RNA-Seq Identification of Peanut Callus-Specific Promoters and Evaluation of Base-Editing Efficiency

TL;DR

This paper identifies peanut callus-specific promoters that can limit CRISPR gene-editing activity to specific plant stages, improving biosafety and reducing unintended effects.

Contribution

The study discovers and validates new callus-specific promoters in peanut for precise CRISPR base editing.

Findings

Five peanut callus-specific promoters were identified and confirmed to be functional in callus tissue.

These promoters enabled cytosine base editing with comparable or higher efficiency than the cauliflower mosaic virus 35S promoter.

Using these promoters reduces off-target effects and metabolic burden in CRISPR-modified peanut plants.

Abstract

Prolonged expression of gene-editing components in CRISPR-modified plants can interfere with phenotypic analysis of target traits, increase the risk of off-target mutations, and lead to unnecessary metabolic burden. To mitigate these issues in peanut (Arachis hypogaea L.), callus-specific promoters were screened to restrict Cas9 expression to the callus stage, minimizing its activity in regenerated plants. In this study, six callus-specific genes in peanut were identified by mining RNA sequencing datasets and validating their expression profiles using quantitative reverse transcriptase PCR. The promoters of Arahy.H0FE8D, Arahy.WT3AEF, Arahy.I20Q6X, Arahy.ELJ55T, and Arahy.N9CMH4 were cloned and assessed for their expression activity. Beta-glucuronidase (GUS) histochemical staining confirmed that all five promoters were functional in peanut callus. Further investigation revealed their ability to drive cytosine base editing via a deaminase-nCas9 fusion protein, with all promoters successfully inducing precise base substitutions in peanut. Notably, PAh-H0FE8D, PAh-WT3AEF, PAh-ELJ55T, and PAh-N9CMH4 exhibited comparable or higher editing efficiencies than the commonly used cauliflower mosaic virus 35S promoter. These findings provide valuable tools for improving the biosafety of CRISPR-based genome editing in peanut breeding programs.

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