Genes Responsive to Elevated CO₂ Concentrations in Triploid White Poplar and Integrated Gene Network Analysis

<div><p>Background</p><p>The atmospheric CO₂ concentration increases every year. While the effects of elevated CO₂ on plant growth, physiology and metabolism have been studied, there is now a pressing need to understand the molecular mechanisms of how plants will respond to future increases in CO₂ concentration using genomic techniques.</p><p>Principal Findings</p><p>Gene expression in triploid white poplar ((<i>Populus tomentosa ×P. bolleana</i>) ×<i>P. tomentosa</i>) leaves was investigated using the Affymetrix poplar genome gene chip, after three months of growth in controlled environment chambers under three CO₂ concentrations. Our physiological findings showed the growth, assessed as stem diameter, was significantly increased, and the net photosynthetic rate was decreased in elevated CO₂ concentrations. The concentrations of four major endogenous hormones appeared to actively promote plant development. Leaf tissues under elevated CO₂ concentrations had 5,127 genes with different expression patterns in comparison to leaves under the ambient CO₂ concentration. Among these, 8 genes were finally selected for further investigation by using randomized variance model corrective ANOVA analysis, dynamic gene expression profiling, gene network construction, and quantitative real-time PCR validation. Among the 8 genes in the network, aldehyde dehydrogenase and pyruvate kinase were situated in the core and had interconnections with other genes.</p><p>Conclusions</p><p>Under elevated CO₂ concentrations, 8 significantly changed key genes involved in metabolism and responding to stimulus of external environment were identified. These genes play crucial roles in the signal transduction network and show strong correlations with elevated CO₂ exposure. This study provides several target genes, further investigation of which could provide an initial step for better understanding the molecular mechanisms of plant acclimation and evolution in future rising CO₂ concentrations.</p></div

Relationship between Modelling Accuracy and Inflection Point Attributes of Several Equations while Modelling Stand Diameter Distributions

<div><p>In this study, seven popular equations, including 3-parameter Weibull, 2-parameter Weibull, Gompertz, Logistic, Mitscherlich, Korf and R distribution, were used to model stand diameter distributions for exploring the relationship between the equations’ inflection point attributes and model accuracy. A database comprised of 146 diameter frequency distributions of Chinese fir (<i>Cunninghamia lanceolata</i> (Lamb.) Hook.) plantations was used to demonstrate model fitting and comparison. Results showed that the inflection points of the stand diameter cumulative percentage distribution ranged from 0.4 to 0.6, showing a 1/2 close rule. The equation’s inflection point attribute was strongly related to its model accuracy. Equation with an inflection point showed much higher accuracy than that without an inflection point. The larger the effective inflection point interval of the fitting curve of the equation was, and the closer the inflection point was to 0.5 for the equations with fixed inflection points, the higher the equation’s accuracy was. It could be found that the equation’s inflection point had close relationship with skewness of diameter distribution and stand age, stand density, which provided a scientific basis for model selection of a stand diameter distribution for Chinese fir plantations and other tree species.</p></div

Skewness and Kurtosis values of DBH from observed stands and equation simulations.

<p>Each circle dot represents a stand.</p

Correlation analysis of skewness of observed stands and seven equations.

<p>Correlation analysis of skewness of observed stands and seven equations.</p

Changes in growth, net photosynthetic rate and endogenous hormones at different CO₂ concentrations.

<p>The three CO₂ concentrations were: T0 treatment (385 µmol·mol⁻¹ CO₂, day 25°C/night 20°C); T1 treatment (550 µmol·mol⁻¹ CO₂, day 28°C/night 23°C); and T2 treatment (720 µmol·mol⁻¹ CO₂, day 31°C/night 26°C). <b>A</b>. Growth parameters of height and diameter of trees measured on June 25 and September 25 at different CO₂ concentrations. Bars represent SE (n = 20). <b>B</b>. Net photosynthetic rates of leaves sampled on June 25 and September 25. <b>C</b>. Levels of four endogenous hormones [gibberellic acid (GA₃, ng/g), abscisic acid (ABA, ng/g), zeatin riboside (ZR, ng/g), and indole acetic acid (IAA, µg/g)] in leaves sampled on September 25 at different CO₂ concentrations. The unit of four hormone concentrations is in fresh weight. Bars represent SE (n = 30 for net photosynthetic rates; n = 9 for endogenous hormone concentrations). Different letters on columns with the same pattern indicate differences at <i>P</i><0.05 according to the LSD test.</p

Expression levels of 8 genes quantified by qRT-PCR.

<p>*<i>P</i><0.05 compared with T0; #<i>P</i><0.05 compared with T1.</p

Frequency percentage of different distribution interval of ordinates of stand inflection points.

<p>Frequency percentage of different distribution interval of ordinates of stand inflection points.</p

Signal transduction network of differentially expressed genes under different CO₂ concentrations.

<p>Cycle nodes represent genes, the sizes of nodes represent the power of the interrelation among the nodes, and the edges between two nodes represent interactions between genes. Details of genes that mapped to each cycle node are listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0098300#pone.0098300.s005" target="_blank">Table S4</a>.</p

Pathway analysis based on genes in the three significant expression profiles.

<p>A, B, and C show significant pathways in profile 12, 10 and 16, respectively. Vertical axis, pathway category; horizontal axis, negative logarithm of <i>P</i>-values of pathways.</p

Relationship of the ordinates and abscissa of inflection points of R distribution to stand age (upper) and planting density (lower).

<p>Relationship of the ordinates and abscissa of inflection points of R distribution to stand age (upper) and planting density (lower).</p