From Wild to Cultivated： Evolution and Regulatory Mechanisms of Tomato Fruit Color

doi:10.13560/j.cnki.biotech.bull.1985.2025-1227

Abstract

Abstract:

During the evolution and domestication from wild relatives to cultivated varieties, the fruits of tomato (Solanum lycopersicum) have gradually developed diverse coloration patterns. The color characteristics of wild tomato fruits (such as green or yellow) are the outcomes of long-term adaptive evolution, endowing the plants with critical ecological adaptability. In contrast, the rich color variations in cultivated tomatoes are mainly shaped by human selection preferences during artificial domestication. This paper systematically summarizes and clarifies the genetic regulatory mechanisms underlying tomato fruit color formation, with a key focus on the regulatory networks of core genes involved in three major metabolic pathways: carotenoid, chlorophyll, and anthocyanin biosynthesis. It further elaborates the interactive effects of natural and artificial selection in driving the diversification of fruit color traits. Currently, a relatively comprehensive and systematic understanding of the mechanisms governing tomato fruit color formation has been established. The major genes controlling the main fruit color phenotypes of tomato, including red, yellow, pink, green, and purple, have been largely identified. Relevant studies are gradually expanding from the functional analysis of individual structural genes to the systematic dissection of complex regulatory networks involving ripening-related regulatory factors (such as RIN and NOR) and transcription factors from the MYB and bHLH families. The integration of multi-omics technologies has further elucidated the multi-layered dynamic regulatory mechanisms underlying fruit color formation. The rapid development of modern breeding technologies, especially the application of gene editing tools, has further expanded the range of fruit color variations. In addition, growing attention is being paid to the coordinated regulation between color formation and other key quality traits (e.g., sugar content, acidity, and aroma), indicating that fruit color is not merely a visual characteristic but also an important indicator of comprehensive fruit quality. Future research should advance from multiple dimensions, including molecular regulation, multi-trait coupling, and breeding translation, to construct a full-chain research system spanning from basic theoretical mechanisms to breeding applications.

Key words: tomato, fruit color, carotenoids, chlorophylls, anthocyanins, metabolic pathways, gene editing

LIU Miao, LIN Tao, JIA Le-song, HU Feng, LI Tao, LI Zhi-wan, LIU Mei-fang, ZHENG Fang-yan, CUI Long. From Wild to Cultivated： Evolution and Regulatory Mechanisms of Tomato Fruit Color[J]. Biotechnology Bulletin, 2026, 42(3): 187-202.

Figures/Tables 8

References 102

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物种名称 Species name	果实直径 Fruit diameter （cm）	心室数 Number of locules	成熟时果皮颜色 Skin color when ripe	条纹（纵贯） Stripes （vertical）
S. habrochaites	1‒1.5	2	均匀淡紫色	深绿色
S. pennellii	1‒1.3	2	均匀绿色	无
S. chmielewskii	1‒1.3	2	绿色	深绿色
S. neorickii	1‒1.3	2	绿色	深绿色
S. arcanum	1‒1.4	2	绿色	深绿色变紫色
S. chilense	1‒1.5	2‒5	绿白色	紫色
S. peruvianum	1‒1.5	2	白紫色/紫色	绿色或紫色
S. huaylasense	1‒1.4	2	绿色	深绿色或紫色
S. corneliomulleri	0.9‒1.3	2	绿色/绿白色	深绿色或紫色
S. cheesmaniae	0.6‒1.4	2	黄色/橙色	无
S. galapagense	0.6‒1.1	2	橙色	无
S. pimpinellifolium	≈1	2	鲜红色	无
S. lycopersicum	1.5‒10+	通常≥2	通常红色	通常无

