Table 3.
Detail of the 110 probe sets identified for processing quality showing at least 10-fold differential expression between good and poor quality wheat varieties in at least one of the three seed developmental stages i.e. 7, 14, and 28 days after anthesis (DAA)
|
Probe set ID |
Putative gene function |
7 DAA |
14 DAA |
28 DAA |
Quality |
Seed development |
Quality x seed development |
|||
|---|---|---|---|---|---|---|---|---|---|---|
| Fold change | Regulation | Fold change | Regulation | Fold change | Regulation | |||||
| Ta.1345.2.S1_x_at |
14 kDa proline-rich protein DC2.15 [Triticum urartu] |
12.1 |
Down |
1.1 |
Down |
1.0 |
Up |
+ |
+ |
+ |
| Ta.1345.1.S1_x_at |
14 kDa proline-rich protein DC2.15 [Triticum urartu] |
11.1 |
Down |
1.0 |
Up |
1.1 |
Down |
+ |
+ |
+ |
| TaAffx.128648.2.A1_at |
2′-deoxymugineic-acid 2′-dioxygenase [Triticum urartu] |
15.3 |
Up |
4.3 |
Up |
1.3 |
Up |
+ |
+ |
- |
| Ta.24114.10.S1_x_at |
Alpha/beta-gliadin [Triticum aestivum] |
54.1 |
Up |
1.1 |
Up |
1.1 |
Up |
+ |
+ |
+ |
| Ta.10028.1.S1_at |
Alpha-amylase/subtilisin inhibitor [Triticum urartu] |
30.9 |
Up |
5.3 |
Up |
1.1 |
Up |
+ |
+ |
- |
| Ta.27778.4.S1_x_at |
Alpha-gliadin [Triticum aestivum] |
284.7 |
Up |
1.3 |
Up |
1.2 |
Down |
+ |
+ |
+ |
| Ta.15268.1.S1_x_at |
Alpha-gliadin [Triticum aestivum] |
110.3 |
Up |
1.1 |
Up |
1.1 |
Up |
+ |
+ |
+ |
| Ta.27778.2.S1_x_at |
Alpha-gliadin [Triticum aestivum] |
209.5 |
Up |
1.5 |
Up |
1.8 |
Down |
+ |
+ |
+ |
| Ta.24114.1.S1_x_at |
Alpha-gliadin protein [Triticum dicoccoides] |
171.4 |
Up |
1.0 |
Up |
1.2 |
Down |
+ |
+ |
+ |
| Ta.21787.1.S1_at |
Aspartic proteinase nepenthesin-1 [Triticum urartu] |
12.5 |
Down |
1.0 |
Down |
1.1 |
Up |
+ |
+ |
+ |
| Ta.27777.1.S2_s_at |
Avenin-like b1 |
122.6 |
Up |
1.1 |
Up |
1.0 |
Up |
+ |
+ |
+ |
| Ta.27777.1.S2_at |
Avenin-like b1 |
57.6 |
Up |
1.0 |
Up |
1.3 |
Up |
+ |
+ |
+ |
| Ta.27712.1.S1_at |
Avenin-like protein [Triticum aestivum] |
86.6 |
Up |
1.1 |
Up |
1.3 |
Up |
+ |
+ |
+ |
| Ta.9799.1.S1_at |
Avenin-like protein [Triticum aestivum] |
45.0 |
Up |
2.7 |
Up |
2.9 |
Up |
+ |
+ |
- |
| Ta.27780.1.S1_x_at |
Beta-amylase [Aegilops tauschii] |
58.6 |
Up |
1.2 |
Down |
1.1 |
Down |
+ |
+ |
+ |
| Ta.27780.2.A1_a_at |
Beta-amylase [Triticum urartu] |
156.1 |
Up |
1.0 |
Down |
1.2 |
Down |
+ |
+ |
+ |
| Ta.27780.2.A1_x_at |
