Research Article

Genome-Wide Transcriptome Analysis of Cadmium Stress in Rice

Table 1

Cadmium-upregulated transcripts identified in roots by RNA-Seq analysis.

Transcript⁢DescriptionFold change
RootShoot
1 d4 d10 d1 d4 d10 d

0.2 µM Cd
Os10t0527400-01Tau class GST protein 327.821.427.51.22.01.7
Os03t0283000-00In2-1 protein27.52.81.01.31.11.5
Os08t0156000-01Conserved hypothetical protein26.421.425.31.31.61.7
Os01t0627967-00Hypothetical protein26.116.524.11.51.91.4
Os04t0178300-02Syn-copalyl diphosphate synthase20.18.020.30.64.21.4
Os04t0301500-01HLH (helix-loop-helix) DNA-binding domain containing protein0.433.10.51.047.59.2
Os02t0676800-01DREB1E (drought responsive element binding protein 1E)0.928.70.91.210.92.0
Os02t0179200-01Glutamine amidotransferase class-I domain containing protein0.828.11.70.93.21.1
Os12t0154800-00RmlC-like jelly roll fold domain containing protein4.021.45.71.01.41.2
Os12t0570700-01MT (metallothionein)-like protein type 118.620.315.80.91.00.9
Os03t0836800-01IAA-amino acid hydrolase 14.36.533.61.01.01.0
Os10t0333700-00Plant disease resistance response protein domain containing protein9.76.021.61.01.01.0
1 µM Cd
Os04t0178300-02Syn-copalyl diphosphate synthase122.032.125.50.51.03.6
Os04t0178300-01Isoform 3 of Syn-copalyl diphosphate synthase109.827.821.50.50.93.1
Os04t0178400-01Cytochrome P450 CYP99A169.821.116.00.81.02.8
Os03t0267000-00Heat shock protein 18057.57.710.91.20.70.7
Os03t0266900-01Heat shock protein 17347.04.95.31.00.40.6
Os01t0136200-01Heat shock protein 1 43.73.91.31.01.01.0
Os07t0190000-011-Deoxy-D-xylulose 5-phosphate synthase 2 precursor42.411.58.60.71.13.9
Os07t0127500-01PR-1a pathogenesis related protein precursor40.05.65.00.80.82.1
Os07t0154100-01Viviparous-1438.85.21.51.11.42.3
Os07t0154201-00Hypothetical gene37.74.71.31.01.32.1
Os12t0555200-01Probenazole-inducible protein PBZ137.713.510.90.30.52.2
Os06t0586000-01Conserved hypothetical protein37.69.36.50.60.91.4
Os10t0527400-01Tau class GST protein 334.318.032.41.11.42.0
Os12t0555000-01Probenazole-inducible protein PBZ133.213.511.00.60.72.5
Os03t0277700-01Protein of unknown function DUF26 domain containing protein32.87.63.41.00.61.0
Os11t0687100-01von Willebrand factor (type A domain)32.54.113.80.70.72.3
Os05t0211700-0028.81.41.21.01.01.0
Os06t0662550-01Conserved hypothetical protein28.57.88.80.80.81.6
Os01t0944100-02Conserved hypothetical protein28.46.39.80.50.61.7
Os06t0568600-01Ent-kaurene oxidase 127.128.111.00.61.44.7
Os12t0418600-01Hypothetical conserved gene26.72.01.31.01.01.0
Os12t0258700-01Cupredoxin domain containing protein26.214.710.60.71.17.1
Os01t0615100-01Substilin/chymotrypsin-like inhibitor25.69.57.90.71.01.8
Os04t0107900-02Heat shock protein 81-125.62.51.61.01.00.9
Os09t0493000-01Conserved hypothetical protein25.32.61.80.91.20.9
Os01t0627967-00Hypothetical protein25.319.521.61.31.81.4
Os01t0944100-03Conserved hypothetical protein25.24.66.30.60.61.8
Os04t0180400-01Cytochrome P450 99A224.44.36.00.50.53.1
Os04t0108101-00Hypothetical protein24.42.31.41.01.01.0
Os02t0269600-00Subtilase22.67.84.10.31.26.0
Os01t0136000-00Heat shock protein 17522.53.11.21.01.41.2
Os04t0180500-00Hypothetical protein22.24.05.40.50.63.1
Os01t0946600-01Conserved hypothetical protein21.816.68.00.70.70.8
Os09t0255400-02Indole-3-glycerol phosphate synthase21.45.13.80.70.92.3
Os01t0348900-01SalT gene product21.26.58.90.10.10.2
Os12t0491800-01Ent-kaurene synthase 1A21.11.51.70.40.85.5
Os01t0132000-01Wound-induced protease inhibitor21.08.811.61.60.50.2
Os11t0592200-01Chitin-binding allergen Bra r 220.73.42.80.70.51.6
Os01t0963000-01Prx (Peroxidase) BP 1 precursor20.63.84.40.71.11.3
Os08t0189600-01Oryza sativa germin-like protein 8-720.611.56.72.11.50.8
Os07t0496250-01Expansin-like B120.52.22.21.51.24.5
Os01t0963000-04Prx (Peroxidase) BP 1 precursor20.33.74.40.71.11.3
Os09t0255400-01Indole-3-glycerol phosphate synthase20.25.23.70.70.92.3
Os11t0601950-01cDNA clone:002-114-B0620.01.71.90.71.01.1
Os03t0129400-01Hypothetical protein10.327.117.61.01.93.6
Os01t0322700-01Nonprotein coding transcript12.225.515.70.91.32.5
Os03t0129400-02EST AU078206 corresponds to a region of the predicted gene9.424.316.31.11.42.8
Os12t0570700-01MT (metallothionein)-like protein type 116.721.217.70.80.83.1
Os12t0571000-01MT (metallothionein)-like protein type 113.920.013.00.91.03.6
Os08t0156000-01Conserved hypothetical protein15.417.926.01.11.51.6
Os03t0836800-01IAA-amino acid hydrolase 10.74.023.71.01.01.0

Reads were mapped to the rice genome and responsive genes were identified by -tests. Transcripts upregulated more than 20-fold in one or more treatments/time points in roots are shown. Transcripts in bold were upregulated under both 1 and 0.2 μM Cd exposure.