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Hybrids between divergent populations commonly show hybrid sterility; this reproductive barrier hinders hybrid breeding of the japonica and indica rice ( Oryza sativa L.) subspecies. Here we show that structural changes and copy number variation at the Sc locus confer japonica–indica hybrid male sterility. The japonica allele, Sc-j , contains a pollen-essential gene encoding a DUF1618-domain protein; the indica allele, Sc-i , contains two or three tandem-duplicated ~ 28-kb segments, each carrying an Sc-j -homolog with a distinct promoter. In Sc-j / Sc-i hybrids, the high-expression of Sc-i in sporophytic cells causes suppression of Sc-j expression in pollen and selective abortion of Sc-j -pollen, leading to transmission ratio distortion. Knocking out one or two of the three Sc-i copies by CRISPR/Cas9 rescues Sc-j expression and male fertility. Our results reveal the gene dosage-dependent allelic suppression as a mechanism of hybrid incompatibility, and provide an effective approach to overcome the reproductive barrier for hybrid breeding. A reproductive barrier between japonica and indica rice subspecies hinders hybrid breeding. Here, the authors reveal that structural and copy number variations of a pollen-essential gene, which encodes a DUF1618-domain protein, result in allelic suppression and subsequently cause hybrid male sterility.

As an efficient gene editing tool, the CRISPR/Cas9 system has been widely employed to investigate and regulate the biosynthetic pathways of active ingredients in medicinal plants. CRISPR technology holds significant potential for enhancing both the yield and quality of active ingredients in medicinal plants. By precisely regulating the expression of key enzymes and transcription factors, CRISPR technology not only deepens our understanding of secondary metabolic pathways in medicinal plants but also opens new avenues for drug development and the modernization of traditional Chinese medicine. This article introduces the principles of CRISPR technology and its efficacy in gene editing, followed by a detailed discussion of its applications in the secondary metabolism of medicinal plants. This includes an examination of the composition of active ingredients and the implementation of CRISPR strategies within metabolic pathways, as well as the influence of Cas9 protein variants and advanced CRISPR systems in the field. In addition, this article examines the long-term impact of CRISPR technology on the progress of medicinal plant research and development. It also raises existing issues in research, including off-target effects, complexity of genome structure, low transformation efficiency, and insufficient understanding of metabolic pathways. At the same time, this article puts forward some insights in order to provide new ideas for the subsequent application of CRISPR in medicinal plants. In summary, CRISPR technology presents broad application prospects in the study of secondary metabolism in medicinal plants and is poised to facilitate further advancements in biomedicine and agricultural science. As technological advancements continue and challenges are progressively addressed, CRISPR technology is expected to play an increasingly vital role in the research of active ingredients in medicinal plants.

Ginsenosides, the primary bioactive components of Panax ginseng, exhibit diverse pharmacological properties, ranging from anticancer to neuroprotective effects. However, traditional production by ginseng cultivation faces limitations due to extended growth cycles, insufficient yields, intricate extraction processes, and significant environmental dependencies. Synthetic biology and synthetic metabolic engineering offer promising alternatives for sustainable manufacturing of essential bioactive compounds, including ginsenosides. First, this review describes the ginsenoside biosynthesis pathways, emphasizing crucial enzymes (e.g., HMG-CoA reductase, squalene epoxidase, dammarenediol-II synthase, amyrin synthase, and various UDP-glycosyltransferases) and their regulatory networks. Understanding these fundamental pathways enables rational engineering of production systems. Second, it examines current synthetic biology approaches, encompassing plant cell, tissue, and hairy root cultures, engineered microbial hosts including Saccharomyces cerevisiae and Escherichia coli, and cell-free enzymatic synthesis. Third, it evaluates the medicinal significance, market prospects, and industrial feasibility of these biomanufactured compounds. Finally, it analyzes the sustainability of production models and explores the emerging potential of engineered plant chassis. These advanced methodologies directly address traditional agricultural constraints and establish a robust framework for future ginsenoside synthesis.

