Table 2.
Differentially expressed gene responses to submergence during germination in contrasting rice genotypes.
| Gene id | Log2 fold change (treatment/control) | ||||||
|---|---|---|---|---|---|---|---|
| IR64 | Nipponbare | F291 | F274-2a | 8391 | 8753 | ||
| 57 DE GENES SIGNIFICANTLY DETECTED IN SIX GENOTYPES (P < 0.05) | |||||||
| LOC_Os01g09030 | 2.54 | 4.18 | 2.46 | 3.73 | 3.88 | 5.62 | Putative uncharacterized protein |
| LOC_Os01g09540 | −2.66 | −6.09 | −4.96 | −2.79 | −4.85 | −6.11 | Putative acid phosphatase |
| LOC_Os01g19820 | 3.46 | 3.75 | 3.65 | 5.78 | 3.55 | 3.22 | Putative ER6 protein |
| LOC_Os01g21120 | 3.11 | 6.04 | 2.97 | 5.58 | 5.27 | 3.96 | Putative ethylene response factor 2 |
| LOC_Os01g22249 | 5.33 | 3.97 | 7.11 | 8.15 | 8.19 | 8.07 | Class III peroxidase 13 |
| LOC_Os01g58290 | 4.34 | 3.33 | 3.35 | 4.87 | 5.06 | 5.89 | Uncharacterized protein |
| LOC_Os01g65830 | 4.18 | 5.73 | 3.39 | 4.89 | 6.36 | 6.60 | Acyl-[acyl-carrier-protein] desaturase 1 |
| LOC_Os01g67010 | 5.56 | 8.20 | 3.84 | 8.48 | 9.05 | 7.75 | Uncharacterized protein |
| LOC_Os01g67030 | 3.81 | 10.53 | 5.75 | 11.27 | 9.42 | 7.96 | Membrane protein-like protein |
| LOC_Os01g68300 | −2.77 | −3.83 | −6.56 | −2.57 | −7.91 | −7.21 | Uncharacterized protein |
| LOC_Os01g68720 | 6.69 | 4.06 | 5.81 | 7.24 | 5.93 | 5.78 | Uncharacterized protein |
| LOC_Os01g74410 | 3.16 | 3.15 | 4.44 | 6.65 | 5.44 | 4.78 | Putative Myb factor protein |
| LOC_Os02g39620 | Inf | 7.21 | 6.54 | 8.94 | 9.92 | Inf | Putative stress-inducible protein |
| LOC_Os02g55890 | 4.32 | 7.11 | 6.80 | 6.13 | 6.46 | 6.91 | Vacuolar proton pyrophosphatase |
| LOC_Os03g01320 | 2.31 | 2.51 | 4.08 | 5.39 | 5.66 | 3.52 | Retrotransposon protein, Ty1-copia subclass |
| LOC_Os03g03034 | 4.10 | 3.87 | 2.75 | 4.06 | 2.94 | 4.64 | Oxidoreductase, 2OG-Fe oxygenase family protein |
| LOC_Os03g08460 | 8.15 | 4.30 | 6.79 | 8.70 | 8.23 | 6.22 | AP2 domain containing protein |
| LOC_Os03g12510 | Inf | 9.63 | 5.16 | 6.83 | Inf | 5.13 | Non-symbiotic hemoglobin 2 |
| LOC_Os03g19270 | 3.16 | 5.37 | 3.13 | 4.49 | 4.54 | 5.47 | Universal stress protein family protein |
| LOC_Os03g19600 | 5.65 | 2.86 | 4.22 | 6.27 | 6.84 | 6.28 | Retrotransposon protein, Ty3-gypsy subclass |
| LOC_Os03g45250 | 5.62 | 6.62 | 4.39 | 6.16 | 7.15 | 7.38 | Uncharacterized protein |
| LOC_Os03g49524 | 4.16 | 4.21 | 3.85 | 7.01 | 4.23 | 5.18 | Uncharacterized protein |
| LOC_Os03g55680 | 6.54 | Inf | 6.58 | 9.34 | 7.25 | 9.13 | Uncharacterized protein |
