Table 1 Zn deficiency-induced or repressed genes returning to basal level after Zn resupply in the shoots. The FPKM value represents mean ± SD (standard deviation) of three biological replicates. Note: MSTRG.18312, MSTRG.5686, and MSTRG.5688 are three new loci. “-” means no description

Os02g0192700

Similar to Thioredoxin peroxidase

0

68.55 ± 60.14

0

Os02g0663100

GRAS transcription factor domain containing protein

0

22.24 ± 4.50

0

Os05g0102000

SAM dependent carboxyl methyltransferase family protein

0

19.82 ± 17.40

0

Os10g0493300

Hypothetical conserved gene

0

13.02 ± 13.99

0

Os04g0382900

Conserved hypothetical protein

0

6.38 ± 9.55

0

Os01g0504100

Protein of unknown function DUF250 domain containing protein

0

6.10 ± 5.29

0

Os10g0528400

Glutathione S-transferase, C-terminal-like domain containing protein

0

5.39 ± 4.72

0

Os12g0103500

Ribosome-inactivating protein domain containing protein

0

4.59 ± 4.11

0

Os09g0116600

Hypothetical gene

0

4.06 ± 5.68

0

Os11g0490300

Hypothetical conserved gene

0

3.26 ± 2.85

0

Os03g0746700

Conserved hypothetical protein

0

3.08 ± 2.72

0

Os01g0532300

Conserved hypothetical protein

0

2.28 ± 2.08

0

Os06g0208951

Conserved hypothetical protein

0

2.00 ± 1.81

0

Os05g0562800

Similar to predicted protein

0

1.90 ± 2.55

0

Os03g0272900

DVL family protein

0

1.69 ± 1.59

0

Os09g0444800

Protein of unknown function DUF716 family protein

0

1.57 ± 1.36

0

Os10g0328600

–

0

1.39 ± 0.88

0

Os02g0550400

Tetratricopeptide-like helical domain containing protein

0

1.10 ± 0.95

0

Os07g0586900

GRAS transcription factor domain containing protein

0

1.02 ± 1.00

0

Os09g0412900

Pentatricopeptide repeat domain containing protein

0

0.64 ± 0.64

0

Os11g0606200

Similar to Leucine Rich Repeat family protein

0

0.49 ± 0.49

0

Os10g0328600

Hypothetical protein

0.02 ± 0.01

8.27 ± 1.81

0.18 ± 0.09

Os04g0280500

Similar to Non-S-locus F-box-like protein 2011

0.03 ± 0.03

10.03 ± 1.61

0.49 ± 0.22

Os04g0561500

Similar to Prolyl endopeptidase (Post-proline cleaving enzyme)

1.78 ± 0.63

204.72 ± 11.10

18.07 ± 8.12

Os06g0566201

–

1.38 ± 0.28

20.93 ± 10.37

1.48 ± 0.19

Os02g0306401

Similar to Nicotianamine aminotransferase A

5.81 ± 1.28

76.61 ± 8.44

15.04 ± 5.84

Os06g0566300

Zinc transporter OsZIP10

2.97 ± 0.26

38.94 ± 10.62

1.84 ± 0.34

MSTRG.18312

–

0.18 ± 0.02

1.92 ± 0.42

0.17 ± 0.08

Os08g0207500

Zinc transporter OsZIP4

1.7 ± 0.42

16.32 ± 8.27

1.9 ± 0.39

Os07g0232800

Zinc transporter OsZIP8

6.84 ± 1.31

50.73 ± 5.05

11.81 ± 6.25

Os03g0293100

Conserved hypothetical protein

7.25 ± 0.67

44.01 ± 14.47

7.78 ± 2.48

Os09g0485900

Similar to 60S ribosomal protein L9 (Gibberellin-regulated protein)

35.05 ± 6.96

164.62 ± 105.32

29.16 ± 13.21

Os11g0577866

Conserved hypothetical protein

9.27 ± 2.32

0

7.93 ± 4.44

Os06g0715200

Conserved hypothetical protein

8.48 ± 7.9

0

15.11 ± 6.49

Os08g0526100

NAD(P)-binding domain containing protein

6.15 ± 5.96

0

4.27 ± 3.76

Os01g0243450

Non-protein coding transcript

3.96 ± 0.68

0

1.66 ± 1.54

Os05g0528701

Non-protein coding transcript

1.81 ± 1.59

0

1.36 ± 1.27

Os01g0856800

Pleckstrin homology-type domain containing protein

0.86 ± 0.8

0

1.14 ± 0.98

Os09g0460300

Alpha/beta hydrolase fold-3 domain containing protein

0.8 ± 0.74

0

9.12 ± 8.68

Os08g0451201

–

0.69 ± 0.67

0

0.85 ± 0.76

Os03g0411900

–

0.64 ± 0.73

0

0.35 ± 0.32

Os01g0880250

Hypothetical protein

6.77 ± 6.57

0.03 ± 0.02

3.64 ± 5.01

MSTRG.5686

–

78.84 ± 109.73

0.42 ± 0.31

227.64 ± 346.33

Os06g0639800

Cytochrome P450 family protein

5.69 ± 0.85

0.06 ± 0.10

5.2 ± 2.26

MSTRG.5688

–

7.28 ± 9.58

0.20 ± 0.06

23.02 ± 34.31

Os03g0592500

–

66.95 ± 83.98

5.22 ± 1.37

30.1 ± 25.42