in rice.
Credit: Horticulture Research
A new study has made significant strides in plant genome editing by developing an A-to-K base editing system for rice and tomato. This technology enables precise genetic alterations, facilitating the creation of specific single-nucleotide polymorphisms (SNPs) that can enhance crop traits and expedite breeding. The research opens new avenues for improving agricultural productivity and crop quality through targeted genetic modifications.
Single nucleotide polymorphisms (SNPs) are critical for generating genetic diversity in plants, influencing essential traits like disease resistance and yield. Traditional base-editing tools—adenine base editors (ABEs) and cytosine base editors (CBEs)—mainly enable A-to-G and C-to-T conversions, limiting the range of genetic modifications possible. This narrow scope restricts researchers’ ability to generate diverse SNPs, thus constraining the potential for comprehensive crop improvement. To address this, researchers have sought more versatile systems capable of broader base substitutions, which could boost genetic variation and accelerate advances in plant breeding.
Researchers from the Chinese Academy of Agricultural Sciences, alongside partners, recently published findings (DOI: 10.1093/hr/uhad250) in Horticulture Research on December 2, 2023,on their new adenine-to-tyrosine (A-to-K) base editor (AKBE) system for plants. This innovative tool enables efficient A-to-T and A-to-C base substitutions, which were successfully tested on multiple loci in rice and tomato. By integrating a protospacer adjacent motif (PAM)-less Cas9 variant, AKBE broadens its target range and achieves heritable, precise edits. Providing a powerful resource for enhancing genetic diversity, this tool marks a substantial advance in plant biotechnology. The study, published in January 2024, represents a critical breakthrough for crop breeding.
In developing the AKBE system, the researchers engineered a mechanism that combines adenosine deaminase with a modified DNA glycosylase (MPG), enabling both A-to-G and A-to-T/C base substitutions with significant efficiency. The use of a PAM-less Cas9 variant further expanded target accessibility, allowing edits in previously challenging genomic regions. Testing on 228 T0 rice plants and 121 T0 tomato plants, AKBE achieved conversion rates averaging 41% for A-to-G and up to 25.9% and 10.5% for A-to-T in rice and tomato, respectively. Additionally, a rice-optimized AKBE enabled A-to-C edits with 1.8% efficiency, further diversifying mutation types. These edits were confirmed to be heritable across generations. Notably, AKBE’s A-to-T editing can create early stop codons, effectively disrupting gene function—an invaluable capability for gene knockout research. For example, edits in the beta-carotene biosynthesis gene (β-OsLCY) in rice led to observable albino phenotypes, affirming successful gene disruption.
Dr. Yifu Tian, a lead researcher from the Chinese Academy of Agricultural Sciences, highlighted the significance of AKBE’s capabilities: “The AKBE system significantly expands the scope of single-base editing in plants, allowing us to explore gene functions with precision and efficiency. By enabling heritable A-to-T and A-to-C conversions, this tool enhances our ability to create genetically diverse crops and opens new possibilities for agricultural biotechnology.”
The AKBE system has substantial potential in advancing crop breeding by enabling precise genetic modifications that could improve resistance to environmental stressors, diseases, and pests in staple crops. This innovation is particularly relevant for developing crop varieties suited to changing climates and addressing global food security challenges. By facilitating controlled gene disruptions, AKBE provides breeders with a precise tool to refine traits like yield, nutritional content, and adaptability. Additionally, as a resource for functional genomics, AKBE allows researchers to explore gene functions in detail, supporting the development of sustainable and resilient agricultural practices.
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References
DOI
Original Source URL
https://doi.org/10.1093/hr/uhad250
Funding information
This study was supported by the China Postdoctoral Science Foundation (No. BX20220098 and No. 2022M720973) and the Hainan Yazhou Bay Seed Laboratory (B22C1000P) to Y.T., Nanfan special project, CAAS (No. ZDXM2314) to M.W., and the National Natural Science Foundation of China (No. 32188102) to J.-K.Z.
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2022. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.