| LOC_Os03g61150 | 6.67 | 5.95 | 3.15 | 6.04 | 7.75 | 7.08 | Uncharacterized protein |
| LOC_Os04g17660 | 2.48 | 3.87 | 5.09 | 5.58 | 4.73 | 6.91 | Uncharacterized protein |
| LOC_Os04g31790 | 4.12 | 5.60 | 3.90 | 5.51 | 4.36 | 4.81 | Uncharacterized protein |
| LOC_Os04g41620 | −4.89 | −7.91 | −Inf | −6.82 | −Inf | −8.60 | CHIT2—Chitinase family protein precursor |
| LOC_Os04g56430 | 6.89 | 6.49 | 7.69 | 7.37 | 10.54 | 7.46 | Putative receptor-like protein kinase |
| LOC_Os05g06920 | −5.18 | −4.22 | −5.81 | −4.89 | −3.80 | −6.06 | Uncharacterized protein |
| LOC_Os05g37780 | Inf | 7.50 | 4.36 | 7.66 | 7.97 | 8.62 | Uncharacterized protein |
| LOC_Os05g39310 | 2.68 | 4.92 | 4.26 | 5.00 | 3.71 | 6.30 | Pyruvate decarboxylase 1 |
| LOC_Os06g04940 | Inf | 8.72 | 7.59 | 7.88 | 8.34 | 9.31 | Uncharacterized protein |
| LOC_Os07g24830 | 9.51 | 5.73 | 7.11 | 9.82 | −3.06 | 6.56 | Uncharacterized protein |
| LOC_Os07g32680 | 3.37 | 3.75 | 4.72 | 5.17 | 8.02 | 6.22 | Putative glycine-rich cell wall structural protein |
| LOC_Os07g32710 | 4.56 | 3.61 | 3.39 | 6.15 | 5.71 | 5.69 | Uncharacterized protein |
| LOC_Os07g41350 | Inf | Inf | 3.86 | 7.52 | 7.86 | 8.27 | Uncharacterized protein |
| LOC_Os07g44140 | 3.12 | 5.04 | 2.80 | 4.68 | 6.17 | 2.67 | Putative cytochrome P450 |
| LOC_Os07g47790 | 6.76 | 9.08 | 6.42 | 7.46 | 9.38 | 8.84 | AP2 domain transcription factor EREBP |
| LOC_Os08g04210 | 6.98 | 6.56 | 8.38 | 9.12 | 7.77 | 9.91 | 33-kDa secretory protein |
| LOC_Os08g08100 | 6.24 | 6.70 | 5.30 | 7.48 | 8.47 | 9.19 | Uncharacterized protein |
| LOC_Os08g40690 | 5.03 | 6.96 | 7.69 | 7.29 | 9.24 | 8.83 | Chitinase |
| LOC_Os09g31000 | Inf | 7.89 | 8.70 | Inf | 8.57 | 8.49 | Uncharacterized protein |
| LOC_Os09g36680 | −5.80 | −5.86 | −4.73 | −6.03 | −6.70 | −11.68 | Drought-induced S-like ribonuclease |
| LOC_Os09g36930 | −3.93 | −6.17 | −5.79 | −4.67 | −Inf | −5.87 | Probable aquaporin PIP2-7 |
| LOC_Os09g38910 | 4.37 | 3.97 | 3.51 | 4.61 | 6.01 | 3.40 | Uncharacterized protein |
| LOC_Os10g30150 | Inf | 10.47 | 2.97 | 6.31 | 7.68 | 8.42 | Universal stress protein family protein |
| LOC_Os10g31420 | Inf | Inf | 9.18 | 5.69 | 6.78 | 6.46 | Uncharacterized protein |
| LOC_Os10g40510 | 6.66 | 7.46 | 7.50 | 8.71 | 8.46 | 8.19 | Cortical cell delineating protein |
| LOC_Os10g40530 | 3.72 | 4.03 | 4.10 | 6.55 | 5.20 | 5.35 | Cortical cell delineating protein |
| LOC_Os11g10510 | 3.39 | 8.38 | 5.29 | 6.16 | 6.03 | 5.90 | Alcohol dehydrogenase 2 |
