Engineering Crop Resilience through Functional Genomics: Multi-Omics Discovery, Transgenics, and Genome Editing for Durable Biotic Stress Resistance

Diseases and insect pests are among the most persistent and damaging constraints on crop productivity and yield stability worldwide. To better counter these threats, high-quality reference genomes and pangenomes, high-throughput phenotyping, and multi-omics tools are accelerating the discovery of resistance and susceptibility determinants and revealing the gene networks that govern plant immunity and anti-herbivore defense. These approaches additionally enable the dissection of links between defense pathways and the biosynthesis of pharmacologically active metabolites, providing opportunities to jointly improve stress resistance and medicinal quality. Particularly, advances in transformation systems and precision engineering—spanning transgenic approaches and genome editing—now enable rapid translation of gene discovery into improved traits in both model plants and a wide range of crops, including non-model economic and medicinal species.

This Research Topic aims to integrate mechanistic insight with practical trait engineering, spanning resistance to fungal, bacterial, oomycete, and viral diseases as well as insect and other arthropod pests. By highlighting innovations that reduce trade-offs, enhance durability, and improve field relevance and scalability, this collection seeks to accelerate functional-genomics-enabled strategies that strengthen crop resilience and support sustainable agriculture.

In this research topic, we welcome original research, reviews, and methods papers that connect gene discovery to trait improvement for resistance against plant diseases and insect pests, across all crop species. We encourage studies that integrate resistance engineering with yield, quality, or bioactive metabolite stability, including but not limited to:

• Identify and functionally validate resistance (R) genes, susceptibility (S) genes, defense regulators, and quantitative loci using forward/reverse genetics and functional genomics

• Integrate multi-omics and systems biology to resolve molecular networks controlling immunity, anti-herbivore defenses, and defense–growth or defense–quality trade-offs

• Dissect hormone crosstalk, defense-related metabolites, and defense priming mechanisms underlying biotic stress responses

• Engineer resistance traits using transgenic approaches and genome editing

• Improve transformation, regeneration, and delivery strategies to enable functional validation and engineering in diverse, non-model, and recalcitrant crops, including medicinal crops.

• Advance durable resistance through stacking, network-aware design, and evaluation of stability, fitness costs, and pathogen/pest adaptation risks, and impacts on yield and medicinal quality.

Article types and fees

This Research Topic accepts the following article types, unless otherwise specified in the Research Topic description:

• Brief Research Report
• Editorial
• FAIR² Data
• FAIR² DATA Direct Submission
• Hypothesis and Theory
• Methods
• Mini Review
• Opinion
• Original Research
• ... View all formats

Articles that are accepted for publication by our external editors following rigorous peer review incur a publishing fee charged to Authors, institutions, or funders.

Article types

This Research Topic accepts the following article types, unless otherwise specified in the Research Topic description:

• Brief Research Report
• Editorial
• FAIR² Data
• FAIR² DATA Direct Submission
• Hypothesis and Theory
• Methods
• Mini Review
• Opinion
• Original Research
• Perspective
• Policy and Practice Reviews
• Review
• Systematic Review
• Technology and Code

Keywords: Functional genomics, Biotic stress, Genome editing, Multi-omics, Plant defense, Hormone crosstalk, Crop resilience, Quality-related traits, Bioactive metabolites

Important note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.