Table 3.
Microarray data validation.
| (A) Quantitative reverse transcriptase‐polymerase chain reaction (qPCR) with RNA from hand‐dissected galls (Ag) at 3 and 7 days post‐infection (dpi) vs. RNA from equivalent uninfected root segments. | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| 3 dpi | 7 dpi | ||||||||
| SGN‐U | Description | qPCR | Ag | TOM1 | CGs/CCs | qPCR | Ag | TOM1 | CGs/CCs |
| SGN‐U152030 | Putative LRP (lateral root primordia) 1 [Oryza sativa (japonica cultivar group)] | 2.40 | 1.71 | 2.40 | 1.85 | ||||
| SGN‐U143838 | Pathogenesis‐related protein PR‐1 precursor [Capsicum annuum] | −0.81 | −2.97 | −2.57 | −4.18 | ||||
| SGN‐U144043 | Peroxidase | −0.64 | −2.68 | −1.15 | −4.58 | ||||
| (B) Comparison of TOM1 log2 ratios with the same data from the homologous genes obtained from the Complete Arabidopsis Transcriptome Microarray (CATMA) hybridized with RNA from whole Arabidopsis galls at 7 dpi vs. control uninfected segments by (Jammes et al., 2005). | |||||
|---|---|---|---|---|---|
| TOM1 3 dpi | TOM1 7 dpi | CATMA 7 dpi | |||
| SGN‐U | Description | GCs/CCs | GCs/CCs | Galls/reference | |
| SGN‐U148611 | Calcium‐binding EF‐hand family protein [Arabidopsis thaliana] | 1.17 | 1.36 | AT3G10300 | 2.21 |
| SGN‐U144918 | Macrophage migration inhibitory factor (MIF) family [A. thaliana] | 1.26 | 1.45 | AT5G01650 | 0.69 |
| SGN‐U143273 | 1‐Aminocyclopropane‐1‐carboxylate oxidase 2 (ACC oxidase 2) (ethylene‐forming enzyme) | −1.73 | −2.05 | At1g05010 | −2.00 |
| SGN‐U145252 | 1‐Aminocyclopropane‐1‐carboxylate oxidase [Solanum tuberosum] | −2.00 | −2.23 | AT1G05010 | −0.76 |
| SGN‐U145393 | At1g17620 [A. thaliana] | −2.46 | −2.65 | AT1G17620 | −1.12 |
| SGN‐U143928 | Xyloglucan endotransglycosylase (XTR4), putative [A. thaliana] | −2.49 | −2.98 | AT1G32170 | −1.26 |
| SGN‐U150639 | Unknown [A. thaliana] | −1.70 | −1.86 | AT1G52200 | −0.96 |
| SGN‐U143303 | Lipoxygenase A | −1.52 | −2.43 | AT1G55020 | *(−1.41) −1.02 |
| SGN‐U143803 | Putative γ TIP [Nicotiana glauca] | −2.39 | −3.12 | AT2G36830 | *(−1.49) −1.60 |
| SGN‐U143455 | Putative peroxidase [Oryza sativa (japonica cultivar group)] | −2.73 | −2.64 | AT2G37130 | −0.95 |
| SGN‐U143822 | Embryo‐abundant protein EMB [Pisum sativum] | −2.53 | −3.12 | AT2G41380 | −1.20 |
| SGN‐U143771 | axi 1 protein from Nicotiana tabacum‐related [A. thaliana] | −1.15 | −1.75 | AT2G44500 | −0.74 |
| SGN‐U146284 | Pathogen‐inducible α‐dioxygenase [Nicotiana attenuata] | −1.76 | −2.01 | AT3G01420 | −1.97 |
| SGN‐U159571 | No apical meristem (NAM) protein family [A. thaliana] | −1.76 | −3.45 | AT3G18400 | −0.73 |
| SGN‐U150800 | Hypothetical protein [A. thaliana] | −1.90 | −3.38 | AT3G48180 | −0.68 |
| SGN‐U152291 | Auxin‐induced (indole‐3‐acetic acid induced) protein family [A. thaliana] | −1.48 | −1.91 | AT3G60690 | −0.73 |
| SGN‐U145645 | Hypothetical protein SENU1, senescence up‐regulated – tomato (fragment) | −1.98 | −3.34 | AT3G62420 | −0.97 |
| SGN‐U143226 | Oxidoreductase, zinc‐binding dehydrogenase family [A. thaliana] | −1.55 | −1.58 | AT4G13010 | −0.77 |
| SGN‐U146724 | Expressed protein [A. thaliana] | −1.49 | −2.04 | AT4G17900 | −0.86 |
| SGN‐U149079 | Hypothetical protein [A. thaliana] | −1.92 | −2.23 | AT4G28050 | −0.70 |
| SGN‐U155547 | Ribulose bisphosphate carboxylase small chain 2A, chloroplast precursor (RuBisCO s.s2A) | −1.58 | −2.12 | AT4G39980 | −0.82 |
| SGN‐U145263 | AT5g25110/T11H3_120 [A. thaliana] | −1.19 | −2.22 | AT5G25110 | −1.32 |
| SGN‐U152349 | bZIP transcription factor, TGA1 [A. thaliana] | −1.53 | −2.8 | AT5G65210 | −0.79 |
The log2 expression ratios obtained from the TOM1 hybridizations with RNA doubly amplified from giant cells (GCs) induced by Meloidogyne javanica at 3 and 7 dpi vs. the corresponding controls (CCs). A positive ratio indicates that the gene is induced in GCs; a negative ratio indicates that the gene is repressed in GCs.
*
Results of qPCR validation (Jammes et al., 2005).