Fig 1.
Phenotypes of germinated seeds of Brassica napus line WH126 at 0, 3, 12 and 24 hours after H2O (control) and salt (1.25% NaCl) treatments.
The names on the figure refer to the corresponding rows of germinated seeds. H indicates H2O treatment, S indicates salt treatment and the adjacent numbers indicate the sampling time points. The names were also used to describe the corresponding cDNA libraries.
Fig 2.
Effect of salt (NaCl) on Brassica napus roots length during the 24-hour time course.
Equal numbers of seeds were placed in three petri dishes under control (H2O treatment) and salt treatment (ST), separately, and placed randomly in the incubator. At each time point, the uniform germinated seeds under both treatments were sampled from every dish to capture root-length values. The whole experiment was carried out on three replicates. The error bars represent the standard error (SE) of the mean root length.
Table 1.
DGE sequencing statistics.
Fig 3.
Summaries of differentially regulated genes during the time course.
Differentially regulated genes were identified either by a comparison of adjacent stages or comparing each stage to H0. “H3/H0” indicates a comparison between the gene expression in the H3 library with that in the H0 library, and the same describes the other labels on the x-axis.
Fig 4.
Total regulated genes at each time point after salt treatment.
Differentially expressed genes were confirmed based on whether the |log2Foldchange| ≥1 and p value ≤0.05.
Fig 5.
Venn diagram describing the exclusion and overlap of regulated genes at three time points.
The left and right diagrams indicate the up- and down-regulated gene numbers, respectively.
Fig 6.
Hierarchical cluster analyses of the 163 common differentially expressed genes (DEGs) at three time points.
This map shows the changes of log2(foldchange) values at the indicated times (3 hours, 12 hours and 24 hours) during salt stress. The genes were assigned into four clusters.
Fig 7.
Gene Ontology (GO) analyses of commonly differentially expressed genes at three time points.
The differentially expressed genes were assigned into three groups, including biological process, cellular components and molecular function. The x-axis represents the most abundant categories of each group, and the y-axis represents the percentages of the total genes in each category.
Fig 8.
Heat-map representation for the regulation by salt stress of the focused genes.
The transcript abundance of each gene at each time point under control or ST was normalized. The top color bar represents the comparative expression level. A redder color indicates more transcript accumulation, and greener indicates less.
Fig 9.
Quantitative real-time PCR (qPCR) validations of gene expression levels from digital gene expression (DGE) analysis.
The qPCR values are presented as the averages of three independent experiments. The genes were randomly selected. “S3/H3” indicates a comparison between the expressions of the corresponding genes in the S3 library with that in the H3 library. The “S12/H12” and “S24/H24” ratios indicate analogous comparisons. The y-axis indicates the fold-changes obtained by two methods. The “A-F” indicates the genes with the assay names of Bra041014, Bra000150, Bra020731, Bra011843, Bra023573 and Bra000090, respectively.
Fig 10.
Proposed model for root-development inhibition under salt stress.
Salt stress caused osmotic stress, oxidative stress and cell wall damage to the roots. Some salt-stress related genes (in red boxes) were regulated by, or responded to, each of these three aspects.