Analysis of Photosynthetic Differences of Rice Germplasm in Southeast Asia Based on Leaf-Tissue Structure, Physiology, and iTRAQ
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Material and Experimental Design
2.2. Investigations and Measurements
2.2.1. Leaf Tissue Structure
2.2.2. Chloroplast Ultrastructure
2.3. Physiological Indicators
2.3.1. Photosynthetic Characteristics
2.3.2. Chlorophyll Fluorescence Parameters
2.3.3. Chlorophyll Content SPAD and RSP
2.3.4. Rubisco Enzyme Activity and Content
2.4. iTRAQ Proteomics
2.4.1. Protein Extraction, Trypsin Digestion and iTRAQ Labeling
2.4.2. High-Performance Liquid Chromatography (HPLC) Fractionation
2.4.3. Liquid Chromatography (LC) Tandem Mass Spectrometry (MS/MS) Analysis
2.4.4. Database Search
2.5. Bioinformatics Analysis
2.5.1. Gene Ontology (GO) Annotation
2.5.2. Domain Annotation
2.5.3. Sequence Subcellular Localization
2.5.4. Enrichment of GO Analysis
2.5.5. Enriched Pathway Analysis
2.6. Real-Time Quantitative PCR Analysis
2.7. Statistics and Analysis
3. Results
3.1. Differences in Leaf Structure
3.2. Differences in Chloroplast Ultrastructure
3.3. Differences in Chlorophyll Value and Photosynthetic Rate
3.4. Differences in Chlorophyll Fluorescence Parameters and Rubisco
3.5. Proteomic Analysis of Different Germplasm Resources
3.5.1. Protein Identification and GO Analysis
3.5.2. Classification of Subcellular Structure Localization
3.5.3. KEGG Analysis
4. Discussion
4.1. Effect of Tissue Structure on Pn
4.2. Effect of Photosynthetic Physiological Indicators on Pn
4.3. Differential Proteins among High- and Low-Light-Efficiency Germplasm Resources
5. Conclusions
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Name | Stomatal Density (pcs) | Stomatal Size (mm) | LT (mm) | No. of BCB (pcs) | No. of SCB (pcs) | BCB Area (mm2) | SCB Area (mm2) | V Diameter (mm) | MC Size (mm2) |
---|---|---|---|---|---|---|---|---|---|
G164 | 3.667 a | 0.001 a | 0.100 a | 9 a | 46 a | 0.016 a | 0.0029 a | 0.0435 a | 2.4 × 10−5 b |
C1 | 6.000 b | 0.004 b | 0.098 a | 20 b | 61 b | 0.015 a | 0.0028 a | 0.0345 b | 1.9 × 10−5 a |
Varieties | Fv/Fm | qP | NPQ | ETR | ΦPSⅡ | Rubisco Activity (nmol/s/g) | Rubisco Content (ng/L) |
---|---|---|---|---|---|---|---|
C1 | 0.813 ± 0.006 a | 0.911 ± 0.011 a | 0.160 ± 0.055 a | 30.429 ± 0.432 a | 0.691 ± 0.009 a | 5.311 ± 9.74 b | 148.933 ± 2.95 a |
G164 | 0.806 ± 0.002 a | 0.874 ± 0.023 a | 0.177 ± 0.042 a | 28.954 ± 0.887 a | 0.660 ± 0.019 a | 5.037 ± 2.43 a | 138.073 ± 4.28 a |
KEGG Pathway | Protein Accession | Protein Description | Coverage [%] | Fold Change | Direction of Change | Subcellular Localization |
---|---|---|---|---|---|---|
Photosynthesis | O23877 | petH; ferredoxin—NADP+ reductase [EC:1.18.1.2] | 10.1 | 1.645 ** | up | chloroplast |
P0C389 | petA; apocytochrome f | 46.2 | 0.764 ** | down | nucleus | |
P12123 | petB; cytochrome b6 | 16.3 | 0.690 * | down | cytoplasm | |
Q0DFC9 | petE; plastocyanin | 20.8 | 0.810 ** | down | chloroplast | |
Q0J8M2 | petF; ferredoxin | 40.3 | 0.790 ** | down | chloroplast | |
Q0JG75 | psb28; PSII 13kDa protein | 16.1 | 0.710 ** | down | chloroplast | |
