Advances in the Elucidation of Metabolic Pathways and Molecular Breeding for Tomato Flavor

doi:10.13560/j.cnki.biotech.bull.1985.2025-1358

Abstract

Abstract:

As one of the most widely consumed fruits and vegetables worldwide, tomato flavor quality directly influences consumer experience and market value. With the rising of income per capita and the upgrading of consumption patterns in China, market demand for high-quality tomatoes has become increasingly urgent. However, the complexity of the genetic regulation of flavor traits, together with limitations in detection technologies and the long-standing emphasis of traditional breeding on agronomic traits such as yield, disease resistance, storage and transport tolerance, has led to a general decline in tomato fruit flavor quality, making it difficult to meet consumer expectations. Therefore, an in-depth understanding of the biosynthetic mechanisms of flavor metabolites and their genetic regulatory networks is critical for the precise improvement of tomato flavor. This review systematically summarizes recent cutting-edge advances, both domestically and internationally, in the biosynthetic and metabolic pathways of tomato flavor compounds and their underlying genetic regulatory mechanisms. It focuses on a multi-omics integration framework for the genetic improvement technology system of tomato flavor. By comprehensively collecting multidimensional omics data—including phenomics, metabolomics, transcriptomics, and genomics—from diverse tomato germplasm resources, and integrating machine learning and bioinformatics approaches, key functional genes and regulatory loci controlling flavor formation can be precisely identified. These discoveries, when combined with modern molecular breeding technologies, enable the efficient and targeted development of new tomato varieties with superior flavor. Furthermore, this review examines major technological bottlenecks in tomato flavor breeding, including the establishment of standardized quantitative evaluation systems for flavor components, the elucidation of genetic regulatory mechanisms underlying flavor traits, and the synergistic improvement of trade-off traits (e.g., flavor vs. yield and resistance). It also proposes targeted future research directions and strategies aimed at promoting a transition in tomato flavor breeding from a traditional producer-oriented paradigm to a consumer-oriented approach. Collectively, this framework provides theoretical foundations and technical pathways for the precise genetic improvement of flavor traits in tomatoes and other crops, thereby supporting the high-quality development of China's agricultural and seed industries.

Key words: tomato, flavor, multi-omics, genetic mechanisms, metabolic pathways, molecular breeding, artificial intelligence, sensory evaluation

JIANG Zhe-hui, WANG Xiao-long, WANG Shou-chuang, ZHOU Ke. Advances in the Elucidation of Metabolic Pathways and Molecular Breeding for Tomato Flavor[J]. Biotechnology Bulletin, 2026, 42(3): 60-78.

