代谢组学技术发展及其在农业动植物研究中的应用

doi:10.16288/j.yczz.19-287

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Hereditas(Beijing) ›› 2020, Vol. 42 ›› Issue (5): 452-465.doi: 10.16288/j.yczz.19-287

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Metabolomics technology and its applications in agricultural animal and plant research

Jing Tian^1,², Yuzhe Wang^1,^2,³(), Shixiong Yan⁴, Shuai Sun⁴, Junjing Jia⁴, Xiaoxiang Hu^1,²()

^1. State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing 100193, China
^2. College of Biological Sciences, China Agricultural University, Beijing 100193, China
^3. College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
^4. Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China

Received:2019-11-04 Revised:2020-03-13 Online:2020-05-20 Published:2020-04-01
Contact: Wang Yuzhe,Hu Xiaoxiang E-mail:yuzhe891@163.com;huxx@cau.edu.cn
Supported by:
Supported by the National Natural Science Foundation of China Nos(31902143);Supported by the National Natural Science Foundation of China Nos(31961133003);Supported by the National Natural Science Foundation of China Nos(U1702232)

Abstract

Abstract:

Metabolomics is a discipline that uses Chromatography-Mass Spectrometry and Nuclear Magnetic Resonance techniques to identify and quantify all small molecule metabolites in living organisms and biological samples, which relies on sensitive, stable analytical procedures and improving databases. Metabolomics has been widely used in medicine, food science, crop and farm animal research, and other fields. Metabolomics can establish a more direct relationship between changes in the type and content of metabolites and phenotypes. Metabolomics has gradually become a new research method for the analysis of genetic mechanisms of complex traits following genomics, transcriptomics, and proteomics with the advances in omics technology. In this review, we firstly introduce common analytical strategies, metabolomics platforms, and metabolomics databases. Then, we review the application of metabolomics in metabolic molecular identification of important economic traits in agricultural animals, disease diagnosis, meat quality and safety detection of animal products. We also introduce the latest achievements in the development, formation and analysis of important traits of animals and plants by using metabolomics, transcriptome, and genomics. Overall, the integrated analysis of metabolomics and other omics can comprehensively explain the genetic mechanism of all kinds of complex traits and help to improve the complete biological process of “mutation-gene-expression-metabolism-phenotype”. Metabolomics provides a new method for the mechanism analysis of complex characters and a novel idea for new agricultural breeding.

Key words: metabolomics, widely targeted metabolomics, metabolome detection platform, agricultural animal, multi-omics association analysis

Jing Tian, Yuzhe Wang, Shixiong Yan, Shuai Sun, Junjing Jia, Xiaoxiang Hu. Metabolomics technology and its applications in agricultural animal and plant research[J]. Hereditas(Beijing), 2020, 42(5): 452-465.

Figures/Tables 5

Fig. 1

Fig. 2

Table 1

Table 2

Characteristic of metabolomics databases"

数据库	优点	缺点	文献
HMDB	(1)公开数据库,免费公开下载; (2)检测定量代谢物18,557个; (3)包含MS/MS谱图22,247个(2265种化合物) GC-MS谱图74,189个(2544种化合物); (4)预测代谢物MS/MS谱图、GC-MS谱图	MS/MS检测中对前体离子大小有限制 (< 20 Da)	[31]
METLIN	(1)公开数据库; (2)包含超过13,000个标准品的高分辨质谱图; (3)不同碰撞能量下的高分辨的MS/MS谱图 >68,000个	(1)所有数据均采自于QTOF质谱; (2)数据不可以下载	[32,33]
NIST v17	(1)公开数据库; (2)包含267,376个化合物的EI 谱图; (3)包含13,808个化合物的574,826个MS/MS谱图	对外部数据来源标识不清	[34]
FiehnLib	(1)包含超过2200个EI谱图,覆盖超过1000种代谢物	(1)数据来源于Angilent公司气相色谱-单四级杆质谱和LECO公司GC-TOF; (2)数据主要来源于植物材料	[35]
LipidSearch	(1)包括超过150万个脂质离子及其预测离子碎片; (2)包括脂质加合离子和MSn信息	(1)商业数据库; (2)数据使用Thermo公司orbitrap类仪器采集; (3)MS/MS数据由计算机算法得到	[32]
LMSD	(1)包含43,402个脂质结构; (2)谱图数据可以下载	(1)在正负电离模式下预测MS/MS谱; (2)MS/MS光谱仅适用于每种脂质的一种加合物	[36]
MassBank	(1)公开数据库; (2)支持输入文本格式的质谱搜索; (3)所有质谱图均是由标准品得到的; (4)有19,000个MS₁和28,000个 MS₂及MSn谱图	(1)数据库中信息未经充分筛选; (2)某些谱图信息包含噪音信号	[37,38]
KEGG	(1)综合性数据库; (2)包含代谢通路和互作网络信息; (3)包含17,268种代谢物和460条通路	图片分辨率较低,不美观	[39]
Reactome	(1)公开数据库; (2)包含1419个化合物及人类2287条通路	数据来源较为单一,主要收集人体主要代谢通路信息	[40]
MetabolomeXchange	(1)公开数据库; (2)包含的数据来源于4个不同数据库; (3)包含代谢物结构及参考光谱、生物学作用、组织和浓度等信息	数据库建设完善难度大

