Dynamic Transcriptome Changes Driven by the Mutation of OsCOP1 Underlie Flavonoid Biosynthesis and Embryogenesis in the Developing Rice Seed

Abstract

CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1), an E3 ubiquitin ligase, functions as a central repressor of light signaling and regulates various light-mediated developmental and metabolic processes in plants. However, detailed mechanisms underlying COP1-regulated flavonoid biosynthesis and embryogenesis in rice seeds remain largely unknown. Here, we performed transcriptome analysis of the rice cop1 (yellowish-pericarp embryo lethal [yel]) null mutant, characterized by flavonoid accumulation in pericarp and abnormal development of embryo, to identify and profile the expression genes involved in flavonoid biosynthesis and embryo development. Comparative transcriptome analysis of yel-hc and wild-type seeds revealed 979 differentially expressed genes (DEGs), of which 577 were upregulated and 402 were downregulated in yel-hc seeds. Functional annotation of DEGs revealed that DEGs were mainly enriched in ‘metabolism’, ‘transcription factors’, ‘secondary metabolites’, and ‘flavonoid biosynthesis’. The DEGs encoding AP2-EREBP, MYB, and bZIP transcription factors (TFs) were predominantly upregulated, whereas those encoding HB, bHLH, and ABI3VP1 TFs were downregulated in yel-hc seeds. Comparative gene expression analysis revealed that genes involved in the C-glycosyl flavone biosynthesis pathway, including OsP1, were activated, whereas anthocyanin biosynthesis genes showed no significant change in expression. In addition, transcript levels of embryo development-related genes, especially homeobox auxin regulation genes, as well as somatic embryogenesis-related genes, were significantly downregulated in yel-hc. Taken together, these results indicate that OsCOP1 plays a crucial role in regulation of flavonoid biosynthesis and embryo structure formation, and changes in the expression of light signal transduction-related genes could have a significant impact on flavonoid biosynthesis and embryogenesis in rice seed.