Metabolomic Variation in Sugarcane Maturation Under a Temperate Climate
Abstract
1. Introduction
2. Materials and Methods
2.1. Plant Material
2.2. Sample Preparation
2.3. Sample Pretreatments for NMR Measurements
2.4. NMR Measurements
2.5. Data Analysis
3. Results
3.1. Growth Characteristics of Sugarcane
3.2. Metabolic Profiles in Sugarcane Maturation
3.3. Key Metabolites in Sugarcane Maturation
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Module | Description/Parameter Options |
---|---|
(1) Data import | |
Loading NMR data | Bruker fid data, Bruker spectra pdata, CSV data |
Loading group data | CSV data |
Loading objective variables | CSV data |
(2) Spectral processing | |
Zero filling (FID only) | Input a value (points) |
Line broadening (FID only) | Input a value (Hz) |
Phase correction (FID only) | Minimization around maximum peak, automated phase correction based on minimization of entropy [38] |
Baseline correction | Distribution-based classification method [39] |
Reference calibration | Select a reference peak range (ppm) |
Field trimming | Select a range (ppm) |
Binning/bucketing | Input binning/bucketing size (ppm) |
Solvent peak removal | Select a range of solvent peaks (ppm) |
Normalization | Reference peak, mean, probabilistic quotient normalization [40] |
Peak alignment | icoshift algorithm |
(3) Multivariate analysis | |
Hierarchical cluster analysis | Method: ward, complete, average, etc. Metric: Euclidean, Bray–Curtis, cosine, etc. |
Nonhierarchical cluster analysis | K-means, g-means, x-means |
PCA | - |
Discriminant analysis | Partial least squares, orthogonal partial least squares |
Correlation heatmap | Pearson, Spearman, and Kendall correlations |
(4) Machine learning | |
Random forest | Classification, regression |
Support vector machine | Classification, regression |
(5) Peak annotation | |
ASICS | - |
Stalk Weight (g) | Stalk Length (cm) | Stalk Diameter (mm) | Internode Count | Stalk Count | |
---|---|---|---|---|---|
Mean ± S.D. | Mean ± S.D. | Mean ± S.D. | Mean ± S.D. | Total | |
Harunoogi | 506.4 ± 205.4 | 176.6 ± 45.2 | 16.9 ± 2.3 | 10.8 ± 2.8 | 92 |
Sep | 489.9 ± 170.9 | 170.9 ± 34.4 | 17.4 ± 1.9 | 10.6 ± 2.3 | 30 |
Oct–Nov | 503.3 ± 224.8 | 170.0 ± 52.5 | 17.0 ± 2.2 | 10.3 ± 3.1 | 34 |
Dec | 527.8 ± 212.6 | 190.8 ± 42.6 | 16.3 ± 2.7 | 11.6 ± 2.7 | 28 |
KTn03-54 | 575.7 ± 280.3 | 137.7 ± 57.8 | 21.4 ± 2.0 | 9.5 ± 4.1 | 43 |