Beta-amylase [Triticum urartu] |
122.4 |
Up |
1.0 |
Up |
1.2 |
Down |
+ |
+ |
+ |
| Ta.27780.3.S1_x_at |
Beta-amylase, partial [Triticum aestivum] |
72.0 |
Up |
1.0 |
Down |
1.1 |
Up |
+ |
+ |
+ |
| Ta.9809.2.S1_at |
Beta-fructofuranosidase, isoenzyme 4 [Aegilops tauschii] |
12.6 |
Up |
1.7 |
Up |
1.1 |
Up |
+ |
+ |
- |
| Ta.27445.1.S1_at |
Cell division protease ftsH-like protein, chloroplastic [Aegilops tauschii] |
9.2 |
Down |
13.4 |
Down |
28.6 |
Down |
+ |
- |
- |
| Ta.6984.1.A1_at |
Chromodomain-helicase-DNA-binding protein 4 [Triticum urartu] |
58.0 |
Down |
7.0 |
Down |
16.9 |
Down |
+ |
+ |
- |
| Ta.14507.2.S1_at |
Cytosolic Fe-S cluster assembly factor NUBP1-like protein [Triticum urartu] |
29.9 |
Down |
3.6 |
Down |
7.6 |
Down |
+ |
- |
- |
| TaAffx.108987.1.S1_at |
DNA-directed RNA polymerase subunit beta [Triticum urartu] |
2.0 |
Down |
5.7 |
Up |
15.2 |
Up |
+ |
+ |
+ |
| Ta.30782.4.S1_at |
Gamma gliadin [Triticum aestivum] |
98.0 |
Up |
1.0 |
Up |
1.0 |
Up |
+ |
+ |
+ |
| Ta.28792.1.S1_x_at |
Gamma-gliadin [Triticum aestivum] |
146.9 |
Up |
1.0 |
Up |
2.2 |
Up |
+ |
+ |
+ |
| Ta.24114.8.S1_x_at |
Gamma-gliadin [Triticum aestivum] |
194.8 |
Up |
1.1 |
Up |
1.8 |
Up |
+ |
+ |
+ |
| Ta.6175.1.S1_at |
Gamma-gliadin [Triticum aestivum] |
105.9 |
Up |
1.2 |
Up |
1.5 |
Down |
+ |
+ |
+ |
| Ta.6175.1.S1_x_at |
Gamma-gliadin [Triticum aestivum] |
80.9 |
Up |
1.4 |
Up |
1.2 |
Down |
+ |
+ |
+ |
| Ta.30782.2.S1_x_at |
Gamma-gliadin [Triticum aestivum] |
51.3 |
Up |
1.2 |
Up |
1.3 |
Up |
+ |
+ |
+ |
| Ta.24114.8.S1_at |
Gamma-gliadin [Triticum aestivum] |
168.9 |
Up |
1.0 |
Up |
1.9 |
Up |
+ |
+ |
+ |
| Ta.30782.2.S1_a_at |
Gamma-gliadin [Triticum aestivum] |
28.2 |
Up |
1.2 |
Up |
1.5 |
Up |
+ |
+ |
- |
| Ta.160.3.S1_x_at |
Gamma-gliadin, partial [Triticum aestivum] |
13.6 |
Up |
3.6 |
Up |
3.5 |
Up |
+ |
+ |
- |
| Ta.160.2.S1_x_at |
Gamma-gliadin, partial [Triticum aestivum] |
13.3 |
Up |
3.8 |
Up |
3.5 |
Up |
+ |
+ |
- |
| Ta.160.1.S1_x_at |
Gamma-gliadin, partial [Triticum aestivum] |
14.6 |
Up |
1.8 |
Up |
2.7 |
Up |
+ |
+ |
- |
| Ta.7430.1.S1_at |
GATA transcription factor 17 [Triticum urartu] |
11.4 |
Up |
5.3 |
Up |
6.4 |
Up |
+ |
- |
- |
| TaAffx.27375.1.S1_at |
General transcription factor IIF subunit 2 [Triticum urartu] |
2.4 |
Down |
5.1 |
Up |
11.4 |
Up |
+ |
+ |
+ |
| Ta.23142.11.S1_x_at |