Figures/Tables 5

References 145

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物质类别 Primary pathway	代谢物 Metabolites	相关基因 Related genes	风味贡献Attributes	参考文献 Reference
糖类 Sugars	果糖、葡萄糖 Fructose， glucose	Lin5， STP11，SWEET， SlNAP2， SlFgr， SlGLK2， SlVPE5	Positive	［27， 80-83］
有机酸 Organic acids	苹果酸 Malic acid	SlME， SlTDT， SlALMT9， SlMIR164A	Positive	［39， 45， 84-85］
有机酸 Organic acids	柠檬酸 Citric acid	SlCS， SlAco， SlPEPCK	Positive	［39， 44， 86］
生物碱类 Alkaloids	甾体糖苷生物碱 Steroidal alkaloids	GAME1， GAME2， GAME5-9， GAME11， GAME12 GAME17， GAME18， GAME25， GAME31	Negative	［87］
氨基酸类 Amino Acids	脯氨酸 Proline	SlP5CS1， SlP5CR	Positive	［88］
氨基酸类 Amino Acids	天冬酰胺、γ-氨基丁酸 Asparagine， GABA	GDSL esterase/lipase	Unknown	［89］
	谷氨酰胺、苏氨酸 Glutamine， threonine		Unknown
醛类 Aldehydes	反式-2-己烯醛 Trans-2-Hexenal	LeHPL	Positive	［90］
	苯乙醛 Phenylacetaldehyde	LeAADCIA， LeAADCIB， LeAADC2	Positive	［91］
	苯甲醛 Benzaldehyde		Positive
	反式-2-庚烯醛 Trans-2-Heptenal		Unknown
	己醛 Hexanal	TomloxC	Unknown	［60］
	庚醛 Heptaldehyde		Unknown
	壬醛 Nonylaldehyde		Negative
	反式-2-戊烯醛 Trans-2-Pentenal	SlscADH1	Unknown	［92］
	顺式柠檬醛 Neral		Unknown
	香叶醛 Geranial	SlADH2	Unknown	［93］
	水杨醛 Salicylaldehyde		Negative
	β-环柠檬醛 β-Cyclocitral	LeCCD4	Unknown	［94］
含氮硫类挥发性代谢物 Nitrogen- and sulfur-containing volatile metabolites	2-异丁基噻唑 2-Isobutylthiazole	SlTNH1	Positive	［95-96］
	3-甲基丁醛肟 3-methylbutyraldehyde oxime		Negative	［95-96］
	苯乙腈 Benzylcyanide		Positive
	3-甲基丁腈 3-methylbutanenitrile		Negative	［95-96］
醇类 Alcohols	2-苯乙醇 2-Phenylethanol	LeAADCIA， LeAADC1B， LeAADC2， PPEAT， FLORAL4	Positive	［97］
	1-戊烯-3-醇 1-Penten-3-ol		Unknown
	3-甲基丁醇 3-Methylbutanol		Unknown
	1-辛烯-3-醇 1-Octen-3-ol	SlFAD7	Negative	［98］
	反式-3-己烯-1-醇 Trans-3-hexen-1-ol	SlADH1	Unknown	［99］
	1-戊醇 1-Pentanol	SlFAD7， Sl-LIP8	Unknown	［100］
	反式-2-己烯-1-醇 E-2-hexen-1-ol		Positive
	己醇 Hexylalcohol	Sl-LIP8	Unknown	［101］
	顺式-3-己烯-1-醇 Z-3-hexen-1-ol	ADH2	Unknown	［101］
	芳樟醇 Linalool	TPS3， TPS5， TPS20， TPS37， TPS39， SlMYB75	Unknown	［102-103］
	橙花叔醇 Nerolidol		Unknown	［102-103］
	2-甲基-1-丁醇 2-Methyl-1-butanol	BCKDC， SlBCAT1， SlBCAT2， AAT1	Unknown	［104］
	3-甲基-1-丁醇 3-Methyl-1-butanol		Positive
酚类 Phenols	丁香酚 Eugenol		Negative
酚类 Phenols	愈创木酚 Guaiacol	E8	Unknown	［105］
酯类 Esters	水杨酸甲酯 Methyl salicylate	SlSAMT	Negative	［106］
	顺式-3-己烯基乙酸酯 cis-3-hexenylacetate		Unknown
	乙酸己酯 Hexylacetate		Unknown
酮类 Ketones	1-戊烯-3-酮 1-Penten-3-one		Unknown
	香叶基丙酮、β-紫罗兰酮 Geranylacetone， β-Ionone	LeCCD1A， LeCCD1B	Positive	［107］
	6-甲基-5-庚烯-2-酮 6-Methyl-5-hepten-2-one		Positive
烷类Alkanes	1-硝基-2-苯乙烷 1-nitro-2-Phenylethane	SlTNH1	Positive	［95-96］
	1-硝基-3-甲基丁烷 1-nitro-3-methylbutane	SlTNH1	Negative	［95-96］

