Table 2 Zn deficiency-induced or repressed genes returning to basal level after Zn resupply in the roots. The FPKM value represents mean ± SD of three biological replicates. Note: MSTRG.6046, MSTRG.22477, and MSTRG.30070 are three new loci. “-” means no description
From: Integrated analyses of miRNAome and transcriptome reveal zinc deficiency responses in rice seedlings
Gene | Description | ZPR (FPKM) | ZMR (FPKM) | ZRR (FPKM) |
|---|---|---|---|---|
Os08g0235800 | Similar to WRKY transcription factor 25 | 0 | 23.49 ± 22.4 | 0 |
Os01g0896400 | Similar to JHL23J11.5 protein | 0 | 11.66 ± 18.26 | 0 |
Os01g0693800 | Similar to Threonine synthase, chloroplast precursor | 0 | 11.17 ± 9.72 | 0 |
Os05g0121500 | Similar to structural constituent of ribosome | 0 | 6.57 ± 6.92 | 0 |
Os03g0191900 | Pathogenesis-related transcriptional factor and ERF domain containing protein | 0 | 5.76 ± 5.66 | 0 |
Os11g0107600 | Similar to prenylated Rab receptor 2 | 0 | 5.35 ± 4.77 | 0 |
Os02g0455400 | Hypothetical conserved gene | 0 | 4.66 ± 4.04 | 0 |
Os03g0852400 | Conserved hypothetical protein | 0 | 4.28 ± 3.71 | 0 |
Os03g0280750 | Plant disease resistance response protein family protein | 0 | 3.48 ± 3.11 | 0 |
Os05g0571600 | Conserved hypothetical protein | 0 | 3.2 ± 2.77 | 0 |
Os02g0310400 | Conserved hypothetical protein | 0 | 3.08 ± 2.68 | 0 |
Os05g0525900 | Similar to Zing finger transcription factor PEI1 | 0 | 2.67 ± 2.32 | 0 |
Os01g0742300 | 3-hydroxyacid dehydrogenase/reductase domain containing protein | 0 | 1.96 ± 1.79 | 0 |
Os03g0253200 | Similar to WAG1; kinase | 0 | 1.91 ± 1.66 | 0 |
Os06g0192800 | Similar to RING-H2 finger protein ATL1R (RING-H2 finger protein ATL8) | 0 | 1.59 ± 1.78 | 0 |
Os01g0234700 | Harpin-induced 1 domain containing protein | 0 | 1.25 ± 1.4 | 0 |
Os03g0103400 | GRAS transcription factor domain containing protein | 0 | 0.99 ± 0.89 | 0 |
Os10g0490100 | Virulence factor, pectin lyase fold family protein | 0 | 0.98 ± 0.88 | 0 |
Os03g0245700 | Similar to senescence-associated protein 15 | 0 | 0.96 ± 0.84 | 0 |
Os05g0578100 | Protein of unknown function DUF1645 family protein | 0 | 0.82 ± 0.15 | 0 |
Os01g0584300 | – | 0 | 2.42 ± 2.23 | 0 |
Os04g0685700 | Similar to H0723C07.4 protein | 0 | 0.75 ± 0.65 | 0 |
Os07g0585900 | Hypothetical conserved gene | 0 | 0.75 ± 0.66 | 0 |
MSTRG.6046 | – | 0 | 0.66 ± 0.7 | 0 |
Os02g0242900 | Similar to hydroquinone glucosyltransferase | 0 | 0.63 ± 0.6 | 0 |
Os11g0256100 | Pentatricopeptide repeat domain containing protein | 0 | 0.41 ± 0.35 | 0 |
Os12g0137700 | Sulfotransferase family protein | 0.01 ± 0.01 | 3.9 ± 3.66 | 0.03 ± 0.04 |
Os04g0280500 | Similar to Non-S-locus F-box-like protein 2011 | 0.07 ± 0.02 | 18.01 ± 5.28 | 0.31 ± 0.22 |