物种名称 Species name	果实直径 Fruit diameter （cm）	心室数 Number of locules	成熟时果皮颜色 Skin color when ripe	条纹（纵贯） Stripes （vertical）
S. habrochaites	1‒1.5	2	均匀淡紫色	深绿色
S. pennellii	1‒1.3	2	均匀绿色	无
S. chmielewskii	1‒1.3	2	绿色	深绿色
S. neorickii	1‒1.3	2	绿色	深绿色
S. arcanum	1‒1.4	2	绿色	深绿色变紫色
S. chilense	1‒1.5	2‒5	绿白色	紫色
S. peruvianum	1‒1.5	2	白紫色/紫色	绿色或紫色
S. huaylasense	1‒1.4	2	绿色	深绿色或紫色
S. corneliomulleri	0.9‒1.3	2	绿色/绿白色	深绿色或紫色
S. cheesmaniae	0.6‒1.4	2	黄色/橙色	无
S. galapagense	0.6‒1.1	2	橙色	无
S. pimpinellifolium	≈1	2	鲜红色	无
S. lycopersicum	1.5‒10+	通常≥2	通常红色	通常无

基因 Gene	作用机制与功能 Mechanisms of action and functions	导致的表型 Resulting phenotype	参考文献 Reference
NOR	NAC家族转录因子，促进类胡萝卜素积累，调控乙烯合成	突变后果实不成熟，呈橙色	［28-30］
CNR	SBP-box转录因子，调控成熟启动，影响类胡萝卜素积累	突变后果实不成熟，颜色为黄色或绿色	［28-30］
RIN	MADS-box转录因子，正向调控成熟过程，促进乙烯合成和类胡萝卜素积累	突变后果实不成熟，颜色为黄色或绿色	［28-30］
SlAP2a	果实成熟的负调控因子，影响类胡萝卜素合成	果实呈橙色，果肉颜色变浅	［31］
TAGL1	表达下调，促进叶绿素合成和叶绿体发育，同时抑制类胡萝卜素积累	未成熟果实出现绿色条纹，成熟后为黄色条纹	［32］
SlMYB72	R2R3-MYB转录因子，负调控叶绿素合成，正调控类胡萝卜素和类黄酮代谢	下调表达导致果实出现深绿色斑点（绿果期）和黄斑（红果期）	［33］
HY5	光信号通路转录因子，促进类胡萝卜素和花青素积累	突变后果实颜色变浅，呈浅红色	［34］
SlIDI1/YFT3	在质体MEP途径中催化IPP和DMAPP的可逆异构化，为类胡萝卜素合成提供必需的前体底物。类异戊二烯代谢通路中的关键酶	功能丧失突变导致酶失活，DMAPP前体严重匮乏，番茄红素合成几乎完全阻断，果实呈黄色。过表达则提供更充足前体，果实红色加深	［35］
SlMCT	MEP途径中的关键酶，萜类化合物生物合成的第2步。该基因突变导致酶功能异常，影响下游类胡萝卜素和激素合成	类胡萝卜素和叶绿素含量显著降低，果实变黄	［36］
PSY1	类胡萝卜素合成的限速酶，催化番茄红素合成第一步	敲除果实呈黄绿色	［37］