Gliadin/avenin-like seed protein [Triticum aestivum] |
124.1 |
Up |
1.1 |
Up |
1.1 |
Down |
+ |
+ |
+ |
| Ta.23142.4.S1_s_at |
Gliadin/avenin-like seed protein [Triticum aestivum] |
175.9 |
Up |
1.0 |
Up |
1.0 |
Up |
+ |
+ |
+ |
| Ta.2415.2.S1_a_at |
Gliadin/avenin-like seed protein [Triticum aestivum] |
17.4 |
Up |
2.1 |
Up |
1.1 |
Down |
+ |
- |
- |
| Ta.24114.7.A1_at |
Granule-bound starch synthase I [Triticum aestivum] |
6.7 |
Down |
26.9 |
Down |
92.8 |
Down |
+ |
+ |
- |
| Ta.5129.2.A1_a_at |
Heat stress transcription factor A-9 [Aegilops tauschii] |
7.5 |
Down |
5.4 |
Down |
25.1 |
Down |
+ |
+ |
- |
| Ta.24963.1.S1_x_at |
HMW-glutenin subunit 1By9, truncated [Triticum aestivum subsp. tibeticum] |
60.4 |
Up |
1.1 |
Down |
1.1 |
Up |
+ |
+ |
+ |
| Ta.24298.1.S1_x_at |
HMW-glutenin subunit Dx5 [Triticum aestivum] |
56.7 |
Up |
1.1 |
Down |
1.0 |
Up |
+ |
+ |
+ |
| Ta.25839.1.A1_a_at |
Hypothetical protein F775_04832 [Aegilops tauschii] |
26.6 |
Up |
4.6 |
Up |
24.9 |
Up |
+ |
+ |
- |
| Ta.7509.3.S1_at |
Hypothetical protein F775_05928 [Aegilops tauschii] |
14.0 |
Down |
26.9 |
Down |
22.0 |
Down |
+ |
- |
- |
| Ta.24550.1.S1_s_at |
Hypothetical protein F775_05934 [Aegilops tauschii] |
16.7 |
Up |
1.4 |
Down |
1.2 |
Down |
+ |
+ |
+ |
| Ta.28759.1.A1_at |
Hypothetical protein F775_09062 [Aegilops tauschii] |
5.7 |
Up |
2.7 |
Up |
14.7 |
Up |
+ |
- |
- |
| Ta.19222.1.S1_at |
Hypothetical protein F775_11525 [Aegilops tauschii] |
29.8 |
Up |
6.9 |
Up |
5.3 |
Up |
+ |
+ |
- |
| Ta.28744.1.S1_at |
Hypothetical protein F775_23873 [Aegilops tauschii] |
11.3 |
Up |
11.0 |
Up |
35.2 |
Up |
+ |
+ |
- |
| Ta.23681.1.S1_a_at |
Hypothetical protein F775_24401 [Aegilops tauschii] |
13.9 |
Up |
8.6 |
Up |
19.3 |
Up |
+ |
+ |
- |
| Ta.9888.1.A1_at |
Hypothetical protein F775_26991 [Aegilops tauschii] |
12.7 |
Up |
1.1 |
Up |
1.1 |
Up |
+ |
+ |
+ |
| Ta.8883.2.S1_at |
Hypothetical protein F775_27368 [Aegilops tauschii] |
12.0 |
Down |
7.9 |
Down |
9.2 |
Down |
+ |
- |
- |
| Ta.14050.1.S1_at |
Hypothetical protein F775_27373 [Aegilops tauschii] |
2.8 |
Up |
3.7 |
Up |
37.3 |
Up |
+ |
- |
- |
| Ta.22853.1.S1_at |
Hypothetical protein F775_27669 [Aegilops tauschii] |
10.1 |
Down |
2.8 |
Down |
1.1 |
Up |
+ |
+ |
+ |
| Ta.12328.2.A1_at |
Hypothetical protein F775_32343 [Aegilops tauschii] |
1.1 |
Down |
2.3 |
Up |
10.1 |
Up |
+ |
+ |
- |
