Gene-to-gene coexpression analysis provides fundamental information and is a promising approach for predicting unknown gene functions in plants. We investigated various associations in the gene expression of tomato (Solanum lycopersicum) to predict unknown gene functions in an unbiased manner. We obtained more than 300 microarrays from publicly available databases and our own hybridizations, and here, we present tomato coexpression networks and coexpression modules. The topological characteristics of the networks were highly heterogenous. We extracted 465 total coexpression modules from the data set by graph clustering, which allows users to divide a graph effectively into a set of clusters. Of these, 88% were assigned systematically by Gene Ontology terms. Our approaches revealed functional modules in the tomato transcriptome data; the predominant functions of coexpression modules were biologically relevant. We also investigated differential coexpression among data sets consisting of leaf, fruit, and root samples to gain further insights into the tomato transcriptome. We now demonstrate that (1) duplicated genes, as well as metabolic genes, exhibit a small but significant number of differential coexpressions, and (2) a reversal of gene coexpression occurred in two metabolic pathways involved in lycopene and flavonoid biosynthesis. Independent experimental verification of the findings for six selected genes was done using quantitative real-time polymerase chain reaction. Our findings suggest that differential coexpression may assist in the investigation of key regulatory steps in metabolic pathways. The approaches and results reported here will be useful to prioritize candidate genes for further functional genomics studies of tomato metabolism.
We assessed the effects of light intensity (photosynthetic photon flux [PPF in µmol·m -2 ·s -1 ]) and number of irradiated leaves on photosynthesis and the fruit growth of individual tomato plants to develop supplemental LED lighting techniques for greenhouse tomato production. In Experiment (Exp.) 1, three PPF levels (P200, P500, and P1000) were applied to a post-anthesis tomato plant for three weeks, each plant pruned to have one leaf and one truss with three flowers. The fruit set and leaf and fruit dry-weight increased with increasing PPF; however, after P500 and P1000 treatments, the leaves showed signs of stress and accompanying disorders. Thus, to increase the fruit set ratio and growth rate of tomato fruits and plants, the total amount of irradiation received by each plant should be increased by increasing the number of irradiated leaves, rather than raising the PPF per leaf. For prolonged cultivation, P200 was the optimal PPF per leaf under the tested treatments. Exp. 2 used standard tomato plants with no leaves or trusses removed. We used an assimilation chamber to examine the effect of the number of leaves receiving P200 irradiation on the photosynthetic rate (Pn) per plant (above ground part). The Pn per plant in treatments where one and two leaves were irradiated by supplemental LED lighting were, respectively, 12 and 28% higher than that in the control (only top lighting). Therefore, fruit growth and yields in tomato cultivation may be raised via acceleration of photosynthesis by increasing the number of leaves that receive P200 irradiation rather than by increasing PPF.
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