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Engineering next-generation crops through CRISPR-mediated horizontal gene transfer
Journal article   Open access

Engineering next-generation crops through CRISPR-mediated horizontal gene transfer

Madhab Kumar Sen, Amit Roy, Rajeev K Varshney FRS and Amrita Chakraborty
New Phytologist, Early View
2026
DOI: https://doi.org/10.1111/nph.70951
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CC BY V4.0,  Open Access

Abstract

crop engineering deep learning horizontal gene transfer microbial genes multi-trait resilience precision agriculture synthetic biology
Crops increasingly face overlapping stresses such as heat, drought, salinity, and pathogens that conventional breeding or genome editing rarely overcome in combination. To address this, we propose CRISPR-enabled horizontal gene transfer (CRISPR-HGT) as a programmable framework that recreates the evolutionary process by which plants historically acquired adaptive microbial genes. Microbial genes, refined under extreme environments, provide a naturally preadapted resource for multi-trait resilience. By integrating tools such as Cas12a, CasΦ, RNA-targeting, and dCas-based epigenome editors with AI-guided microbial gene discovery, CRISPR-HGT enables modular and inducible stress regulation. This approach shifts genome editing from allelic modification to evolution-guided design. We outline a conceptual pipeline spanning microbial gene mining to adaptive field deployment, highlighting the ecological, biosafety, and regulatory dimensions, from the European Union's cautious oversight to the UK's product-based framework. CRISPR-HGT thus introduces an evolution-informed paradigm for engineering crops that anticipate stress and sustain yield under climate uncertainty.

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