Project description:The metabolic response of maize source leaves to low nitrogen supply was analyzed in maize seedlings by parallel measurements of transcriptome and metabolome profiling. Inbred lines A188 and B73 were cultivated under controlled growth chamber conditions and supplied with either sufficient (15mM) or limiting (0.15mM) nitrate supply. Leaf lamina material was harvested at day 20 and day 30 after germination with the fifth and sixth leaf representing the main source leaf respectively. Four replicates were collecetd from individual plants for each combination of genotype, growth stage and nitrogen treatment. The leaf material was frozen, homogenised and aliquoted for transcriptome and metabolome analysis. The molecular data was further supplemented by phenotypic characterisation of the maize seedlings under investigation. Limited availability of nitrogen caused strong shifts in the metabolite profile of leaves. The transcriptome was less affected by the nitrogen stress but showed strong genotype and age dependent patterns. Nitrogen starvation initiated the selective down-regulation of processes involved in nitrate reduction and amino acid assimilation; ammonium assimilation related transcripts on the other hand were not influenced. Carbon assimilation related transcripts were characterized by high transcriptional coordination and general down-regulation under low nitrogen conditions. Nitrogen deprivation caused a slight accumulation of starch, but also directed increased amounts of carbohydrates into the cell wall and secondary metabolites. The decrease in N availability also resulted in accumulation of phosphate and by strong down-regulation of genes usually involved in phosphate starvation response, underlining the great importance of phosphate homeostasis control under stress conditions. Maize inbred lines A188 and B73 were cultivated in pots containing nutrient poor peat soil under the controlled conditions of a growth chamber. The plants were fertilized with modified Hoagland solutions containing either 15mM (high N) or 0.15mM nitrate (low N). Source leaf lamina were harvested at day 20 and day 30 after start of germination for parallel analysis of transcriptome and metabolome profiles. The molecular data is further supplemented by phenotypic characterization of the maize seedlings under investigation.

Project description:To investigate the developmental gradient of the third maize leaf, the light exposed area of the leaf (corresponding to 18cm of leaf) and 2cm shaded by the sheath were sampled in ten slices. Four replicates were collected, immediately shock frozen in liquid nitrogen and subsequently cut into 2cm slices. At least 10 plants were pooled for each biological replicate. We have systematically analyzed a developmental gradient of the third maize leaf from the point of emergence into the light to the tip in ten continuous leaf slices to study organ development and physiological and biochemical functions. Transcriptome analysis, oxygen sensitivity of photosynthesis, delta-13C values, and photosynthetic rate measurements showed that the maize leaf undergoes a sink to source transition without an intermediate phase of C3 photosynthesis or operation of a photorespiratory carbon pump. Metabolome and transcriptome analysis, chlorophyll and protein measurements, as well as dry weight determination showed continuous gradients for all analyzed items. The absence of binary on-off switches and regulons pointed to a morphogradient along the leaf as the determining factor of developmental stage. Analysis of transcription factors for differential expression along the leaf gradient defined a list of putative regulators orchestrating the sink-to-source transition and establishment of C4 photosynthesis. Finally, transcriptome and metabolome analysis, as well as enzyme activity measurements, and absolute quantification of selected metabolites revised the current model of maize C4 photosynthesis. All datasets are included within the publication to serve as a resource for maize leaf systems biology. For the transcriptional analysis, the goal of the study was to (i) identify whether the leaf contains binary switches for genes involved in photosynthesis, (ii)characterize the patterns of gene expression in the leaf, (iii) provide independent validation of maize leaf expression experiments published in Li et al. (2011) and (iv) determine transcripts co-expressed with key transcripts of C4 photosynthesis. To this end, changed transcripts were determined by ANOVA and characterized by K-means and hierachical clustering. Four replicates were collected for each of the ten consecutive leaf slices resulting in 40 one color arrays. Slice 1 represents the tip of the leaf, slice 10 the lowermost slice which is shaded by the sheath with all slices in between consecutively numbered.

Project description:To investigate the developmental gradient of the third maize leaf, the light exposed area of the leaf (corresponding to 18cm of leaf) and 2cm shaded by the sheath were sampled in ten slices. Four replicates were collected, immediately shock frozen in liquid nitrogen and subsequently cut into 2cm slices. At least 10 plants were pooled for each biological replicate. We have systematically analyzed a developmental gradient of the third maize leaf from the point of emergence into the light to the tip in ten continuous leaf slices to study organ development and physiological and biochemical functions. Transcriptome analysis, oxygen sensitivity of photosynthesis, delta-13C values, and photosynthetic rate measurements showed that the maize leaf undergoes a sink to source transition without an intermediate phase of C3 photosynthesis or operation of a photorespiratory carbon pump. Metabolome and transcriptome analysis, chlorophyll and protein measurements, as well as dry weight determination showed continuous gradients for all analyzed items. The absence of binary on-off switches and regulons pointed to a morphogradient along the leaf as the determining factor of developmental stage. Analysis of transcription factors for differential expression along the leaf gradient defined a list of putative regulators orchestrating the sink-to-source transition and establishment of C4 photosynthesis. Finally, transcriptome and metabolome analysis, as well as enzyme activity measurements, and absolute quantification of selected metabolites revised the current model of maize C4 photosynthesis. All datasets are included within the publication to serve as a resource for maize leaf systems biology. For the transcriptional analysis, the goal of the study was to (i) identify whether the leaf contains binary switches for genes involved in photosynthesis, (ii)characterize the patterns of gene expression in the leaf, (iii) provide independent validation of maize leaf expression experiments published in Li et al. (2011) and (iv) determine transcripts co-expressed with key transcripts of C4 photosynthesis. To this end, changed transcripts were determined by ANOVA and characterized by K-means and hierachical clustering.

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Implications of transcriptomics, proteomics and metabolomics analysis of maize seeds for food safety

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