De novo transcriptome analysis two types of barley (Hordeum vulgare) and exploring the mechanism of high anthocyanin content in black barley

Barley is a major food crop which is also utilized as a medicinal plant due to having considerable flavonoid content. Among all flavonoids, anthocyanins, a group of flavonoids, play a crucial role in plants for pigmentation, pollination and seed dispersal, as well as acting as antioxidants. Black barley contains a significant higher anthocyanin than yellow barley. To explore the molecular mechanism of higher anthocyanin content in black barley, transcriptome analysis were done to elucidate the involvement and expression of new genes in anthocyanin biosynthesis in two barley. Following transcriptomic analyses, 10579 new genes were identified, and 5912 were functionally annotated. Twelve types of alternative splicing were found in 10579 unigenes. Among 7113 differentially expressed genes (DEGs), 3235 were significantly up-regulated. The existence of the highest PPI and involvement of many DEGs in various BP, CC, and MF might reveal their significant influence on plant growth, development, and yield. Involvement of DEGs in phenylpropanoid and flavonoid biosynthesis in the black variety might be due to their great involvement in flavonoid biosynthesis, including anthocyanin. Higher expression of ANS1, LDOX1, LDOX2, and LDOX3 genes that are involved in anthocyanin biosynthesis in the grain maturation stage than the grain filling stage might reveal their great involvement in biosynthesis, accumulation and transformation of anthocyanin into the seed in that stage. Therefore, the current first report on DEGs in two barley cultivars, their expression, the unigenes and expression of major genes in anthocyanin might guide plant biologists in reprogramming the anthocyanin biosynthesis pathway to develop barley with improved anthocyanin content by developing and transforming synthetic genetic circuits into black barley.