Table 4.
Genes most likely contributing to the variation in BPH performance on Bt rice.
| Probe set ID | BPH-infested/non-infested | Gene ID and annotation | Classification | |||
|---|---|---|---|---|---|---|
| Bt | non-Bt | |||||
| FC | RP | FC | RP | |||
| Os.50961.1.S1_at | 4.125 | D | 1.046 | – | LOC_Os03g58890//oxidoreductase, 2OG-Fe oxygenase family protein | Carbohydrates metabolism |
| Os.11244.3.S1_x_at | 3.643 | D | 0.884 | – | LOC_Os06g04200//Granule-bound starch synthase 1, chloroplast precursor | |
| Os.10546.1.S1_s_at | 3.458 | D | 0.901 | – | LOC_Os09g34230//UDP-glucoronosyl and UDP-glucosyltransferase family protein | |
| Os.21369.1.S1_at | 3.383 | D | 1.740 | – | LOC_Os08g32780//bifunctionalmonodehydroascorbate reductase and carbonic anhydrasenectarin-3 precursor | |
| Os.27281.1.S1_at | 3.147 | D | 0.880 | – | LOC_Os04g02620//oxidoreductase, short chain dehydrogenase/reductase family protein | |
| Os.49281.1.S1_at | 3.025 | D | 0.926 | – | LOC_Os06g21240//Glycine rich protein family protein | |
| OsAffx.27459.2.S1_s_at | 9.600 | D | 0.685 | – | LOC_Os06g05000//Early nodulin 93 ENOD93 protein | Growth regulation |
| Os.38638.3.S1_x_at | 7.855 | D | 0.958 | – | LOC_Os06g05010//Early nodulin 93, putative | |
| Os.38638.1.S1_at | 5.593 | D | 2.311 | U | LOC_Os06g04990//Early nodulin 93, putative | |
| Os.11212.1.S1_at | 4.388 | D | 1.132 | – | LOC_Os07g18750//LTPL42—Protease inhibitor/seed storage/LTP family protein precursor, | Lipids metabolm |
| Os.27520.1.S1_at | 3.508 | D | 0.632 | – | LOC_Os12g02320//LTPL12—Protease inhibitor/seed storage/LTP family protein precursor, | |
| Os.13246.1.S1_at | 2.174 | U | 16.584 | D | LOC_Os01g59870//LTPL65—Protease inhibitor/seed storage/LTP family protein precursor, | |
| Os.13835.2.S3_a_at | 2.147 | U | 2.028 | D | LOC_Os01g51920//phosphotransferase | |
| Os.9538.1.S1_s_at | 3.415 | U | 1.344 | – | LOC_Os06g39870//26S protease regulatory subunit 8 | Nucleotides and protein metabolism |
| Os.27804.1.S1_at | 4.783 | D | 0.629 | – | LOC_Os08g10310//SHR5-receptor-like kinase | |
| Os.10246.4.S1_x_at | 4.709 | D | 0.572 | – | LOC_Os06g06510//Histone H3 | |
| Os.16899.1.S1_at | 3.617 | D | 0.718 | – | LOC_Os07g30150//phosphoribosyl transferase | |
| Os.8570.3.S1_s_at | 3.416 | D | 0.845 | – | LOC_Os03g19600//retrotransposon protein, putative, Ty3-gypsy subclass | Others |
| Os.10255.1.S1_s_at | 2.254 | D | 3.048 | U | LOC_Os01g37350//retrotransposon protein, putative, Ty3-gypsy subclass | |
| Os.5044.1.S1_at | 4.864 | U | 1.966 | – | LOC_Os01g50410//STE_MEKK_ste11_MAP3K.6 | Signal transduction |
| OsAffx.26237.1.S1_at | 4.28 | D | 0.998 | – | LOC_Os04g29770//wall–associated receptor kinase-like 3 precursor | |
| Os.12535.1.S1_at | 6.262 | U | 1.769 | – | LOC_Os01g52230//phosphoethanolamine/phosphocholine phosphatase | Stress response |
| Os.53670.1.S1_at | 4.675 | U | 1.710 | – | LOC_Os05g15880//glycosyl hydrolase | |
| Os.25329.1.A1_at | 3.827 | U | 1.087 | – | LOC_Os12g43440//Thaumatin-like protein precursor | |
| Os.20260.1.S1_at | 6.624 | D | 1.475 | – | LOC_Os01g22352//peroxidase 2 precursor | |
