Scientia Agricultura Sinica ›› 2023, Vol. 56 ›› Issue (7): 1359-1376.doi: 10.3864/j.issn.0578-1752.2023.07.013

• HORTICULTURE • Previous Articles     Next Articles

Identification and Comparative Analysis of Metabolites in Grape Seed Based on Widely Targeted Metabolomics

SHENG HongJie2(), LU SuWen1(), ZHENG XuanAng1, JIA HaiFeng1, FANG JingGui1   

  1. 1 College of Horticulture, Nanjing Agricultural University, Nanjing 210095
    2 Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing 210014
  • Received:2022-05-20 Accepted:2022-08-17 Online:2023-04-01 Published:2023-04-03


【Objective】 Grape seeds have high bioactivity because they are rich in many metabolites. The objective of this study was to comprehensively identify the metabolite components in grape seeds, to compare and to analyze the differences of metabolites among different varieties, and to explore the relationship between metabolites in grape seeds and skin color and variety origin, so as to provide a reference basis for further development and utilization of grape seeds. 【Method】 The mature seeds of purple-skinned Kyoho (V. labruscana: V. labrusca × V. vinifera, JFS), pink-skinned Wink (V. vinifera, WKS), and yellow-skinned Italia (V. vinifera, YDS) were used for widely targeted metabolomics analysis by UPLC-MS/MS. The metabolites were identified and compared by multivariate statistical methods. 【Result】 The quality of metabolomics data was good, and the data of samples within groups was repetitive and the differences in the data of samples among groups were existed. A total of 514 metabolites were identified in the seeds of three grape varieties, including 6 primary metabolites, such as amino acids and lipids, and 20 secondary metabolites, such as proanthocyanidins and resveratrol. Among different varieties, the metabolite components were similar but the metabolite contents were significantly different. The relative contents of most metabolites were high in the dark variety Kyoho, followed by the light variety Wink, but low in the colorless variety Italy, indicating that the metabolite contents in grape seeds might be positively correlated with the skin color. The relative contents of metabolites in the seeds of Wink and Italia were similar, while they were greatly different from those of Kyoho, indicating that the metabolite contents in grape seeds might be related to the variety origin. The differential metabolites among different varieties were mainly involved in phenylpropane biosynthesis, anthocyanin synthesis, lipid metabolism, etc. pathway. There were many phenolic compounds in the differential metabolites and the metabolites with the large difference were mainly flavonoids. Grape seeds were rich in phenols and lipids. In addition to monomeric flavane-3-ols and their polymers, the relative contents of other phenolic compounds such as flavones and flavonols were also high. There was no significant difference in the relative contents of resveratrol among the three varieties. The relative contents of glyceryl phosphatide such as lysophosphatidylcholine were high, while those of linolenic acid were low. There was little difference in the relative contents of lipids among different varieties. 【Conclusion】 The metabolite components in grape seeds of different varieties were similar, while the metabolite contents were related to the skin color and the variety origin. Phenols and lipids were important components of metabolites in grape seeds and could be used as good sources for food and other processing industries.

Key words: grape (Vitis vinifera), seed, metabolomics, metabolite, phenol, lipid

Fig. 1

Berries and seeds from Kyoho, Wink and Italia JFS: Kyoho; WKS: Wink; YDS: Italia. The white lines represent 1 cm. The same as below"

Fig. 2

Overlap diagrams pf total ion chromatogram detected by mass spectrometry of grape seed samples"

Fig. 3

Correlation analysis (A), hierarchical clustering analysis (B), PCA analysis (C), and OPLS-DA model (D) of metabolites in grape seeds"

Table 1

Classes and numbers of metabolites in grape seeds"

