Integrated Metabolome and Transcriptome Analyses Reveal Amino Acid Biosynthesis Mechanisms during the Physiological Maturity of Grains in Yunnan Hulled Wheat (Triticum aestivum ssp. yunnanense King)
Abstract
:1. Introduction
2. Results
2.1. Plant Material and Physiological Maturity Selection of Two YHW Lines
2.2. Phenotype and Total Amino Acid Contents of D and Y
2.3. Metabolome Analyses of AAs and Derivatives in WG and MG of Y and D
2.4. Changes in AADCs during Developmental Stages Differed between the Two Wheat Lines
2.5. Transcriptome Analyses of the Two Wheat Lines at Different Developmental Stages
2.6. Differential Expression of AA Biosynthesis and Regulatory Genes between WG and MG
2.7. Confirmation of RNA-Seq Data Using Quantitative Real-Time Polymerase Chain Reaction (qRT-PCR)
2.8. Weighted Gene Co-Expression Network Analysis (WGCNA) of AA Biosynthesis during Physiological Maturity
2.9. Identification of the Expression Patterns and Metabolic Pathways of AA Biosynthesis Genes in YHW Lines at Different Stages of Physiological Maturity
2.10. Correlation Analysis of EAAs and Transcriptome of YHW Grains at Different Levels of Physiological Maturity
3. Discussion
4. Materials and Methods
4.1. Plant Material and Samples
4.2. Measurement of Grain Characteristics
4.3. Metabolite Extraction and Profiling
4.4. Transcriptome Sequencing and Data Analysis
4.5. RT-qPCR
4.6. Co-Expression Network Construction
4.7. CCA
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
References
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Compounds | Molecular Weight (Da) | Formula | Class |
---|---|---|---|
L-Valine | 1.17 × 102 | C5H11NO2 | Essential amino acid |
L-Threonine | 1.19 × 102 | C4H9NO3 | Essential amino acid |
L-Leucine | 1.31 × 102 | C6H13NO2 | Essential amino acid |
L-Isoleucine | 1.31 × 102 | C6H13NO2 | Essential amino acid |
L-Lysine | 1.46 × 102 | C6H14N2O2 | Essential amino acid |
L-Methionine | 1.49 × 102 | C5H11NO2S | Essential amino acid |
L-Histidine | 1.55 × 102 | C6H9N3O2 | Essential amino acid |
L-Phenylalanine | 1.65 × 102 | C9H11NO2 | Essential amino acid |
L-Tryptophan | 2.04 × 102 | C11H12N2O2 | Essential amino acid |
L-Alanine | 8.90 × 101 | C3H7NO2 | Amino acids |
L-Serine | 1.05 × 102 | C3H7NO3 | Amino acids |
L-Proline | 1.15 × 102 | C5H9NO2 | Amino acids |
L-Homoserine | 1.19 × 102 | C4H9NO3 | Amino acids |
L-Cysteine | 1.21 × 102 | C3H7NO2S | Amino acids |
L-Norleucine | 1.31 × 102 | C6H13NO2 | Amino acids |
L-Asparagine | 1.32 × 102 | C4H8N2O3 | Amino acids |
L-Ornithine | 1.32 × 102 | C5H12N2O2 | Amino acids |
L-Aspartic acid | 1.33 × 102 | C4H7NO4 | Amino acids |
L-Glutamine | 1.46 × 102 | C5H10N2O3 | Amino acids |
L-Glutamic acid | 1.47 × 102 | C5H9NO4 | Amino acids |
L-Homomethionine | 1.63 × 102 | C6H13NO2S | Amino acids |
L-Arginine | 1.74 × 102 | C6H14N4O2 | Amino acids |
L-Tyrosine | 1.81 × 102 | C9H11NO3 | Amino acids |
L-Homocystine | 2.68 × 102 | C8H16N2O4S2 | Amino acids |
N-Methylglycine | 8.90 × 101 | C3H7NO2 | Amino acid derivatives |
L-Azetidine-2-carboxylic acid | 1.01 × 102 | C4H7NO2 | Amino acid derivatives |
Methyl 3-aminopropanoate | 1.03 × 102 | C4H9NO2 | Amino acid derivatives |
N,N-Dimethylglycine | 1.03 × 102 | C4H9NO2 | Amino acid derivatives |
N-Acetyl-L-glycine | 1.17 × 102 | C4H7NO3 | Amino acid derivatives |
