A Systemic View of Carbohydrate Metabolism in Rice to Facilitate Productivity
Abstract
:1. Introduction
2. Materials and Methods
2.1. Integration of Carbohydrate Metabolism Annotation Data
2.2. Collection and Clustering of Microarray Data
2.3. Functional Classification via Literature Search
2.4. Gene Ontology (GO) Enrichment Analysis
2.5. KEGG Enrichment Analysis
2.6. RNA Extraction and qRT-PCR
2.7. Construction of the Conceptual Carbohydrate Metabolism Model
3. Results
3.1. Identification of Genome-Wide Candidate Genes Related to Carbohydrate Metabolism
3.2. Functional Analysis of the Characterized Carbohydrate Metabolism-Related Genes
3.3. Anatomical Dissection of Carbohydrate Metabolism-Related Genes via Meta-Expression Analysis
3.4. Functional Comparison and Enrichment Analysis of 11 Anatomical Clusters
3.5. In Silico and In Vitro Expression Verification of Tissue-Preferred Genes
3.6. Construction of a Conceptual Carbohydrate Metabolism Model
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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LOC_id | Symbol | Character_major 1 | Character_minor | Method 2 | Detailed Functions | Reference |
---|---|---|---|---|---|---|
Os02g44230 | OsTPP1 | R or T | Cold tolerance | OX | Cold and salinity tolerance | [37] |
Os05g44210 | OsTPS1 | R or T | Cold tolerance | OX | Cold, drought, and salinity tolerance | [38] |
Os01g64660 | moc2 | MT | Culm leaf | KO | Tiller bud outgrowth; tillering | [39] |
Os12g44380 | ossut2 | MT | Culm leaf | KO | Sugar export; growth retardation | [40] |
Os05g44210 | OsTPS1 | R or T | Drought tolerance | OX | Cold, drought, and salinity tolerance | [38] |
Os06g36560 | OsMIOX | R or T | Drought tolerance | OX | Drought tolerance | [41] |
Os03g07480 | OsSUT1 | MT | Dwarf | KD | Dwarfism; flowering time | [42] |
Os04g56320 | OsrcaA2 | MT | Dwarf | KD/OX | Dwarfism | [43] |
Os07g05820 | OsGLO4 | R or T | Dwarf | KD | Growth inhibition | [44] |
Os11g05110 | OsPK1 | MT | Dwarf | KO | Elongation of uppermost internode; dwarfism | [45] |
Os11g05110 | ospk1 | MT | Dwarf | KO | Dwarfism; seed color; internode color; regulation of gibberellin and ABA biosynthesis | [46] |
Os12g44380 | ossut2 | MT | Dwarf | KO | Sugar export; growth retardation | [40] |
Os01g44220 | osagpl2 | PT | Eating quality | KO | Starch biosynthesis | [47] |
Os01g55540 | OsAAT2 | PT | Eating quality | OX | Seed amino acid and protein content | [48] |
Os02g52710 | Amy1A | PT | Eating quality | KD | Seed starch content; high temperature-triggered grain chalkiness | [49] |
Os03g03720 | OsGAPDHB | PT | Eating quality | KD | Fragrance rice | [50] |
Os03g09250 | RINO1 | PT | Eating quality | KD | Seed phytic acid content | [51] |
Os03g09250 | RINO1 | PT | Eating quality | KD | Seed phytic acid content | [52] |
Os03g52760 | lpaN15-186 | PT | Eating quality | KO | Seed phytic acid content | [53] |
Os03g55090 | pho1 | PT | Eating quality | KO | Seed starch content; grain maturation | [54] |
Os05g32710 | OsISA2 | PT | Eating quality | OX | Seed starch content | [55] |
Os05g33570 | flo4 | PT | Eating quality | KO | Seed protein and lipid content | [56] |
Os06g04200 | wx | PT | Eating quality | NV | Seed amylose content | [57] |
Os06g06560 | OsSSI | PT | Eating quality | KO | Seed amylopectin content | [58] |
Os06g12450 | SSIIa | PT | Eating quality | KD | Chalky kernel; amylose content | [59] |
Os06g12450 | ALK | PT | Eating quality | NV | Gelatinization temperature; gel consistency | [60] |
Os08g09230 | SSIIIa | PT | Eating quality | KD | Chalky kernel; amylose content | [59] |
Os08g09230 | flo5 | PT | Eating quality | KO | Seed starch content | [61] |
Os08g09230 | ss3a | PT | Eating quality | KO | Seed starch content | [62] |
Os08g25734 | osagps2 | PT | Eating quality | KO | Seed starch content | [47] |
Os08g40930 | OsISA1 | PT | Eating quality | OX | Seed starch content | [55] |
Os09g28400 | Amy3A | PT | Eating quality | KD | Seed starch content; high temperature-triggered grain chalkiness | [49] |
Os09g28420 | Amy3B | PT | Eating quality | KD | Seed starch content; high temperature-triggered grain chalkiness | [49] |
Os09g29404 | isa3 | PT | Eating quality | KO | Seed starch content | [63] |
Os01g72090 | se13 | PT | Flowering | KO | Photoperiodic response | [64] |
Os02g34560 | Oscyt-inv1 | PT | Flowering | KO | Root cell development; flowering time; fertility | [65] |
Os03g07480 | OsSUT1 | PT | Flowering | KD | Dwarfism; flowering time | [42] |
Os02g52710 | AmyI-1 | PT | Germination dormancy | KD/OX | Starch degradation; seed germination; seedling growth | [66] |