Sep | 646.1 ± 235.5 | 150.3 ± 44.5 | 22.1 ± 1.9 | 10.4 ± 3.2 | 13 |
Oct–Nov | 534.9 ± 284.1 | 125.5 ± 58.9 | 21.5 ± 1.9 | 8.5 ± 4.2 | 16 |
Dec | 557.0 ± 301.3 | 140.1 ± 64.3 | 20.6 ± 2.0 | 9.9 ± 4.6 | 14 |
Kurokaido | 449.4 ± 182.2 | 153.3 ± 42.7 | 17.2 ± 1.9 | 8.1 ± 2.2 | 95 |
Sep | 431.2 ± 147.9 | 148.1 ± 30.1 | 17.1 ± 1.8 | 8.0 ± 1.6 | 32 |
Oct–Nov | 454.7 ± 191.5 | 148.2 ± 47.6 | 17.6 ± 1.6 | 7.8 ± 2.4 | 28 |
Dec | 461.8 ± 200.6 | 162.2 ± 46.7 | 16.9 ± 2.1 | 8.5 ± 2.4 | 35 |
NCo310 | 398.3 ± 205.8 | 155.8 ± 60.8 | 16.1 ± 2.1 | 9.2 ± 3.5 | 83 |
Sep | 365.9 ± 151.0 | 149.2 ± 45.3 | 16.0 ± 2.1 | 8.8 ± 2.6 | 26 |
Oct–Nov | 416.4 ± 223.5 | 162.2 ± 67.1 | 16.0 ± 1.8 | 9.5 ± 3.8 | 29 |
Dec | 409.8 ± 226.3 | 155.4 ± 65.6 | 16.4 ± 2.3 | 9.4 ± 3.8 | 28 |
Ni22 | 639.5 ± 220.4 | 200.6 ± 48.6 | 18.3 ± 1.6 | 10.6 ± 2.7 | 69 |
Sep | 576.1 ± 208.4 | 180.2 ± 37.1 | 18.5 ± 1.7 | 9.4 ± 2.3 | 20 |
Oct–Nov | 673.8 ± 201.5 | 204.8 ± 45.7 | 18.4 ± 1.6 | 10.8 ± 2.3 | 27 |
Dec | 655.0 ± 240.3 | 213.9 ± 55.0 | 18.0 ± 1.5 | 11.5 ± 3.1 | 22 |
Ni27 | 897.7 ± 274.6 | 203.1 ± 37.7 | 21.9 ± 2.2 | 11.6 ± 2.5 | 66 |
Sep | 855.2 ± 254.4 | 186.7 ± 41.4 | 22.8 ± 1.7 | 10.6 ± 2.7 | 19 |
Oct–Nov | 872.3 ± 313.0 | 200.1 ± 38.5 | 21.6 ± 2.5 | 11.4 ± 2.4 | 22 |
Dec | 952.4 ± 242.3 | 218.3 ± 26.3 | 21.6 ± 1.9 | 12.5 ± 2.0 | 25 |
NiF8 | 691.8 ± 356.3 | 166.2 ± 63.3 | 20.9 ± 3.3 | 9.3 ± 3.5 | 56 |
Sep | 623.3 ± 370.9 | 147.6 ± 63.6 | 21.0 ± 4.5 | 8.5 ± 3.5 | 17 |
Oct–Nov | 721.8 ± 339.8 | 171.5 ± 58.0 | 21.0 ± 2.3 | 9.3 ± 3.3 | 20 |
Dec | 721.5 ± 351.5 | 177.4 ± 64.7 | 20.6 ± 2.9 | 10.2 ± 3.4 | 19 |
NiTn18 | 450.2 ± 266.4 | 150.4 ± 75.4 | 17.5 ± 2.0 | 9.7 ± 4.9 | 88 |
Sep | 472.6 ± 229.2 | 155.8 ± 56.1 | 17.9 ± 1.7 | 9.8 ± 3.7 | 28 |
Oct–Nov | 443.7 ± 297.9 | 144.9 ± 83.0 | 17.4 ± 2.1 | 9.5 ± 5.5 | 31 |
Dec | 435.4 ± 262.6 | 150.9 ± 82.4 | 17.2 ± 2.1 | 9.8 ± 5.2 | 29 |
RK03-3010 | 450.7 ± 250.2 | 123.0 ± 59.7 | 20.5 ± 1.6 | 7.4 ± 3.3 | 36 |
Sep | 361.7 ± 188.6 | 105.8 ± 48.7 | 19.9 ± 2.0 | 6.4 ± 2.6 | 13 |
Oct–Nov | 421.4 ± 243.6 | 115.2 ± 58.8 | 20.5 ± 1.1 | 7.0 ± 3.2 | 13 |
Dec | 604.4 ± 258.8 | 155.5 ± 61.2 | 21.4 ± 1.2 | 9.3 ± 3.3 | 10 |
Juice Extraction Efficiency (%) | Brix (%) | pH | |
---|---|---|---|
Mean ± S.D. | Mean ± S.D. | Mean ± S.D. | |
Harunoogi | 51.1 ± 2.7 | 13.3 ± 2.2 | 5.20 ± 0.09 |
Sep | 51.6 ± 2.2 | 10.8 ± 0.9 | 5.11 ± 0.04 |
Oct–Nov | 50.8 ± 3.0 | 13.6 ± 1.4 | 5.21 ± 0.05 |