| Ta.8621.1.S1_at |
Hypothetical protein F775_43701 [Aegilops tauschii] |
10.8 |
Down |
1.2 |
Up |
1.1 |
Up |
+ |
+ |
+ |
| Ta.24736.1.S1_at |
Hypothetical protein F775_43830 [Aegilops tauschii] |
550.2 |
Up |
31.2 |
Up |
8.0 |
Up |
+ |
+ |
- |
| Ta.24218.1.S1_at |
Hypothetical protein TRIUR3_02605 [Triticum urartu] |
11.6 |
Up |
6.9 |
Up |
3.6 |
Up |
+ |
- |
- |
| Ta.5278.1.S1_at |
Hypothetical protein TRIUR3_04715 [Triticum urartu] |
10.1 |
Down |
4.2 |
Down |
3.0 |
Down |
+ |
- |
- |
| Ta.14446.1.A1_at |
Hypothetical protein TRIUR3_05569 [Triticum urartu] |
14.8 |
Down |
13.2 |
Down |
9.9 |
Down |
+ |
- |
- |
| Ta.5243.2.S1_a_at |
Hypothetical protein TRIUR3_06223 [Triticum urartu] |
2.3 |
Down |
4.9 |
Down |
19.0 |
Down |
+ |
+ |
- |
| Ta.2025.1.S1_at |
Hypothetical protein TRIUR3_06809 [Triticum urartu] |
1.6 |
Down |
86.3 |
Down |
1727.5 |
Down |
+ |
+ |
+ |
| Ta.23013.3.S1_s_at |
Hypothetical protein TRIUR3_09069 [Triticum urartu] |
31.5 |
Down |
1.4 |
Down |
1.4 |
Down |
+ |
+ |
+ |
| Ta.6018.1.S1_x_at |
Hypothetical protein TRIUR3_12951 [Triticum urartu] |
10.7 |
Up |
1.1 |
Up |
1.0 |
Up |
+ |
+ |
+ |
| Ta.24550.2.S1_s_at |
Hypothetical protein TRIUR3_13108 [Triticum urartu] |
28.6 |
Up |
1.4 |
Down |
1.2 |
Down |
+ |
+ |
+ |
| Ta.24550.2.S1_at |
Hypothetical protein TRIUR3_13108 [Triticum urartu] |
21.1 |
Up |
1.5 |
Down |
1.1 |
Down |
+ |
+ |
+ |
| TaAffx.80038.1.S1_at |
Hypothetical protein TRIUR3_13205 [Triticum urartu] |
11.9 |
Down |
1.4 |
Up |
1.1 |
Up |
+ |
+ |
+ |
| TaAffx.82110.1.S1_at |
Hypothetical protein TRIUR3_18607 [Triticum urartu] |
1.4 |
Down |
2.5 |
Up |
10.5 |
Up |
+ |
+ |
- |
| Ta.7158.1.S1_at |
Hypothetical protein TRIUR3_24125 [Triticum urartu] |
108.1 |
Up |
6.8 |
Up |
4.5 |
Up |
+ |
+ |
- |
| Ta.11896.1.A1_s_at |
Hypothetical protein TRIUR3_24659 [Triticum urartu] |
24.9 |
Up |
7.9 |
Up |
3.7 |
Up |
+ |
- |
- |
| TaAffx.80118.1.S1_at |
Hypothetical protein TRIUR3_25902 [Triticum urartu] |
20.1 |
Down |
5.8 |
Down |
32.6 |
Down |
+ |
+ |
- |
| Ta.4497.1.S1_at |
Hypothetical protein TRIUR3_27348 [Triticum urartu] |
10.3 |
Down |
1.2 |
Up |
1.1 |
Up |
+ |
+ |
+ |
| TaAffx.5865.2.A1_at |
Hypothetical protein TRIUR3_27593 [Triticum urartu] |
1.4 |
Down |
2.9 |
Up |
14.2 |
Up |
+ |
+ |
- |
| TaAffx.78552.1.S1_at |
Hypothetical protein TRIUR3_27901 [Triticum urartu] |
14.7 |
Up |
1.9 |