物质类别 Primary pathway	代谢物 Metabolites	相关基因 Related genes	风味贡献Attributes	参考文献 Reference
糖类 Sugars	果糖、葡萄糖 Fructose， glucose	Lin5， STP11，SWEET， SlNAP2， SlFgr， SlGLK2， SlVPE5	Positive	［27， 80-83］
有机酸 Organic acids	苹果酸 Malic acid	SlME， SlTDT， SlALMT9， SlMIR164A	Positive	［39， 45， 84-85］
有机酸 Organic acids	柠檬酸 Citric acid	SlCS， SlAco， SlPEPCK	Positive	［39， 44， 86］
生物碱类 Alkaloids	甾体糖苷生物碱 Steroidal alkaloids	GAME1， GAME2， GAME5-9， GAME11， GAME12 GAME17， GAME18， GAME25， GAME31	Negative	［87］
氨基酸类 Amino Acids	脯氨酸 Proline	SlP5CS1， SlP5CR	Positive	［88］
氨基酸类 Amino Acids	天冬酰胺、γ-氨基丁酸 Asparagine， GABA	GDSL esterase/lipase	Unknown	［89］
	谷氨酰胺、苏氨酸 Glutamine， threonine		Unknown
醛类 Aldehydes	反式-2-己烯醛 Trans-2-Hexenal	LeHPL	Positive	［90］
	苯乙醛 Phenylacetaldehyde	LeAADCIA， LeAADCIB， LeAADC2	Positive	［91］
	苯甲醛 Benzaldehyde		Positive
	反式-2-庚烯醛 Trans-2-Heptenal		Unknown
	己醛 Hexanal	TomloxC	Unknown	［60］
	庚醛 Heptaldehyde		Unknown
	壬醛 Nonylaldehyde		Negative
	反式-2-戊烯醛 Trans-2-Pentenal	SlscADH1	Unknown	［92］
	顺式柠檬醛 Neral		Unknown
	香叶醛 Geranial	SlADH2	Unknown	［93］
	水杨醛 Salicylaldehyde		Negative
	β-环柠檬醛 β-Cyclocitral	LeCCD4	Unknown	［94］
含氮硫类挥发性代谢物 Nitrogen- and sulfur-containing volatile metabolites	2-异丁基噻唑 2-Isobutylthiazole	SlTNH1	Positive	［95-96］
	3-甲基丁醛肟 3-methylbutyraldehyde oxime		Negative	［95-96］
	苯乙腈 Benzylcyanide		Positive
	3-甲基丁腈 3-methylbutanenitrile		Negative	［95-96］
醇类 Alcohols	2-苯乙醇 2-Phenylethanol	LeAADCIA， LeAADC1B， LeAADC2， PPEAT， FLORAL4	Positive	［97］
	1-戊烯-3-醇 1-Penten-3-ol		Unknown
	3-甲基丁醇 3-Methylbutanol		Unknown
	1-辛烯-3-醇 1-Octen-3-ol	SlFAD7	Negative	［98］
	反式-3-己烯-1-醇 Trans-3-hexen-1-ol	SlADH1	Unknown	［99］
	1-戊醇 1-Pentanol	SlFAD7， Sl-LIP8	Unknown	［100］
	反式-2-己烯-1-醇 E-2-hexen-1-ol		Positive
	己醇 Hexylalcohol	Sl-LIP8	Unknown	［101］
	顺式-3-己烯-1-醇 Z-3-hexen-1-ol	ADH2	Unknown	［101］
	芳樟醇 Linalool	TPS3， TPS5， TPS20， TPS37， TPS39， SlMYB75	Unknown	［102-103］
	橙花叔醇 Nerolidol		Unknown	［102-103］
	2-甲基-1-丁醇 2-Methyl-1-butanol	BCKDC， SlBCAT1， SlBCAT2， AAT1	Unknown	［104］
	3-甲基-1-丁醇 3-Methyl-1-butanol		Positive
酚类 Phenols	丁香酚 Eugenol		Negative
酚类 Phenols	愈创木酚 Guaiacol	E8	Unknown	［105］
酯类 Esters	水杨酸甲酯 Methyl salicylate	SlSAMT	Negative	［106］
	顺式-3-己烯基乙酸酯 cis-3-hexenylacetate		Unknown
	乙酸己酯 Hexylacetate		Unknown
酮类 Ketones	1-戊烯-3-酮 1-Penten-3-one		Unknown
	香叶基丙酮、β-紫罗兰酮 Geranylacetone， β-Ionone	LeCCD1A， LeCCD1B	Positive	［107］
	6-甲基-5-庚烯-2-酮 6-Methyl-5-hepten-2-one		Positive
烷类Alkanes	1-硝基-2-苯乙烷 1-nitro-2-Phenylethane	SlTNH1	Positive	［95-96］
	1-硝基-3-甲基丁烷 1-nitro-3-methylbutane	SlTNH1	Negative	［95-96］