Combined Application of Multi-omics Technologies in Plant Metabolic Pathway Resolution

doi:10.13560/j.cnki.biotech.bull.1985.2024-0814

Abstract

Abstract:

Multi-omics technology refers to a combination of two or more omics, such as genomics, transcriptomics, proteomics or metabolomics, etc. By analyzing batches of data from different biomolecular levels, it establishes the internal relations among biomolecules at different them. It is an effective tool for the systematic study of complex biological systems by an approach of the systematic study of biological samples. The metabolic pathways of plants are extremely complex, including the primary metabolic pathways that provide energy and nutrients for plant growth and the secondary metabolic pathways that produce a wide variety of small molecules. The relevant metabolites not only support plant growth and development but also play a pivotal role in the plant's responses to environmental stresses. For mankind, these metabolites serve as vital sources of food, energy and bio-materials. Moreover, numerous drug molecules or lead compounds with therapeutic effects discovered from plant metabolites have contributed greatly to human health. In recent years, because of the high-throughput and comprehensive detection advantages, technology of combined omics has been more and more widely used in plant metabolic pathway analysis and have yielded many excellent results due to the advantages of its high through-put and complete detection. From three aspects, namely, resistance to environmental stress, agronomic traits research, and natural product synthesis, this paper presents a classification and elaboration of related studies on plant metabolic pathway resolution using technology of combined application of omics. Finally, this paper discusses the current challenges and future potentials of this technology.

Key words: plant metabolic pathway analysis, omics analysis technology, combined multi-omics analysis

TANG You, ZHAO Jun-wei, SUN Lan-xi, LI Xiang. Combined Application of Multi-omics Technologies in Plant Metabolic Pathway Resolution[J]. Biotechnology Bulletin, 2025, 41(4): 76-87.