Research into plant gene function is crucial for developing strategies to increase crop yields. The recent introduction of large language models (LLMs) offers a means to aggregate large amounts of data into a queryable format, but the output can contain inaccurate or false claims known as hallucinations. To minimize such hallucinations and produce high‐quality knowledge‐based outputs, the s of over 60 000 plant research articles are compiled into a Chroma database for retrieval‐augmented generation (RAG). Then linguistic data are used from 13 993 Arabidopsis (Arabidopsis thaliana) phenotypes and 23 323 gene functions to fine‐tune the LLM Llama3‐8B, producing PlantGPT, a virtual expert in Arabidopsis phenotype–gene research. By evaluating answers to test questions, it is demonstrated that PlantGPT outperforms general LLMs in answering specialized questions. The findings provide a blueprint for functional genomics research in food crops and demonstrate the potential for developing LLMs for plant research modalities. To provide broader access and facilitate adoption, the online tool http://www.plantgpt.icu is developed, which will allow researchers to use PlantGPT in their scientific investigations. PlantGPT integrates 60 000+ plant research articles with Arabidopsis phenotype‐gene data through retrieval‐augmented generation and fine‐tuning of Llama3‐8B. This open‐source, specialized AI system outperforms general large language models in plant gene‐phenotype relationships, establishing a new paradigm for functional genomics research and molecular design breeding.

Proanthocyanidins (PAs) play an important role in plant disease defense and have beneficial effects on human health. We isolated and characterized a novel R2R3 MYB-type PA-regulator SsMYB3 from a well-known ornamental plant, coleus (Solenostemon scutellarioides), to study the molecular regulation of PAs and to engineer PAs biosynthesis. The expression level of SsMYB3 was correlated with condensed tannins contents in various coleus tissues and was induced by wounding and light. A complementation test in the Arabidopsis tt2 mutant showed that SsMYB3 could restore the PA-deficient seed coat phenotype and activated expression of the PA-specific gene ANR and two related genes, DFR and ANS. In yeast two-hybrid assays, SsMYB3 interacted with the Arabidopsis AtTT8 and AtTTG1 to reform the ternary transcriptional complex, and also interacted with two tobacco bHLH proteins (NtAn1a and NtJAF13-1) and a WD40 protein, NtAn11-1. Ectopic overexpression of SsMYB3 in transgenic tobacco led to almost-white flowers by greatly reducing anthocyanin levels and enhancing accumulation of condensed tannins. This overexpression of SsMYB3 upregulated the key PA genes (NtLAR and NtANR) and late anthocyanin structural genes (NtDFR and NtANS), but downregulated the expression of the final anthocyanin gene NtUFGT. The formative SsMYB3-complex represses anthocyanin accumulation by directly suppressing the expression of the final anthocyanin structural gene NtUFGT, through competitive inhibition or destabilization of the endogenous NtAn2-complex formation. These results suggested that SsMYB3 may form a transcription activation complex to regulate PA biosynthesis in the Arabidopsis tt2 mutant and transgenic tobacco. Our findings suggest that SsMYB3 is involved in the regulation of PA biosynthesis in coleus and has the potential as a molecular tool for manipulating biosynthesis of PAs in fruits and other crops using metabolic engineering.

Base editing enables precise nucleotide substitutions within a relatively broad editing window (5–6 nucleotides). However, considerable bystander editing significantly compromise its accuracy. Point mutagenesis, a powerful approach for gradient‐tuning protein function, facilitates the generation of diverse plant phenotypes to meet the demands of complex environments and consumer preferences. Here, a series of plant base editors is engineered by fusing three optimized TadA8e variants, TadA9, TadA‐LM, and TadA‐dual, with a PAM‐flexible SpRY nickase (SpRYn, with 5′‐NNN PAM recognition). These editors enable A‐to‐G, C‐to‐T, and dual‐base (simultaneous A‐to‐G and C‐to‐T) conversions within a highly condensed active window (1–3 nucleotides). Performance evaluations reveal that the TadDBE (TadA Dual‐Base Editor) achieves the most robust outcomes, delivering dual‐base editing efficiencies ranging from 2.3% to 61.4%, while maintaining minimal off‐target activity. Utilizing TadDBE, targeted point mutagenesis is performed on OsBadh2, a gene encoding betaine aldehyde dehydrogenase that plays a critical role in the biosynthesis of 2‐acetyl‐1‐pyrroline (2‐AP), a key aromatic compound. This approach yields rice lines exhibiting gradient‐tuned aromatic profiles and optimized levels of 2‐AP and γ‐aminobutyric acid (GABA). These evolved TadA‐derived editors provide a precise, PAM‐flexible platform for base editing and represent a versatile strategy for generating genome‐edited plants with gradient‐tuned agronomic traits. Base editing enables precise nucleotide substitutions but limited by bystander editing. This study engineers plant base editors by fusing optimized TadA variants with PAM‐flexible SpRY nickase, enabling A‐to‐G, C‐to‐T, and dual‐base conversions in a highly condensed window (≤3 nucleotides). Additionally, TadDBE (TadA Dual‐Base Editor)‐mediated directed evolution in OsBadh2 generats gradient‐tuned 2‐AP and GABA contents in rice, offering a precise and effective platform for crop breeding.