| Os.49627.1.S1_at | 5.695 | D | 0.552 | – | LOC_Os06g37150//L-ascorbate oxidase | |
| OsAffx.14201.1.S1_at | 5.063 | D | 1.017 | – | LOC_Os04g39360//heavy metal transport/detoxification protein | |
| OsAffx.32039.1.S1_x_at | 5.013 | D | 0.518 | – | LOC_Os12g35610//respiratory burst oxidase homolog | |
| Os.7611.1.S1_at | 4.413 | D | 0.737 | – | LOC_Os03g06670//Core histone H2A/H2B/H3/H4 domain containing protein | |
| Os.35510.1.S1_at | 4.211 | D | 0.517 | – | LOC_Os02g01220//Rhodanese-like domain containing protein | |
| Os.5338.1.S1_at | 3.597 | D | 0.644 | – | LOC_Os10g30150//universal stress protein family protein | |
| Os.5583.1.S1_at | 3.328 | D | 1.242 | – | LOC_Os03g19270//universal stress protein family protein | |
| OsAffx.11838.1.S1_x_at | 3.154 | D | 1.0783 | – | LOC_Os01g73250//abscisic stress-ripening | |
| Os.22580.1.S1_s_at | 3.033 | D | 0.902 | – | LOC_Os01g73250//abscisic stress-ripening | |
| Os.1479.1.S1_at | 6.91 | D | 0.871 | – | LOC_Os07g48980//Nicotianamine synthase 3 | |
| Os.54454.1.S1_at | 5.698 | D | 0.516 | – | LOC_Os11g32650//chalcone synthase | |
| OsAffx.27442.1.S1_at | 3.035 | U | 0.683 | – | LOC_Os06g03670//dehydration-responsive element-binding protein 1A | Transcription factors |
| Os.21231.1.S1_at | 6.147 | D | 0.600 | – | LOC_Os01g38610//Helix-loop-helix DNA-binding domain containing protein | |
| Os.7512.1.S1_at | 3.464 | U | 1.698 | – | LOC_Os04g56990//myb-like DNA-binding domain, SHAQKYF class family protein | |
| Os.9303.1.S1_at | 4.955 | D | 0.559 | – | LOC_Os02g46460//peptide transporter PTR3-A | Transport |
| Os.57361.1.S1_at | 7.482 | U | 1.948 | – | LOC_Os08g13400//hypothetical protein | Unknown |
| Os.9886.1.S1_at | 3.544 | U | 1.227 | – | LOC_Os04g02530//Conserved hypothetical protein | |
| Os.56964.1.S1_at | 6.937 | D | 0.912 | – | LOC_Os06g46980//expressed protein | |
| Os.5390.1.S1_at | 6.669 | D | 0.582 | – | LOC_Os12g33130//expressed protein | |
| Os.8558.1.S1_at | 4.388 | D | 0.629 | – | LOC_Os02g11770//hypothetical protein | |
| OsAffx.23641.1.S1_at | 3.635 | D | 0.595 | – | LOC_Os01g43230//expressed protein | |
| OsAffx.31409.1.S1_s_at | 3.558 | D | 1.314 | – | LOC_Os11g40660//hypothetical protein | |
| Os.50018.1.S1_at | 3.475 | D | 0.623 | – | LOC_Os07g47750//expressed protein | |
| Os.53428.1.S1_at | 3.391 | D | 0.600 | – | LOC_Os09g26370//expressed protein | Unknown |
| Os.7382.1.S1_at | 3.274 | D | 0.939 | – | LOC_Os05g46950//expressed protein | |
| OsAffx.16877.1.S1_at | 3.117 | D | 0.795 | – | LOC_Os08g07490//expressed protein | |
Nine Bt rice-specific upregulated and 37 (38 probe-sets) Bt rice-specific downregulated genes, as well as four genes showing opposite responses to BPH between Bt and non Bt rice plants were identified. These genes are involved in carbohydrate, lipid, nucleotide and protein metabolism, growth regulation, signal transduction, stress responses, or they encode transcription factors and transporters. FC, fold change value; RP, regulation pattern; D, down regulated; U, up regulated; –, no significant change.