Table 2

Table 3

Summary of the metabolome combined with multi-omics analysis in agricultural animal study"

物种	研究群体	样本类型	研究性状	代谢物分子	研究结论	文献
猪	白杜洛克猪×二花脸猪 (n=591)、苏太猪(n=282)	背最长肌腹部脂肪	脂肪酸组成	长链脂肪酸	腹部脂肪中C20:0与16号染色体中SNP显著关联;肌肉中C18:0与14号染色体中SNP显著关联;脂肪酸组成的候选基因：SCD和ELOVL7	[73]
	杜洛克猪×长白猪× 约克夏猪DLY(n=610)	背最长肌	酸肉	肌糖原、葡萄糖 (RG)和乳酸	PRKAG3基因中低频错义突变R200Q和PHKG1g.8283C> A引起猪RG含量显著升高,导致DLY猪酸肉性状	[74]
	未阉割公猪(n=1282)	颈下脂肪	公猪肉膻味	雄烯酮	SULT2A1、SULT2B1、HSD17B14和CYP2A19基因与公猪膻味性状有关	[75]
牛	挪威红牛(n=878)	牛乳	牛乳脂肪酸组成	短链、中长链和长链脂肪酸	在BTA1、BTA13和BTA15中检测到重要的与牛奶脂肪酸相关QTL,鉴定到脂肪酸从头合成重要候选基因NCOA6	[76]
	意大利西门塔尔牛(n=416) 意大利荷斯坦牛(n=436)	牛乳	牛乳脂肪酸组成	脂肪酸	在西门塔尔牛中鉴定到ECI2、PCYT2、DCXR、G6PC3、PYCR1和ALG12与牛乳脂肪酸组成相关基因;在荷斯坦牛中CYP17A1、ACO2、PI4K2A、GOT1、GPT、NT5C2、PDE6G、POLR3H和COX15与牛乳脂肪酸组成相关基因	[77]
	荷斯坦-弗里斯兰奶牛 (n=248)	牛乳	奶牛酮症预后研究	磷酸胆碱和甘油磷酸胆碱	位于25号染色体的APOBR基因中QTL与代谢物显著相关	[78]
	荷斯坦牛(n=1217)	血清	血清电解质 QTL鉴定	钙、氯、钠、钾和镁离子	GATA2、TMEM123和SCN5A基因与牛电解质平衡相关	[79]
	中国西门塔尔牛(n=723)	最长肌	脂肪酸组成	中链脂肪酸	FASN和ELOVL5基因组脂肪酸有关	[80]
	内洛尔肉牛(表型n=963; 基因型n=1616)	最长肌	脂肪酸含量	中链和长链脂肪酸	鉴定到与脂肪酸相关基因ELOVL5、ESSRG、PCYT1A、ABC5、ABC6和ABC10	[81]
	日本黑牛(n=574)	最长肌	牛肉鲜味	牛磺酸、肌苷和次黄嘌呤	鉴定到与牛磺酸相关基因SLC6A6、RAB7A、RPN1和CCDC12;与肌苷和次黄嘌呤相关基因NT5E	[82]
	日本黑牛(n=1836)	最长肌	氨基酸组成	β-丙氨酸和牛磺酸	鉴定到与氨基酸有关基因STT3B、SUV420H1、CPT1A、MRPL21和IGHMBP2	[83]
鸡	伊朗Urmia鸡×AA肉鸡 F₂群体(n=270)	血浆	代谢性状相关基因座鉴定	甘油三酯、胆固醇和葡糖糖	鉴定到与甘油三酯相关基因DOCK10和AP1S3	[84]

Table 3

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质谱名称	检测质量范围 (质荷比: m/z,单位: Da)	分辨率	优点	缺点
傅里叶变换离子回旋共振质谱 (Fourier transform Ion cyclotron resonance, FT-ICR MS)	100~10,000	100,000~1,000,000以上	分辨率和灵敏度最高	仪器体积大; 售价高; 维护费用昂贵; 扫描速度慢
静电场轨道阱质谱 (Orbitrap-MS)	LC-MS 50~6000 GC-MS 30~3000	140,000(在m/z =272时) 100,000(在m/z =272时)	分辨率和灵敏度仅次于FT-ICR; 价格比FT-ICR低	扫描速度慢; 不能单独做串极质谱
四级杆飞行时间质谱 (QTOF-MS)	LC-MS 20~4000 GC-MS 20~3000	最高可达40,000以上	提供高分辨谱图; 速度快; 适合复杂样品分析; 对更小分子量代谢物检测较好	分辨力和灵敏度不及 Orbitrap

Metabolomics technology and its applications in agricultural animal and plant research

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