CARBON Newsletter (28 January 2025) - Your Latest News About CRISPR in AgroBio

Top picks

• China’s Ministry of Agriculture and Rural Affairs have granted Qi Biodesign three approvals for gene edited crop traits for nationwide cultivation until the end of 2029. The edited crops are: 1) Soybean with mutant GmLn gene for improved yield; 2) Wheat with mutant TaALS gene for ALS herbicide resistance; and 3) Rice with mutant waxy Wx gene for improved quality. Read the official statement in Chinese here.
• Qi Biodesign, based in China, has also secured funding of $75 million in total funding to advance its proprietary CRISPR-Cas-based SEEDIT platform, featuring RNA-guided nucleases, base editors, and PrimeRoot editors for precision genome editing. The funds will support R&D, product development, and commercialisation of gene-edited crops, including high oleic acid soybean and disease-resistant wheat, driving innovations in agriculture for sustainability and food security.

Technical advances

• Researchers in Germany have developed CRISPR-Cas9 tools for the fern Ceratopteris richardii, including Cas9 expression under the CaMV 35S promoter and U6 promoters for sgRNA transcription. These advances simplify genome engineering in ferns, overcoming past technical barriers and enabling studies on fern physiology, development, and evolution, with potential applications in understanding plant biology and evolution more broadly.
• American researchers present a tRNA-processing-based strategy to enhance CRISPR-Cas9 multiplex genome editing, enabling precise production of multiple gRNAs from a single polycistronic gene. Applied in rice, the system achieved high-efficiency multiplex editing and chromosomal deletions, offering a versatile and broadly applicable tool for improving CRISPR-Cas9 targeting and editing capabilities across diverse organisms.
• A new CRE.AI.TIVE platform leverages CRISPR-Cas and machine learning to upregulate plant gene activity by predicting and validating sequence variants without prior knowledge of cis-regulatory elements. Using transcriptomic and epigenomic datasets, the system combines in silico mutagenesis with protoplast-based massively parallel reporter assay (MPRA). Functional promoter variants of the tomato gene SlbHLH96 were successfully identified and validated, providing a scalable approach for precision gene regulation in plant biotechnology.
• DNA-free CRISPR-Cas9 genome editing in raspberry has been achieved for the first time by developing a novel protoplast isolation protocol. Using ribonucleoprotein complexes, researchers edited the phytoene desaturase gene with an efficiency of 19%. This method, which has not yet been peer-reviewed, preserves elite cultivar genetics and regulatory non-transgenic status, providing a platform for precision breeding and functional genomics in raspberry.
• Researchers have engineered the hypercompact CRISPR-Cas12j-8 nuclease and its crRNA, significantly boosting genome editing efficiency in soybean and rice. The enhancements enabled previously uneditable target sites to be modified and, in some cases, matched SpCas9 efficiency. Engineered Cas12j-8-based cytosine base editors showed a 5.36- to 6.85-fold increase in C-to-T editing efficiency without indels, establishing it as a powerful tool for plant genome editing and base editing.
• An optimised tape sandwich method for chili leaf protoplast isolation has achieved high yields and a 48.71% efficiency in GFP plasmid transfection using PEG-mediated delivery. Cas9 protein transfection efficiency reached 2.94%, limited by protein aggregation. This streamlined protocol significantly reduces isolation time and improves transfection efficiency, advancing genetic studies in recalcitrant crops like chili.

Disease and stress control

• CRISPR-Cas9 mutagenesis of SlHP2 and SlHP3 in tomato improved drought tolerance by reducing stomatal density, enhancing water retention, and promoting deeper root growth. Double mutants (slhp2,3-10 and slhp2,3-11) exhibited lower oxidative stress and downregulated cytokinin signalling and stomatal differentiation genes under PEG-induced stress.

Agronomic traits

• CRISPR-Cas base editing has been used to repair a deleterious mutation in the SSP2 gene of domesticated tomatoes, improving shoot architecture and enabling early fruit yield. This study demonstrates how correcting harmful mutations accumulated during domestication can fine-tune crop traits, providing a precise approach for predictable agricultural improvements.
• CRISPR-Cas9 has been used to knock out FIS1 and PL genes, enhancing tomato firmness without compromising overall fruit quality. Double knockouts showed the greatest firmness improvement, demonstrating the tool’s efficiency in generating transgenic-free mutants across fewer generations. This approach provides a promising strategy for accelerating tomato breeding with improved storability.

Industry

• The American biotech company Inari has raised $144 million, bringing its total equity funding to over $720 million, to advance its CRISPR-Cas-driven multiplex gene editing technology SEEDesign. The company focuses on AI-powered seed design for large-acre crops, aiming to enhance yields and sustainability in soybeans, corn, and wheat.
• Cibus Inc. has standardised its proprietary RTDS gene editing process, enabling precise, multi-edit trait development in crops like rice (herbicide tolerance) and canola (disease resistance) within 12 months. This timebound, predictable system accelerates trait commercialisation and supports regulatory classification akin to natural or conventionally bred traits, avoiding GMO designation.
• The UK-based startup Phytoform Labs has used CRISPR-Cas gene editing to create a compact tomato plant tailored for vertical farming, producing up to 400% more fruit per square metre. The miniaturised variety allows denser planting and faster crop cycles without reducing fruit size.
• The plant breeding market, valued at USD 14.8 billion in 2023, is set to grow at a 12.8% CAGR through 2032, with CRISPR-Cas9 driving transformative advancements. This powerful genome editing tool enables precise genetic modifications, fostering crops with enhanced nutrition, pest resistance, and stress tolerance to meet the rising demand for resilient, high-yielding varieties. North America leads the way, leveraging CRISPR technologies alongside strong R&D investments and government support to shape the future of sustainable agriculture.

