CRISPR and Artificial Intelligence in Crop Improvement: A Critical Synthesis for Precision Plant Breeding

CRISPR-Cas9 Precision Breeding for Climate-resilient Vegetable Crops: A Critical Appraisal of Evidence, Inference and Deployment

Confidence in current claims of climate resilience remains low for most targets, and progress will depend on multi-environment field testing, yield-based endpoints, and extension of editing capability beyond the few genotypes that presently regenerate reliably.

Genome editing in tetraploid potato: CRISPR technologies, multi-omics target discovery, and applications for trait-oriented breeding

Programmable Domestication: CRISPR, Pan‐Genomics and System Level Engineering for Next‐Generation Crops

ABSTRACT Global agriculture is increasingly challenged by climate instability, genetic erosion, emerging pathogens and rising food demands, exposing the limitations of conventional breeding and traditional domestication strategies. Recent advances in CRISPR‐based genome editing, pangenomic, synthetic biology, artificial intelligence (AI)‐assisted breeding and predictive phenomics are transforming de novo domestication from a slow evolutionary process into a programmable framework for rational crop redesign. This review synthesises recent advances in programmable de novo domestication and highlights how crop wild relatives and underutilised germplasm can be harnessed to develop resilient, climate‐adaptive and sustainable crop systems. The integration of multiplex genome editing, pan‐genomic variation discovery, AI‐driven genomic prediction and predictive breeding enables precise engineering of key domestication traits governing plant architecture, yield potential, stress resilience and nutritional quality. Furthermore, we propose a trajectory‐based framework for programmable domestication comprising Adaptive Rescue, Agronomic Refinement and Novel Chassis Engineering, which illustrates distinct evolutionary pathways, engineering complexity and crop redesign objectives. We also examine the major system level challenges that constrain programmable domestication, including cryptic genetic variation, epistasis, gene regulatory network complexity, genotype phenotype predictability, biodiversity conservation and regulatory considerations. Collectively, programmable domestication represents a transformative shift from conventional crop improvement towards system‐level engineering of next‐generation crops, providing a strategic foundation for enhancing global food security, agricultural sustainability and environmental resilience in the face of accelerating climate change.

AI-Guided DNA-Free and Genotype-Independent Genome Editing for Soybean Improvement

Soybean is a strategic crop for global protein and vegetable oil supply chains; however, genetic improvement remains constrained by genotype-dependent regeneration, variable transformation efficiency, and regulatory concerns regarding stable transgene integration. This review synthesizes emerging DNA-free and genotype-independent genome-editing frameworks for soybean, where genotype independence is defined as the ability to recover fertile, non-chimeric edited plants across elite germplasm. We critically examine the soybean genome-editing toolbox, including CRISPR-Cas9, Cas12a, multiplex editing systems, base editing, and prime editing, and discuss persistent bottlenecks associated with target selection, off-target assessment, editability, and plant recovery. Particular emphasis is placed on artificial intelligence (AI)-assisted approaches that integrate genomic, epigenomic, chromatin-accessibility, and multi-omics datasets to improve target prioritization, guide RNA design, off-target prediction, and locus- and genotype-specific editability assessment. We further evaluate DNA-free genome-editing technologies, including CRISPR-Cas ribonucleoproteins, transient RNA-based systems, and nanocarrier-mediated delivery platforms, highlighting their potential to generate non-integrative edits while reducing prolonged nuclease exposure. In addition, we discuss regeneration reprogramming strategies based on developmental regulators and morphogenic modules, including BBM-WUS, GRF-GIF, de novo meristem induction, and somatic embryogenesis, as enabling technologies for overcoming cultivar-dependent regeneration barriers. Importantly, this review proposes an integrated AI-to-field framework that connects target discovery, editability prediction, DNA-free editing, regeneration reprogramming, phenotypic validation, and breeding deployment into a unified soybean improvement pipeline. We further highlight emerging opportunities in multi-omics-guided target discovery, genotype-aware prediction models, regeneration-aware editing strategies, and closed-loop machine-learning systems that continuously improve editing decisions through experimental feedback. Collectively, these convergent innovations provide a practical foundation for accelerating the development of climate-resilient, nutritionally enhanced, and industry-ready soybean cultivars.

CRISPR–Cas technologies for precision genome editing in plants: advances, applications, and future perspectives

This review provides a comprehensive synthesis of a recent advances in CRISPR–Cas technologies and their strategic applications in crop genetics and hybrid breeding, and showcases how these technologies accelerate hybrid breeding by engineering male sterility systems, fixing heterosis, and generating high-throughput mutant libraries for trait discovery.

CRISPR-Cas9: an emerging and precise genome editing system for crops to combat food insecurity

Genome editing has emerged as a transformative tool to improve crop productivity, resilience, and nutritional quality, helping address global food insecurity. Among gene-editing platforms, clustered regularly interspaced short palindromic repeats (CRISPR)/ Cas systems (notably CRISPR-Cas9) offer simple, efficient, and scalable methods for targeted modifications, including knockouts, base edits, and precise “search-and-replace” prime edits. In plants, recent advances such as improved base editors, optimized prime-editing platforms, and DNA-free delivery methods have expanded the scope of edits achievable while reducing off-target effects and regulatory concerns. This review summarizes CRISPR principles, highlights technical breakthroughs and crop applications that mitigate biotic and abiotic stresses, and outlines practical challenges and future directions necessary for responsible deployment in agriculture.