Figures/Tables 2

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组学方法 Research method based on omics	研究领域 Research area	研究对象 Research object	具体研究内容 Research content	参考文献Reference
基因组学 + 代谢组学 Genomics + metabolomics	植物农艺性状 Agronomic traits	番茄	现代商业番茄风味缺失的解析	［40］
转录组学 + 代谢组学 Transcriptomics + metabolomics	天然产物合成 Natural product synthesis	秋水仙、本氏烟草	秋水仙碱生物合成	［55］
		桃儿七、本氏烟草	鬼臼毒素生物合成	［21］
		水仙花青蒿青蒿青蒿山茱萸金线兰三叶崖爬藤枣叶白及烟草茶树苦荞麦板蓝根灵芝	石蒜科生物碱的生物合成途径解析青蒿毛状体发育和青蒿素生物合成调控青蒿腺毛状体的发育和角质层生物合成青蒿非腺毛细胞中的青蒿合成山茱萸主要活性物质的合成与积累金线兰中黄酮类化合物合成基因研究三叶崖爬藤不同生境下黄酮类化合物合成研究枣叶成熟过程黄酮类化合物积累机制研究高产和低产白及多糖和黄酮含量差异成因研究烟草吡啶生物碱相关合成基因研究茶叶茶多酚、茶氨酸和咖啡因合成基因研究苦荞麦黄酮类化合物生物合成及调控基因挖掘板蓝根木质素生物合成的合成特征和调控机制茉莉酸甲酯促进灵芝酸合成的分子机制	［56］［61］［71］［72］［73］［74］［75］［76］［63］［64］［65］［77］［78］［66］
	植物农艺性状 Agronomic traits	牡丹	牡丹花不同颜色（黄色和紫红色）形成与黄酮类物质含量及相关合成和调控基因互作关系研究	［43］
		石榴	突尼斯软籽石榴的风味相关基因和转录因子挖掘	［44］
		山茶	山茶花颜色改变与香气之间的关系及代谢分配研究	［45］
		猕猴桃	红肉猕猴桃果实成熟颜色转换相关结构基因和转录因子挖掘	［46］
		枇杷	野生到栽培枇杷果实色素演变的代谢背景和相关基因研究	［47］
		水稻	水稻生命周期不同组织样本中代谢物和基因表达共性分析及新转录因子鉴定	［48］
	植物抗环境胁迫（生物） Environmental stress resistance （biotic）	番茄、本氏烟草	番茄生产法卡林二醇所需的生物合成基因簇及其抗菌活性	［18］
	植物抗环境胁迫（非生物） Environmental stress resistance （abiotic）	当归肉苁蓉水稻天麻黄芪甘草	当归盐胁迫适应机制肉苁蓉适应碱地、草地和沙地等不同生境的机制探究亚洲栽培稻的耐寒适应性研究低温胁迫对天麻生长发育的影响研究黄芪的干旱胁迫适应性研究甘草适应紫外线-B照射研究	［31］［79］［32］［80］［34］［39］
转录组学 + 蛋白质组学 Transcriptomics + proteomics	植物农艺性状 Agronomic traits	粳稻	粳稻的休眠调控信号网络研究	［49］
	植物抗环境胁迫（非生物） Environmental stress resistance （abiotic）	高羊茅	高羊茅的低氮胁迫适应机制	［30］
	天然产物合成 Natural product synthesis	鹅掌草萱草叶小金梅草罂粟	鹅掌草三萜皂苷生物合成基因挖掘萱草叶小金梅草萜类化合物合成相关萜烯合酶研究罂粟中血根碱生物合成酶研究	［67］［81］［82］
转录组学 + 空间代谢组学 Transcriptomics + spatial metabolomics	天然产物合成 Natural product synthesis	丹参、大叶鼠尾草	二萜类化合物在丹参和大叶鼠尾草中生成和积累机制	［58］
转录组学 + 表型组学 Transcriptomics + phenomics	植物抗环境胁迫（非生物） Environmental stress resistance （abiotic）	当归	当归在紫外线-B辐射增强条件下的适应机制	［38］
代谢组学 + 表型组学 Metabolomics + phenomics	植物抗环境胁迫（非生物） Environmental stress resistance （abiotic）	黄芪	黄芪主要品种应对紫外线-B的策略研究	［37］
蛋白质组学 + 代谢组学 Proteomics + metabolomics	植物抗环境胁迫（非生物） Environmental stress resistance （abiotic）	苹果	不同海拔对苹果成熟代谢物-蛋白质网络的影响	［36］