Detection

• Researchers in China have developed a PCR-based screening method to efficiently identify CRISPR-Cas-induced mutations in large T1 plant populations. By leveraging T0 sequencing data, the approach uses dual-primer PCR for ≥4 bp indels and dCAPS for 1–2 bp indels to distinguish wild-type, heterozygous, and homozygous genotypes.
• A novel LAMP-HNB assay can detect Cas9 cassettes in genome-edited plants, enabling rapid, cost-effective identification of modifications. The method amplifies DNA in 30 minutes with a colour change from violet to sky blue, detecting single DNA copies. This isothermal system provides a sensitive tool for monitoring CRISPR-Cas edits, addressing biosecurity concerns in agricultural biotechnology.
• Researchers in South Africa have developed an recombinase polymerase amplification (RPA) and Cas12a assay for rapid, sensitive detection of Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4), a major threat to banana production. The isothermal assay detects as little as 10 fg of target DNA with no cross-reactivity and enables field detection via blue-light visualisation. This portable method could enhance early detection and containment of Foc TR4 outbreaks.

Commentaries and perspectives

• According to a blog post on the ISAAA website, 2024 brought significant strides globally to gene editing, with crops like high-protein soybeans, disease-resistant wheat, and reduced-lignin maize gaining approvals and field trials. Countries including Thailand, Uruguay, and New Zealand updated regulations to support genome-edited crops, while the EU confirmed the safety of new genomic techniques. These advancements highlight gene editing’s growing role in sustainable agriculture and global food security.
• To ensure food security amidst the growing challenges of climate change, a new study proposes two primary strategies to improve crops’ abiotic stress tolerance: "rewilding" domesticated crops by reintroducing stress tolerance genes lost during domestication and de novo domestication of resilient wild plants. The study underscores that both strategies face technical and societal barriers, including the need for policy reforms to streamline gene-editing regulations and broader public acceptance of genetically engineered crops.
• An article in Food Engineering Magazine examines the regulatory and patent challenges surrounding CRISPR gene editing in agriculture, highlighting its potential to sustainably boost crop production while addressing environmental and food security issues. It explores the distinction between gene-edited and genetically modified crops, the complex global patent landscape, and differing regulatory frameworks across countries, emphasising the need for adaptive strategies to advance CRISPR’s adoption in agriculture.
• A feature in Seed World finds that legal complexities surrounding CRISPR-Cas9 patents are complicating its commercial use, with disputes among key players like the Broad Institute, UC Berkeley, and ToolGen affecting access and licensing globally. Calgary-based AgGene is navigating this uncertain landscape while seeking licensing for its gene editing platform, balancing costs, efficiency, and long-term IP considerations. Canada’s evolving CRISPR patent system exemplifies how these disputes influence biotech innovation and accessibility.

Reviews

• Application of CRISPR/Cas9 in the Improvement of Industrially Important Crops. This book chapter highlights the transformative potential of CRISPR-based genome editing for precisely enhancing traits in industrial crops, emphasising its efficiency, non-transgenic applications, and capacity to accelerate breeding while addressing regulatory and technical challenges.
• Genetic Improvement of rice Grain size Using the CRISPR/Cas9 System. This review highlights key genes influencing grain size and explores how precise gene modifications using CRISPR-Cas9 can optimise these traits.
• CRISPR/Cas9 and its derivatives to improve crop biotic stress resistance: Current status and prospects. This review summarises recent advancements in CRISPR-Cas9 and related genome editing technologies for enhancing plant resistance to biotic stressors, including pathogens, pests, and parasites, while discussing future challenges and opportunities in this field.
• Application and development of CRISPR technology in the secondary metabolic pathway of the active ingredients of phytopharmaceuticals. This review explores the applications of CRISPR-Cas9 in regulating secondary metabolism and enhancing active ingredient yield and quality in medicinal plants, while addressing challenges and future prospects in this field.
• Critical considerations and computational tools in plant genome editing. This review explores recent advances in CRISPR-Cas plant genome editing, focusing on regulatory exemptions, essential factors for experimental design, and the critical role of computational tools in construct optimisation, mutation detection, and minimising off-target effects.
• CRISPR/Cas9-Based Genome Engineering in Plants for Enhancing Disease Resistance. This book chapter discusses the application of CRISPR-Cas9 in enhancing plant disease resistance, focusing on its potential as a sustainable alternative to pesticides, strategies for improving precision and efficiency, and its transformative role in developing durable, pathogen-resistant crops.
• Breeding Plants Resilient to Climate Change. This book chapter highlights how CRISPR-Cas genome editing and advanced breeding techniques can develop climate-resilient crops to mitigate the impacts of climate change on biodiversity, agriculture, and food security.

Conferences

• The 7th CRISPR AgBio Congress will be held on 4-6 February 2025 in Raleigh, NC, focusing on cutting-edge gene editing for agriculture. Key themes include CRISPR advancements, delivery systems, regulatory pathways, commercialisation, and consumer acceptance. Sessions highlight innovations in crop resilience, biocontrol, and product development, showcasing strategies to accelerate gene-edited products while addressing sustainability and global food security challenges.