Abstract
Black and red rice are rich in both anthocyanin and proanthocyanin content, which belong to a large class of flavonoids derived from a group of phenolic secondary metabolites. However, the molecular pathways and mechanisms underlying the flavonoid biosynthetic pathway are far from clear. Therefore, this study was undertaken to gain insight into physiological factors that are involved in the flavonoid biosynthetic pathway in rice cultivars with red, black, and white colors. RNA sequencing of caryopsis and isobaric tags for relative and absolute quantification (iTRAQ) analyses have generated a nearly complete catalog of mRNA and expressed proteins in different colored rice cultivars. A total of 31,700 genes were identified, of which 3417, 329, and 227 genes were found specific for red, white, and black rice, respectively. A total of 13,996 unique peptides corresponding to 3916 proteins were detected in the proteomes of black, white, and red rice. Coexpression network analyses of differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) among the different rice cultivars showed significant differences in photosynthesis and flavonoid biosynthesis pathways. Based on a differential enrichment analysis, 32 genes involved in the flavonoid biosynthesis pathway were detected, out of which only CHI, F3H, ANS, and FLS were detected by iTRAQ. Taken together, the results point to differences in flavonoid biosynthesis pathways among different colored rice cultivars, which may reflect differences in physiological functions. The differences in contents and types of flavonoids among the different colored rice cultivars are related to changes in base sequences of Os06G0162500, Os09G0455500, Os09G0455500, and Os10G0536400. Current findings expand and deepen our understanding of flavonoid biosynthesis and concurrently provides potential candidate genes for improving the nutritional qualities of rice.
Highlights
Asian cultivated rice (Oryza sativa L.) is an important global crop that feeds approximately half of the human population [1]
We compared the differences in abundance of mRNAs and proteins in the caryopses of different pigmented rice cultivars, and we found several key genes that were differentially expressed in the flavonoid biosynthesis pathways
Transcriptomes of caryopses of three rice cultivars were determined by RNA sequencing (RNA-Seq) using a high-throughput Illumina platform
Summary
Asian cultivated rice (Oryza sativa L.) is an important global crop that feeds approximately half of the human population [1]. In the current study we performed an expression analysis of the transcription factors involved in flavonoid biosynthesis among different pigmented rice cultivars. We compared the differences in abundance of mRNAs and proteins in the caryopses of different pigmented rice cultivars, and we found several key genes that were differentially expressed in the flavonoid biosynthesis pathways. We argue that the joint analysis of gene and protein expression data provides a comprehensive representation of the physiological factors that regulate flavonoid biosynthesis in different pigmented rice cultivars. This approach expands and deepens our understanding of flavonoid biosynthesis while concurrently providing potential candidate genes for improving the nutritional qualities of rice
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