CARBON Newsletter (19 June 2026) - Your Latest News About CRISPR in AgroBio

Top picks

• The European Parliament has given final approval to the EU's New Genomic Techniques regulation, completing the legislative process after the Council's adoption in April. The framework treats NGT-1 plants – including many produced by CRISPR-Cas editing – as equivalent to conventionally bred varieties, exempting them from the stricter GMO rules in force since 2001. NGT-2 that have undergone more extensive or complex genetic modifications are still covered by the existing strict GMO rules and will be subject to risk assessment.
• Multiplex CRISPR-Cas editing of Sl7-DR2, SlGAD3, SlSGR1, SlGGP1 and SlGGP2 generated tomato lines simultaneously enriched in seven health-promoting compounds, including vitamins D₃ and C, β-carotene, lycopene and GABA. The multibiofortified tomatoes showed no major growth or fruit-quality penalties and exhibited enhanced suppression of colorectal tumour growth in both in vitro and mouse models, demonstrating the potential of multiplex editing to create nutrient-dense functional foods.

Technical advances

• Prime editing efficiency in soybean was substantially improved by engineering the editor, including modification of the reverse transcriptase, incorporation of a viral nucleocapsid protein and suppression of mismatch repair through a dominant-negative GmMLH1 allele. The resulting GmPEplus system achieved editing efficiencies of up to 81.3%, while a Csy4-mediated multiplex platform enabled simultaneous editing of up to 12 genes, providing efficient and heritable genome-editing tools for soybean breeding.
• Researchers have expanded CRISPR-Combo technology by incorporating iSpyMacCas9, enabling simultaneous genome editing and activation of the morphogenic gene OsBBM1 in rice. Activation of OsBBM1 increased hormone-free plant regeneration rates to 42% and improved both single-target and multiplex editing efficiencies, establishing iSpyMacCas9-Combo as a more effective platform for editing challenging genomic targets in rice.
• Researchers have developed a highly efficient Agrobacterium-mediated transformation platform for black pepper using nucellar apomixis-derived embryos, overcoming a major barrier to genetic improvement in this crop. The method achieved >90% transformation efficiency, 99% survival of transgenic plants and 89% CRISPR-Cas9 editing efficiency of Pds, while bioreactor-based propagation enabled large-scale production of transformed and genome-edited plants.
• An AI-designed CRISPR nuclease, OpenCRISPR-1, was adapted for rice and shown to support efficient gene knockout, base editing and prime editing with performance broadly comparable to SpCas9. The platform also enabled stable genome editing in regenerated plants and, in some contexts, achieved higher base-editing efficiencies, highlighting the potential of AI-generated nucleases for plant genome engineering.
• A new efficient protoplast platform for pear and other woody species enables DNA-free multiplex genome editing using CRISPR-Cas9 ribonucleoproteins. Simultaneous editing of PbrARC3, PbrPARC6 and PbrFtsZ2-1a reproduced chloroplast division defects and revealed downstream stress-signalling responses, thereby demonstrating a rapid system for trait validation, functional genomics and transgene-free precision breeding in woody crops.
• A twin prime editing-based knockout system (TKO) introduced stop codon clusters to generate precise gene knockouts with fewer in-frame mutations than Cas9, achieving high editing efficiencies in rice, maize and wheat. The approach enabled multiplex knockout of up to ten genes and, when combined with conventional prime editing in the TRIM1 and TRIM2 platforms, supported simultaneous gene disruption, precise sequence editing and kilobase-scale DNA insertion.
• To improve CRISPR-Cas9 editing in kenaf (Hibiscus cannabinus), a team identified two endogenous U6 promoters – HcU6-1 and HcU6-14 – using the AtU6-26 promoter as a reference, finding HcU6-14 to be the more transcriptionally active in GUS assays. Vectors targeting the ALS gene via Agrobacterium rhizogenes-induced hairy roots yielded mutations only with the HcU6-14 promoter, not the exogenous cotton GbU6-9 promoter, confirming the endogenous promoter's superior editing efficiency.
• Researchers optimised tissue culture, Agrobacterium-mediated transformation and CRISPR-Cas9 delivery for several commercially relevant heirloom tomato cultivars, overcoming a major barrier to genome editing in these varieties. The improved platform enabled the generation of edited plants targeting traits such as plant architecture and flowering time, establishing a foundation for precision breeding of heirloom tomatoes while preserving their distinctive flavour characteristics.

