Genome editing of the flavanone 3-hydroxylase gene produces a green Perilla line with elevated luteolin accumulation

Perilla frutescens var. crispa is widely cultivated in East Asia and produces a diverse range of secondary metabolites with nutritional and medicinal value. Based on anthocyanin content, perilla is classified into red and green chemotypes. The anthocyanin biosynthetic pathway is highly conserved among plants, and the flavanone 3-hydroxylase gene (F3H) in red perilla is considered essential for this pathway. Here, we used CRISPR-Cas9 genome editing to generate novel Perilla lines with altered metabolite profiles. In four edited T plants, multiple biallelic indels, including a -3 bp in-frame deletion, were introduced at the target site. In the T generation, these mutations and the transgene segregated in a Mendelian manner, resulting in recovery of null-segregant plants. Metabolite analysis revealed strong suppression of anthocyanin biosynthesis and a significant increase in luteolin accumulation in edited lines compared with the wild type. Transcriptome analysis further confirmed the loss of F3H function, demonstrating a metabolic shift of the flavonoid pathway toward luteolin production. This study provides the first functional validation of F3H in perilla and highlights its potential application in breeding cultivars with controlled bioactive compound contents. Our findings also demonstrate practical strategies for implementing genome editing in non-model crops and developing high-value functional cultivars. Practitioner PointsO_LIEditing a single flavonoid biosynthetic gene (F3H) effectively alters pigment composition in perilla leaves. C_LIO_LIIncreased accumulation of luteolin-related compounds suggests potential for enhancing functional metabolites without complex pathway engineering. C_LIO_LIGenome editing offers a feasible tool for perilla improvement in breeding and functional food development. C_LI