Os03g07480 | OsSUT1 | R or T | Insect resistance | Others | Upregulation by aphid feeding; transfer sucrose | [67] |
Os02g47020 | SBPase | R or T | Other stress resistance | OX | Photosynthetic ability under high-temperature condition | [68] |
Os02g01150 | OsHPR1 | PT | Others | KD/OX | Photorespiratory pathway | [69] |
Os05g50380 | LSU3 | Others | Others | KO | Culm starch content | [70] |
Os01g69030 | OsSPS1 | PT | Panicle flower | KO | Pollen germination through sucrose synthesis | [71] |
Os02g34560 | Oscyt-inv1 | MT | Root | KO | Root cell development; flowering time; fertility | [65] |
Os12g44380 | ossut2 | MT | Root | KO | Sugar export; growth retardation | [40] |
Os02g17500 | OsGMST1 | R or T | Salinity tolerance | KD | Salinity tolerance | [72] |
Os02g44230 | OsTPP1 | R or T | Salinity tolerance | OX | Cold and salinity tolerance | [37] |
Os03g07480 | OsSUT1 | R or T | Salinity tolerance | KD | Salinity tolerance | [73] |
Os05g44210 | OsTPS1 | R or T | Salinity tolerance | OX | Cold, drought, and salinity tolerance | [38] |
Os08g03290 | OsGAPC3 | R or T | Salinity tolerance | OX | Salinity tolerance | [74] |
Os01g44220 | OsAGPL2 | MT | Seed | KO | Glassy/vitreous, shrunken grain | [75] |
Os03g55090 | pho1 | MT | Seed | KO | Seed starch content; grain maturation | [54] |
Os04g33740 | GIF1 | MT | Seed | NV | Grain filling; grain size | [12] |
Os08g25734 | OsAGPS2b | PT | Seed | KO | Seed weight; starch content; AGPase activities from developing endosperms of the seed | [75] |
Os11g05110 | ospk1 | MT | Seed | KO | Dwarfism; seed color; internode color; Regulation of gibberellin and ABA biosynthesis | [46] |
Os02g52710 | AmyI-1 | MT | Shoot seedling | KD/OX | Starch degradation; seed germination; seedling growth | [66] |
Os01g11054 | Osppc4 | PT | Source activity | KD | Ammonium assimilation in leaves | [76] |
Os01g64660 | oscfbp1 | PT | Source activity | KO | Photosynthetic sucrose biosynthesis; growth retardation | [77] |
Os01g64960 | qNPQ1-2 | PT | Source activity | NV | Nonphotochemical quenching capacity; protection from photoinhibition | [78] |
Os01g64960 | PsbS | PT | Source activity | KD/OX | Nonphotochemical quenching capacity; photosynthetic rate in fluctuating light conditions | [79] |
Os02g32660 | BE2b | PT | Source activity | Others | Starch biosynthesis in endosperm; amylopectin biosynthesis; branch formation | [80] |
Os03g57220 | OsGLO1 | PT | Source activity | KD | Photorespiration | [81] |
Os04g56320 | rca | PT | Source activity | KD | Rubisco activity | [82] |
Os05g40180 | OsSTN8 | PT | Source activity | KO | Photosystem II repair during high light illumination | [83] |
Os06g06560 | SS1 | PT | Source activity | Others | Starch biosynthesis in endosperm; chain elongation | [80] |
Os06g51084 | BE1 | PT | Source activity | Others | Starch granule binding; amylopectin structure | [80] |
Os07g05820 | OsGLO4 | PT | Source activity | KD | Rubisco activation; photosynthesis rate | [44] |
Os08g45190 | PGR5 | PT | Source activity | KD | Photosynthetic capacity | [84] |
Os10g37180 | OsGDCH | PT | Source activity | KD | Leaf senescence induced by reactive oxygen species | [85] |
Os12g17600 | rbcS | PT | Source activity | KD | Rubisco content; photosynthetic capacity | [86] |
Os12g17600 | OsRBCS2 | PT | Source activity | KD | Rubisco content | [87] |
Os12g17600 | rbcS | PT | Source activity | KD/OX | Rubisco content; photosynthetic capacity | [88] |
Os12g19381 | OsRBCS5 | PT | Source activity | KD | Rubisco content | [87] |
Os12g19470 | OsRBCS4 | PT | Source activity | KD | Rubisco content | [87] |
Os12g44380 | ossut2 | PT | Source activity | KO | Sugar export; growth retardation | [40] |
Os02g34560 | Oscyt-inv1 | PT | Sterility | KO | Root cell development; flowering time; fertility | [65] |
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Hong, W.-J.; Jiang, X.; Choi, S.-H.; Kim, Y.-J.; Kim, S.-T.; Jeon, J.-S.; Jung, K.-H. A Systemic View of Carbohydrate Metabolism in Rice to Facilitate Productivity. Plants 2021, 10, 1690. https://doi.org/10.3390/plants10081690
Hong W-J, Jiang X, Choi S-H, Kim Y-J, Kim S-T, Jeon J-S, Jung K-H. A Systemic View of Carbohydrate Metabolism in Rice to Facilitate Productivity. Plants. 2021; 10(8):1690. https://doi.org/10.3390/plants10081690
Chicago/Turabian StyleHong, Woo-Jong, Xu Jiang, Seok-Hyun Choi, Yu-Jin Kim, Sun-Tae Kim, Jong-Seong Jeon, and Ki-Hong Jung. 2021. "A Systemic View of Carbohydrate Metabolism in Rice to Facilitate Productivity" Plants 10, no. 8: 1690. https://doi.org/10.3390/plants10081690