Disease and stress control

• CRISPR-Cas9 knockout and overexpression analyses revealed that SlASR4 is a positive regulator of drought tolerance in tomato. The transcription factor enhanced water retention, antioxidant defences and stress-responsive gene expression under drought conditions, while its interaction with phloem protein 2 (SlPP2) identified a previously unknown mechanism linking SlASR4 to reactive oxygen species homeostasis and stress adaptation.
• CRISPR-Cas9 knockout of OsDCR revealed that this BAHD acyltransferase-like protein positively regulates salt tolerance in rice. Overexpression of OsDCR enhanced tolerance to salinity, reduced oxidative damage and increased abscisic acid accumulation, while interaction studies identified OsPRP3 as a downstream partner contributing to the stress-response pathway.
• A tissue-specific CRISPR-Cas9 knockout strategy targeting OsPHO2 or OsSPX1/2 in rice vascular tissues improved phosphate-deficiency tolerance without the growth penalties typically associated with whole-plant disruption of phosphate-starvation regulators. The edited plants maintained phosphate homeostasis, increased tiller number and grain yield under low-phosphate field conditions, demonstrating how spatially restricted genome editing can balance stress adaptation with crop productivity.
• A CRISPR-Cas9 genetic screen identified OsDT2 as a positive regulator of drought tolerance in rice. OsDT2 forms a conserved transcriptional complex with OsbZIP66 and OsNF-YC4 to activate drought-responsive genes such as OsLEA3, and overexpression enhanced drought resistance. The DT2-bZIP66-NF-YC4 regulatory module was conserved across rice, wheat, maize and Arabidopsis, highlighting a promising target for engineering drought-resilient crops.

Agronomic traits

• CRISPR-Cas9-mediated mutagenesis of HWS and GAD3 generated tomato plants with increased sugar and GABA content alongside facultative parthenocarpy, particularly under high-temperature conditions. The study linked the parthenocarpic phenotype to altered hormone-regulated fruit development, suggesting that simultaneous editing of HWS and GAD3 could improve both fruit quality and climate resilience in tomato.
• CRISPR-Cas9-generated osbadh1osbadh2 double mutants accumulated 7.1-fold more 2-acetyl-1-pyrroline than wild-type rice, exceeding the increase seen in osbadh2 single mutants. However, the enhanced fragrance was accompanied by reduced GABA levels and markedly lower tolerance to drought and salinity stress, revealing a trade-off between aroma improvement and abiotic stress resilience.
• Multiplex CRISPR-Cas9 knockout of all 10 TREHALOSE-6-PHOSPHATE PHOSPHATASE (TPP) genes in Arabidopsis uncovered extensive functional redundancy that had masked their biological roles. The resulting mutants showed increased branching, earlier flowering, disrupted trehalose 6-phosphate metabolism, iron deficiency and chlorosis, revealing that TPP-mediated signalling coordinates plant development, sugar metabolism, iron homeostasis and photosynthetic function.
• CRISPR-Cas9 knockout of MeSSI in cassava increased resistant starch content 6.7-fold and amylose levels by 16.4% without reducing total starch accumulation or root yield. The edits altered amylopectin structure, starch granule morphology and thermal properties, while triggering compensatory changes in carbon metabolism, identifying MeSSI as a key target for improving the nutritional quality of cassava.
• CRISPR-Cas9 adenine base editing was used to introduce a W545R substitution in the sorghum SbALS gene, generating plants with strong resistance to the ALS-inhibiting herbicide imazethapyr. The edited allele conferred herbicide tolerance in greenhouse and field trials without affecting key agronomic traits, demonstrating the feasibility of precise base editing for sorghum improvement.
• CRISPR-Cas9 editing of a cis-regulatory element in the SD1 promoter enhanced TCP19 binding and strengthened repression of SD1 expression in Kam sweet rice. The resulting reduction in gibberellin production shortened plants without affecting yield, nitrogen-use efficiency or grain quality, demonstrating a precise alternative to gene knockout for crop improvement.

