Synergistic design nearly triples potato base editing efficiency

A research team has developed a highly efficient cytosine base editing platform for potato, overcoming a major barrier to precise improvement of this genetically complex crop. By combining stronger expression elements with strategies that open chromatin, the researchers increased average editing efficiency from 26.8% to 76.7% in a hairy-root test system. The optimized editor also precisely modified two acetolactate synthase genes, StALS1 and StALS2, and produced potato lines that resisted the herbicide chlorsulfuron without obvious growth penalties. The work provides a practical route for creating targeted traits in potato while limiting unwanted insertions and deletions, and it offers a broader design framework for improving clustered regularly interspaced short palindromic repeats (CRISPR)-based editing tools in crops. 

Potato (Solanum tuberosum) is a major food crop, but its highly heterozygous and often tetraploid genome makes conventional breeding and functional gene analysis unusually difficult. Because potato is mainly propagated vegetatively, harmful mutations can accumulate and may remain tightly linked to valuable alleles, making them hard to remove through repeated crossing. Cytosine base editors (CBEs), which convert selected cytosines to thymines without cutting both strands of deoxyribonucleic acid (DNA), could address this problem, yet previously reported potato systems have offered limited efficiency, narrow functional choice, or insufficient species-specific optimization. Based on these challenges, in-depth research is needed to develop efficient, precise, and adaptable base editing systems tailored to potato breeding and gene-function studies.

Researchers from the Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences; the School of Life Sciences at Henan University and its Shenzhen Research Institute; and the Yunnan Key Laboratory of Potato Biology at Yunnan Normal University reported (DOI: 10.1093/hr/uhag122) the study in Horticulture Research on April 7, 2026. The team systematically compared cytidine deaminases, expression-control elements, and chromatin-accessibility strategies, then combined the strongest components into optimized potato CBEs. They further tested whether the best-performing editor could create stable herbicide-resistant germplasm through simultaneous editing of StALS1 and StALS2.

The researchers first compared five cytidine deaminases in an Agrobacterium rhizogenes-mediated hairy-root assay. Sdd7 delivered the highest mean editing efficiency, 46.7%, with a low insertion and deletion (InDel) frequency, whereas CDA1 provided a broader editing window. They then strengthened editor expression with the Arabidopsis thaliana ribosomal protein S5A (RPS5A) promoter and tobacco mosaic virus (TMV) Ω enhancer, and co-expressed the human fat mass and obesity-associated gene (hFTO), which encodes a ribonucleic acid (RNA) N6-methyladenosine demethylase, to improve chromatin accessibility. Adding chromatin-modulating peptides (CMPs) derived from high mobility group protein HMGN1 and human histone H1 produced further gains: CDA1-HNHN reached an average efficiency of 80.6%, compared with 25.9% for CDA1, without a significant increase in InDels. The final mini-Sdd7-based editor, RF-Sdd7-HNHN, achieved 65.6%–87.4% editing across three test loci and raised the mean to 76.7%, about 2.9-fold above the unoptimized editor. In stable potato plants, it precisely edited the target residues in both StALS1 and StALS2 in 85.7% of lines, with no off-target changes detected at predicted sites. Edited plants rooted and grew on chlorsulfuron-containing medium and remained healthy after greenhouse spraying, while wild-type controls either failed to root in culture or wilted after spraying.

In explaining the significance of the results, the authors said the advance lies not in a single molecular component, but in combining several complementary improvements into one editing system. Stronger expression increased the amount of editing machinery, while chromatin-focused strategies made target DNA more accessible and helped the editor work more consistently. They said the comparison between Sdd7- and CDA1-based systems also gives researchers a clear choice: a narrower, cleaner editing window for precision breeding, or a broader window for applications such as saturation mutagenesis. This modular approach could make crop genome editing easier to adapt to different biological goals.

The optimized platform could accelerate potato functional genomics, repair harmful alleles that are difficult to separate from useful traits, and support faster development of varieties with improved agronomic performance. Its successful use in herbicide-resistance breeding also suggests a route for coupling acetolactate synthase (ALS) editing with selection of other desired edits, potentially helping researchers recover edited plants more efficiently. Beyond potato, the same design logic may improve adenine base editors, prime editors, and other genome-editing systems in crops with limited editing resources. Before agricultural deployment, however, the approach will require broader testing across potato genotypes, multi-season field evaluation, careful assessment of unintended edits, and consideration of regulatory and stewardship requirements for herbicide-resistant germplasm.

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References

DOI

10.1093/hr/uhag122

Original Source URL

https://doi.org/10.1093/hr/uhag122

Funding information

This study is supported by China National Key Research and Development Program (2023YFF1000400) and China Postdoctoral Science Foundation (2023 M733833).

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, 2023. 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.