Os10g0553600 | Exostosin-like family protein | 0.01 ± 0.01 | 1.69 ± 0.89 | 0.01 ± 0.01 |
Os08g0207401 | Hypothetical gene | 0.01 ± 0.03 | 0.97 ± 0.34 | 0.04 ± 0.03 |
Os10g0328600 | Hypothetical protein | 0.11 ± 0.09 | 6.52 ± 1.13 | 0.13 ± 0.03 |
Os06g0566201 | – | 0.4 ± 0.03 | 13.82 ± 8.44 | 0.88 ± 0.15 |
Os06g0566300 | Zinc transporter OsZIP10 | 0.88 ± 0.12 | 23.97 ± 7.22 | 1.58 ± 0.07 |
Os04g0561500 | Similar to Prolyl endopeptidase (Post-proline cleaving enzyme) | 7.38 ± 0.4 | 155.99 ± 10.59 | 10.99 ± 4.64 |
Os05g0472400 | Similar to Zinc transporter 9 | 1.48 ± 0.25 | 29.79 ± 5.17 | 5.12 ± 2.05 |
Os07g0232800 | Zinc transporter OsZIP8 | 0.75 ± 0.23 | 14.84 ± 1.15 | 0.99 ± 0.31 |
Os04g0304400 | Similar to MADS-box protein AGL16-II | 0.51 ± 0.04 | 8.26 ± 3.48 | 1.83 ± 0.09 |
Os08g0207500 | Zinc transporter OsZIP4 | 2.9 ± 0.24 | 28.12 ± 9.16 | 4.29 ± 1.91 |
MSTRG.22477 | – | 0.34 ± 0.11 | 3.12 ± 0.97 | 0.09 ± 0.06 |
MSTRG.30070 | – | 21.6 ± 19.8 | 91.8 ± 29.43 | 0.46 ± 0.24 |
Os06g0131300 | Arginine decarboxylase, Chilling stress respons | 98.89 ± 73.37 | 0 | 123.68 ± 112.96 |
Os03g0244950 | Heat shock protein DnaJ, N-terminal domain containing protein | 6.6 ± 7.68 | 0 | 3.45 ± 3.04 |
Os06g0505501 | Non-protein coding transcript | 3.46 ± 1.52 | 0 | 1.61 ± 1.6 |
Os02g0756850 | Hypothetical protein | 2.36 ± 0.31 | 0 | 1.33 ± 1.33 |
Os11g0706200 | GRAS transcription factor domain containing protein | 1.8 ± 1.63 | 0 | 1.98 ± 1.91 |
Os12g0124700 | CDC45-like protein family protein | 1.16 ± 1.08 | 0 | 1.83 ± 2.03 |
Os09g0412900 | Pentatricopeptide repeat domain containing protein | 1.12 ± 0.98 | 0 | 0.96 ± 0.84 |
Os03g0140300 | Conserved hypothetical protein | 0.99 ± 1.07 | 0 | 0.62 ± 0.54 |
Os04g0277400 | Membrane bound O-acyl transferase, MBOAT family protein | 0.84 ± 0.71 | 0 | 1.14 ± 1.09 |
Os10g0328700 | Tetratricopeptide-like helical domain containing protein | 0.58 ± 0.47 | 0 | 0.39 ± 0.34 |
Os07g0172600 | Pentatricopeptide repeat domain containing protein | 0.55 ± 0.58 | 0 | 0.67 ± 0.63 |
Os01g0163000 | Leucine-rich repeat, N-terminal domain containing protein | 0.46 ± 0.1 | 0 | 0.4 ± 0.38 |
Os03g0821700 | Pentatricopeptide repeat domain containing protein | 0.45 ± 0.15 | 0 | 0.53 ± 0.19 |
Os02g0621600 | Similar to OSIGBa0157K09-H0214G12.24 protein | 0.44 ± 0.59 | 0 | 0.62 ± 0.4 |
Os11g0133500 | Serine/threonine protein kinase-related domain containing protein | 0.35 ± 0.31 | 0 | 0.71 ± 0.8 |
Os12g0585300 | Cyclin-like F-box domain containing protein | 1.17 ± 1 | 0 | 1.53 ± 1.33 |
Os11g0111000 | Conserved hypothetical protein | 1.1 ± 0.92 | 0.01 ± 0.01 | 1.07 ± 1.11 |
Os03g0758500 | Similar to blue copper protein | 6.31 ± 5.39 | 0.15 ± 0.1 | 11.47 ± 3.69 |