Industry

• Belgian startup Rainbow Crops has raised €9.7 million in seed funding to advance an AI-guided multiplex gene-editing platform designed to improve complex traits such as yield, drought tolerance and heat resilience. The company combines artificial intelligence, large-scale genome editing and high-throughput phenotyping to identify and engineer combinations of genes and regulatory elements, with the goal of accelerating crop breeding through the simultaneous modification of dozens of targets.
• Dutch plant biotechnology company Hudson River Biotechnology⁠ has licensed the Fulcrum gene-editing platform from Pairwise⁠, expanding its genome-editing capabilities for crop improvement programmes. The agreement gives Hudson River access to additional CRISPR-based editing tools, enzymes and trait libraries, which will be integrated into its services for vegetable, soft-fruit and other crop breeders developing transgene-free improved varieties.
• Tropic Bioscience, a UK biotechnology company, is using CRISPR-Cas gene editing to develop Cavendish bananas resistant to Tropical Race 4 (TR4), a fungal disease threatening global banana production. Field trials are underway in major growing regions, and the company expects commercial cultivation to begin in 2027, with harvests potentially reaching consumers in 2028.

Regulation

• Seed company KWS⁠ welcomes the new EU approval of New Genomic Techniques (NGT), saying it will allow genome editing to move from research into product development and field trials, potentially accelerating the development of crop varieties with improved resilience, plant health and resource-use efficiency.
• Agricultural biotechnology company Cibus⁠ said the framework validates its long-standing gene-editing approach and could accelerate deployment of crops with traits such as disease resistance, improved resource-use efficiency and reduced reliance on agricultural chemicals across European markets.

Detection

• A CRISPR-Cas12a-based fluorescence assay was developed to detect economically motivated adulteration in fruit juice by coupling target recognition to hybridisation chain reaction-mediated signal amplification. Applied to blueberry juice, the method enabled visual detection with high specificity and a detection limit of 19.5 fM, demonstrating sensitive identification of trace adulterants in complex food samples.

Reviews

• Engineering abiotic stress tolerance in cereal crops: current advances and future directions. This review examines how CRISPR-Cas genome editing, alongside genomic selection, multi-omics, artificial intelligence and speed breeding, is being integrated to improve abiotic stress tolerance and accelerate the development of climate-resilient cereal crops.
• Systematic review using PRISMA on CRISPR based genome editing and artificial intelligence approaches to enhance ornamental crops. This review highlights recent advancements in CRISPR-Cas technologies and AI applications, demonstrating their potential to improve ornamental traits such as flower colour and longevity while addressing challenges in precision and efficiency.
• Advancements in genome editing tools and technologies for improvement of horticultural crops. This review traces the evolution of genome editing in horticultural crops, from early site-directed nucleases to CRISPR-Cas and next-generation base and prime editors, alongside plant transformation systems and applications spanning architecture, nutritional quality, stress resistance and yield.
• Prime editing: evolution of CRISPR–Cas system for a robust next-generation genome editing in plants. This review traces the evolution of prime editors from PE1 to advanced variants such as PE7 and TwinPE, detailing protein engineering, pegRNA architecture and DNA-repair modulation alongside plant-adapted refinements – codon optimisation, promoter tuning and plant-compatible Cas9 and reverse transcriptase variants – for precision crop improvement.
• Genome engineering of plant photosynthesis for carbon sequestration. This review maps the molecular and physiological innovations needed to realise plant-based carbon dioxide removal at climate-relevant scales, surveying CRISPR-based strategies to boost photosynthetic efficiency and carbon sequestration alongside the regulatory and deployment challenges for genome-edited crops.
• CRISPR revolution in plant genetics: promises, challenges and future prospects. This review surveys CRISPR-Cas applications for crop improvement, contrasting the widely used Cas9 with Cas12a – noted for recognising A/T-rich sequences and processing its own guide RNA – across uses spanning trait enhancement, disease and pest management, stress tolerance and biofortification.
• Advances in CRISPR-Cas technology, mechanisms, applications, and ethical challenges. This review comprehensively examines the mechanisms, applications, and ethical considerations of CRISPR-Cas systems, highlighting their potential to revolutionize plant sciences while addressing concerns related to off-target effects and biosafety.
• Writing Big in Plant Genomes: Advances, Challenges and Strategies for Targeted Large-Fragment DNA Insertion. This review compares four toolkits for targeted DNA insertion in plants – nuclease-dependent strategies, recombinases, transposon-derived systems and CRISPR-Cas-coupled platforms – assessing capacity, efficiency and precision, and highlighting emerging approaches such as AI-guided design and RNA-guided transposition.
• Genome Editing in Root and Tuber Crop Development in Sub-Saharan Africa. This review synthesises recent advances in CRISPR-Cas9 editing of root and tuber crops – potato, cassava, sweet potato and yam – covering traits such as disease resistance, abiotic stress tolerance and nutritional quality, alongside transformation and regulatory constraints and emerging genotype-independent and DNA-free editing strategies.