| LOC_Os11g42500 | −4.17 | −5.49 | −6.00 | −3.44 | −6.08 | −6.88 | Dirigent-like protein |
| LOC_Os11g47500 | 3.87 | 5.97 | 7.31 | 7.28 | 8.39 | 7.49 | Xylanase inhibitor protein 1 |
| LOC_Os11g47570 | 4.00 | 5.34 | 6.13 | 7.69 | 8.36 | 6.45 | Uncharacterized protein |
| LOC_Os11g47600 | 5.22 | 8.20 | 4.97 | 8.90 | 8.52 | 6.55 | Xylanase inhibitor protein 1 |
| LOC_Os12g09540 | 3.20 | 4.09 | 3.99 | 4.05 | 4.45 | 6.30 | Phosphoribosylamine-glycine ligase |
| LOC_Os12g35610 | 2.83 | 6.17 | 3.97 | 5.77 | 5.03 | 6.49 | Respiratory burst oxidase |
| LOC_Os12g38770 | 4.49 | 4.34 | 6.49 | 5.93 | 6.65 | 5.60 | Nucleotide pyrophosphatase/phosphodiesterase |
| 43 DE GENES STRONGLY REGULATED IN FIVE TOLERANT GENOTYPES (P < 0.05) BUT LESS SIGNIFICANT IN SENSITIVE IR64 (P > 0.05) | |||||||
| LOC_Os01g13690 | −2.03 | −5.05 | −4.75 | −3.64 | −3.56 | −5.19 | Branched-chain amino acid aminotransferase-like protein |
| LOC_Os01g45274 | −1.04 | −3.21 | −2.76 | −2.35 | −2.59 | −4.57 | Carbonic anhydrase |
| LOC_Os01g46120 | −1.26 | −4.39 | −4.97 | −4.21 | −4.94 | −5.51 | Lipase-like protein |
| LOC_Os01g70520 | −1.70 | −6.51 | −6.36 | −5.38 | −Inf | −8.73 | Beta-glucosidase 5 |
| LOC_Os02g02400 | −1.61 | −6.40 | −8.44 | −5.19 | −8.12 | −9.24 | Catalase isozyme A |
| LOC_Os02g18650 | Inf | 7.09 | 7.53 | 6.61 | 6.18 | 7.30 | Pectinesterase |
| LOC_Os02g20540 | −1.60 | −5.60 | −5.97 | −3.18 | −7.50 | −5.82 | Putative fasciclin-like arabinogalactan-protein |
| LOC_Os02g30080 | −1.91 | −4.73 | −7.27 | −4.79 | −6.78 | −5.46 | Cytochrome P450 family protein |
| LOC_Os02g38920 | 1.60 | 3.04 | 4.35 | 4.17 | 4.98 | 4.35 | Glyceraldehyde-3-phosphate dehydrogenase 3, cytosolic |
| LOC_Os03g13300 | 1.62 | 7.58 | 2.68 | 4.28 | 5.95 | 2.78 | Glutamate decarboxylase |
| LOC_Os03g27190 | −1.63 | −4.27 | −6.02 | −6.46 | −6.48 | −8.55 | ICE-like protease p20 domain containing protein |
| LOC_Os03g31750 | 2.08 | 5.43 | 6.38 | 5.00 | 6.24 | 6.78 | Pyruvate, phosphate dikinase |
| LOC_Os03g45619 | −1.95 | −9.38 | −5.41 | −4.31 | −6.70 | −13.01 | Cytochrome P450 family protein |
| LOC_Os03g57490 | 1.40 | 5.28 | 4.68 | 5.86 | 5.35 | 4.71 | Beta-Ig-H3 domain-containing protein |
| LOC_Os04g25650 | 1.65 | 4.50 | 5.94 | 4.87 | 6.20 | 3.75 | Uncharacterized protein |
| LOC_Os04g54220 | 4.12 | 5.94 | 6.65 | 8.03 | 7.53 | 7.48 | Uncharacterized protein |
| LOC_Os04g56230 | −1.21 | −6.00 | −Inf | −6.43 | −5.76 | −6.83 | Polyprenyl synthetase |
| LOC_Os05g10650 | 1.68 | 5.50 | 3.96 | 4.87 | 5.65 | 4.21 | Uncharacterized protein |
