Efficient prime editors for heritable multiplex precision genome editing in soybean

Jun 9, 2026Nature plants

Efficient gene editors for precise, heritable changes to multiple soybean genes

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CRISPR Gene Editing on OpenScience ↗PubMed ↗DOI ↗

Abstract

GmPEplus achieves editing efficiencies of up to 81.3% in stable transgenic soybean lines.

An optimized prime editing system for soybean was developed by modifying key components of the editing machinery.
Nicking the non-edited strand with an additional guide RNA improved editing efficiency significantly.
Optimizing the expression of components with a separate cassette increased efficiency by 13.1-fold.
A multiplex editing system enables the simultaneous editing of 2-12 genes in soybean hairy roots.
Up to 3 genes can be edited simultaneously in stable transgenic soybean lines.

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Prime editing (PE) is limited by low efficiency in dicot plants. Here we develop an optimized PE system for soybean, GmPEplus, by deleting the RNase H domain, introducing a V223A substitution within the reverse transcriptase domain, inserting a viral nucleocapsid protein between Cas9 and reverse transcriptase, and co-expressing a dominant-negative engineered allele of the endogenous GmMLH1. GmPEplus achieves editing efficiencies of up to 81.3% in stable transgenic lines. Subsequently, we show that nicking the non-edited strand using an additional sgRNA via the tRNA processing system enhances editing efficiency, and that optimizing its expression with an independent AtU6 cassette boosts efficiency by 13.1-fold. Importantly, a Csy4-mediated multiplex PE system (CMMPE) is established for simultaneous editing of 2-12 genes in soybean hairy roots and up to 3 genes in stable transgenic lines. GmPEplus and CMMPE offer powerful, versatile tools for precise, multiplex and heritable genome editing in soybean breeding.