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Mining plant metabolomes:Methods,applications,and perspectives

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Plant Communications 2021年第5期2卷 92-105页

作者： Aimin Ma xiaoquan qi Key Laboratory of Plant Molecular Physiology Institute of BotanyChinese Academy of SciencesBeijing 100093China Innovation Academy for Seed Design Chinese Academy of SciencesBeijing 100049China

Plants produce a variety of metabolites that are essential for plant growth and human *** fully understand the diversity of metabolites in certain plants,lots of methods have been developed for metabolites detection and data *** the data-processing procedure,how to effectively reduce false-positive peaks,analyze large-scale metabolic data,and annotate plant metabolites remains *** this review,we introduce and discuss some prominent methods that could be exploited to solve these problems,including a five-step filtering method for reducing false-positive signals in LC-MS analysis,QPMASS for analyzing ultra-large GC-MS data,and MetDNA for annotating *** main applications of plant metabolomics in species discrimination,metabolic pathway dissection,population genetic studies,and some other aspects are also *** further promote the development of plant metabolomics,more effective and integrated methods/platforms for metabolite detection and comprehensive databases for metabolite identification are highly *** the improvement of these technologies and the development of genomics and transcriptomics,plant metabolomics will be widely used in many fields.

关键词： plant metabolomics metabolites data-processing methods application

Plant metabolomics and metabolic biology

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Journal of Integrative Plant Biology 2014年第9期56卷 814-815页

作者： xiaoquan qi Dabing Zhang Institute of Botany the Chinese Academy of Sciences Shanghai Jiaotong University

Plants produce a large array of specialized metabolites（natural products）that not only are essential for growth and development,but also play important roles in adaptation to the variable stressful ***,many plant metabolites are essential nutrient elements for humans and serve as natural ***,study of the biosynthesis of natural products is still in its infancy,because more than 90%of plant metabolites are unknown and only a small number of genes/ enzymes involved in metabolism are identified in the model plants Arabidopsis and rice.

关键词： specialized nutrient adaptation biosynthesis environments genomics mutant anthocyanin biologic transcripts

The global integrative network:integration of signaling and metabolic pathways

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aBIOTECH 2022年第4期3卷 281-291页

作者： Yuying Lin Shen Yan Xiao Chang xiaoquan qi Xu Chi Department of Dermatology Xuan Wu HospitalBeijing100053China Agricultural Information Institute Chinese Academy of Agricultural ScienceBeijing100081China Key Laboratory of Plant Molecular Physiology Institute of BotanyChinese Academy of SciencesBeijing100093China The Innovative Academy of Seed Design Chinese Academy of SciencesBeijing100101China CAS Key Laboratory of Genomic and Precision Medicine Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing100101China

The crosstalk between signaling and metabolic pathways has been known to play key roles in human diseases and plant biological *** integration of signaling and metabolic pathways can provide an essential reference framework for crosstalk ***,current databases use distinct structures to present signaling and metabolic pathways,which leads to the chaos in the integrated ***,for the metabolic pathways,the metabolic enzymes and the reactions are disconnected by the current widely accepted layout of edges and nodes,which hinders the topological analysis of the integrated ***,we propose a novel“meta-pathway”structure,which uses the uniformed structure to display the signaling and metabolic pathways,and resolves the difficulty in linking the metabolic enzymes to the reactions *** compiled a comprehensive collection of global integrative networks(GINs)by merging the meta-pathways of 7077 *** demonstrated the assembly of the signaling and metabolic pathways using the GINs of four species—human,mouse,Arabidopsis,and *** all of the nodes were assembled into one major network for each of the four species,which provided opportunities for robust crosstalk and topological analysis,and knowledge graph construction.

关键词： Signaling pathways Metabolic pathways Integration Crosstalk of pathways

Identification and Validation of a Major Quantitative Trait Locus for Slow-rusting Resistance to Stripe Rust in Wheat

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Journal of Integrative Plant Biology 2012年第5期54卷 330-344页

作者： Xiaohua Cao Jianghong Zhou Xiaoping Gong Guangyao Zhao Jizeng Jia xiaoquan qi Key Laboratory of Plant Molecular Physiology Institute of BotanyChinese Academy of SciencesBeijing 100093China Graduate University of Chinese Academy of Sciences Beijing 100049China Institute of Crop Sciences Chinese Academy of Agricultural SciencesBeijing 100081China These authors contributed equally to this article.

