Discovery of genes involved in anthocyanin biosynthesis from the rind and pith of three sugarcane varieties using integrated metabolic profiling and RNA-seq analysis

Abstract

Background Sugarcane (Saccharum officinarum) is one of the most valuable feedstocks for sugar production. In addition to the production of industrial raw materials such as alcohol, papermaking, the fiber of livestock feed, respectively, sugarcane can produce bioactive compounds such as anthocyanins. Elucidation of the anthocyanin biosynthesis pathway is critical for the molecular breeding of sugarcane varieties with favorable traits. We aimed to identify candidate genes involved in anthocyanin biosynthesis by transcriptomic and metabolomic analyses. Results Three varieties of sugarcane displaying different colors were used in this study: FN15 (greed rind), ROC22 (red rind), and Badila (purple rind). Sample materials were subjected to metabolomic analysis using UPLC-Q-TOF/MS and RNA-seq analysis. The metabolomic profiling results showed Cyanidin, Cyanidin (6’-malonylglucoside), Cyanidin O-glucoside, and Peonidin O-glucoside were the main components responsible for the rind color. Then, through RNA-seq analysis, we identified a total of 3137, 3302, 3014 differentially expressed genes (DEGs) between the rind and pith tissues for the corresponding varieties Badila rind, ROC22, and FN15. We then compared the expression levels of genes among the rind tissues from the three varieties. We identified 2901, 2821, and 3071 DEGs between Badila rind vs. ROC22 rind, Badila rind vs. FN15 rind, ROC22 rind vs. FN15 rind, respectively. We identified two enriched pathways, including phenylpropanoid biosynthesis and flavonoid biosynthesis. Sequencing similarity search identified a total of 50 unigenes belonging to 15 enzyme families as putative genes involved in anthocyanin biosynthesis in sugarcane rind. Seven of them were identified as candidate genes related to anthocyanin biosynthesis in the rind of sugarcane through co-localization analysis with the anthocyanin content in sugarcane. In total, 25 unigenes were selected and subjected to RT-qPCR analysis, and qRT-PCR results were consistent with those obtained with the RNA-Seq experiments. Conclusions We proposed a pathway for anthocyanin biosynthesis in sugarcane rind. This is the first report on the biosynthesis of anthocyanin in sugarcane using the combined transcriptomic and metabolomic methods. The results obtained from this study will lay the foundation for breeding purple pith sugarcane varieties with high anthocyanin contents.

The Transcriptome and Metabolome Reveal Stress Responses in Sulfur-Fumigated Cucumber (Cucumis sativus L.)

“…The read counts were estimated as the number of fragments per kilobase of the transcript sequences per million base pairs mapped (FPKM) values of expressed genes. The differentially expressed genes (DEGs) were identified using DESeq (2012) in R package ( Anders and Huber, 2013 ) with false discovery rate (FDR) < 0.05 and | log2(Fold Change)| > = 1 ( Ni et al, 2021 ).…”

Novel Insights into Anthocyanin Metabolism and Molecular Characterization of Associated Genes in Sugarcane Rinds Using the Metabolome and Transcriptome

“…In the past decade, anthocyanins have been deliberated as important food materials having a variety of biological activities such as anti-aging activity, minimizing the risk of diabetes and cancers, acting as a strong antioxidant, lowering cholesterol and blood lipids, and specific functions in protecting vision and treating glaucoma [ 5 ]. Enhancing anthocyanin contents in plants is one of the most popular research topics [ 4 , 6 , 7 ].…”

“…Sugarcane is an excellent breeding material to enhance its anthocyanin content to extract more valuable anthocyanins for commercial uses [ 6 , 15 ]. Flavonoids and anthocyanins are naturally found in the Saccharum species such as S. barberi , S. robustum , S. officinarum , and their inter-generic and interspecific crosses.…”

“…Flavonoids and anthocyanins are naturally found in the Saccharum species such as S. barberi , S. robustum , S. officinarum , and their inter-generic and interspecific crosses. The cultivation of purple-hearted and red color sugarcane gives high anthocyanin content [ 6 ]. Chemical and spectroscopic analysis revealed two flavonoids in S. officinarum ; from Chinese sugarcane ( S. sinensis Roxb), valuable flavonoids and anthocyanin have been isolated [ 16 ].…”

“…Thirteen anthocyanins and their derivatives were characterized in different cultivated sugarcane cultivars [ 18 ]. Recently, seven anthocyanins have been identified and quantified in three cultivated sugarcane ( S. officinarum ) varieties [ 6 ].…”