氨基酸 Amino acid 78 79 78 79
脂类 Lipid 65 64 65 65
有机酸Organic acid 55 55 51 58
核苷酸Nucleotide 57 57 58 58
糖类 Carbohydrate 16 19 18 19
醇类Alcohol 7 7 7 7
黄酮 Flavone 35 32 31 38
黄酮醇 Flavonol 29 26 28 30
黄烷酮 Flavanone 14 14 14 15
儿茶素Catechin 11 11 11 11
花青素 Anthocyanin 6 8 5 8
异黄酮 Isoflavone 5 5 5 6
原花青素 Proanthocyanidin 4 4 4 4
羟基肉桂酰 Hydroxycinnamoyl 21 22 22 23
苯甲酸 Benzoic acid 12 12 12 12
奎宁酸 Quinate 4 5 4 5
香豆素 Coumarin 3 4 4 4
维生素 Vitamin 13 13 13 13
酚胺 Phenolamide 11 12 12 12
吲哚 Indole 5 4 4 5
生物碱 Alkaloid 3 4 3 4
色胺 Tryptamine 3 4 4 4
胆碱 Choline 3 3 3 3
吡啶 Pyridine 2 2 2 2
烟酸 Nicotinic acid 3 3 3 3
萜类 Terpenoid 2 2 2 2
其他 Other 24 23 24 24
总计 Total 491 494 487 514

Fig. 4

Volcano plots of differential metabolites Each dot in the volcano plots represents a metabolite. The x-axis indicates log2 of estimated fold represent significantly up-regulated and down-regulated metabolites, respectively, while gray dots represent non-significantly accumulated metabolites"

Fig. 5

Hierarchical clustering analysis of differential metabolites The x-axis indicates samples and the y-axis indicates differential metabolites. Changes in metabolite concentration is indicated by color scales"

Fig. 6

Venn diagram of differential metabolites"

Table 2

The common differential metabolites in the three comparisons"

比较组 Comparison group
肌醇 Inositol 其他 Other 上调 Up 上调 Up 上调 Up
羟基金雀异黄素 2'-Hydroxygenistein 黄酮 Flavone 上调 Up 上调 Up 上调 Up
肌酸 Creatine 有机酸 Organic acid 上调 Up 上调 Up 上调 Up
紫丁香苷 Syringin 羟基肉桂酰 Hydroxycinnamoyl 上调 Up 下调 Down 上调 Up
N-芥子酰腐胺 N-Sinapoyl putrescine 酚胺 Phenolamide 上调 Up 下调 Down 上调 Up
对香豆酰五羟色胺己糖苷 N-hexosyl-p-coumaroyl serotonin 色胺 Tryptamine 上调 Up 下调 Down 上调 Up
3-Hydroxy-3-methylpentane-1,5-dioic acid
Amino acid
上调 Up 下调 Down 下调 Down
矢车菊素 3-O-葡萄糖苷 Cyanidin 3-O-glucoside 花青素 Anthocyanin 上调 Up 下调 Down 下调 Down
花青素苷 Cyanidin 3,5-O-diglucoside 花青素 Anthocyanin 上调 Up 下调 Down 下调 Down
迷迭香酸 Rosmarinic acid 有机酸 Organic acid 下调 Down 上调 Up 上调 Up
2'-脱氧鸟苷 Deoxyguanosine 核苷酸 Nucleotide 下调 Down 上调 Up 上调 Up
2-脱氧肌苷2'-Deoxyinosine 核苷酸 Nucleotide 下调 Down 上调 Up 上调 Up
2-脱氧腺苷 Deoxyadenosine 核苷酸 Nucleotide 下调 Down 上调 Up 上调 Up
毡毛美洲茶素 Velutin 黄酮 Flavone 下调 Down 上调 Up 下调 Down
麦黄酮 4'-O-丁香醇醚7-O-己糖苷
Tricin 4'-O-(syringyl alcohol) ether 7-O-hexoside
下调 Down 上调 Up 下调 Down
反式-4-羟基-3-甲氧基肉桂酸 Hydroxy-methoxycinnamate 羟基肉桂酰 Hydroxycinnamoyl 下调 Down 上调 Up 下调 Down
单酰甘油酯(酰基18:3)异构3 MAG (18:3) isomer3 脂质 Lipid 下调 Down 上调 Up 下调 Down
壬二酸 Azelaic Acid 有机酸 Organic acid 下调 Down 下调 Down 下调 Down
2-(甲酰氨基)苯甲酸 2-(Formylamino) benzoic acid 有机酸 Organic acid 下调 Down 下调 Down 下调 Down
DL-高半胱氨酸 DL-homocysteine 氨基酸 Amino acid 下调 Down 下调 Down 下调 Down
N-乙酰-L-谷氨酸 N-Acetyl-L-glutamic acid 氨基酸 Amino acid 下调 Down 下调 Down 下调 Down
蛋氨酸亚砜 Methionine sulfoxide 氨基酸 Amino acid 下调 Down 下调 Down 下调 Down
香兰素 Vanillin 苯甲酸 Benzoic acid 下调 Down 下调 Down 下调 Down
黄苷 Xanthosine 核苷酸 Nucleotide 下调 Down 下调 Down 下调 Down
杨梅苷 Myricetin 3-O-rhamnoside 黄酮醇 Flavonol 下调 Down 下调 Down 下调 Down
乔松素 Pinocembrin 黄烷酮 Flavanone 下调 Down 下调 Down 下调 Down
5-O-对香豆酰莽草酸 5-O-p-Coumaroyl shikimic acid 奎宁酸 Quinate 下调 Down 下调 Down 下调 Down
3,4-二甲氧基肉桂酸 3,4-Dimethoxycinnamic acid 羟基肉桂酰 Hydroxycinnamoyl 下调 Down 下调 Down 下调 Down
4-Methoxycinnamic acid
Hydroxycinnamoyl derivatives
下调 Down 下调 Down 下调 Down
阿魏酸 Ferulic acid 羟基肉桂酰 Hydroxycinnamoyl 下调 Down 下调 Down 下调 Down
松柏醛 Coniferylaldehyde 羟基肉桂酰 Hydroxycinnamoyl 下调 Down 下调 Down 下调 Down
松柏醇 Coniferyl alcohol 羟基肉桂酰 Hydroxycinnamoyl 下调 Down 下调 Down 下调 Down