Dec | 51.0 ± 2.7 | 15.5 ± 0.9 | 5.30 ± 0.04 |
KTn03-54 | 58.7 ± 2.7 | 11.6 ± 2.0 | 5.22 ± 0.10 |
Sep | 58.4 ± 1.5 | 9.9 ± 1.2 | 5.11 ± 0.05 |
Oct–Nov | 58.8 ± 3.1 | 12.0 ± 1.5 | 5.22 ± 0.08 |
Dec | 58.8 ± 3.2 | 12.6 ± 2.1 | 5.31 ± 0.06 |
Kurokaido | 55.4 ± 2.7 | 15.7 ± 2.8 | 5.15 ± 0.08 |
Sep | 54.9 ± 2.3 | 13.2 ± 0.8 | 5.15 ± 0.09 |
Oct–Nov | 55.2 ± 2.5 | 16.2 ± 2.7 | 5.13 ± 0.06 |
Dec | 55.9 ± 3.1 | 17.6 ± 2.3 | 5.17 ± 0.07 |
NCo310 | 55.9 ± 3.3 | 10.2 ± 2.8 | 5.11 ± 0.13 |
Sep | 55.0 ± 3.5 | 8.9 ± 1.8 | 5.00 ± 0.06 |
Oct–Nov | 55.5 ± 3.0 | 10.1 ± 3.0 | 5.15 ± 0.12 |
Dec | 57.3 ± 2.9 | 11.4 ± 2.8 | 5.19 ± 0.10 |
Ni22 | 55.2 ± 2.2 | 13.2 ± 2.1 | 5.22 ± 0.09 |
Sep | 55.4 ± 2.0 | 10.7 ± 0.7 | 5.16 ± 0.06 |
Oct–Nov | 54.8 ± 2.7 | 13.7 ± 0.8 | 5.23 ± 0.08 |
Dec | 55.4 ± 1.8 | 15.0 ± 1.8 | 5.28 ± 0.07 |
Ni27 | 57.5 ± 2.1 | 13.6 ± 2.4 | 5.23 ± 0.10 |
Sep | 57.7 ± 1.5 | 10.8 ± 1.4 | 5.13 ± 0.06 |
Oct–Nov | 56.5 ± 2.3 | 14.5 ± 1.8 | 5.22 ± 0.09 |
Dec | 58.2 ± 1.8 | 14.8 ± 1.6 | 5.32 ± 0.05 |
NiF8 | 55.6 ± 2.6 | 11.4 ± 2.4 | 5.13 ± 0.11 |
Sep | 54.1 ± 2.8 | 8.8 ± 1.2 | 5.01 ± 0.03 |
Oct–Nov | 56.6 ± 2.0 | 12.3 ± 1.1 | 5.14 ± 0.08 |
Dec | 56.1 ± 2.3 | 12.9 ± 2.2 | 5.25 ± 0.04 |
NiTn18 | 56.7 ± 2.5 | 10.6 ± 2.6 | 5.19 ± 0.11 |
Sep | 56.4 ± 1.7 | 8.7 ± 1.9 | 5.11 ± 0.06 |
Oct–Nov | 56.6 ± 3.2 | 11.5 ± 2.1 | 5.19 ± 0.13 |
Dec | 57.1 ± 2.3 | 11.6 ± 2.5 | 5.25 ± 0.07 |
RK03-3010 | 52.3 ± 2.5 | 9.4 ± 2.9 | 5.20 ± 0.12 |
Sep | 50.9 ± 2.6 | 7.6 ± 1.3 | 5.08 ± 0.05 |
Oct–Nov | 52.7 ± 2.4 | 9.8 ± 2.7 | 5.23 ± 0.10 |
Dec | 53.5 ± 1.6 | 11.4 ± 3.1 | 5.31 ± 0.05 |
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Date, Y.; Ishikawa, C.; Ono, H. Metabolomic Variation in Sugarcane Maturation Under a Temperate Climate. Metabolites 2025, 15, 558. https://doi.org/10.3390/metabo15080558
Date Y, Ishikawa C, Ono H. Metabolomic Variation in Sugarcane Maturation Under a Temperate Climate. Metabolites. 2025; 15(8):558. https://doi.org/10.3390/metabo15080558
Chicago/Turabian StyleDate, Yasuhiro, Chiaki Ishikawa, and Hiroshi Ono. 2025. "Metabolomic Variation in Sugarcane Maturation Under a Temperate Climate" Metabolites 15, no. 8: 558. https://doi.org/10.3390/metabo15080558
APA StyleDate, Y., Ishikawa, C., & Ono, H. (2025). Metabolomic Variation in Sugarcane Maturation Under a Temperate Climate. Metabolites, 15(8), 558. https://doi.org/10.3390/metabo15080558