CARBON Newsletter (26 November 2024) - Your Latest News About CRISPR in AgroBio

Top picks

• Europe's first field trial of CRISPR-edited Chardonnay vines has begun in Italy, targeting a DMR6 gene to enhance resistance to downy mildew. The gene encodes a protein that typically suppresses the plant's immune defence by limiting salicylic acid production. Conducted by EdiVite, the trial avoids GMO restrictions by excluding foreign DNA. The field study will test whether reduced susceptibility translates into lower fungicide use. Parallel efforts in Italy are advancing edited vines for powdery mildew resistance, signalling a shift in EU agricultural innovation towards sustainability. EdiVite also posted the news in a company press release.
• A new CRISPR-Cas system delivered via an RNA rhabdovirus vector has enabled non-transgenic gene editing in tobacco. The method targeted six berberine bridge enzyme-like protein (BBL) family genes, which are implicated in the last steps of pyridine alkaloid biosynthesis. Mutants with BBLa and BBLb inactivation showed drastic nicotine declines, with minor effects from other BBL genes. The agronomic evaluation identified viable low-nicotine lines, offering new genetic resources for breeding and insights into alkaloid biosynthesis pathways.

Technical advances

• Scientists in Japan have used CRISPR-Cas9 to generate hypomorphic alleles of the lethal ArabidopsisHPY2 gene by targeting mRNA splicing sites. Severe mutants caused seedling lethality, but the hypomorphic hpy2-cr3 allele produced partial-function proteins, allowing plants to survive and reproduce. This approach highlights CRISPR-Cas9's utility in creating viable knockdowns for functional analysis of essential genes.
• Scientists in India have demonstrated the use of Streptococcus pyogenestracr-L and its truncated variant Δtracr-L for genome editing in rice, alongside the standard tracr-S. While tracr-S showed superior cleavage efficiency in vitro, all tracrRNAs generated comparable indels in vivo at target genes. These findings expand the CRISPR-Cas toolkit for plant and eukaryotic genome editing with diverse tracrRNA options.
• The first chromosome-level genome assembly of Cryptomeria japonica (9.1 Gbp) has been achieved using PacBio HiFi and Hi-C sequencing. With CRISPR-Cas9 established for gene editing in this species, the high-quality assembly and ∼91% conserved genes identified via BUSCO provide a robust foundation for genetic studies, including precise genome editing, and insights into Cupressaceae and Pinaceae evolution.
• Indian researchers have established an Agrobacterium-mediated hairy root transformation and CRISPR-Cas9 editing system for Lathyrus sativus. Editing LsOCS, a gene linked to oxalate metabolism, caused oxalate accumulation without altering β-ODAP levels, which causes the motor neuron disease neurolathyrism. Complementation in Arabidopsis mutants confirmed LsOCS function. This system enables rapid functional analysis of Lathyrus genes, aiding efforts to reduce neurotoxin content and improve agronomic traits.

Disease and stress control

• CRISPR-Cas9 has been used to mutate OsCTS11, a novel cold-responsive gene in rice, enhancing seedling cold tolerance. The Chinese researchers used fine mapping to identify OsCTS11 within the qCTS11 QTL on chromosome 11. The gene, encoding a stress-enhanced protein, localises to chloroplasts and the nucleus. This research advances the understanding of cold tolerance mechanisms and offers genetic tools for developing resilient rice varieties.
• The crucial role of OsNCED4, an ABA biosynthesis gene, in rice tolerance to salt, cold, and drought stresses has been revealed by CRISPR-Cas9 knockout of the gene. Mutants showed reduced ABA levels, excessive ROS accumulation, and increased stress sensitivity. OsNCED4 offers a promising target for developing rice varieties with enhanced resilience to multiple abiotic stresses.
• CRISPR-Cas9 editing has confirmed the role of GL12, a MYB transcription factor from wild rice, in improving salt tolerance and grain length in cultivated rice. GL12W mutants showed reduced grain size and salt sensitivity, while overexpression increased cell expansion and regulated stress-related genes.