Fig. 7

KEGG classifications of differential metabolites The x-axis represents the rich factor of differential metabolites and the y-axis indicates the KEGG pathways. Rich factor indicates the ratio of the number of enriched differential metabolites (sample number) to the number of the total metabolites (Background number) in the pathway. The number of enriched differential metabolites in each pathway is shown on the corresponding column"

Table 3

Categories and numbers of differential metabolites from grape seeds"

总数目 Total numbers 170 71 99 121 40 81 189 70 119
氨基酸 Amino acid 18 9 9 16 3 13 34 13 21
脂类 Lipid 18 7 11 9 1 8 27 6 21
有机酸 Organic acid 16 8 8 17 7 10 15 9 6
核苷酸 Nucleotide 17 5 12 16 8 8 16 8 8
糖类 Carbohydrate 6 5 1 3 1 2 3 2 1
醇类 Alcohol 3 2 1 1 1 0 2 2 0
黄酮 Flavone 18 4 14 13 7 6 15 2 13
黄酮醇 Flavonol 14 2 12 7 5 2 16 4 12
黄烷酮 Flavanone 2 1 1 6 1 5 5 1 4
儿茶素 Catechin 3 3 0 2 0 2 2 1 1
花青素 Anthocyanin 5 5 0 4 0 4 3 1 2
异黄酮 Isoflavone 4 2 2 2 2 0 4 3 1
原花青素 Proanthocyanidin 1 1 0 0 0 0 2 2 0
羟基肉桂酰 Hydroxycinnamoyl 14 2 12 9 1 8 13 2 11
苯甲酸 Benzoic acid 3 1 2 3 0 3 3 1 2
奎宁酸 Quinate 2 1 1 1 0 1 3 2 1
香豆素 Coumarin 0 0 0 0 0 0 0 0 0
维生素 Vitamin 2 1 1 3 1 2 4 2 2
酚胺 Phenolamide 7 4 3 4 1 3 4 3 1
吲哚 Indole 1 0 1 0 0 0 1 0 1
生物碱 Alkaloid 1 1 0 1 0 1 0 0 0
色胺 Tryptamine 2 1 1 2 0 2 3 1 2
胆碱 Choline 0 0 0 0 0 0 0 0 0
吡啶 Pyridine 0 0 0 0 0 0 0 0 0
烟酸 Nicotinic acid 1 0 1 0 0 0 2 0 2
萜类 Terpenoid 2 0 2 0 0 0 2 0 2
其他 Other 10 6 4 2 1 1 10 5 5

