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Supplementary Materials Figure S1: Metabolite distribution by PCA analysis in sweet corn cultivars. A clear distinction can be observed among the three cultivars. The three dots in each group are representative of the pooled samples performed for this study. In total, 30 biological replications were performed per cultivar, every ten of which were pooled to give one pooled sample. Mix is the mixture of JZY, JBT and CPL. Figure S2. HCA analysis of sweetcorn kernels from the three accessions. Figure S3. OPLS-DA analysis of sweetcorn kernels from the three accessions in pairs. (A), OPLS-DA model; (B), OPLS-DA scores plot, the three dots in each group are representative of the pooled samples performed for this study. In total, 30 biological replications were performed per cultivar, every ten of which were pooled to give one pooled sample; (C), OPLS-DA S-plot, red dots indicate the distinctive compounds (VIP≥1); (D), OPLS-DA permutation test (n=200), the horizontal lines indicate R2Y and Q2 in the original model, red dot and blue dot represent R2Y’ and Q2’ of the model after Y replacement, respectively. All R2Y’ dots are below the original R2Y line, and all Q2’ dots are below the original Q2 line, indicating the OPLS-DA model is validate and suitable. Figure S4. Mass spectrum of potential metabolite markers related to grain quality traits in sweet corn. (A), skimmin; (B), N’,N’’-diferuloylspermidine; (C), 3-hydroxyanthranilic acid. Table S1. The gradient program for HPLC analysis in various sweet corn kernels. Time Flow rate % A % B (min) (mL/min) 0.0 0.4 95 5 Gradient program 11.0 0.4 5 95 12.0 0.4 5 95 12.1 0.4 95 5 15.0 0.4 95 5 Table S2. A list of differential metabolites in kernels among the three sweet corn cultivars using UPLC-QTRAP-MS/MS (Q2 > 0.5 in PLS-DA plot). Molec JBT vs. JZY JBT vs. CPL JZY vs. CPL ular Rt Q1 Q3 Weigh Ionization Class (min) (Da) (Da) t (Da) model Compounds VIP a Log2FC b VIP Log2FC VIP Log2FC 0.76 204 102 205 [M-H]- Pantothenol 1.16 -0.71 1.31 -1.35 1.14 -0.64 0.77 151 71 152 [M-H]- D-Arabitol 0.4 0.23 1.23 1.14 1.12 0.91 Alcohols 4-(Aminomethyl)-5-(hydroxymethyl)-2- 0.77 169 134 168 [M+H]+ methylpyridin-3-ol 1.4 -0.59 1.42 -1.59 1.25 -1 0.79 138 94 137 [M+H]+ Trigonelline 1.52 -2.58 0.49 -0.247 1.37 2.33 2.68 219 146 218 [M+H]+ Abrine 1.05 -0.43 1.37 -1.04 1.32 -0.61 Protonate 2.73 250 147 250 d Coumaroyl choline 