Integrated proteogenomic, quantitative redox proteomic and metabolomic approaches reveal signatures of seed dormancy control in wheat

ROS generation, antioxidative systems, phytohormonal regulation and their reciprocal signaling were shown to play important roles in releasing embryo cells from the quiescent state during seed dormancy alleviation. Phenotype- and genotype-specific proteomic signatures of seed dormancy and association of dormancy release with ROS-mediated protein oxidation were studied using spring wheat doubled haploid populations and integration of proteogenomic, pharmacological, redox proteomic and metabolomic approaches. Dormancy-related alterations in aleurone and embryo proteomes and transcriptomes during early imbibition were studied using iTRAQ-based quantitative proteomics, mRNA-Seq differential gene expression analysis, and association with QTL regions. In dormant embryos, significant phenotype-specific changes were found for proteins involved in redox control, signaling associated with flowering, phytohormones and lipid second messengers, development and growth repression, cell cycle control and epigenetic regulation of gene expression, translational dynamics, cell wall metabolism, and ubiquitin 26S proteasome pathway. In embryos with non-dormant phenotype energy metabolism showed high capacity for the provision of NADPH reducing equivalents, pyruvate and TCA cycle intermediates for biosynthetic processes. Pathways for energy provision in non-dormant aleurone showed increased flux through the glycolytic pathway, high metabolic network flexibility, and an important role of inorganic pyrophosphate metabolism as an alternative energy donor. Inhibition of ROS production in the presence of ABA had synergistic effect on blocking germination in non-dormant seeds. Differential thiol-specific blocking followed by quantitative iodoTMT labeling-based proteomic analysis revealed sets of 813 and 535 redox responding target proteins identified in embryo and aleurone, respectively. Our results demonstrate that germination induction is mediated through the redox control, the NADPH oxidases are at least one source of that control, and wheat seeds appear to use antioxidative pathways to maintain dormancy. The total glutathione levels were significantly higher in dormant than in non-dormant and after-ripened embryos, whereas the total ascorbate levels increased upon after-ripening indicating high capacity for ascorbate regeneration.