Multi-omics reveals the metabolic changes and genetic basis of post-flowering rice caryopsis under blue light

• Published in: Chemical and biological technologies in agriculture Vol. 11; no. 1; pp. 128 - 19
• Main Authors: Zhang, Ping, Tang, Yongsheng, Liu, Junna, Wang, Qianchao, Li, Li, Li, Hanxue, Wang, Xuqin, Zhang, Lingyuan, Bai, Yutao, Jiang, Guofei, Huang, Liubin, Qin, Peng
• Format: Journal Article
• Language: English
• Published: Cham Springer International Publishing 31.08.2024; Springer Nature B.V; SpringerOpen
• Subjects: Accumulation; Agriculture; Auxins; Biological analysis; Biomedical and Life Sciences; Blue light; Developmental stages; Differentiation (biology); Down-regulation; Flavonoids; Flowering; Genes; Genetic analysis; Gluten; Granular materials; Hormones; Jasmonic acid; Life Sciences; Light; Lipid metabolism; Lipids; Metabolism; Metabolites; Morphogenesis; Multi-omics; Organic acids; Organic Chemistry; Organs; Phenolic acids; Phenols; Photosynthesis; Plant Biochemistry; Plant Physiology; Pollination; Proteins; Proteomes; Rice; Secondary metabolites; Seeds; Soil Science & Conservation; Starch; Terpenes; Transcription factors; Transcription regulation; Transcriptomes; Secondary metabolites; Blue light; Starch; Multi-omics; Rice; Transcription regulation
• ISSN: 2196-5641; 2196-5641
• DOI: 10.1186/s40538-024-00654-1

Background The effects of blue light on photosynthetic organs have been studied. However, its effects on non-photosynthetic organs, in particular, on the early stages of rice caryopsis development, are unclear. Thus, we aimed to determine the metabolic characteristics of caryopsis development under blue light to improve the metabolic quality of crop kernels. Results We conducted a multi-omics analysis of each of the three periods from the beginning of cellular differentiation to the end of morphogenesis in post-pollination seeds of a japonica rice variety to explore the effect of blue light on metabolic levels during these metabolic changes and its genetic basis. It was found that blue light caused a gradual decrease in auxin content, a significant increase in the accumulation of JA and flavonoids, and a downregulation of the expression of many starch-related genes and proteins, leads to reduced starch synthesis and smaller starch granules. In addition, the gene co-expression network identified three transcription factors that may regulate starch and two that may regulate flavonoids. Conclusions It was found through multi-omics testing that hormones such as jasmonic acid and auxins, and metabolites including alkaloids, flavonoids, lipids, organic acids, phenolic acids, and terpenoids altered significantly. Transcriptome and proteome analyses showed that blue light affected the seed nutrient repository activity. Specifically, starch- and gluten-related genes and proteins were significantly downregulated. Co- and WGCNA analyses identified several transcription factors that were regulated under blue light and identified key regulators of starch. Our study provides an understanding of the effects of blue light on post-flowering development in Gramineae and provides a framework for blue light-induced synthesis of secondary metabolites. Graphical Abstract Highlights Evaluate the impact of blue light on the secondary metabolite accumulation. Confirm the accumulation of hormones and flavonoids in different blue light. Identify key candidate genes related to starch and flavonoid. Blue light leads to reduced starch synthesis and smaller starch granules.