1.55 -2.66 1.09 -0.929 1.18 1.73 Protonate 3.08 310 251 310 d Sinapoylcholine 1.56 1.96 0.315 0.192 1.32 -1.77 Alkaloids 3.39 157 103 156 [M+H]+ 2,3'-Bipyridine 0.86 0.62 1.4 2.38 1.25 1.76 3.79 485 323 484 [M+H]+ N-hexosyl-p-coumaroyl serotonin 0.55 -0.24 1.48 -13.6 1.4 -13.36 3.84 219 174 218 [M+H]+ 5-Methoxy-N,N-dimethyltryptamine 1.12 -11.3 0.0434 -0.621 1.01 10.68 4.38 162 116 161 [M+H]+ Indole-3-carboxylic 1.49 2.13 1.42 2.5 0.63 0.37 4.50 164 149 165 [M-H]- Coixol 0.73 -0.83 1.12 -1.62 1.11 -0.78 6.09 327 171 350 [M]- Acid orange 20 1.2 0.75 0.869 -0.587 1.37 -1.34 0.73 175 116 174 [M+H]+ L-(+)-Arginine 0.74 -0.14 1.4 -1.92 1.32 -1.78 0.75 116 74 117 [M-H]- Guanidineacetic acid 1.05 -0.67 1.46 -2.03 1.14 -1.36 0.75 159 88 160 [M-H]- D-Alanyl-D-Alanine 0.85 -0.37 1.44 -1.52 1.23 -1.15 0.76 118 74 119 [M-H]- L-Threonine 0.84 0.48 1.36 1.09 1.08 0.61 0.76 147 84 146 [M+H]+ L-Glutamine 1.12 0.16 1.39 1.02 1.3 0.86 Amino acid 0.77 307 145 308 [M-H]- L-Glutamine O-hexside 0.84 -0.72 1.28 -1.52 0.99 -0.8 and 0.77 122 76 121 [M+H]+ L-Cysteine 0.74 0.2 1.24 1.22 1.13 1.01 derivatives 0.77 399 250 398 [M+H]+ S-(5'-Adenosyl)-L-methionine 1.12 -2.08 0.67 -0.712 0.47 1.37 0.78 147 84 146 [M+H]+ L-(+)-Lysine 1.13 0.17 1.44 1 1.37 0.83 0.78 131 114 132 [M-H]- L-Asparagine 1.39 -0.74 1.42 -1.62 1.29 -0.88 0.78 133 116 132 [M+H]+ L(+)-Ornithine 1.03 -0.82 1.27 -1.33 0.88 -0.51 0.78 88 71 89 [M-H]- L-Alanine 1.48 -0.39 1.44 -1.03 1.33 -0.64 0.79 174 131 175 [M-H]- L-Citrulline 0.89 -0.25 1.41 -1.11 1.19 -0.86 0.79 275 257 276 [M-H]- L-Saccharopine 1.5 0.86 1.45 3.07 1.35 2.21 2-Aminoadipic acid (L-Homoglutamic 0.80 162 98 161 [M+H]+ acid) 0.68 0.28 1.45 3.56 1.37 3.28 0.80 235 118 234 [M+H]+ Lysine butyrate 1.5 -1.9 1.27 -1.49 0.48 0.41 0.80 308 146 309 [M-H]- L-Glutamic acid O-glucoside 1.27 -1.4 0.64 0.339 1.28 1.73 0.84 112 95 111 [M+H]+ Histamine 0.53 -0.31 1.15 1.55 1.19 1.87 0.87 150 61 149 [M+H]+ DL-Methionine 1.56 0.88 1.17 -0.353 1.37 -1.23 0.73508 1.13523 0.52395 - 1.11 187 125 188 [M-H]- Nα-Acetyl-L-glutamine 9 -0.80328 5 -3.01054 1 2.20726 0.32101 1.31013 1.19861 1.31909 1.12174 1.13 251 84 250 [M+H]+ γ-Glu-Cys 6 0.076869 9 4 8 5 1.14 187 145 188 [M-H]- N6-Acetyl-L-lysine 1.47 -0.99 1.1 0.269 1.36 1.26 1.46395 1.39921 0.76400 - 1.14 217 158 216 [M+H]+ Nα-Acetyl-L-arginine 7 -0.9678 9 -1.17645 4 0.20866 1.15 150 61 149 [M+H]+ L-Methionine 1.37 0.67 1.26 -0.41 1.37 -1.08 1.16 308 233 307 [M+H]+ Glutathione reduced form 1 0.4 1.25 1.13 1.05 0.74 1.16 128 82 129 [M-H]- L-Pipecolic acid 0.82 -0.3 1.39 -1.05 1.23 -0.75 1.16 217 199 218 [M-H]- (5-L-Glutamyl)-L-amino acid 1.09 -1.44 0.824 -0.527 0.95 0.91 1.18 188 128 189 [M-H]- N-Acetyl-L-glutamic acid 0.22 0.06 1.39 -1.6 1.32 -1.66 1.26 132 86 131 [M+H]+ L-Isoleucine 1.02 -0.24 1.41 0.785 1.36 1.02 1.26 138 103 137 [M+H]+ L-Tyramine 1.31 -0.93 1.32 1.5 1.33 2.43 1.27 174 88 175 [M-H]- N-Acetylaspartate 0.69 -10.46 1.04 1.6 1.41 12.06 1.29 132 57 131 [M+H]+ N-Propionylglycine 1.09 -0.23 1.4 0.799 1.38 1.02 1.35 132 86 131 [M+H]+ alpha-Aminocaproic acid 1.01 -0.27 1.4 0.757 1.36 1.02 1.44 162 73 161 [M+H]+ S-Allyl-L-cysteine 0.8 2.96 1.1 -2.53 1.11 -5.49 (-)-3-(3,4-Dihydroxyphenyl)-2- 1.45 212 166 211 [M+H]+ methylalanine 0.8 0.32 1.05 -1.14 1.17 -1.47 3-(6-Hydroxy-3,4-dioxo-1,5- 1.50 210 135 211 [M-H]- cyclohexadien-1-yl)-L-alanine 1.19 -0.41 1.46 -1.24 1.27 -0.83 3-Hydroxy-3-methylpentane-1,5-dioic 1.59 161 99 162 [M-H]- acid 1.18 -0.59 1.15 0.623 1.36 1.21 1.91 216 170 215 [M+H]+ 3-Chloro-L-tyrosine 1.12 -14 0.457 -0.291 0.64 13.71 1.92 166 77 165 [M+H]+ D-(+)-Phenylalanine 1.12 -19.04 0.0141 0.0969 1.01 19.14 1.98 237 192 236 [M+H]+ N'-Formylkynurenine 1.12 -2.06 0.956 -0.756 0.06 1.31 2.57 145 101 146 [M-H]- 2,3-dimethylsuccinic acid 1.48 -1.78 1.42 -2.69 0.96 -0.91 2.61 224 136 223 [M+H]+ N-Acetyl-L-tyrosine 1.25 -1.18 1.32 -1.29 0.06 -0.12 3.51 172 130 173 [M-H]- N-Acetyl-l-leucine 1.4 0.78 1.46 2.16 1.33 1.38 3.62 313 166 312 [M+H]+ Phe-Phe 1.41 1.75 0.37 0.11 1.29 -1.64 3.84 206 147 207 [M-H]- N-Acetyl-L-phenylalanine 1.25 3.74 0.596 2.85 0.67 -0.88 4.07 245 88 246 [M-H]- N-(3-Indolylacetyl)-L-alanine 0.69 -9.93 1.05 1.72 1.41 11.65 7.49 302 109 301 [M+H]+ D-erythro-sphinganine 1.52 1.05 0.787 0.348 1.19 -0.7 0.76 649 145 650 [M-H]- D(+)-Melezitose O-rhamnoside 0.97 -0.43 1.33 -1.39 1.12 -0.96 Carbohydrates 1.07 289 97 290 [M-H]- D-Sedoheptuiose 7-phosphate 0.22 0.05 1.31 2.82 1.24 2.77 Hesperetin 7-O-neohesperidoside 4.07 609 301 610 [M-H]- (Neohesperidin) 1.44 2.35 0.291 -0.38 1.37 -2.73 4.08 609 301 610 [M-H]- Hesperetin 7-rutinoside (Hesperidin) 1.45 2.14 0.522 -0.451 1.31 -2.59 4.22 433 271 434 [M-H]- Naringenin 7-O-glucoside (Prunin) 1.53 18.46 - d - 1.37 -18.46 5.05 289 153 288 [M+H]+ Eriodictyol 0.28 -0.12 1.46 -12.5 1.4 -12.39 5.57 271 151 272 [M-H]- Naringenin chalcone 1.3 8.27 0.491 1.2 1.01 -7.07 5.59 271 151 