Transcriptome and Metabolome Analysis Provides Insights into the Heterosis of Yield and Quality Traits in Two Hybrid Rice Varieties (Oryza sativa L.)
Abstract
:1. Introduction
2. Results
2.1. Yield and Quality Analysis
2.2. Metabolite Profiles of Rice Grains
2.3. Transcriptome Profiles of Rice Grains
2.4. Identification of WGCNA Modules Associated with Yield and Rice Quality in Different Varieties
2.5. Functional Annotation of Hub Genes Highly Associated with Yield and Quality Traits
3. Discussion
4. Materials and Methods
4.1. Plant Materials, Field Experiments, and Sampling
4.2. RNA Extraction and Profiling Analysis
4.3. Metabolite Extraction, Identification, and Profiling Analysis
4.4. Yield and Rice Quality Determination
4.5. Quantitative Real-Time Polymerase Chain Reaction (qRT‒PCR)
4.6. Statistical Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
WGCNA | weighted gene coexpression network |
GO | Gene Ontology |
KEGG | Kyoto Encyclopedia of Genes and Genomes |
DEG | differentially expressed gene |
PCA | principal component analysis |
DMs | differential metabolites |
TY871 | Taiyou 871 |
CH | Changhui 871 |
TF | Taifeng B |
TY398 | Taiyou 398 |
GH | Guanghui 398 |
PL | panicle length |
TGNPP | total grain number per panicle |
1000-GW | 1000-grain weight |
EPP | effective panicle per plant |
PBN | primary branch number |
SBN | secondary branch number |
YPP | yield per plant |
SSR | seed setting rate |
BR | brown rice rate |
MR | milled rice rate |
HMR | head milled rice rate |
CD | chalkiness degree |
GC | gel consistency |
AC | amylose content |
qRT‒PCR | quantitative real-time polymerase chain reaction |
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Variety | EPP | PL (cm) | PBN | SBN | TGNPP | SSR (%) | 1000-GW (g) | YPP (g) |
---|---|---|---|---|---|---|---|---|
TY398 | 12.67 ± 0.58 a | 25.63 ± 0.46 a | 13.78 ± 0.69 bc | 43.78 ± 5.23 ab | 196.83 ± 4.01 b | 81.79 ± 0.85 a | 23.55 ± 0.59 b | 39.25 ± 4.65 ab |
GH | 9.67 ± 0.58 b | 22.68 ± 0.19 b | 12.47 ± 1.12 c | 36.58 ± 6.57 b | 163.33 ± 8.97 c | 80.48 ± 1.28 ab | 20.53 ± 0.32 cd | 22.94 ± 1.52 c |
TF | 8.00 ± 1.00 b | 21.81 ± 0.59 b | 12.00 ± 0.58 c | 23.22 ± 2.12 c | 109.89 ± 0.69 d | 70.65 ± 1.16 d | 19.95 ± 0.18 e | 13.14 ± 0.88 d |
TY871 | 12.67 ± 0.58 a | 27.38 ± 2.00 a | 15.11 ± 0.69 b | 52.22 ± 1.71 a | 215.00 ± 2.52 b | 78.55 ± 0.65 b | 24.97 ± 0.09 a | 44.91 ± 2.43 a |
CH | 9.00 ± 1.00 b | 27.24 ± 0.17 a | 18.00 ± 0.00 a | 51.00 ± 3.18 a | 253.44 ± 14.69 a | 75.61 ± 0.97 c | 20.95 ± 0.42 c | 35.96 ± 1.99 b |
Variety | BR | MR | HMR | CD | GC | AC |
---|---|---|---|---|---|---|
TY398 | 75.39 ± 0.07 b | 63.23 ± 0.25 d | 49.73 ± 2.99 bc | 3.67 ± 0.34 bc | 73.00 ± 1.00 a | 16.03 ± 0.81 ab |
GH | 77.18 ± 0.36 a | 67.25 ± 0.10 a | 53.72 ± 0.74 ab | 4.39 ± 0.13 ab | 63.33 ± 3.79 b | 17.15 ± 0.58 a |
TF | 73.71 ± 0.26 c | 64.15 ± 0.23 c | 55.08 ± 2.06 b | 2.08 ± 0.48 d | 80.00 ± 1.00 a | 13.93 ± 0.07 c |
TY871 | 74.03 ± 0.66 c | 65.29 ± 0.30 b | 56.85 ± 2.41 a | 3.39 ± 0.37 c | 64.33 ± 2.52 b | 15.14 ± 0.84 bc |
CH | 72.54 ± 0.25 d | 61.82 ± 0.09 e | 47.31 ± 0.28 d | 4.80 ± 0.17 a | 49.00 ± 4.36 c | 16.23 ± 0.34 ab |
Module | Core Gene | Gene Function |
---|---|---|
Honeydew1 | Os04g0350700 | Basic helix–loop–helix protein, Regulation of awn development, grain size, and grain number |
Ivory | Os06g0318500 | Sodium/hydrogen exchanger |
Ivory | Os03g0793700 | RmlC-like jelly roll fold domain containing protein |
Grey60 | Os05g0363200 | UDP-glucuronic acid decarboxylase |
Grey60 | Os05g0154700 | Kinesin 13 protein, Regulation of grain length and plant height |
Lavenderblush3 | Os06g0254300 | EF-hand calcium binding protein |
Lavenderblush3 | Os03g0168100 | Late embryogenesis abundant protein repeat containing protein |
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Zhou, D.; Zhou, X.; Sun, C.; Tang, G.; Liu, L.; Chen, L.; He, H.; Xiong, Q. Transcriptome and Metabolome Analysis Provides Insights into the Heterosis of Yield and Quality Traits in Two Hybrid Rice Varieties (Oryza sativa L.). Int. J. Mol. Sci. 2022, 23, 12934. https://doi.org/10.3390/ijms232112934
Zhou D, Zhou X, Sun C, Tang G, Liu L, Chen L, He H, Xiong Q. Transcriptome and Metabolome Analysis Provides Insights into the Heterosis of Yield and Quality Traits in Two Hybrid Rice Varieties (Oryza sativa L.). International Journal of Molecular Sciences. 2022; 23(21):12934. https://doi.org/10.3390/ijms232112934
Chicago/Turabian StyleZhou, Dahu, Xinyi Zhou, Changhui Sun, Guoping Tang, Lin Liu, Le Chen, Haohua He, and Qiangqiang Xiong. 2022. "Transcriptome and Metabolome Analysis Provides Insights into the Heterosis of Yield and Quality Traits in Two Hybrid Rice Varieties (Oryza sativa L.)" International Journal of Molecular Sciences 23, no. 21: 12934. https://doi.org/10.3390/ijms232112934