Unlocking the black pericarp sorghum (Sorghum bicolor (L.) Moench) trait through genome assembly and integrated omics analysis of key genes in 3-deoxyanthocyanidin biosynthesis

Abstract Background Sorghum ( Sorghum bicolor (L.) Moench) is a staple C4 cereal used for fuel, food, and animal feed and a resource for functional genomics in monocots. Tx3362 is a rare black sorghum genotype producing high levels of 3-deoxyanthocyanidins (3-DOAs) in pericarp tissue under UV-B light. Black grain sorghum is presently the only food source of these potent antioxidants for human health and natural food colorants. Lack of a reference genome for this phenotype has hindered the characterization of the complex genetic architecture underlying 3-DOA biosynthesis in pericarp tissues. Additionally, black sorghum may contain unique features contributing to the induction of this rare tissue specific response. Results A high-quality genome assembly and annotation of sorghum genotype Tx3362 was generated using a hybrid sequencing approach resulting in 46,941 gene models including 5,217 gene models absent from existing pan-genome references. Comparative analysis revealed extensive structural variation, including inversions, translocations, duplications, as well as expansions and contractions of flavonoid structural gene families between Tx3362, red pericarp genotype, Wray, and BTx623. Lineage-specific duplications and contractions were revealed within flavonoid gene families. Using Tx3362 as a reference genome for a weighted gene co-expression network analysis (WGCNA) in pericarp tissues refined a network of 292 genes highly correlated with 3-DOAs. Together with this refined network of genes, DAP-Seq profiling of nine transcription factors (MYB, NAC, WRKY, bHLH, and C2H2) demonstrated coordinated regulation of 3-DOA pathway genes during black pericarp maturation, with temporal activation from early (2–5 days post-anthesis) to late stages (10–17 days after anthesis (DAA)). Finally, early transcriptional correlations for environmentally induced 3-DOAs in black sorghum were found in developing floral meristem tissues. Conclusions The Tx3362 reference genome harbors Tx3362-specific gene models for key flavonoid structural gene families, critical transcription factors, and gene networks responsible for 3-DOA biosynthesis and provides a framework for understanding black pericarp sorghum and 3-DOA biosynthesis. Integration of WGCNA and DAP-Seq revealed the temporal and coordinated regulation of key 3-DOA biosynthesis related genes. This resource enables exploration of flavonoid metabolism, stress response, and developmental pathways in sorghum, and supports efforts toward enhancing nutrition and economically valuable grain traits.