Stripe （yellow） rust, caused by Puccinia striiformis Westend. f. sp. tritici Eriks （Pst）, is one of the most important wheat （Triticum aestivum L.） diseases and causes significant yield losses. A recombinant inbred （RI） population derived from a cross between Yanzhan 1 and Xichang 76-9 cultivars was evaluated for resistance to wheat stripe rust strain CYR32 at both the seedling and adult plant stages. Four resistance quantitative trait loci （QTLs） were detected in this population, in which the major one, designated as Yrql, was mapped on chromosome 2DS. The strategy of using the Brachypodium distachyon genome, wheat expressed sequence tags and a draft DNA sequences （scaffolds） of the D-genome （Aegilops tauschfi Coss.） for the development of simple sequence repeat （SSR） markers was successfully used to identify 147 SSRs in hexaploid wheat. Of the 19 polymorphic SSRs in the RI population, 17 SSRs were mapped in the homeologous group 2 chromosomes near Yrql region and eight SSRs were genetically mapped in the 2.7 cM region of Yrql, providing abundant DNA markers for fine-mapping of Yrql and marker-assisted selection in wheat breeding program. The effectiveness of Yrql was validated in an independent population, indicating that this resistance QTL can be successfully transferred into a susceptible cultivar for improvement of stripe rust resistance.

关键词： Quantitative trait locus slow-rusting stripe rust wheat.

Discrimination and Quantification of True Biological Signals in Metabolomics Analysis Based on Liquid Chromatography-Mass Spectrometry

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Molecular Plant 2016年第8期9卷 1217-1220页

作者： Duan, Lixin Molnar, Istvan Snyder, John Hugh Shen, Guo-an qi, xiaoquan Chinese Acad Sci Inst Bot Key Lab Plant Mol Physiol 20 NanxincunXiangshan Rd Beijing 100093 Peoples R China Univ Arizona Nat Prod Ctr Sch Nat Resources & Environm 250 East Valencia Rd Tucson AZ 85706 USA

Dear Editor Metabolomics is a rapidly emerging field of post-genomic research that aims to comprehensively analyze all metabolites in biological samples. Potential biomarkers that distinguish prostate cancer samples were successfully identified through metabolomics analysis （Sreekumar et al., 2009）. Metabolome quantitative trait loci （mQTL） and genome-wide association studies coupled with metabolomics analysis （mGWAS） also became efficient tools to decipher the genetic basis of complex metabolic traits in large populations （Gong et al., 2013; Chen et al., 2014）.

关键词： Metabolomics comprehensively successfully

Identification and fine mapping of quantitative trait loci for seed vigor in germination and seedling establishment in rice

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Journal of Integrative Plant Biology 2014年第8期56卷 749-759页

作者： Lixia Xie Zhengwei Tan Yuan Zhou Rongbao Xu Laibao Feng Yongzhong Xing xiaoquan qi Key Laboratory of Plant Molecular Physiology Institute of Botany the Chinese Academy of Sciences University of Chinese Academy of Sciences Department of Continuing Education Shandong Television University National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural University

Seed vigor is an index of seed quality that is used to describe the rapid and uniform germination and the establish- ment of strong seedlings in any environmental conditions. Strong seed vigor in low-temperature germination conditions is particularly important in direct-sowing rice production systems. However, seed vigor has not been selected as an important breeding trait in traditional breeding programs due to its quantitative inherence. In this study, we identified and mapped eight quantitative trait loci （QTLs） for seed vigor by using a recombinant inbred population from a cross between rice （Oryza sativa L. ssp. indica） cultivars ZS97 and MH63. Conditional QTL analysis identified qSV-1, qSV-Sb, qSV-6a, qSV- 6b, and qSV-11 influenced seedling establishment and that qSV- 5a, qSV-Sc, and qSV-8 influenced only germination. Of these, qSV-1, qSV-Sb, qSV-6a, qSV-6b, and qSV-8 were low-tempera- ture-specific QTLs. Two major-effective QTLs, qSV-1, and qSV-5cwere narrowed down to 1.13-Mbp and 4oo-kbp genomic regions, respectively. The results provide tightly linked DNA markers for the marker-assistant pyramiding of multiple positive alleles for increased low-temperature germination seed vigor in both normal and environments.