N-Methyl-α-aminoisobutyric acid | 1.17 × 102 | C5H11NO2 | Amino acid derivatives |
5-Oxoproline | 1.29 × 102 | C5H7NO3 | Amino acid derivatives |
5-Oxo-L-proline | 1.29 × 102 | C5H7NO3 | Amino acid derivatives |
Cycloleucine | 1.29 × 102 | C6H11NO2 | Amino acid derivatives |
N-Acetyl-beta-alanine | 1.31 × 102 | C5H9NO3 | Amino acid derivatives |
Trans-4-hydroxy-L-proline | 1.31 × 102 | C5H9NO3 | Amino acid derivatives |
S-Methyl-L-cysteine | 1.35 × 102 | C4H9NO2S | Amino acid derivatives |
L-Cyclopentylglycine | 1.43 × 102 | C7H13NO2 | Amino acid derivatives |
N-Methyl-trans-4-hydroxy-L-proline | 1.45 × 102 | C6H11NO3 | Amino acid derivatives |
L-Threo-3-methylaspartate | 1.47 × 102 | C5H9NO4 | Amino acid derivatives |
O-Acetylserine | 1.47 × 102 | C5H9NO4 | Amino acid derivatives |
(2S,3R,4S)-4-Hydroxyisoleucine | 1.47 × 102 | C6H13NO3 | Amino acid derivatives |
4-Hydoxy-L-isoleucine | 1.47 × 102 | C6H13NO3 | Amino acid derivatives |
N-Acetyl-L-threonine | 1.61 × 102 | C6H11NO4 | Amino acid derivatives |
N-Methyl-L-glutamate | 1.61 × 102 | C6H11NO4 | Amino acid derivatives |
3-Hydroxy-3-methylpentane-1,5-dioic acid | 1.62 × 102 | C6H10O5 | Amino acid derivatives |
4-Hydroxy-L-glutamic acid | 1.63 × 102 | C5H9NO5 | Amino acid derivatives |
L-Methionine methyl ester | 1.63 × 102 | C6H13NO2S | Amino acid derivatives |
L-Methionine sulfoxide | 1.65 × 102 | C5H11NO3S | Amino acid derivatives |
L-Glycyl-L-proline | 1.72 × 102 | C7H12N2O3 | Amino acid derivatives |
N-Acetyl-L-leucine | 1.73 × 102 | C8H15NO3 | Amino acid derivatives |
N-Alpha-acetyl-L-asparagine | 1.74 × 102 | C6H10N2O4 | Amino acids derivatives |
N-α-Acetyl-L-ornithine | 1.74 × 102 | C7H14N2O3 | Amino acid derivatives |
N-Acetyl-L-aspartic acid | 1.75 × 102 | C6H9NO5 | Amino acid derivatives |
O-Phospho-L-serine | 1.85 × 102 | C3H8NO6P | Amino acid derivatives |
N-Acetyl-L-glutamine | 1.88 × 102 | C7H12N2O4 | Amino acid derivatives |
N-Glycyl-L-leucine | 1.88 × 102 | C8H16N2O3 | Amino acid derivatives |
L-Glycyl-L-isoleucine | 1.88 × 102 | C8H16N2O3 | Amino acid derivatives |
N6-Acetyl-L-lysine | 1.88 × 102 | C8H16N2O3 | Amino acid derivatives |
Homoarginine | 1.88 × 102 | C7H16N4O2 | Amino acid derivatives |
N-Monomethyl-L-arginine | 1.88 × 102 | C7H16N4O2 | Amino acid derivatives |
Trimethyllysine | 1.88 × 102 | C9H20N2O2 | Amino acid derivatives |
N-Acetyl-L-glutamic acid | 1.89 × 102 | C7H11NO5 | Amino acid derivatives |
N-Acetyl-L-methionine | 1.91 × 102 | C7H13NO3S | Amino acid derivatives |
L-Tyrosine methyl ester | 1.95 × 102 | C10H13NO3 | Amino acid derivatives |
3,4-Dihydroxy-L-phenylalanine (L-dopa) | 1.97 × 102 | C9H11NO4 | Amino acid derivatives |
NG,NG-Dimethyl-L-arginine | 2.02 × 102 | C8H18N4O2 | Amino acid derivatives |
N-Acetyl-L-phenylalanine | 2.07 × 102 | C11H13NO3 | Amino acid derivatives |
6-Hydroxydopaquinone | 2.11 × 102 | C9H9NO5 | Amino acid derivatives |
N-Acetyl-L-arginine | 2.16 × 102 | C8H16N4O3 | Amino acid derivatives |
5-L-Glutamyl-L-amino acid | 2.18 × 102 | C8H14N2O5 | Amino acid derivatives |
5-Hydroxy-L-tryptophan | 2.20 × 102 | C11H12N2O3 | Amino acid derivatives |
Glycylphenylalanine | 2.22 × 102 | C11H14N2O3 | Amino acid derivatives |
L-Glycyl-L-phenylalanine | 2.22 × 102 | C11H14N2O3 | Amino acid derivatives |
N-Acetyl-L-tyrosine | 2.23 × 102 | C11H13NO4 | Amino acid derivatives |
