Insight into Differential Responses of Upland and Paddy Rice to Drought Stress by Comparative Expression Profiling Analysis
Abstract
:1. Introduction
2. Results and Discussion
2.1. Performance of Upland and Paddy Rice under Normal and Drought Conditions
2.2. Different Drought-Responsive Profiles of the Two Rice Genotypes
2.3. Dynamic Patterns of the Drought-Responsive Genes
2.4. Differentially Expressed Genes in the Intervals of Drought Resistance-Related QTL
2.5. Differential Expression Patterns of Drought-Responsive Genes in the QTL Intervals
2.6. Discussion
2.6.1. Mechanism of Drought Resistance at the Reproductive Stage
2.6.2. Candidate Genes for QTL Related to Drought Resistance
3. Experimental Methods
3.1. Plant Materials, Cultivation and Stress Treatment
3.2. Microarray and Initial Data Analysis
3.3. Physiological Analysis
3.4. Quantitative Gene Expression Level by Real-Time PCR Analysis
3.5. Accession Numbers
4. Conclusions
Supplementary Information
ijms-14-05214-s001.docAcknowledgments
Conflict of Interest
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Trait | Normal growth | Drought stress | Relative value b | |||
---|---|---|---|---|---|---|
ZS97 | IRAT109 | ZS97 | IRAT109 | ZS97 | IRAT109 | |
PH | 87.34 ± 6.96 | 103.95 ± 7.58 **a | 80.81 ± 6.63 | 95.33 ± 6.63 ** | 0.926 | 0.917 |
GY | 41.72 ± 5.41 * | 38.45 ± 7.11 | 19.83 ± 7.4 | 25.55 ± 10.14 ** | 0.475 | 0.662 |
TPP | 31.57 ± 2.27 ** | 24.85 ± 2.13 | 23.84 ± 8.12 ** | 13.13 ± 5.94 | 0.753 | 0.526 |
SPP | 93.34 ± 17.81 | 114.18 ± 24.94 ** | 75.44 ± 12.57 ** | 72.14 ± 16.51 | 0.808 | 0.631 |
SF | 0.91 ± 0.06 ** | 0.67 ± 0.08 | 0.47 ± 0.10 | 0.46 ± 0.20 | 0.516 | 0.687 |
KGW | 23.48 ± 2.02 | 32.28 ± 2.14 ** | 19.69 ± 2.27 | 31.26 ± 3.84 ** | 0.838 | 0.969 |
RV | 36.62 ± 9.43 | 60.51 ± 10.27 ** | 20.82 ± 8.43 | 31.56 ± 9.15 ** | 0.568 | 0.522 |
RVT | 1.16 ± 0.37 | 2.43 ± 0.57 ** | 0.86 ± 0.27 | 2.38 ± 0.50 ** | 0.741 | 0.979 |
GO.ID | Term | IRAT109 | ZS97 | |||||
---|---|---|---|---|---|---|---|---|
Level a | Significant b | Expected c | Classic d | Significant b | Expected c | Classic d | ||
Up | ||||||||
GO:0006950 | response to stress | 3 | 233 | 180.79 | 9.60 × 10−6 | 250 | 180.61 | 8.50 × 10−9 |
GO:0009605 | response to external stimulus | 3 | 69 | 43.5 | 8.10 ×10−5 | 80 | 43.46 | 5.90×10−8 |
GO:0005975 | carbohydrate metabolic process | 4 | 111 | 77.88 | 7.00 ×10−5 | 131 | 77.8 | 1.00 × 10−9 |
GO:0009991 | response to extracellular stimulus | 4 | 16 | 7.84 | 0.00475 | 21 | 7.83 | 2.60 × 10−5 |
GO:0000271 | polysaccharide biosynthetic process | 6 | 10 | 4.3 | 0.00949 | 12 | 4.29 | 0.00093 |
GO:0042221 | response to chemical stimulus | 3 | - | - | - | 32 | 19.36 | 0.00338 |
GO:0006725 | cellular aromatic compound metabolic process | 4 | - | - | - | 24 | 12.88 | 0.00225 |
GO:0017144 | drug metabolic process | 4 | - | - | - | 10 | 3.54 | 0.00224 |
