# Chromatin accessibility directly governs flavonoid biosynthesis and indirectly orchestrates cannabinoid production in Cannabis

## TL;DR

This study explores how chromatin accessibility influences the production of flavonoids and cannabinoids in Cannabis, offering new insights for breeding improved cannabis varieties.

## Contribution

The study reveals chromatin accessibility as a direct regulator of flavonoid biosynthesis and an indirect driver of cannabinoid production in Cannabis.

## Key findings

- Increased chromatin accessibility at flavonoid-biosynthetic gene promoters up-regulates their expression and flavonoid accumulation.
- Differential chromatin accessibility in fatty acid and trichome-related genes drives cannabinoid divergence between cultivars.
- Multi-omics integration identified 491 DAMs, 8343 DEGs, and 11376 DAGs between two hemp cultivars.

## Abstract

Secondary metabolites in hemp enhance its pharmaceutical and nutraceutical value, yet the epigenetic regulatory network underlying secondary metabolite biosynthesis remains poorly understood in hemp. Here, we profiled the inflorescences of two cultivars with different trichome density by integrating metabolomics, transcriptomics and ATAC-seq. Multi-omics data revealed pronounced differences in metabolites (491 differentially accumulated metabolites (DAMs)), transcripts (8343 differentially expressed genes (DEGs)), and chromatin accessibility (11376 different accessibility genes, (DAGs)) between two cultivars. Integrated analyses reveal that increased chromatin accessibility at the promoters of several flavonoid-biosynthetic genes up-regulated their expression, resulting in the accumulation of flavonoids. Although chromatin accessibility of cannabinoid biosynthetic gene promoters modulates content, differential chromatin accessibility of the promoter of fatty acid biosynthetic and trichome density (trichome initiation, MeJA signaling, and identity of floral organ) related genes constitutes the key driver underlying cannabinoid divergence between two cultivars. Our study advances the understanding of epigenetic regulation of plant secondary metabolites and offers a novel strategy for enhancing cannabinoid and flavonoid content in Cannabis, providing efficient and precise molecular markers for the selection and breeding of new cannabis varieties.