Project description:These data are associated with the following peer-reviewed scientific paper: Peng Zhang, Robert Sharwood, Adam Carroll, Gonzalo M Estavillo, Susanne von Caemmerer and Robert T Furbank (2024) Systems analysis of long-term heat stress responses in the C4 grass Setaria viridis, The Plant Cell Corresponding Author: Robert Sharwood (R.Sharwood@westernsydney.edu.au) Abstract A substantial number of C4 plants are utilized as food and fodder crops and often display improved resource use efficiency compared to C3 plants. However, the response of C4 plants to future extreme conditions such as heatwaves is less understood. Here, Setaria viridis, an emerging C4 model grass closely related to important C4 crops, was grown under long-term high temperature stress for two weeks (42C, compared to 28C). High temperature resulted in stunted growth, but surprisingly had little impact on leaf thickness, leaf area-based photosynthetic rates and bundle sheath leakiness. Dark respiration rates increased significantly (p<0.05 two-tailed Student's t-test assuming equal variance) and there were major alterations in carbon and nitrogen metabolism in the heat-stressed plants, including reduced starch levels, accumulation of soluble sugars and increased leaf nitrogen content. Quantification of major phytohormones revealed a dramatic increase in abscisic acid and accumulation of IAA-amino acid conjugates in the heat-stressed plants, consistent with transcriptional changes of genes in these pathways. Leaf transcriptomics, proteomics and metabolomics analyses were carried out and mapped onto the metabolic pathways of photosynthesis, respiration, carbon/nitrogen metabolism and phytohormone biosynthesis and signaling. While poor correlations were observed between transcript and protein log2(FoldChange) values for some photosynthetic genes, we provide an in-depth analysis of 37 hierarchical functional groups. Overall, many stress signaling pathways were upregulated, consistent with multiple potent signals leading to reduced plant growth. A systems-based model of the plant response to long-term heat stress is presented based on the oxidative stress, phytohormone and sugar signaling pathways.

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.

Project description:This study was designed to identify changes in gene expression when corn was placed under various related stresses including being grown with a competing weed (canola) to the V4 or V8 stage, or when 40% shade cloth was present to the V4 or V8 stage, or under low nitrogen (no added nitrogen fertilizer), or under weed/shade free fertilized control conditions. In all 5 treatments and the control, samples were harvested at V8. Mechanisms underlying early season weed stress on crop growth are not well described. Corn vegetative growth and development, yield, and gene expression response to nitrogen (N), light (40% shade), and weed stresses were compared with the response of nonstressed plants. Vegetative parameters, including leaf area and biomass, were measured from V2 toV12 corn stages. Transcriptome (2008) or quantitative Polymerase Chain Reaction (q PCR) (2008/09) analyses examined differential gene expression in stressed versus nonstressed corn at V8. Vegetative parameters were impacted minimally by N stress although grain yield was 40% lower. Shade, present until V2, reduced biomass and leaf area > 50% at V2 and, at V12, recovering plants remained smaller than nonstressed plants. Grain yields of shade-stressed plants were similar to nonstressed controls, unless shade remained until V8. Growth and yield reductions due to weed stress in 2008 were observed when weeds remained until V6. In 2009, weed stress at V2 reduced vegetative growth, and weed stress until V4 or later reduced yield. Principle component analysis of differentially expressed genes indicated that shade and weed stress had more similar gene expression patterns to each other than to nonstressed or low N stressed tissues. Weed-stressed corn had 630 differentially expressed genes compared with the nonstressed control. Of these genes, 259 differed and 82 were shared with shade-stressed plants. Corn grown in N-stressed conditions shared 252 differentially expressed genes with weed-stressed plants. Ontologies associated with light/photosynthesis, energy conversion, and signaling were down-regulated in response to all three stresses. Although shade and weed stress clustered most tightly together, only three ontologies were shared by these stresses, O-methyltransferase activity (lignification processes), Poly U binding activity (post-transcriptional gene regulation), and stomatal movement. Based on both morphologic and genomic observations, results suggest that shade, N, and weed stresses to corn are regulated by both different and overlapping mechanisms.

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.

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Systems analysis of long-term heat stress responses in the C4 grass Setaria viridis

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