GO:0016051 | carbohydrate biosynthetic process | 5 | - | - | - | 19 | 9.49 | 0.00275 |
GO:0016999 | antibiotic metabolic process | 5 | - | - | - | 10 | 3.54 | 0.00224 |
GO:0044270 | nitrogen compound catabolic process | 5 | - | - | - | 7 | 2.18 | 0.00483 |
GO:0017000 | antibiotic biosynthetic process | 6 | - | - | - | 8 | 3.01 | 0.00889 |
GO:0034637 | cellular carbohydrate biosynthetic process | 6 | - | - | - | 13 | 5.65 | 0.00369 |
GO:0009250 | glucan biosynthetic process | 8 | - | - | - | 10 | 3.84 | 0.0042 |
GO:0016787 | hydrolase activity | 3 | - | - | - | 290 | 246.07 | 0.00093 |
GO:0016491 | oxidoreductase activity | 3 | - | - | - | 53 | 37.37 | 0.0065 |
GO:0006139 | nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 4 | 286 | 250.98 | 0.00506 | - | - | - |
GO:0022402 | cell cycle process | 4 | 6 | 1.36 | 0.00153 | - | - | - |
GO:0044262 | cellular carbohydrate metabolic process | 5 | 24 | 13.95 | 0.00629 | - | - | - |
GO:0016311 | dephosphorylation | 6 | 13 | 5.81 | 0.0047 | - | - | - |
GO:0044042 | glucan metabolic process | 6 | 13 | 6.11 | 0.00727 | - | - | - |
GO:0006073 | cellular glucan metabolic process | 7 | 13 | 6.11 | 0.00727 | - | - | - |
GO:0006350 | transcription | 7 | 187 | 145.2 | 9.70 × 10−5 | - | - | - |
GO:0006470 | protein amino acid dephosphorylation | 9 | 13 | 5.81 | 0.0047 | - | - | - |
GO:0045735 | nutrient reservoir activity | 2 | 11 | 4.78 | 0.00753 | - | - | - |
GO:0003676 | nucleic acid binding | 3 | 325 | 286.7 | 0.00509 | - | - | - |
Down
| ||||||||
GO:0050896 | response to stimulus | 2 | 608 | 465.77 | 2.90 × 10−17 | 583 | 447.76 | 2.80 × 10−16 |
GO:0065007 | biological regulation | 2 | 441 | 378 | 4.30 × 10−5 | 416 | 363.39 | 0.00042 |
GO:0022414 | reproductive process | 3 | 82 | 52.03 | 1.90 ×10−5 | 71 | 50.02 | 0.0015 |
GO:0048856 | anatomical structure development | 3 | 73 | 46.77 | 7.40 × 10−5 | 66 | 44.96 | 0.00092 |
GO:0006793 | phosphorus metabolic process | 4 | 252 | 158.57 | 3.70 × 10−5 | 231 | 152.44 | 1.10 ×10−11 |
GO:0009908 | flower development | 6 | 66 | 40.61 | 4.80 × 10−5 | 60 | 39.04 | 0.00049 |
GO:0016310 | phosphorylation | 6 | 242 | 147.35 | 2.90 × 10−16 | 221 | 141.65 | 1.90 × 10−12 |
GO:0043687 | post-translational protein modification | 8 | 278 | 194.01 | 3.50 × 10−11 | 255 | 186.51 | 2.70 ×10−8 |
GO:0006468 | protein amino acid phosphorylation | 9 | 233 | 136.72 | 1.40 × 10−17 | 215 | 131.44 | 3.00 × 10−14 |
GO:0009653 | anatomical structure morphogenesis | 4 | 50 | 26.71 | 9.20 × 10−6 | 42 | 25.68 | 0.00096 |
GO:0030154 | cell differentiation | 4 | 83 | 49.94 | 2.10 × 10−6 | 76 | 48.01 | 3.40 ×10−5 |
GO:0048608 | reproductive structure development | 5 | 71 | 43.49 | 2.10 × 10−5 | 64 | 41.81 | 0.00036 |
GO:0006464 | protein modification process | 7 | 340 | 266.3 | 1.50 × 10−7 | 307 | 256 | 0.00014 |
GO:0006725 | cellular aromatic compound metabolic process | 4 | - | - | - | 27 | 16.32 | 0.00619 |