比较基因组学 + 代谢组学 Comparative genomics + metabolomics	植物农艺性状 Agronomic traits	甜瓜、西瓜	甜瓜、西瓜中葫芦素合成途径解析	［42］
比较基因组学 + 转录组学 Comparative genomics + transcriptomics	植物抗环境胁迫（非生物） Environmental stress resistance （abiotic）	水稻水稻	水稻抗金属离子胁迫性状基因座研究水稻苗期耐不同金属离子的数量性状基因座研究	［28］［29］
转录组学 + 表观组学 Transcriptomics + epigenomics	植物抗环境胁迫（非生物） Environmental stress resistance （abiotic）植物抗环境胁迫 Environmental stress resistance	小麦玉米、小麦	DNA甲基化与小麦的金属胁迫耐受玉米、小麦组蛋白修饰在生物和非生物胁迫中的作用	［83］［84］
转录组学 + 蛋白质组学 + 代谢组学 Transcriptomics + proteomics + metabolomics	植物农艺性状 Agronomic traits	油茶	中国海南岛热带油茶种子成熟过程中主要代谢成分的合成与积累及基因共表达分析	［50］
		苹果	高氮施肥对苹果碳水化合物和黄酮类化合物的积累影响及成因研究	［52］
		荔枝	荔枝果肉在常温贮藏过程中的质量及代谢变化	［53］
基因组学 + 转录组学 + 代谢组学 Genomics + transcriptomics + metabolomics	植物农艺性状 Agronomic traits	黄瓜	黄瓜苦味驯化丢失过程的解析	［41］
		黄瓜	基于基因组变异图谱的黄瓜驯化和多样性遗传基础分析	［85］
		番茄	全球范围内育种如何改变番茄果实代谢物含量研究	［51］
	天然产物合成 Natural product synthesis	丹参	丹参酮14，16-醚（杂）环化形成D环机制	［57］
		罂粟	罂粟苄基异喹啉生物碱生物合成基因挖掘	［59］
		雷公藤	雷公藤甲素合成中间步骤研究	［62］
	植物抗环境胁迫（生物） Environmental stress resistance （biotic）	野生烟草	烟草植物对食草动物叶蝉的一条保守的非寄主抗性通路	［17］
		玉米	玉米抵抗蚜虫的候选基因挖掘	［22］
		番茄	番茄代谢物与果实成熟及病原体防御的关联研究	［23］
	植物抗环境胁迫（非生物） Environmental stress resistance （abiotic）	月腺大戟、狼毒大戟	不同纬度条件对月腺大戟或狼毒大戟两种同科植物的代谢影响	［33］
比较基因组学 + 转录组学 + 代谢组学 Comparative genomics + transcriptomics + metabolomics	天然产物合成 Natural product synthesis	铁皮石斛	铁皮石斛萜类合成酶基因及转录因子挖掘	［69］
	天然产物合成 Natural product synthesis	罂粟	罂粟苄基异喹啉生物碱生物合成途径及合成进化历史挖掘	［70］
比较基因组学 + 转录组学 + 表观组学 Comparative genomics + transcriptomics + epigenomics	天然产物合成 Natural product synthesis	桔梗	桔梗根中桔梗皂苷生物合成基因挖掘	［68］
表观组学 + 转录组学 + 代谢组学 Epigenomics + transcriptomics + metabolomics	植物抗环境胁迫（非生物） Environmental stress resistance （abiotic）	大麦	野生大麦对干燥和潮湿土壤环境的适应机理	［35］
基因组学 + 转录组学 + 泛转录组学 + 代谢组学 Genomics + transcriptomics + pan-transcriptomics + metabolomics	植物农艺性状 Agronomic traits	茶树	茶树风味相关代谢产物的调控网络及候选调控基因研究	［54］
微生物组学 + 转录组学 + 代谢组学 Microbiomics + transcriptomics + metabolomics	植物抗环境胁迫（生物） Environmental stress resistance （biotic）	柑橘金线兰	土壤环境和根瘤微生物对柑橘萜烯合成的影响金线兰根共生真菌对其黄酮类化合物合成的影响	［25］［27］