Up |
3.4 |
Up |
+ |
+ |
+ |
| TaAffx.78552.1.S1_x_at |
Hypothetical protein TRIUR3_27901 [Triticum urartu] |
11.7 |
Up |
1.7 |
Up |
2.9 |
Up |
+ |
- |
- |
| Ta.5785.1.S1_at |
Hypothetical protein TRIUR3_27988 [Triticum urartu] |
1.1 |
Up |
1.1 |
Up |
14.3 |
Up |
+ |
+ |
+ |
| TaAffx.5496.1.S1_at |
Hypothetical protein TRIUR3_29836 [Triticum urartu] |
16.7 |
Up |
10.6 |
Up |
2.9 |
Up |
+ |
+ |
- |
| Ta.21106.1.A1_at |
Hypothetical protein TRIUR3_30277 [Triticum urartu] |
4.9 |
Up |
5.7 |
Up |
16.2 |
Up |
+ |
+ |
- |
| Ta.14723.1.S1_at |
Hypothetical protein TRIUR3_33733 [Triticum urartu] |
1.7 |
Down |
3.5 |
Up |
11.3 |
Up |
+ |
+ |
+ |
| Ta.3527.1.S1_at |
Hypothetical protein TRIUR3_34067 [Triticum urartu] |
6.2 |
Up |
8.1 |
Up |
28.3 |
Up |
+ |
+ |
- |
| TaAffx.30606.1.S1_at |
Katanin p80 WD40 repeat-containing subunit B1-like Protein 1 [Triticum urartu] |
1.2 |
Down |
2.3 |
Up |
14.0 |
Up |
+ |
+ |
- |
| Ta.23142.5.S1_x_at |
LMW-glutenin [Triticum aestivum] |
57.8 |
Up |
1.0 |
Up |
1.3 |
Up |
+ |
+ |
+ |
| Ta.14625.1.S1_x_at |
LMW-glutenin [Triticum aestivum] |
106.0 |
Up |
1.1 |
Down |
1.2 |
Down |
+ |
+ |
+ |
| Ta.131.1.S1_at |
LMW-glutenin subunit, partial [Triticum aestivum] |
58.9 |
Up |
1.1 |
Up |
1.2 |
Up |
+ |
+ |
+ |
| TaAffx.109582.1.S1_s_at |
LRR receptor-like serine/threonine-protein kinase FLS2 [Triticum urartu] |
3.7 |
Down |
9.2 |
Up |
10.3 |
Up |
+ |
+ |
+ |
| Ta.12643.5.S1_x_at |
No significant similarity found |
92.5 |
Up |
1.2 |
Up |
1.0 |
Up |
+ |
+ |
+ |
| Ta.7825.1.S1_s_at |
No significant similarity found |
1.0 |
Up |
13.5 |
Up |
1.2 |
Up |
+ |
+ |
+ |
| TaAffx.104444.1.S1_at |
No significant similarity found |
47.5 |
Down |
5.4 |
Down |
4.4 |
Down |
+ |
+ |
- |
| TaAffx.31445.1.S1_at |
No significant similarity found |
1.4 |
Down |
3.6 |
Up |
11.1 |
Up |
+ |
+ |
- |
| Ta.19222.1.S1_x_at |
No significant similarity found |
14.1 |
Up |
3.9 |
Up |
3.2 |
Up |
+ |
- |
- |
| TaAffx.91902.1.A1_at |
No significant similarity found |
4.2 |
Up |
5.5 |
Up |
32.6 |
Up |
+ |
- |
- |
| Ta.23896.1.S1_at |
Omega gliadin [Triticum aestivum] |
33.1 |
Up |
1.4 |
Up |
1.5 |
Up |
+ |
+ |
- |
| Ta.23366.2.S1_at |
Peroxidase 66 [Triticum urartu] |
2.6 |
Up |
10.0 |
Up |
60.0 |
Up |
+ |
+ |
- |
| Ta.23366.2.S1_x_at |
Peroxidase 66 [Triticum urartu] |
2.4 |
Up |
5.6 |
Up |
28.9 |
Up |
+ |
+ |
- |
| Ta.4957.1.S1_at |