GO:0006979 | response to oxidative stress | 4 | - | - | - | 27 | 15.65 | 0.00347 |
GO:0009991 | response to extracellular stimulus | 4 | - | - | - | 18 | 9.93 | 0.00921 |
GO:0046164 | alcohol catabolic process | 4 | - | - | - | 21 | 12.22 | 0.00959 |
GO:0009225 | nucleotide-sugar metabolic process | 5 | - | - | - | 18 | 8.11 | 0.00094 |
GO:0019318 | hexose metabolic process | 6 | - | - | - | 24 | 13.75 | 0.00482 |
GO:0046365 | monosaccharide catabolic process | 6 | - | - | - | 21 | 11.74 | 0.00608 |
GO:0007155 | cell adhesion | 3 | 9 | 3.67 | 0.00876 | - | - | - |
GO:0006810 | transport | 4 | 222 | 188.16 | 0.00338 | - | - | - |
GO:0006811 | ion transport | 5 | 63 | 40.11 | 0.00019 | - | - | - |
GO:0015837 | amine transport | 5 | 18 | 8.54 | 0.00171 | - | - | - |
GO:0015849 | organic acid transport | 5 | 18 | 8.74 | 0.00224 | - | - | - |
GO:0055085 | transmembrane transport | 5 | 31 | 19.16 | 0.00487 | - | - | - |
GO:0006812 | cation transport | 6 | 49 | 34.65 | 0.00803 | - | - | - |
GO:0006820 | anion transport | 6 | 11 | 4.57 | 0.00452 | - | - | - |
GO:0006855 | multidrug transport | 6 | 10 | 4.37 | 0.00966 | - | - | - |
GO:0009309 | amine biosynthetic process | 6 | 24 | 14.3 | 0.00781 | - | - | - |
GO:0006865 | amino acid transport | 7 | 18 | 8.54 | 0.00171 | - | - | - |
GO:0015698 | inorganic anion transport | 7 | 10 | 3.08 | 0.00057 | - | - | - |
GO:0008652 | cellular amino acid biosynthetic process | 8 | 22 | 12.81 | 0.00809 | - | - | - |
GO:0009064 | glutamine family amino acid metabolic process | 8 | 10 | 3.97 | 0.00475 | - | - | - |
GO:0009069 | serine family amino acid metabolic process | 8 | 11 | 4.96 | 0.00876 | - | - | - |
GO:0004553 | hydrolase activity, hydrolyzing O-glycosyl compounds | 5 | 47 | 32.8 | 0.00784 | - | - | - |
TIGR Locus | Annotation (TIGR version 6.1) | Normal a | Drought b | ||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
ZS97 | IRAT109 | NIL-ZS | NIL-IR | ZS97 | IRAT109 | NIL-ZS | NIL-IR | C1 c | C2 d | ||
LOC_Os02g32250 | retrotransposon protein | − | + | − | + | ↑ | ↑ | ↑ | ↑ | 4 | a |
LOC_Os02g40240 | receptor kinase | + | − | ↓ | ↓ | ↑ | 1 | d | |||
LOC_Os02g41710 | cyclic nucleotide-gated ion channel | + | − | + | − | ↑ | ↑ | ↓ | ↑ | 2 | d |
LOC_Os02g44780 | polyprenyl synthetase | ↑ | ↑ | ↑ | ↑ | 4 | a | ||||
LOC_Os02g48360 | pyrophosphate-fructose 6-phosphate 1-phosphotransferase subunit alpha | − | + | − | + | ↑ | ↑ | ↑ | ↑ | 4 | a |
LOC_Os02g48710 | expressed protein | + | − | ↑ | ↑ | ↑ | 3 | b | |||
LOC_Os02g51840 | expressed protein | + | − | ↑ | 3 | d | |||||
LOC_Os02g53200 | glucan endo-1,3-beta-glucosidase precursor | + | − | + | − | ↓ | ↑ | ↓ | ↑ | 4 | c |
LOC_Os02g54254 | saccharopine dehydrogenase | + | − | ↑ | ↑ | ↑ | ↑ | 4 | a | ||
LOC_Os03g03034 | flavonol synthase/flavanone 3-hydroxylase | − | + | ↑ | ↑ | ↓ | 1 | d | |||
LOC_Os03g03050 | expressed protein | + | − | ↑ | ↑ | ↑ | ↑ | 4 | a | ||
LOC_Os03g03790 | AMP-binding domain containing protein | − | + | ↓ | ↓ | ↓ | ↓ | 4 | a | ||