关键词： Conditional quantitative trait locus mapping germination seedling establishment seed vigor rice

Functional Analysis of a Rice Oxidosqualene Cyclase through Total Gene Synthesis

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Molecular Plant 2013年第5期6卷 1726-1729页

作者： Juncong Sun Xia Xu Zheyong Xue John Hugh Snyder xiaoquan qi Key Laboratory of Plant Molecular Physiology Institute of Botany Chinese Academy of Sciences Nanxincun 20 Fragrant Hill. Beijing 100093 China Graduate University of Chinese Academy of Sciences Yuquan Road 19 Beijing 100049 China

Dear Editor, Plants produce a large range of triterpenoids that serve as chemical defenses against pathogens. For example, β-amyrin synthase （AsbAS1） performs the initial enzymatic step in the biosynthesis of the potent antimicrobial avencins in oats （Haralampidis et al., 2001）. Additionally, other triterpenoids such as glycyrrhizin and QS21 are known to have beneficial or detrimental effects for human health （Osbourn et al., 2011）. For some time, heterologous expression of plant oxidos- qualene cyclases （OSCs） in yeast has been a powerful meth- odology for the functional characterization of this important family of triterpene biosynthetic enzymes.

关键词： Saccharomyces cerevisiae lanosterol-deficient plant OSC

Biosynthesis and functions of metabolites

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Science China(Life Sciences) 2017年第11期60卷 1280-1282页

作者： juncong sun bing leng guoan sheng xin fang laigeng li jirong huang xiaoquan qi xiaoya chen institute of botany chinese academy of sciences Beijing 100093China chinese society for plant biology Shanghai 200031China institute of plant phystology and ecology shanghai institutes for biological scienceschinese academy of sciencesShanghai 200032China college of life and environmental sciences shanghai normal universityShanghai 200234China

Metabolism is the basic activity of life. Two in- ternational conferences, including the 4th Interna- tional Conference on Plant Metabolism （ICPM2017, http：//***/2017/***）, and the 13th International Meeting on Biosynthesis, Function and Synthetic Biology of Isoprenoids （TERPNET2017,http：//***/2017/***） were concurrently convened side by side in Dalian from July 16 to 20, 2017.

关键词： Biosynthesis functions of metabolites

Functional diversity and metabolic engineering of plantspecialized metabolites

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Life Metabolism 2022年第2期1卷 109-121页

作者： Shaoqun Zhou Yongshuo Ma Yi Shang xiaoquan qi Sanwen Huang Jiayang Li Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenGuangdong 518120China Department of Chemical Engineering Massachusetts Institute of TechnologyCambridgeMA 02142USA Yunnan Key Laboratory of Potato Biology The CAAS-YNNU-YINMORE Joint Academy of Potato SciencesYunnan Normal UniversityKunmingYunan 650500China Key Laboratory of Plant Molecular Physiology Institute of BotanyChinese Academy of SciencesBeijing 100093China State Key Laboratory of Plant Genomics National Center for Plant Gene ResearchInstitute of Genetics and Developmental BiologyInnovation Academy for Seed DesignChinese Academy of SciencesBeijing 100101China

Plants are talented biochemists that produce a broad diversity of small *** so-called specialized metabolites(SMs)play critical roles in the adaptive evolution of plants to defend against biotic and abiotic stresses,attract pollinators,and modulate soil microbiota for their own *** plant SMs have been used as nutrition and flavor compounds in our daily food,as well as drugs for treatment of human *** multi-omics tools have significantly accelerated the process of biosynthetic pathway elucidation in plants through correlation analyses,genetic mapping,and de novo biosynthetic gene cluster *** the biosynthesis of plant SMs has enabled reconstitution of naturally occurring specialized metabolic pathways in microbial hosts,providing a sustainable supply of these high-value *** this review,we illustrate the general functions of several typical plant SMs in natural ecosystems and for human *** then provide an overview of current methods elucidating the biosynthetic pathways of plant SMs,and synthetic biology strategies that optimize the efficiency of heterologous biosynthetic pathways in microbial *** forward,dissection of the functions and application of plant SMs by using current multidiscipline approaches would be greatly benefit to the scientific community and human societies.

关键词： plant specialized metabolites metabolic engineering