Fig. 8

The most significant different metabolite multiples of grape seeds of three comparison groups"

Fig. 9

The heatmap showing the Log2 Fold change of differential metabolites in three comparisons Changes in metabolite concentration is indicated by color scales"

Table 4

Important polyphenols in grape seeds"

葡萄种子 Grape seed 比较组 Comparison group
花青素 Anthocyanin
矢车菊素 3-O-葡萄糖苷 Cyanidin 3-O-glucoside 7.86E+06 3.66E+07 1.91E+06 2.22 -4.26 -2.04
矢车菊素 3-O-芸香糖苷 Cyanidin 3-O-rutinoside 2.27E+06 5.78E+06 3.68E+06 1.35
天竺葵素-3-O-葡萄糖苷 Pelargonidin 3-O-glucoside 9.00E+00 1.09E+07 9.00E+00 20.21 -20.21
花青素苷 Cyanidin 3,5-O-diglucoside 4.78E+05 1.63E+06 9.00E+00 1.77 -17.47 -15.70
芍药花青素O-己糖苷 Peonidin O-hexoside 1.98E+05 1.64E+06 9.00E+00 -17.48
天竺葵色素苷 Pelargonin 9.00E+00 7.50E+05 7.63E+05 16.35 16.37
儿茶素 Catechin
原儿茶醛 Protocatechuic aldehyde 1.51E+07 1.48E+07 1.12E+07
三儿茶素 Catechin-catechin-catechin 1.33E+07 9.29E+06 5.89E+06
原儿茶酸 Protocatechuic acid 8.58E+06 4.22E+06 5.53E+06
原花青素 Proanthocyanidin
原花青素B2 Procyanidin B2 1.47E+07 1.80E+07 1.70E+07
原花青素A2 Procyanidin A2 1.07E+07 7.82E+06 1.21E+07
原花青素A3 Procyanidin A3 9.21E+06 2.73E+07 2.37E+07 1.57 1.37
黄酮 Flavone
木犀草苷 Luteolin 7-O-glucoside 4.98E+07 8.40E+07 8.14E+07
紫铆素 Butin 5.04E+06 6.04E+06 3.32E+06
葡萄种子 Grape seed 比较组 Comparison group
圣草酚 C-己糖 Eriodictyol C-hexoside 3.80E+07 4.05E+07 5.22E+07
金圣草黄素 7-O-芸香糖苷 Chrysoeriol 7-O-rutinoside 2.38E+05 7.82E+04 9.00E+00 -13.08 -14.69
麦黄酮 7-O-己糖苷 Tricin 7-O-hexoside 1.47E+05 8.46E+04 9.00E+00 -13.20 -14.00
麦黄酮 5-O-己糖苷 Tricin 5-O-hexoside 1.40E+05 9.00E+00 2.76E+04 -13.93
菠叶素 Spinacetin 8.48E+04 9.00E+00 9.00E+00 -13.20 -13.20
麦黄酮 7-O-己糖基-O-己糖苷 Tricin 7-O-hexosyl-O-hexoside 9.00E+00 1.55E+05 2.70E+04 14.07
麦黄酮 4'-O-丁香醇醚 7-O-己糖苷
Tricin 4'-O-(syringyl alcohol) ether 7-O-hexoside
1.25E+05 9.00E+00 1.21E+04 -13.76 10.39 -3.37
6-C-己糖苷-芹菜素 O-阿魏酰己糖苷 6-C-hexosyl-apigenin O-feruloylhexoside 1.34E+06 9.00E+00 9.00E+00 -17.19 -17.19
氧甲基柚皮素 C-戊糖苷 O-methylnaringenin C-pentoside 2.35E+05 9.00E+00 9.00E+00 -14.67 -14.67
异黄酮 Isoflavone
染料木苷 Genistein 7-O-Glucoside 1.61E+06 2.71E+06 3.31E+06 1.04
黄酮醇 Flavonol
三叶豆甙 Kaempferol 3-O-galactoside 4.13E+07 7.39E+07 6.62E+07
黄颜木素 Fustin 1.02E+07 1.22E+07 2.09E+07 1.03
绣线菊甙 Quercetin 4'-O-glucoside 8.10E+06 1.46E+07 1.56E+07
异鼠李素-3-O-新橙皮糖苷 Isorhamnetin 3-O-neohesperidoside 8.53E+05 9.00E+00 9.67E+04 -16.53
3,7-二-O-甲基槲皮素 3,7-Di-O-methylquercetin 4.01E+04 9.00E+00 6.98E+04 -12.12 12.92
黄烷酮 Flavanone
橙皮素 5-O-葡萄糖苷 Hesperetin 5-O-glucoside 8.39E+06 1.55E+07 1.66E+07
柚皮素 Naringenin 5.20E+06 6.70E+06 3.76E+06
柚皮苷查尔酮 Naringenin chalcone 4.98E+06 5.16E+06 2.76E+06
新橙皮苷 Hesperetin 7-O-neohesperidoside 2.77E+05 1.20E+05 9.00E+00 -13.70
7-氧甲基圣草酚 7-O-Methyleriodictyol 9.00E+00 9.00E+00 1.89E+04 11.04 11.04
苯甲酸 Benzoic acid
2,5-二羟基苯甲酸 O-己糖苷
2,5-dihydroxy benzoic acid O-hexside
2.92E+07 3.39E+07 5.05E+07
对-氨基苯甲酸 p-Aminobenzoate 1.71E+07 9.05E+06 8.87E+06
没食子酸甲酯 Methyl gallate 6.47E+06 7.47E+06 1.36E+07 1.07
奎宁酸 Quinate
奎宁酸 Quinic acid 1.67E+06 1.56E+06 9.13E+05
5-O-对香豆酰莽草酸 5-O-p-Coumaroyl shikimic acid 1.27E+05 4.34E+04 9.00E+00 -12.24 -13.78
O-阿魏酰奎尼酸 O-Feruloyl quinic acid 9.00E+00 2.08E+04 5.65E+04 12.62
羟基肉桂酰 Hydroxycinnamoyl
松柏醛 Coniferylaldehyde 1.93E+07 1.08E+06 2.31E+05 -4.16 -2.23 -6.39
松脂醇 Pinoresinol 1.21E+07 3.84E+05 4.33E+05 -4.97 -4.80
高香草酸 Homovanillic acid 5.95E+06 1.10E+06 1.18E+06 -2.44 -2.34
芥子酸吡喃葡萄糖苷 1-O-beta-D-Glucopyranosyl sinapate 9.00E+00 3.54E+04 3.63E+04 11.94 11.98
白藜芦醇 Resveratrol 8.71E+05 6.19E+05 5.17E+05