Agronomic traits

• Chinese scientists have achieved a significant advance in tomato agriculture by leveraging CRISPR-Cas9 to enhance sweetness without yield loss. Through a genome-wide association study (GWAS), SlCDPK27 and SlCDPK26 were identified as negative regulators that promote the degradation of a sucrose synthase by phosphorylating it, thereby functioning as a sugar brake. CRISPR-Cas9 was employed to inactivate these genes in cultivated tomato varieties, leading to up to 30% higher glucose and fructose levels in the fruits while overcoming the trade-off between fruit size and sugar content.
• CRISPR-Cas9 knockout of PtoCYP90D1 in Populus tomentosa has revealed its critical role in biomass production. Mutants show reduced growth compared to wild-type plants. Overexpression increased plant height, stem diameter, and cell wall components, enhancing biomass yield. These findings highlight PtoCYP90D1 as a target for the genetic improvement of poplar for industrial and agricultural applications.
• A high-efficiency tissue culture and CRISPR-Cas9 system has been developed for the medical plant Hemsleya chinensis, which contains antibacterial and anti-inflammatory compounds. Genome editing of HcOSC6, a key gene in the biosynthesis of cucurbitadienol, was successfully achieved, and edited lines showed reduced cucurbitadienol levels, while overexpression increased production. This platform facilitates functional studies and molecular breeding, advancing the understanding of medicinal compound biosynthesis in this species.

Industry

• A partnership between Pairwise and the International Institute of Tropical Agriculture (IITA) has received $3.9 million from the Bill & Melinda Gates Foundation to boost yam (Dioscorea spp) production through gene editing. The project goal is to reduce labour and environmental impact associated with traditional plant staking while also enabling mechanised farming in Nigeria, where yam is an important staple food crop.
• Corteva has announced a 2024-2027 strategy focused on tackling food security, climate change, and biofuel demand. Key initiatives include advanced gene editing for transformative farming, hybrid wheat with drought resilience, and $1 billion in annual revenues from biologicals by 2030. The company plans $1 billion in incremental sales, $1 billion in cost savings, and $4.5 billion in shareholder returns, underpinned by significant R&D investment.
• Corteva also reported third-quarter financial results, with a net loss of $519 million and $2.42 billion in cash. The loss was driven by a revenue decline, increased costs for raw materials and iR&D, and restructuring charges.
• Caribou Biosciences reported third-quarter financial results, with a net loss of $34.7 million and $281.0 million in cash.
• Bayer has reported third-quarter financial results, with a net loss of €4.18 billion and €1.148 billion in free cash flow. Sales in the company's Crop Science division decreased by 3.6 per cent to €3.986 billion.

Screening

• Researchers in Hong Kong have described a simple, rapid, low-cost, and sensitive method for screening CRISPR-Cas9-induced mutants in several plant species. The technique, PCR-Bsl I-associated analysis (PCR-BAA), combines standard PCR, Bsl I restriction digestion, and agarose gel electrophoresis to efficiently identify mutants, even in low-efficiency editing events, making it ideal for large populations of transformants.

Commentaries and perspectives

• An article in MIT Technology Review takes a closer look at how CRISPR is driving a "climate-adapted" revolution in agriculture, enabling precise genetic tweaks to enhance resilience in crops and livestock. Advances include drought-tolerant rice, storm-resistant corn, and methane-reducing cattle, but regulatory and ethical considerations remain critical as adoption grows. The author also interviews Jennifer Doudna, and she highlights CRISPR's efficiency over traditional breeding and its potential for scalable, sustainable food production, which is vital in combating climate-induced challenges.

Reviews

• Technological advancements in the CRISPR toolbox for improving plant salt tolerance. This review emphasises the transformative potential of CRISPR in modifying the central dogma to develop salt-tolerant crops, thereby contributing to sustainable agriculture and global food security.
• Genome editing in future crop protection: utilising CRISPR/Cas9 to improve crop resistance against diseases, pests, and weeds. This review highlights the transformative potential of genome editing in crop protection and calls for continued research and development in this field.
• Engineering cold resilience: implementing gene editing tools for plant cold stress tolerance. This review highlights the need for innovative approaches to enhance cold tolerance and underscores how genome-editing tools can deepen our understanding of genes involved in cold stress.
• CRISPR-based microalgal genome editing and the potential for sustainable aquaculture: a comprehensive review. This review shows microalgae's potential in sustainable aquaculture. It provides an assessment of current developments and successes in CRISPR-based genome editing in microalgae and the potential future uses of its metabolic engineering and gene editing strategies.
• CRISPR/Cas technology: fueling the future of Biofuel production with sugarcane. This review provides a scientific overview of sugarcane as a potential feedstock for biofuel and the use of a genome editing approach for the improvement of industrial and agronomical traits in sugarcane.
• Integration of CRISPR/Cas9 with multi-omics technologies to engineer secondary metabolite productions in medicinal plant: Challenges and Prospects. This review briefly discusses omics and CRISPR/Cas9-based methods to improve secondary metabolite production in medicinal plants.