Peroxisomal acyl-coenzyme A oxidase 1 [Triticum urartu] |
26.6 |
Down |
3.6 |
Down |
7.9 |
Down |
+ |
+ |
- |
| Ta.12764.1.A1_at |
Peroxisomal multifunctional enzyme type 2 [Aegilops tauschii] |
1.5 |
Down |
1.3 |
Down |
14.5 |
Down |
+ |
+ |
+ |
| Ta.14489.1.S1_at |
pTACR7 [Triticum aestivum] |
2.4 |
Down |
7.6 |
Down |
29.0 |
Down |
+ |
+ |
- |
| TaAffx.118782.1.A1_at |
Putative disease resistance protein RGA4 [Triticum urartu] |
2.8 |
Down |
1.7 |
Down |
10.7 |
Down |
+ |
+ |
+ |
| Ta.23352.1.S1_at |
Putative serine/threonine-protein kinase-like protein CCR3 [Aegilops tauschii] |
10.8 |
Up |
5.8 |
Up |
6.1 |
Up |
+ |
- |
- |
| TaAffx.112770.1.S1_x_at |
Retrovirus-related Pol polyprotein from transposon TNT 1-94 [Triticum urartu] |
2.6 |
Down |
6.4 |
Up |
12.3 |
Up |
+ |
+ |
+ |
| TaAffx.112770.1.S1_at |
Retrovirus-related Pol polyprotein from transposon TNT 1-94 [Triticum urartu] |
1.7 |
Down |
5.4 |
Up |
10.7 |
Up |
+ |
+ |
+ |
| TaAffx.27343.2.S1_at |
Serine/threonine-protein phosphatase 7 long form-like Protein [Triticum urartu] |
1.3 |
Down |
2.1 |
Up |
11.5 |
Up |
+ |
+ |
+ |
| Ta.2434.3.A1_at |
S-formylglutathione hydrolase [Aegilops tauschii] |
13.7 |
Down |
11.9 |
Down |
9.6 |
Down |
+ |
- |
- |
| Ta.1622.2.S1_at |
Sugar transporter ERD6-like protein 5 [Aegilops tauschii] |
10.0 |
Down |
2.4 |
Down |
1.4 |
Down |
+ |
+ |
- |
| TaAffx.109268.1.S1_x_at |
TaCBF11 [Triticum aestivum] |
1.2 |
Down |
2.1 |
Up |
10.0 |
Up |
+ |
+ |
+ |
| Ta.10170.1.S1_at |
Trypsin inhibitor CMc [Aegilops tauschii] |
32.9 |
Up |
1.2 |
Up |
1.7 |
Up |
+ |
+ |
- |
| Ta.13439.1.S1_a_at |
Trypsin inhibitor-Bowman-Birk type |
84.5 |
Up |
2.1 |
Up |
3.0 |
Up |
+ |
+ |
- |
| TaAffx.6814.1.S1_at |
Wall-associated receptor kinase 5 [Aegilops tauschii] |
1.2 |
Down |
1.9 |
Up |
11.0 |
Up |
+ |
+ |
+ |
| TaAffx.111195.1.S1_at |
Zf-MYND domain-containing protein [Triticum aestivum] |
1.7 |
Down |
3.5 |
Up |
13.3 |
Up |
+ |
+ |
+ |
| TaAffx.86295.1.S1_at | Zf-MYND domain-containing protein [Triticum aestivum] | 1.3 | Down | 2.1 | Up | 10.4 | Up | + | + | - |
The majority of the probe sets also involved in seed development stage and interaction (quality x development) as identified through gene-specific two-way ANOVA analysis. The function to the probe sets was assigned through blastx at NCBI website.
+ = involved, - = not involved.