L-Prolyl-L-leucine | 2.28 × 102 | C11H20N2O3 | Amino acid derivatives |
L-Valyl-L-leucine | 2.30 × 102 | C11H22N2O3 | Amino acid derivatives |
L-Lysine-butanoic acid | 2.34 × 102 | C10H22N2O4 | Amino acid derivatives |
L-Alanyl-L-phenylalanine | 2.36 × 102 | C12H16N2O3 | Amino acid derivatives |
L-Leucyl-L-leucine | 2.44 × 102 | C12H24N2O3 | Amino acid derivatives |
N-Acetyl-L-tryptophan | 2.46 × 102 | C13H14N2O3 | Amino acid derivatives |
L-Isoleucyl-L-aspartate | 2.46 × 102 | C10H18N2O5 | Amino acid derivatives |
γ-Glutamyl-L-valine | 2.46 × 102 | C10H18N2O5 | Amino acid derivatives |
L-γ-Glutamyl-L-leucine | 2.60 × 102 | C11H20N2O5 | Amino acid derivatives |
Glycyl-tryptophan | 2.61 × 102 | C13H15N3O3 | Amino acid derivatives |
L-Prolyl-L-phenylalanine | 2.62 × 102 | C14H18N2O3 | Amino acid derivatives |
Phenylacetyl-L-glutamine | 2.64 × 102 | C13H16N2O4 | Amino acid derivatives |
L-Valyl-L-phenylalanine | 2.64 × 102 | C14H20N2O3 | Amino acid derivatives |
γ-Glutamylmethionine | 2.78 × 102 | C10H18N2O5S | Amino acid derivatives |
L-Aspartyl-L-phenylalanine | 2.80 × 102 | C13H16N2O5 | Amino acid derivatives |
γ-Glutamylphenylalanine | 2.94 × 102 | C14H18N2O5 | Amino acid derivatives |
Glutathione reduced form | 3.07 × 102 | C10H17N3O6S | Amino acid derivatives |
γ-Glutamyltyrosine | 3.10 × 102 | C14H18N2O6 | Amino acid derivatives |
L-Phenylalanyl-L-phenylalanine | 3.12 × 102 | C18H20N2O3 | Amino acid derivatives |
S-(Methyl)glutathione | 3.21 × 102 | C11H19N3O6S | Amino acid derivatives |
Tryptophan glutamic acid | 3.33 × 102 | C16H19N3O5 | Amino acid derivatives |
S-(5′-Adenosy)-L-homocysteine | 3.84 × 102 | C14H20N6O5S | Amino acid derivatives |
Oxiglutatione | 6.12 × 102 | C20H32N6O12S2 | Amino acid derivatives |
L-Alanyl-L-alanine | 1.60 × 102 | C6H12N2O3 | Oligopeptides |
Cyclo(L-Ala-L-Pro) | 1.68 × 102 | C8H12N2O2 | Oligopeptides |
Cyclo(D-Leu-L-Pro) | 2.10 × 102 | C11H18N2O2 | Oligopeptides |
Cyclo(D-Phe-L-Pro) | 2.44 × 102 | C14H16N2O2 | Oligopeptides |
Cyclo(Pro-Phe) | 2.44 × 102 | C14H16N2O2 | Oligopeptides |
γ-Glu-Cys | 2.50 × 102 | C8H14N2O5S | Oligopeptides |
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Zhang, C.; Zhang, P.; Zhang, X.; Wang, Q.; Liu, J.; Li, L.; Cheng, S.; Qin, P. Integrated Metabolome and Transcriptome Analyses Reveal Amino Acid Biosynthesis Mechanisms during the Physiological Maturity of Grains in Yunnan Hulled Wheat (Triticum aestivum ssp. yunnanense King). Int. J. Mol. Sci. 2023, 24, 13475. https://doi.org/10.3390/ijms241713475
Zhang C, Zhang P, Zhang X, Wang Q, Liu J, Li L, Cheng S, Qin P. Integrated Metabolome and Transcriptome Analyses Reveal Amino Acid Biosynthesis Mechanisms during the Physiological Maturity of Grains in Yunnan Hulled Wheat (Triticum aestivum ssp. yunnanense King). International Journal of Molecular Sciences. 2023; 24(17):13475. https://doi.org/10.3390/ijms241713475
Chicago/Turabian StyleZhang, Chuanli, Ping Zhang, Xuesong Zhang, Qianchao Wang, Junna Liu, Li Li, Shunhe Cheng, and Peng Qin. 2023. "Integrated Metabolome and Transcriptome Analyses Reveal Amino Acid Biosynthesis Mechanisms during the Physiological Maturity of Grains in Yunnan Hulled Wheat (Triticum aestivum ssp. yunnanense King)" International Journal of Molecular Sciences 24, no. 17: 13475. https://doi.org/10.3390/ijms241713475