PDS	类胡萝卜素生物合成中的一种关键酶，可将植物烯转化为ζ-胡萝卜素	PDS沉默的果实出现黄色表型	［38］
ZDS	在类胡萝卜素合成途径中，负责将ζ-胡萝卜素转化为链孢红素，是生成番茄红素的关键步骤之一	ZDS功能缺失导致果实呈黄色/橙色	［39］
CRTISO	催化胡萝卜素去饱和过程中的顺反异构化，合成全反式番茄红素和下游环化类胡萝卜素（如β-胡萝卜素、叶黄素）的关键酶	突变果实呈橙色	［40］
CYC-B	编码番茄红素β-环化酶，将番茄红素转化为β-胡萝卜素	功能获得突变使β-胡萝卜素大增，果肉呈橙色	［41］
og/og^c	beta基因的无效等位基因。发生移码突变，无法产生有功能的番茄红素β-环化酶	果实呈深红色	［41］
SlCCD4b	催化类胡萝卜素在C9-C10位点裂解，生成挥发性芳香物质；负调控番茄果实中β-胡萝卜素和番茄红素的积累	过表达导致果实呈深橙色	［42］
ClpR1	敲低ClpR1会削弱Clp蛋白酶活性，导致蛋白质降解受阻，引发蛋白质折叠应激；进而上调ClpB3和OR/OR-like等分子伴侣基因表达，促进DXS和PSY酶稳定性，增加β-胡萝卜素积累，同时抑制番茄红素积累	沉默导致成熟果实呈橙色	［43］
Delta	催化番茄红素生成δ-胡萝卜素	突变体成熟果实为橙色	［44］
WRKY32	RNAi生成品系的番茄果实中，乙烯信号传导减少，导致乙烯释放受到抑制，染色体发育延迟，类胡萝卜素积累减少	果实表型呈黄色	［45］
YFT1	调控乙烯合成、信号转导、质体发育和类胡萝卜素积累	突变体果实呈黄色	［46］
SNAC9	正向调控番茄果实成熟过程中的类胡萝卜素代谢	敲除后果实成熟延迟，果实颜色变浅	［47］
SlNAP7	影响番茄叶绿体发育和番茄红素积累	沉默使得果皮和果肉呈现黄色	［48］
DXS1	催化MEP途径第一步，合成质体类异戊二烯的关键限速酶	绿熟期果实呈白色，红熟期颜色变浅	［49］
CRY1a	促进果实中类胡萝卜素的积累	过表达果实颜色加深，红熟期呈深红色；敲除果实颜色变浅	［50］
GH	质体末端氧化酶，参与类胡萝卜素合成	突变体果实为橙黄色	［51］
hp-3	催化玉米黄质向紫黄质的转化，影响类胡萝卜素（尤其是番茄红素）的合成与储存能力	果实颜色加深（红色增强）	［52］
SlBEL11	作为转录抑制因子，直接结合下游基因番茄红素β-环化酶2的启动子，抑制其转录	沉默时果实成熟时呈黄色	［53］
SlCHRC	色粒体相关类胡萝卜素结合蛋白（CHRC）调节色粒体发育和类胡萝卜素积累	敲除导致果实成熟延迟，类胡萝卜素含量降低，果实表型更绿	［54］
SlDML2	DNA去甲基化酶，影响类胡萝卜素（如β-胡萝卜素和番茄红素）积累	突变体果实保持绿色	［55］
SlBBX20 （Solyc01g110180）	促进类胡萝卜素合成	过表达使未成熟果实呈深绿色，成熟果实颜色加深	［56］
SlCMB1	MADS-box转录因子，正调控果实成熟；促进乙烯合成和类胡萝卜素积累；与RIN、TAGL1等蛋白互作	抑制后果实成熟延迟，颜色变浅，呈浅橙或橙色	［57］

