Metabolite profiling and associated gene expression reveal two metabolic shifts during the seed-to-seedling transition in Arabidopsis thaliana

• Published in: Plant molecular biology Vol. 95; no. 4-5; pp. 481 - 496
• Main Authors: Silva, Anderson Tadeu, Ligterink, Wilco, Hilhorst, Henk W. M.
• Format: Journal Article
• Language: English
• Published: Dordrecht Springer Netherlands 01-11-2017; Springer Nature B.V
• Subjects: Amino Acids - metabolism; Arabidopsis - genetics; Arabidopsis - metabolism; Arabidopsis Proteins - genetics; Arabidopsis Proteins - metabolism; Biochemistry; Biomedical and Life Sciences; Citric Acid Cycle; Correlation analysis; Cotyledon - genetics; Cotyledon - metabolism; Cotyledons; Developmental stages; Flowers & plants; Gene expression; Gene Expression Profiling; Gene Expression Regulation, Developmental; Gene Expression Regulation, Plant; Germination; Life cycles; Life Sciences; Metabolic flux; Metabolic networks; Metabolic pathways; Metabolic response; Metabolism; Metabolites; Metabolomics; Plant Pathology; Plant Sciences; Seed germination; Seedlings; Seedlings - genetics; Seedlings - metabolism; Seeds; Seeds - genetics; Seeds - metabolism; Transcription; Transcriptome; Transportation networks; Metabolite-transcription correlation; Seedling establishment; Seed-to-seedling metabolism; Metabolite profile; Network analysis; Metabolite–metabolite correlation
• ISSN: 0167-4412; 1573-5028
• DOI: 10.1007/s11103-017-0665-x

Key message
Metabolic and transcriptomic correlation analysis identified two distinctive profiles involved in the metabolic preparation for seed germination and seedling establishment, respectively. Transcripts were identified that may control metabolic fluxes.
The transition from a quiescent metabolic state (dry seed) to the active state of a vigorous seedling is crucial in the plant’s life cycle. We analysed this complex physiological trait by measuring the changes in primary metabolism that occur during the transition in order to determine which metabolic networks are operational. The transition involves several developmental stages from seed germination to seedling establishment, i.e. between imbibition of the mature dry seed and opening of the cotyledons, the final stage of seedling establishment. We hypothesized that the advancement of growth is associated with certain signature metabolite profiles. Metabolite–metabolite correlation analysis underlined two specific profiles which appear to be involved in the metabolic preparation for seed germination and efficient seedling establishment, respectively. Metabolite profiles were also compared to transcript profiles and although transcriptional changes did not always equate to a proportional metabolic response, in depth correlation analysis identified several transcripts that may directly influence the flux through metabolic pathways during the seed-to-seedling transition. This correlation analysis also pinpointed metabolic pathways which are significant for the seed-to-seedling transition, and metabolite contents that appeared to be controlled directly by transcript abundance. This global view of the transcriptional and metabolic changes during the seed-to-seedling transition in Arabidopsis opens up new perspectives for understanding the complex regulatory mechanism underlying this transition.