Table 1.
Summary of sequencing results and their matches in the Oryza sativa japonica.
Fig 1.
Verification of RNA-Seq results through (A) principal component analysis and (B) real-time PCR.
Correlation between data obtained from RNA-Seq and RT-PCR data. Data are the mean of three biological replicates.
Fig 2.
Summary of the numbers of differentially expressed genes upon exposure to saline-alkaline stress in Dongdao-4 and Jigeng-88.
(A) The number of genes up- or downregulated in shoots of Dongdao-4 and Jigeng-88. (B) The number of genes up- or downregulated in roots of Dongdao-4 and Jigeng-88.
Fig 3.
Venn diagram of differentially expressed genes (DEGs) in Dongdao-4 and Jigeng-88.
(A) Upregulated DEGs in shoots; (B) downregulated DEGs in shoot; (C) upregulated DEGs in roots; (D) downregulated DEGs in roots. The numbers of genes shared and distinct to each genotype are shown.
Table 2.
Functional category annotations of upregulated genes in both rice genotypes.
Table 3.
Functional category annotations of downregulated genes in both rice genotypes.
Fig 4.
Significantly enriched GO terms at the biological process ontology level for differentially regulated genes in Dongdao-4 and Jigeng-88.
(A) GO terms specifically enriched by downregulated DEGs in shoots, (B) GO terms specifically enriched by upregulated DEGs in roots, (C) GO terms specifically downregulated DEGs in roots. GO terms were defined as significantly enriched if the false discovery rate (FDR) was ≤ 0.05. Green and red bars represent significantly enriched GO terms in Dongdao-4 and Jigeng-88, respectively. Blue and gray bars represent GO terms that are not significantly enriched in Dongdao-4 and Jigeng-88, respectively.
Fig 5.
KEGG terms significantly enriched by differentially regulated genes in Dongdao-4 and Jigeng-88.
(A) KEGG terms specifically enriched by upregulated DEGs in shoots, (B) KEGG terms specifically enriched by downregulated DEGs in shoots, (C) KEGG terms specifically enriched by upregulated DEGs in roots, (D) KEGG terms specifically enriched by downregulated DEGs in roots.
Table 4.
Differentially regulated genes involved in iron homeostasis in Dongdao-4 and Jigeng-88 seedlings.
Table 5.
The upregulated genes involved in GA and phenylpropanoid biosynthesis in Dongdao-4 seedlings.