LOC_Os03g36550 | transposon protein | + | − | ↑ | ↑ | ↑ | 2 | d | |||
LOC_Os03g37960 | acyl CoA binding protein | ↑ | ↑ | 1 | c | ||||||
LOC_Os03g38800 | AAA family ATPase | − | + | ↓ | ↓ | ↓ | 2 | b | |||
LOC_Os04g07890 | AGAP002737-PA | + | − | ↑ | ↑ | ↑ | 2 | d | |||
LOC_Os04g08280 | retrotransposon protein,Ty3-gypsy subclass | + | − | − | + | ↑ | ↑ | ↑ | ↓ | 3 | d |
LOC_Os04g08800 | expressed protein | − | + | ↑ | ↑ | ↑ | ↑ | 4 | a | ||
LOC_Os04g52450 | aminotransferase | + | − | + | − | ↑ | ↑ | 4 | c | ||
LOC_Os04g52640 | SHR5-receptor-like kinase | − | + | − | + | ↑ | ↑ | ↓ | 1 | d | |
LOC_Os04g52670 | OsSAUR21 - Auxin-responsive SAUR gene family member | + | − | + | − | ↑ | ↑ | 4 | c | ||
LOC_Os05g37450 | starch binding domain containing protein | − | + | ↑ | ↑ | ↑ | 3 | b | |||
LOC_Os05g37830 | expressed protein | + | − | ↑ | ↑ | ↑ | 2 | b | |||
LOC_Os05g38360 | DHHC zinc finger domain containing protein | + | − | ↑ | 3 | b | |||||
LOC_Os07g10970 | leucine zipper protein-like | − | + | ↓ | ↑ | 1 | c | ||||
LOC_Os07g15770 | CCT motif family protein | − | + | − | + | ↓ | ↑ | ↑ | 1 | c | |
LOC_Os09g13440 | expressed protein | + | − | + | − | ↑↓ | ↓ | ↑ | 1 | c | |
LOC_Os09g14450 | pollen signaling protein with adenylyl cyclase activity | − | + | ↓ | ↑ | 3 | c | ||||
LOC_Os11g29790 | receptor kinase | − | + | ↑ | ↓ | ↓ | ↓ | 2 | b | ||
LOC_Os11g35274 | protein kinase domain containing protein | + | − | + | − | ↑ | ↑ | ↑ | 2 | b | |
LOC_Os12g03740 | OsFBX438 - F-box domain containing protein | ↑ | ↑ | ↑ | ↑ | 4 | a | ||||
LOC_Os12g07280 | ZOS12-02 - C2H2 zinc finger protein | − | + | − | + | ↓ | ↓↑ | ↓ | 1 | c | |
LOC_Os12g08260 | dehydrogenase E1 component domain containing protein | + | − | ↑ | ↑ | ↑ | ↑ | 4 | a | ||
LOC_Os12g39360 | aspartic proteinase nepenthesin precursor | + | − | ↓ | ↓ | ↓ | ↓ | 4 | a | ||
LOC_Os12g39520 | OsFBDUF66 - F-box and DUF domain containing protein | + | − | ↑ | ↑ | ↑ | ↑ | 4 | a | ||
LOC_Os12g44100 | peptide transporter PTR2 | + | − | ↓ | ↑ | ↓ | ↓ | 3 | b |
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Ding, X.; Li, X.; **ong, L. Insight into Differential Responses of Upland and Paddy Rice to Drought Stress by Comparative Expression Profiling Analysis. Int. J. Mol. Sci. 2013, 14, 5214-5238. https://doi.org/10.3390/ijms14035214
Ding X, Li X, **ong L. Insight into Differential Responses of Upland and Paddy Rice to Drought Stress by Comparative Expression Profiling Analysis. International Journal of Molecular Sciences. 2013; 14(3):5214-5238. https://doi.org/10.3390/ijms14035214
Chicago/Turabian StyleDing, **peng, **aokai Li, and Lizhong **ong. 2013. "Insight into Differential Responses of Upland and Paddy Rice to Drought Stress by Comparative Expression Profiling Analysis" International Journal of Molecular Sciences 14, no. 3: 5214-5238. https://doi.org/10.3390/ijms14035214