Table 5

Important lipids in grape seeds"

葡萄种子 Grape seed 比较组 Comparison group
脂质-甘油磷脂 Lipids-Glycerophospholipids
溶血磷脂酰胆碱 16:0 LysoPC 16:0 2.57E+08 1.98E+08 1.61E+08
溶血磷脂酰胆碱 16:0 LysoPC 16:0 2.46E+08 1.88E+08 1.51E+08
溶血磷脂酰胆碱 18:1 LysoPC 18:1 7.60E+07 1.17E+08 1.14E+08
脂质-甘油酯 Lipids-Glycerolipids
单酰甘油酯 (酰基 18:3) MAG (18:3) 2.19E+06 9.92E+05 8.17E+05 -1.14 -1.42
单酰甘油酯单糖 (18:2) MGMG (18:2) 7.71E+05 3.62E+05 3.84E+05 -1.09 -1.01
单酰甘油酯二糖 (18:2) DGMG (18:2) 7.52E+05 2.67E+05 2.64E+05 -1.49 -1.51
脂质-脂肪酸 Lipids-Fatty acids
十八碳-三烯酸 Octadeca-trienoic acid 6.76E+07 3.64E+07 3.28E+07 -1.05
4-羟基鞘氨醇 4-Hydroxysphinganine 2.71E+07 7.94E+06 6.55E+06 -1.77 -2.05
石榴酸 Punicic acid 1.27E+07 1.77E+07 6.12E+06 -1.53
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