Abstract

Over the past five years, plant science has undergone a paradigm shift fueled by genome-editing platforms, single-cell/spatial omics, and synthetic-biology toolkits. Yet the pace and diversity of publications challenge researchers and breeders seeking a coherent view of translational progress. Systematically mapped peer-reviewed research from 2020 to mid-2025 was conducted to quantify the adoption of CRISPR-derived editors, track omics-enabled discoveries in stress resilience and metabolic engineering and identify bottlenecks limiting large-scale deployment across major crops.

PubMed, Web of Science, Scopus, AGRICOLA, and ScienceDirect were queried using PRISMA 2020 guidelines. Inclusion required a molecular focus (genome editing, transcriptomics, metabolomics, plant–microbe interactions) and higher-plant subject matter. Of 3,112 records retrieved, 247 high-quality articles and 42 reviews met eligibility. Dual-reviewer screening, JBI and SANRA appraisal, and narrative synthesis were employed; effect sizes were calculated where datasets were comparable.

It was observed that Genome editing dominated (46 % of studies), with prime editing and multiplex CRISPR rising from <2 % (2020) to 14 % (2024). Single-cell RNA-seq revealed novel stress-responsive cell types in rice and maize, while spatial transcriptomics linked ion gradients to root developmental zones. Metabolic-engineering papers (21 %) reported >25 % increases in provitamin A, specialty lipids, or pharmaceutical precursors without growth penalties. Persistent challenges include transformation recalcitrance in 28 % of crop species, off-target verification gaps (35 % of studies), and fragmented regulatory trajectories.

The evidence indicated that there is a progression from descriptive to design-driven plant biology, yet transformation bottlenecks and regulatory uncertainty impede full commercialization. A three-pronged roadmap integrating tissue-culture innovations, standardized off-target pipelines, and harmonized policy frameworks is required to accelerate sustainable crop development.

Keywords: CRISPR, single-cell omics, metabolic engineering, plant stress physiology, systematic review