| LOC_Os05g12400 | −2.83 | −5.56 | −8.49 | −3.46 | −6.12 | −8.47 | BURP domain-containing protein 1 |
| LOC_Os05g12630 | −3.12 | −6.63 | −4.22 | −3.02 | −4.74 | −7.14 | BURP domain-containing protein 7 |
| LOC_Os05g13970 | Inf | 6.16 | 6.59 | 6.29 | 9.22 | 5.65 | Uncharacterized protein |
| LOC_Os06g03520 | 2.14 | 6.07 | 2.90 | 2.85 | 8.35 | 6.83 | Uncharacterized protein |
| LOC_Os06g05020 | 1.88 | 8.48 | 2.84 | 3.17 | 8.41 | 8.75 | Putative early nodulin |
| LOC_Os06g49340 | 1.89 | Inf | 4.95 | 6.46 | 5.38 | 9.90 | Uncharacterized protein |
| LOC_Os07g01560 | 1.71 | 5.13 | 3.56 | 4.56 | 6.11 | 3.45 | Putative monosaccharide transport protein MST1 |
| LOC_Os07g04990 | −2.19 | −4.58 | −3.97 | −3.92 | −3.38 | −6.39 | Aldo/keto reductase family-like protein |
| LOC_Os07g09630 | 1.82 | 5.43 | 4.12 | 4.35 | 3.84 | 6.40 | Uncharacterized protein |
| LOC_Os07g34570 | −1.53 | −3.29 | −7.22 | −4.45 | −5.66 | −7.52 | Thiamine thiazole synthase, chloroplastic |
| LOC_Os07g37454 | 2.56 | 6.46 | 3.44 | 5.13 | 7.48 | 6.40 | Uncharacterized protein |
| LOC_Os07g46480 | −1.67 | −4.32 | −3.36 | −2.77 | −4.33 | −6.03 | Nucleoid DNA-binding-like protein |
| LOC_Os07g47990 | 1.32 | 3.71 | 5.32 | 4.68 | 6.51 | 3.34 | Putative peroxidase |
| LOC_Os07g49110 | −1.26 | −4.80 | −5.03 | −3.86 | −5.39 | −5.11 | Uncharacterized protein |
| LOC_Os08g25720 | 0.35 | 2.58 | 3.07 | 3.08 | 2.45 | 2.94 | Putative pyrophosphate-dependent phosphofructokinase |
| LOC_Os08g27840 | −0.65 | −4.07 | −4.71 | −2.62 | −3.74 | −4.04 | Phosphoenolpyruvate carboxylase |
| LOC_Os09g16520 | 1.23 | 4.29 | 6.19 | 5.60 | 7.09 | 6.56 | Cytochrome b5-like Heme/Steroid binding domain containing protein |
| LOC_Os09g31040 | 2.18 | 5.90 | 6.71 | 5.93 | 7.98 | 8.21 | Uncharacterized protein |
| LOC_Os10g23180 | −2.22 | −7.12 | −7.18 | −6.30 | −8.44 | −7.37 | Cytochrome P450 family protein |
| LOC_Os10g26700 | 1.97 | Inf | 6.49 | 6.97 | 5.64 | 8.27 | YGL010w |
| LOC_Os10g31460 | −0.69 | 5.25 | 8.41 | 4.38 | 10.02 | 3.95 | Uncharacterized protein |
| LOC_Os11g43860 | −0.64 | −4.19 | −4.17 | −7.00 | −3.94 | −4.48 | Magnesium/proton exchanger 1 |
| LOC_Os11g47550 | NA | Inf | 10.47 | 7.02 | 8.27 | 5.88 | Xylanase inhibitor protein 2 |
| LOC_Os11g47560 | 4.19 | Inf | 5.90 | 7.24 | Inf | Inf | Xylanase inhibitor protein 2 |
| LOC_Os11g47590 | Inf | 6.02 | 6.25 | Inf | 7.40 | 7.80 | Xylanase inhibitor protein 1 |
The original P-value for each gene is listed in Table S7. Gene descriptions were extracted from the Gramene BioMart database and MSU gene annotation.