组学方法 Research method based on omics	研究领域 Research area	研究对象 Research object	具体研究内容 Research content	参考文献Reference
基因组学 + 代谢组学 Genomics + metabolomics	植物农艺性状 Agronomic traits	番茄	现代商业番茄风味缺失的解析	［40］
转录组学 + 代谢组学 Transcriptomics + metabolomics	天然产物合成 Natural product synthesis	秋水仙、本氏烟草	秋水仙碱生物合成	［55］
		桃儿七、本氏烟草	鬼臼毒素生物合成	［21］
		水仙花青蒿青蒿青蒿山茱萸金线兰三叶崖爬藤枣叶白及烟草茶树苦荞麦板蓝根灵芝	石蒜科生物碱的生物合成途径解析青蒿毛状体发育和青蒿素生物合成调控青蒿腺毛状体的发育和角质层生物合成青蒿非腺毛细胞中的青蒿合成山茱萸主要活性物质的合成与积累金线兰中黄酮类化合物合成基因研究三叶崖爬藤不同生境下黄酮类化合物合成研究枣叶成熟过程黄酮类化合物积累机制研究高产和低产白及多糖和黄酮含量差异成因研究烟草吡啶生物碱相关合成基因研究茶叶茶多酚、茶氨酸和咖啡因合成基因研究苦荞麦黄酮类化合物生物合成及调控基因挖掘板蓝根木质素生物合成的合成特征和调控机制茉莉酸甲酯促进灵芝酸合成的分子机制	［56］［61］［71］［72］［73］［74］［75］［76］［63］［64］［65］［77］［78］［66］
	植物农艺性状 Agronomic traits	牡丹	牡丹花不同颜色（黄色和紫红色）形成与黄酮类物质含量及相关合成和调控基因互作关系研究	［43］
		石榴	突尼斯软籽石榴的风味相关基因和转录因子挖掘	［44］
		山茶	山茶花颜色改变与香气之间的关系及代谢分配研究	［45］
		猕猴桃	红肉猕猴桃果实成熟颜色转换相关结构基因和转录因子挖掘	［46］
		枇杷	野生到栽培枇杷果实色素演变的代谢背景和相关基因研究	［47］
		水稻	水稻生命周期不同组织样本中代谢物和基因表达共性分析及新转录因子鉴定	［48］
	植物抗环境胁迫（生物） Environmental stress resistance （biotic）	番茄、本氏烟草	番茄生产法卡林二醇所需的生物合成基因簇及其抗菌活性	［18］
	植物抗环境胁迫（非生物） Environmental stress resistance （abiotic）	当归肉苁蓉水稻天麻黄芪甘草	当归盐胁迫适应机制肉苁蓉适应碱地、草地和沙地等不同生境的机制探究亚洲栽培稻的耐寒适应性研究低温胁迫对天麻生长发育的影响研究黄芪的干旱胁迫适应性研究甘草适应紫外线-B照射研究	［31］［79］［32］［80］［34］［39］
转录组学 + 蛋白质组学 Transcriptomics + proteomics	植物农艺性状 Agronomic traits	粳稻	粳稻的休眠调控信号网络研究	［49］
	植物抗环境胁迫（非生物） Environmental stress resistance （abiotic）	高羊茅	高羊茅的低氮胁迫适应机制	［30］
	天然产物合成 Natural product synthesis	鹅掌草萱草叶小金梅草罂粟	鹅掌草三萜皂苷生物合成基因挖掘萱草叶小金梅草萜类化合物合成相关萜烯合酶研究罂粟中血根碱生物合成酶研究	［67］［81］［82］
转录组学 + 空间代谢组学 Transcriptomics + spatial metabolomics	天然产物合成 Natural product synthesis	丹参、大叶鼠尾草	二萜类化合物在丹参和大叶鼠尾草中生成和积累机制	［58］
转录组学 + 表型组学 Transcriptomics + phenomics	植物抗环境胁迫（非生物） Environmental stress resistance （abiotic）	当归	当归在紫外线-B辐射增强条件下的适应机制	［38］
代谢组学 + 表型组学 Metabolomics + phenomics	植物抗环境胁迫（非生物） Environmental stress resistance （abiotic）	黄芪	黄芪主要品种应对紫外线-B的策略研究	［37］
蛋白质组学 + 代谢组学 Proteomics + metabolomics	植物抗环境胁迫（非生物） Environmental stress resistance （abiotic）	苹果	不同海拔对苹果成熟代谢物-蛋白质网络的影响	［36］
比较基因组学 + 代谢组学 Comparative genomics + metabolomics	植物农艺性状 Agronomic traits	甜瓜、西瓜	甜瓜、西瓜中葫芦素合成途径解析	［42］
比较基因组学 + 转录组学 Comparative genomics + transcriptomics	植物抗环境胁迫（非生物） Environmental stress resistance （abiotic）	水稻水稻	水稻抗金属离子胁迫性状基因座研究水稻苗期耐不同金属离子的数量性状基因座研究	［28］［29］
转录组学 + 表观组学 Transcriptomics + epigenomics	植物抗环境胁迫（非生物） Environmental stress resistance （abiotic）植物抗环境胁迫 Environmental stress resistance	小麦玉米、小麦	DNA甲基化与小麦的金属胁迫耐受玉米、小麦组蛋白修饰在生物和非生物胁迫中的作用	［83］［84］
转录组学 + 蛋白质组学 + 代谢组学 Transcriptomics + proteomics + metabolomics	植物农艺性状 Agronomic traits	油茶	中国海南岛热带油茶种子成熟过程中主要代谢成分的合成与积累及基因共表达分析	［50］
		苹果	高氮施肥对苹果碳水化合物和黄酮类化合物的积累影响及成因研究	［52］
		荔枝	荔枝果肉在常温贮藏过程中的质量及代谢变化	［53］
基因组学 + 转录组学 + 代谢组学 Genomics + transcriptomics + metabolomics	植物农艺性状 Agronomic traits	黄瓜	黄瓜苦味驯化丢失过程的解析	［41］
		黄瓜	基于基因组变异图谱的黄瓜驯化和多样性遗传基础分析	［85］
		番茄	全球范围内育种如何改变番茄果实代谢物含量研究	［51］
	天然产物合成 Natural product synthesis	丹参	丹参酮14，16-醚（杂）环化形成D环机制	［57］
		罂粟	罂粟苄基异喹啉生物碱生物合成基因挖掘	［59］
		雷公藤	雷公藤甲素合成中间步骤研究	［62］
	植物抗环境胁迫（生物） Environmental stress resistance （biotic）	野生烟草	烟草植物对食草动物叶蝉的一条保守的非寄主抗性通路	［17］
		玉米	玉米抵抗蚜虫的候选基因挖掘	［22］
		番茄	番茄代谢物与果实成熟及病原体防御的关联研究	［23］
	植物抗环境胁迫（非生物） Environmental stress resistance （abiotic）	月腺大戟、狼毒大戟	不同纬度条件对月腺大戟或狼毒大戟两种同科植物的代谢影响	［33］
比较基因组学 + 转录组学 + 代谢组学 Comparative genomics + transcriptomics + metabolomics	天然产物合成 Natural product synthesis	铁皮石斛	铁皮石斛萜类合成酶基因及转录因子挖掘	［69］
	天然产物合成 Natural product synthesis	罂粟	罂粟苄基异喹啉生物碱生物合成途径及合成进化历史挖掘	［70］
比较基因组学 + 转录组学 + 表观组学 Comparative genomics + transcriptomics + epigenomics	天然产物合成 Natural product synthesis	桔梗	桔梗根中桔梗皂苷生物合成基因挖掘	［68］
表观组学 + 转录组学 + 代谢组学 Epigenomics + transcriptomics + metabolomics	植物抗环境胁迫（非生物） Environmental stress resistance （abiotic）	大麦	野生大麦对干燥和潮湿土壤环境的适应机理	［35］
基因组学 + 转录组学 + 泛转录组学 + 代谢组学 Genomics + transcriptomics + pan-transcriptomics + metabolomics	植物农艺性状 Agronomic traits	茶树	茶树风味相关代谢产物的调控网络及候选调控基因研究	［54］
微生物组学 + 转录组学 + 代谢组学 Microbiomics + transcriptomics + metabolomics	植物抗环境胁迫（生物） Environmental stress resistance （biotic）	柑橘金线兰	土壤环境和根瘤微生物对柑橘萜烯合成的影响金线兰根共生真菌对其黄酮类化合物合成的影响	［25］［27］