Papaya (Carica papaya L.) is widely valued for vitamins, minerals, dietary fiber, and papain, an enzyme used in food, pharmaceutical, and cosmetic industries. Yet papaya improvement remains difficult because production is affected by papaya ringspot virus (PRSV), limited genetic diversity, and sex separation. Modern genome editing offers new possibilities, but conventional Agrobacterium-mediated transformation in papaya is inefficient, time-consuming, and strongly influenced by genotype. Base editing can introduce precise single-nucleotide changes, but suitable tools for papaya have been lacking. Due to these challenges, in-depth research is needed to develop faster, more efficient, and more precise genome-editing systems for papaya.
Researchers from Fujian Agriculture and Forestry University, Southern University of Science and Technology, the Chinese Academy of Tropical Agricultural Sciences, and the University of Illinois at Urbana-Champaign reported (DOI: 10.1093/hr/uhag049) the study in Horticulture Research on February 20, 2026. The paper presents a streamlined cut–dip–budding (CDB)-based hairy-root system for papaya gene editing. The study further reports ABE and cytosine base editor (CBE) toolboxes, marking the first precise single-nucleotide editing systems developed for papaya and offering a new platform for papaya genome research and breeding.
The researchers first used Agrobacterium rhizogenes K599 and the RUBY reporter gene to induce and visually identify transformed hairy roots. Tests across explant types and seedling stages showed that young true leaves were suitable materials for hairy-root induction. The team then targeted two sex-related candidate genes, CpGASA and CpWIP3, using clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 constructs. In hairy-root assays, about 43% of transgene-positive roots targeting CpGASA and 55% targeting CpWIP3 carried edits at the intended sites. After pre-validating active CpWIP3 single-guide ribonucleic acids (sgRNAs), the researchers moved to stable transformation and detected CRISPR/Cas9-induced mutations in 23 of 29 transgenic lines, reaching 79.3% editing efficiency. They also screened promoters to build adenine base editor (ABE) and CBE systems. Some ABE combinations achieved 100% adenine-to-guanine conversion, while optimized CBE constructs produced efficient cytosine editing at selected CpGASA sites.
The authors said the study changes how gene-editing tools can be tested in papaya. Instead of spending months on stable transformation before knowing whether a guide or editor works, researchers can first evaluate candidate tools in hairy roots and select the most promising ones. They said this pre-screening step is especially important for crops with slow or difficult transformation systems. By combining rapid validation with precise base editing, the platform gives papaya researchers a more reliable way to connect candidate genes with useful traits and to move precision breeding closer to practical application.
The implications extend beyond one technical workflow. A reliable editing system can help researchers investigate papaya sex determination, fruit quality, disease resistance, and other traits important for breeding. Editing genes such as CpWIP3 and CpGASA may deepen understanding of reproductive development and support the future design of more predictable breeding materials. The ABE and CBE toolboxes also enable single-base changes without relying mainly on insertions or deletions from conventional CRISPR/Cas9 editing. Although further optimization is still needed, especially for root-to-shoot regeneration and target-dependent editing performance, this platform lays an important foundation for precision papaya breeding and may benefit other recalcitrant tropical crops.
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References
DOI
10.1093/hr/uhag049
Original Source URL
https://doi.org/10.1093/hr/uhag049
Funding information
This work was supported by the National Natural Science Foundation of China (grant no. 32472697) to J.J.Y. and Natural Science Foundation of Fujian Province of China (2024 J09026) to J.J.Y..
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.