Innovations in Computational Design and Multi-Omics Validation for Plant Genome Editing

The field of plant genome editing is rapidly evolving, driven by the advent of sophisticated computational tools and multi-omics technologies. While CRISPR/Cas and related platforms have revolutionized targeted DNA modification, recent years have seen a surge of innovation in computational methods to enhance guide RNA design, predict off-target effects, and optimize editing efficiency. Despite these advances, challenges remain in reliably predicting functional outcomes, connecting genomic edits to complex traits, and validating results beyond simple genotyping. Pangenome-scale datasets and benchmarking efforts are highlighting variability in tool performance across diverse species and genetic backgrounds, further underscoring the need for integrative approaches. Ongoing debates focus on how best to link computational predictions with biological reality, leveraging growing high-throughput resources and diverse multi-omics datasets to ensure predictive power and biological relevance.This Research Topic aims to explore pioneering research and new methodologies at the cutting edge of computational design and validation for plant genome editing. We seek to answer how next-generation computational frameworks—for guide RNA selection, off-target detection, and editing activity prediction—can be robustly benchmarked at scale, and how these predictions can be validated using functional genomics approaches such as transcriptomics, epigenomics, and proteomics. Special emphasis will be placed on strategies that connect editing outcomes with phenotypic and agronomic traits in crop plants, helping close the gap between genetic modification and real-world performance.The scope of this Research Topic is centered on innovative computational strategies and multi-omics validation in the context of precision plant genome editing. We encourage submissions that address the following themes, among others:• Advanced computational tools for guide RNA design and off-target prediction• Benchmarking of genome editing platforms using high-throughput and pangenome-scale datasets• Integration of transcriptomics, epigenomics, and proteomics for edited locus validation• Data-driven methods linking genome editing to phenotypic and agronomic traits in crops• Application of artificial intelligence and machine learning in genome editing• Case studies demonstrating translational impact in precision breedingWe welcome a wide range of article types, including original research, methodological advances, comprehensive reviews, perspectives, and case reports, to provide a broad and insightful view on the interface of computational biology and functional genomics in plant genome editing. Topic editors: Kalenahalli Yogendra, Raviraj Banakar Source: https://www.frontiersin.org/research-topics/83931/innovations-in-computational-design-and-multi-omics-validation-for-plant-genome-editing