基因 Gene	作用机制与功能 Mechanisms of action and functions	导致的表型 Resulting phenotype	参考文献 Reference
NOR	NAC家族转录因子，促进类胡萝卜素积累，调控乙烯合成	突变后果实不成熟，呈橙色	［28-30］
CNR	SBP-box转录因子，调控成熟启动，影响类胡萝卜素积累	突变后果实不成熟，颜色为黄色或绿色	［28-30］
RIN	MADS-box转录因子，正向调控成熟过程，促进乙烯合成和类胡萝卜素积累	突变后果实不成熟，颜色为黄色或绿色	［28-30］
SlAP2a	果实成熟的负调控因子，影响类胡萝卜素合成	果实呈橙色，果肉颜色变浅	［31］
TAGL1	表达下调，促进叶绿素合成和叶绿体发育，同时抑制类胡萝卜素积累	未成熟果实出现绿色条纹，成熟后为黄色条纹	［32］
SlMYB72	R2R3-MYB转录因子，负调控叶绿素合成，正调控类胡萝卜素和类黄酮代谢	下调表达导致果实出现深绿色斑点（绿果期）和黄斑（红果期）	［33］
HY5	光信号通路转录因子，促进类胡萝卜素和花青素积累	突变后果实颜色变浅，呈浅红色	［34］
SlIDI1/YFT3	在质体MEP途径中催化IPP和DMAPP的可逆异构化，为类胡萝卜素合成提供必需的前体底物。类异戊二烯代谢通路中的关键酶	功能丧失突变导致酶失活，DMAPP前体严重匮乏，番茄红素合成几乎完全阻断，果实呈黄色。过表达则提供更充足前体，果实红色加深	［35］
SlMCT	MEP途径中的关键酶，萜类化合物生物合成的第2步。该基因突变导致酶功能异常，影响下游类胡萝卜素和激素合成	类胡萝卜素和叶绿素含量显著降低，果实变黄	［36］
PSY1	类胡萝卜素合成的限速酶，催化番茄红素合成第一步	敲除果实呈黄绿色	［37］
PDS	类胡萝卜素生物合成中的一种关键酶，可将植物烯转化为ζ-胡萝卜素	PDS沉默的果实出现黄色表型	［38］
ZDS	在类胡萝卜素合成途径中，负责将ζ-胡萝卜素转化为链孢红素，是生成番茄红素的关键步骤之一	ZDS功能缺失导致果实呈黄色/橙色	［39］
CRTISO	催化胡萝卜素去饱和过程中的顺反异构化，合成全反式番茄红素和下游环化类胡萝卜素（如β-胡萝卜素、叶黄素）的关键酶	突变果实呈橙色	［40］
CYC-B	编码番茄红素β-环化酶，将番茄红素转化为β-胡萝卜素	功能获得突变使β-胡萝卜素大增，果肉呈橙色	［41］
og/og^c	beta基因的无效等位基因。发生移码突变，无法产生有功能的番茄红素β-环化酶	果实呈深红色	［41］
SlCCD4b	催化类胡萝卜素在C9-C10位点裂解，生成挥发性芳香物质；负调控番茄果实中β-胡萝卜素和番茄红素的积累	过表达导致果实呈深橙色	［42］
ClpR1	敲低ClpR1会削弱Clp蛋白酶活性，导致蛋白质降解受阻，引发蛋白质折叠应激；进而上调ClpB3和OR/OR-like等分子伴侣基因表达，促进DXS和PSY酶稳定性，增加β-胡萝卜素积累，同时抑制番茄红素积累	沉默导致成熟果实呈橙色	［43］
Delta	催化番茄红素生成δ-胡萝卜素	突变体成熟果实为橙色	［44］
WRKY32	RNAi生成品系的番茄果实中，乙烯信号传导减少，导致乙烯释放受到抑制，染色体发育延迟，类胡萝卜素积累减少	果实表型呈黄色	［45］
YFT1	调控乙烯合成、信号转导、质体发育和类胡萝卜素积累	突变体果实呈黄色	［46］
SNAC9	正向调控番茄果实成熟过程中的类胡萝卜素代谢	敲除后果实成熟延迟，果实颜色变浅	［47］
SlNAP7	影响番茄叶绿体发育和番茄红素积累	沉默使得果皮和果肉呈现黄色	［48］
DXS1	催化MEP途径第一步，合成质体类异戊二烯的关键限速酶	绿熟期果实呈白色，红熟期颜色变浅	［49］
CRY1a	促进果实中类胡萝卜素的积累	过表达果实颜色加深，红熟期呈深红色；敲除果实颜色变浅	［50］
GH	质体末端氧化酶，参与类胡萝卜素合成	突变体果实为橙黄色	［51］
hp-3	催化玉米黄质向紫黄质的转化，影响类胡萝卜素（尤其是番茄红素）的合成与储存能力	果实颜色加深（红色增强）	［52］
SlBEL11	作为转录抑制因子，直接结合下游基因番茄红素β-环化酶2的启动子，抑制其转录	沉默时果实成熟时呈黄色	［53］
SlCHRC	色粒体相关类胡萝卜素结合蛋白（CHRC）调节色粒体发育和类胡萝卜素积累	敲除导致果实成熟延迟，类胡萝卜素含量降低，果实表型更绿	［54］
SlDML2	DNA去甲基化酶，影响类胡萝卜素（如β-胡萝卜素和番茄红素）积累	突变体果实保持绿色	［55］
SlBBX20 （Solyc01g110180）	促进类胡萝卜素合成	过表达使未成熟果实呈深绿色，成熟果实颜色加深	［56］
SlCMB1	MADS-box转录因子，正调控果实成熟；促进乙烯合成和类胡萝卜素积累；与RIN、TAGL1等蛋白互作	抑制后果实成熟延迟，颜色变浅，呈浅橙或橙色	［57］