272 [M-H]- Naringenin C 1.51 16.74 0.671 9.52 1.11 -7.23 5.59 271 151 272 [M-H]- Butin 1.3 7.98 0.0322 0.604 1.13 -7.38 5.66 271 151 272 [M-H]- 4',5,7-Trihydroxyflavanone 1.29 8.02 0.0373 0.705 1.11 -7.31 Flavonoids 5.75 301.1 164 302 [M-H]- Hesperetin 1.26 5.35 0.669 -7.71 1.37 -13.07 and 5.75 301.1 151 302 [M-H]- Homoeriodictyol 1.28 5.71 0.669 -7.2 1.37 -12.91 proanthocyani 2.63 487 163 488 [M-H]- Acacetin O-acetyl hexoside 1.47 1.09 1.27 0.582 1.05 -0.51 ns 2.78 627 465 626 [M+H]+ 8-C-hexosyl-hesperetin O-hexoside 0.86 0.19 1.42 1.18 1.33 0.98 Luteolin O-hexosyl-O-hexosyl-O- 2.83 771 609 772 [M-H]- hexoside 1.27 -1.51 0.174 0.0781 0.9 1.59 3.39 565 433 564 [M+H]+ C-hexosyl-apigenin C-pentoside 1.19 1.98 0.038 -0.14 1.17 -2.12 3.72 669 331 668 [M+H]+ Tricin 5-O-feruloylhexoside 1.46 2.03 0.872 -0.779 1.33 -2.81 3.77 565 499 564 [M+H]+ C-pentosyl-C-hexosyl-apigenin 1.14 1.92 0.519 -0.481 1.14 -2.4 3.78 433.1 283.1 432 [M+H]+ Apigenin C-glucoside 1.2 3.04 1.07 2.02 0.84 -1.02 3.78 433.1 283 432 [M+H]+ Isovitexin 0.59 2.53 1.07 1.87 0.47 -0.66 3.84 419 383 418 [M+H]+ O-methylnaringenin C-pentoside 1.24 -1.05 0.623 -0.313 0.67 0.74 3.87 609 463 608 [M+H]+ Chrysoeriol C-hexosyl-O-rhamnoside 1.24 4.33 1.09 -3.79 1.22 -8.11 3.89 463 313 462 [M+H]+ Chrysoeriol 8-C-hexoside 1.06 4.98 1.05 -11.2 1.39 -16.15 3.94 503 341 504 [M-H]- Chrysoeriol O-acetylhexoside 0.76 -0.53 1.08 -2.06 1.01 -1.53 4.00 491 329 492 [M-H]- Tricin 5-O-hexoside 0.7 0.53 0.786 1.64 1.28 1.11 4.07 637 329 638 [M-H]- Tricin 5-O-rutinoside 1.43 -1.36 0.931 0.691 1.32 2.05 1.30951 0.75397 0.75021 0.95440 - 4.11 527 331 526 [M+H]+ Tricin 5-O-β-guaiacylglycerol 5 1.621293 5 2 8 0.87108 4.30 491 315 492 [M-H]- Tricin 7-O-hexoside 0.97 0.86 1.48 -11.3 1.4 -12.19 4.56 579 331 578 [M+H]+ Tricin O-malonylhexoside 0.09 1.1 1.04 -9.87 1 -10.97 5.23 403 313 404 [M-H]- Tricin O-glycerol 0.49 -0.14 1.17 -3.32 1.09 -3.18 5.48 435 331 434 [M+H]+ Tricin O-phenylformic acid 1.1 10.57 1.04 11.6 0.08 1.08 5.73 329 314 330 [M-H]- Tricin 1.34 2.46 1.1 -2.18 1.32 -4.63 5.76 299 284 300 [M-H]- Chrysoeriol 1.05 10.9 0.99 10.87 6.00 523 329 524 [M-H]- Tricin O-eudesmic acid 1.19 1.69 1.12 -3.28 1.17 -4.97 3.34 563 353 596 [M-H]- Schaftoside 1.21 1.85 0.892 -0.79 1.22 -2.64 3.50 563 353 564 [M-H]- Vicenin-3 1.17 1.68 0.759 -0.676 1.2 -2.35 3.52 565 409 564 [M+H]+ Isoschaftoside 1.08 1.45 0.808 -0.719
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