Figure 1.
Differential responsiveness of rice japonica variety (Nipponbare) and indica variety (93-11) to MV treatment.
A. 93-11 (up) and Nipponbare (down) sprouted seeds were mock-treated (water) or treated with 10 µM MV. B. The chlorophyll content of seedling plants after treatment.
Figure 2.
Summary of the transcription profiles of different rice cultivars (Nipponbare vs 93-11) under 10 µM MV treatment.
A. The Venn diagram illustrates probe level expression affected by two factors -cultivar (Nipponbare vs. 93-11) and treatment (10 µM MV vs. mock). The number of probes showing a significant change at P< = 0.01 is shown. B. The cultivar and treatment effects of Core Intersectional Probesets (CIPs). The blue circles at top-right represent the CIPs preferentially expressed in Nipponbare and up-regulated by MV treatment. The brown triangles at bottom-left represent the CIPs preferentially expressed in 93-11 and down-regulated by MV treatment. The yellow squares at upper-left represent the CIPs preferentially expressed in Nipponbare and down-regulated by MV treatment. The green diamonds at bottom-right represents the CIPs preferentially expressed in 93-11 and up-regulated by MV treatment.
Table 1.
Gene Ontology Analysis of 1062 CIPs.
Figure 3.
The expression pattern of the Core Intersectional Probesets (CIPs) in highlighted gene superfamilies.
A. The probe sets were derived from peroxidases, GSTs, UGTs, P450s, UDP-glucoronosyl transferase, and NB-ARC domain-containing proteins. B. The probe sets were from transporters, kinases, and TFs. The color scale (representing expression level) is shown at bottom-right. Red indicates a higher expression level, whereas blue indicates a lower expression level. White indicates the average expression level.
Table 2.
Real-time RT-PCR for selected genes in 10 µM MV treated Nipponbare and 93-11 seedlings.
Figure 4.
InDel analysis of selected genes between indica and japonica varieties.
Lanes 1–5: PCR products obtained using genomic DNA of indica varieties: 93-11, 37760, 03A-11, TP34, and ShuiYuan349, respectively. Lanes 6–10: PCR products obtained using genomic DNA of japonica varieties: Nipponbare, IR66746-76-3-2, REIMEL, ShangZhou10, and YunFeng7, respectively. LOC_Os11g12340–disease resistance protein RPM1; LOC_Os02g56700–Cinnamoyl-CoA reductase (OsCCR10); LOC_Os11g10550–NBS-LRR disease resistance protein; LOC_Os07g33690–NBS-LRR type disease resistance protein Hom-F; LOC_Os10g38360–glutathione S-transferase.
Figure 5.
The sketch map for GSTs in the 20.15 to 20.17 Mb region of chromosome 10.
This map highlights three glutathione S-transferase genes within the CIP list, LOC_Os10g38340, LOC_Os10g38350, and LOC_Os10g38360, including their locations, transcript direction, the positions of indel regions different between japonica and indica, motifs in promoter regions, and expression patterns.
Figure 6.
The expression pattern of selected phenylpropanoid pathway related genes in 10 µM MV treated seedling plants from rice japonica variety (Nipponbare) and indica variety (93-11).
The black bars indicate relative expression (fold-change by real-time PCR) of the gene in Nipponbare samples. The grey bars indicate relative expression (fold-change by real-time PCR) of the gene in 93-11 samples. Error bars represent the standard error of three replicates. LOC_Os05g12240–Chalcone synthase 8 (CHS8); LOC_Os10g12080–Cytochrome P450 98A15p (C3H); LOC_Os02g56460–Cinnamoyl-CoA reductase (OsCCR1); LOC_Os02g56700–Cinnamoyl-CoA reductase (OsCCR10).