基因 Gene	作用机制与功能 Mechanisms of action and functions	导致的表型 Resulting phenotype	参考文献 Reference
SlSGR1	促进果实成熟过程中叶绿素的降解	突变后果实保持绿色，成熟后呈褐色	［37］
SlGLK2	调控叶绿体发育，影响叶绿素分布	过表达果实肩部持续深绿色，形成“内绿果”；功能缺失导致果实肩部绿色变浅	［65］
SlBEL2	负调控叶绿体发育和叶绿素合成，影响果实绿色肩部形成	过表达果肩绿色消失，果实整体呈浅绿色；敲除SlBEL2果肩绿色加深	［66］
SlZHD17	影响番茄果实叶绿体的发育，促进了叶绿素的积累	下调导致未成熟和绿熟阶段果实更绿，成熟时期明显色素沉着不均匀	［67］
SlARF10	正向调控一些叶绿素合成相关基因表达，促进叶绿体发育和光合作用	过表达后果实在绿熟期呈深绿色；RNAi敲低后果实在绿熟期呈浅绿色	［68］
SlBL4	负调控叶绿素合成与叶绿体发育；抑制细胞壁代谢相关基因	下调后果实颜色略深绿，成熟后果实着色不均，不完全变红	［69］
SlBEL11	负调控叶绿素合成与叶绿体发育	沉默后未熟果实叶绿素显著积累，果色深绿；成熟延迟，出现斑驳绿粉相间表型	［70］
SlAPRR2-LIKE	调控质体数目与面积，影响叶绿素与类胡萝卜素积累	过表达增加质体数与色素含量，果色深绿	［70］
TKN2	Class I KNOX转录因子；正调控叶绿体发育	功能获得性突变体果实叶绿素含量增加，果色深绿且均匀	［71］
TKN4	Class I KNOX转录因子；正调控叶绿体发育梯度	功能缺失突变体（ug）果实肩部绿色缺失，成熟后果实颜色更均匀	［71］
HP1	负调控光形态建成；突变导致叶绿体和质体区室增大	突变体叶绿素和类胡萝卜素含量增加，果色更深	［71-72］
DR12/SlARF4	属于ARF转录因子家族，参与生长素响应；抑制其表达导致叶绿素含量增加、叶绿体数量增多、果实成熟不均匀	未熟果实呈深绿色；成熟果实呈斑驳状	［73］
SlGRAS9	负调控叶绿素积累和叶绿体发育	敲除或敲低后果实呈深绿色	［74］
SlELP2L	功能缺失会导致番茄果实叶绿素降解受阻	基因沉默（RNAi）后，番茄果实在未成熟阶段呈现深绿色	［75］
TDET1/HP-2	负调控光形态建成和光信号传导；影响绿体和花青素积累	突变导致未成熟果实深绿色	［76］
SlDXR	MEP途径限速酶，调控类胡萝卜素、叶绿素、类黄酮合成；影响叶绿体发育	突变体果实呈橙黄色，果肉为黄/白色	［77］
SlMYB72	R2R3-MYB转录因子，负调控叶绿素合成，正调控类胡萝卜素和类黄酮代谢	下调表达导致果实出现深绿色斑点（绿果期）和黄斑（红果期）	［33］
su	调控质体分裂；突变导致叶片和绿色果实中质体数量减少、体积增大（巨型叶绿体）	su-1/su-3突变体的未成熟果实呈浅绿色	［78］
SlKN5	与BLH1-clade蛋白形成复合物，抑制叶绿体生物发生、叶绿素合成和赤霉素降解相关基因的表达；在果实发育早期抑制叶绿素积累	敲除导致未成熟果实颜色更深绿	［79］