J Integr Plant Biol.

• Research Article • Previous Articles    

Optimized TadA-derived base editors efficiently manipulate mRNA splicing by A-to-G and C-to-K editing in potato

Kaiyuan Chen1†*, Yan Zhang1†, Jiuzhou Deng1, Lumin Zhang2,3, Huiying Zhou4, Yaxin Duan4, Enle Xiao4, Guangtao Zhu4 and Chunzhi Zhang1*   

  1. 1. State Key Laboratory of Genome and Multi-omics Technologies, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
    2. School of Life Sciences, Henan University, Kaifeng 475004, China
    3. Shenzhen Research Institute of Henan University, Shenzhen 518000, China
    4. School of Life Sciences, Yunnan Key Laboratory of Potato Biology, Southwest United Graduate School, Yunnan Normal University, Kunming 650500, China
    These authors contributed equally to this article.
    *Correspondences: Chunzhi Zhang (zhangchunzhi01@caas.cn, Dr. Zhang is fully responsible for the distribution of all materials associated with this article); Kaiyuan Chen (chenkaiyuan@caas.cn)
  • Received:2025-12-16 Accepted:2026-03-26 Online:2026-04-20
  • Supported by:
    This study is supported by the National Key Research and Development Program of China (2021YFD1201400), the National Natural Science Foundation of China (32488302 and U2002204), the Agricultural Science and Technology Innovation Program (CAAS-ZDRW240204), and China Postdoctoral Science Foundation (2023M733833).

Abstract: Pre-messenger RNA (pre-mRNA) splicing is a critical mechanism for post-transcriptional regulation in plants. Through alternative splicing, plants produce diverse transcriptomes and proteomes that finely regulate development as well as responses to biotic and abiotic stresses. However, modulating the generation of specific splicing isoforms for functional characterization remains challenging, particularly in the non-model crop potato. Here, we show that two optimized TadA-derived base editors efficiently induce diverse mRNA splice variants by targeting specific splice sites. By evaluating multiple adenosine deaminases and performing multi-dimensional optimization, we developed an efficient adenine base editor RTF-ABE8e for potato. RTF-ABE8e achieved 100% editing efficiency at two StDL1 target sites in stable transgenic potato, with homozygous editing frequencies as high as 93.3% and 91.1%, respectively. We also developed RTF-TadDE, a dual-base editor based on a TadA-derived dual deaminase, for A-to-G and C-to-K (K = T/G) mutations in potato with an overall editing efficiency comparable to that of RTF-ABE8e. By targeting different splice sites with these base editors, we obtained diverse splicing isoforms carrying premature termination codons (PTCs) at StDL1 and StPDS and robust mutant phenotypes. These base editors enable efficient and precise editing of splice sites to trigger missplicing, making them powerful tools for manipulating splicing in plants.

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