De novo transcriptome analysis in three types of barley following exploring the mechanism of quercetin content in purple barley (Hordeum vulgare)

In addition to being a major food crop, barley is also utilized as a medicinal plant due to having lots of bioactive compounds like flavonoids. Among all flavonoids, quercetin is very important due to anti-inflammatory, anti-cancer, antibacterial, and antioxidant effects. Among yellow, black and purple barley, only purple barley contains quercetin. To explore the molecular mechanism of quercetin content in purple barley, transcriptome analysis, following involvement and expression of new genes in quercetin biosynthesis were examined through a series of analyses. Following transcriptomic analyzes, 6,393 genes were structurally optimized and 4,986 were functionally annotated. A number of 6,393 unigenes, 12 types of alternative splicing and 561,743 putative SNPs (mostly intronic) were found. Among 4540 differentially expressed genes, the highest upregulated genes were in purple barley. The existence of the highest PPI and involvement of many DEGs (differentially expressed genes) in many BP, CC and MF might reveal their great influence in plant growth, development and yield. Involvement of significant unigenes and DEGs in phenylpropanoid and flavonoid biosynthesis in the purple variety might be due to their great involvement in flavonoid biosynthesis, including quercetin. Therefore, the current first report on DEGs in three barley cultivars, their expression, unigenes and expression of major genes in quercetin might guide the plant biologist to reprogram the quercetin biosynthesis pathway to develop barley with improved quercetin content through developing and transforming synthetic genetic circuits into the yellow barley.