Q109L0 | psbP; photosystem II oxygen-evolving enhancer protein 2 | 17.7 | 0.645 ** | down | chloroplast | |
Q10LV7 | psb27; photosystem II Psb27 protein | 34.5 | 0.745 ** | down | chloroplast | |
Q69S39 | petC; cytochrome b6-f complex iron-sulfur subunit [EC:1.10.9.1] | 49.8 | 0.720 ** | down | chloroplast | |
Q6ZFJ3 | petH; ferredoxin--NADP+ reductase [EC:1.18.1.2] | 56.3 | 0.770 ** | down | chloroplast | |
Carbon fixation in photosynthetic organism | A0A0P0WP33 | PGK; phosphoglycerate kinase [EC:2.7.2.3] | 63.6 | 0.800 ** | down | chloroplast |
A0A0P0XLG164 | PEPC; phosphoenolpyruvate carboxylase [EC:4.1.1.31] | 20.3 | 1.635 * | up | cytoplasm | |
A0A0P0XUE4 | GPT; alanine transaminase [EC:2.6.1.2] | 22.4 | 1.425 * | up | cytoplasm | |
Q0JJQ7 | E1.1.1.40; malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) [EC:1.1.1.40] | 29.1 | 1.500 ** | up | chloroplast | |
Q2QTJ1 | rbcS; ribulose-bisphosphate carboxylase small chain [EC:4.1.1.39] | 53.1 | 0.790 ** | down | chloroplast | |
Q42972 | MDH2; malate dehydrogenase [EC:1.1.1.37] | 15.7 | 1.465 ** | up | cytoplasm | |
Q655Y9 | FBP; fructose-1,6-bisphosphatase I [EC:3.1.3.11] | 27.7 | 1.315 ** | up | chloroplast | |
Q69K00 | TPI; triosephosphate isomerase (TIM) [EC:5.3.1.1] | 53 | 0.745 ** | down | chloroplast | |
Q69UU3 | GGAT; glutamate--glyoxylate aminotransferase [EC:2.6.1.4 2.6.1.2 2.6.1.44] | 58.4 | 0.815 ** | down | peroxisome | |
Q6H6C7 | PGK; phosphoglycerate kinase [EC:2.7.2.3] | 55.7 | 1.300 ** | up | chloroplast | |
Q6YYW3 | E1.1.1.82; malate dehydrogenase (NADP+) [EC:1.1.1.82] | 47.8 | 0.795 ** | down | chloroplast | |
Q7X8A1 | GAPA; glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) [EC:1.2.1.13] | 51 | 0.775 ** | down | chloroplast | |
Q7XDC8 | MDH1; malate dehydrogenase [EC:1.1.1.37] | 31.6 | 1.225 ** | up | cytoplasm | |
Q7XZW5 | MDH2; malate dehydrogenase [EC:1.1.1.37] | 57.9 | 0.750 ** | down | chloroplast | |
Q8H4V1 | pepc; phosphoenolpyruvate carboxylase [EC:4.1.1.31] | 35.7 | 1.310 ** | up | cytoplasm | |
Q9SNK3 | GAPA; glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) [EC:1.2.1.13] | 55 | 0.815 ** | down | chloroplast | |
Q0J8A4 | GAPDH; glyceraldehyde 3-phosphate dehydrogenase [EC:1.2.1.12] | 64.1 | 1.390 ** | up | cytoplasm |
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Zhang, X.; Tang, M.; Wang, H.; Tao, W.; Wang, Q.; Chen, L.; Gao, G.; Lv, R.; Liang, T. Analysis of Photosynthetic Differences of Rice Germplasm in Southeast Asia Based on Leaf-Tissue Structure, Physiology, and iTRAQ. Agronomy 2022, 12, 3207. https://doi.org/10.3390/agronomy12123207
Zhang X, Tang M, Wang H, Tao W, Wang Q, Chen L, Gao G, Lv R, Liang T. Analysis of Photosynthetic Differences of Rice Germplasm in Southeast Asia Based on Leaf-Tissue Structure, Physiology, and iTRAQ. Agronomy. 2022; 12(12):3207. https://doi.org/10.3390/agronomy12123207
Chicago/Turabian StyleZhang, Xiaoli, Maoyan Tang, Hui Wang, Wei Tao, Qiang Wang, Lei Chen, Guoqing Gao, Ronghua Lv, and Tianfeng Liang. 2022. "Analysis of Photosynthetic Differences of Rice Germplasm in Southeast Asia Based on Leaf-Tissue Structure, Physiology, and iTRAQ" Agronomy 12, no. 12: 3207. https://doi.org/10.3390/agronomy12123207