Integrative analysis of metabolome and transcriptome reveals anthocyanins biosynthesis regulation in grass species Pennisetum purpureum

Genes or metabolites involved in the same biological process will have same or similar change rules, so association analysis of transcriptome and metabolome is an effective way to find key metabolic pathways, key genes and explain the molecular mechanisms. Anthocyanin-rich forage is rare but a powerful antioxidant, which is good for both humans and animals. Pennisetum purpureum cv. Purple is abundant in anthocyanins and has higher biomass than most forage grasses. To study the mechanisms underlying the purple color of P. purpureum, transcriptomic and metabolomics analyses were performed with the purple-leaved cultivar 'Purple' and the green-leaved cultivar 'Mott'. Metabolites, including luteolin, kaempferol, quercetin, malvidin, apigenin, pelargonidin and cyanidin were present at different levels between the cultivars. High levels of malvidin correlated with purple color, suggesting that this compound probably plays a dominant role in making the purple leaves in P. purpureum considering its high content and strong correlation with the color expression. A total of 16 differentially expressed genes (DEGs) in the flavonoid biosynthesis pathway were discovered between the purple and green varieties, and these were selected as candidate genes possibly involved in purple color formation and accumulation. Moreover, 47 differentially expressed transcription factors (TFs) were identified, including 15 upregulated and 12 down-regulated TFs between 'Purple' and 'Mott'. Furthermore, 55 SNPs in 11 DEGs and 231 SNPs in 41 differentially expressed TFs were found between 'Purple' and 'Mott', suggesting that SNPs may play an important role in regulating gene expression. This study provides crucial information on leaf color development and anthocyanins production of P. purpureum, and will facilitate the development of breeding forage varieties with high-anthocyanins contents.