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Chen J, Zhang Y, Wei J, Hu X, Yin H, Liu W, Li D, Tian W, Hao Y, He Z, Fernie AR, Chen W. Beyond pathways: Accelerated flavonoids candidate identification and novel exploration of enzymatic properties using combined mapping populations of wheat. Plant Biotechnol J 2024. [PMID: 38408119 DOI: 10.1111/pbi.14323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 02/06/2024] [Accepted: 02/12/2024] [Indexed: 02/28/2024]
Abstract
Although forward-genetics-metabolomics methods such as mGWAS and mQTL have proven effective in providing myriad loci affecting metabolite contents, they are somehow constrained by their respective constitutional flaws such as the hidden population structure for GWAS and insufficient recombinant rate for QTL. Here, the combination of mGWAS and mQTL was performed, conveying an improved statistical power to investigate the flavonoid pathways in common wheat. A total of 941 and 289 loci were, respectively, generated from mGWAS and mQTL, within which 13 of them were co-mapped using both approaches. Subsequently, the mGWAS or mQTL outputs alone and their combination were, respectively, utilized to delineate the metabolic routes. Using this approach, we identified two MYB transcription factor encoding genes and five structural genes, and the flavonoid pathway in wheat was accordingly updated. Moreover, we have discovered some rare-activity-exhibiting flavonoid glycosyl- and methyl-transferases, which may possess unique biological significance, and harnessing these novel catalytic capabilities provides potentially new breeding directions. Collectively, we propose our survey illustrates that the forward-genetics-metabolomics approaches including multiple populations with high density markers could be more frequently applied for delineating metabolic pathways in common wheat, which will ultimately contribute to metabolomics-assisted wheat crop improvement.
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Affiliation(s)
- Jie Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Yazhouwan National Laboratory, Sanya, China
| | - Yueqi Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Jiaqi Wei
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Wuhan Academy of Agricultural Sciences, Wuhan, China
| | - Xin Hu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Huanran Yin
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Wei Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Dongqin Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Wenfei Tian
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuanfeng Hao
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhonghu He
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Wei Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
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Zhu A, Liu M, Tian Z, Liu W, Hu X, Ao M, Jia J, Shi T, Liu H, Li D, Mao H, Su H, Yan W, Li Q, Lan C, Fernie AR, Chen W. Chemical-tag-based semi-annotated metabolomics facilitates gene identification and specialized metabolic pathway elucidation in wheat. Plant Cell 2024; 36:540-558. [PMID: 37956052 PMCID: PMC10896294 DOI: 10.1093/plcell/koad286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 10/19/2023] [Accepted: 10/19/2023] [Indexed: 11/15/2023]
Abstract
The importance of metabolite modification and species-specific metabolic pathways has long been recognized. However, linking the chemical structure of metabolites to gene function in order to explore the genetic and biochemical basis of metabolism has not yet been reported in wheat (Triticum aestivum). Here, we profiled metabolic fragment enrichment in wheat leaves and consequently applied chemical-tag-based semi-annotated metabolomics in a genome-wide association study in accessions of wheat. The studies revealed that all 1,483 quantified metabolites have at least one known functional group whose modification is tailored in an enzyme-catalyzed manner and eventually allows efficient candidate gene mining. A Triticeae crop-specific flavonoid pathway and its underlying metabolic gene cluster were elucidated in further functional studies. Additionally, upon overexpressing the major effect gene of the cluster TraesCS2B01G460000 (TaOMT24), the pathway was reconstructed in rice (Oryza sativa), which lacks this pathway. The reported workflow represents an efficient and unbiased approach for gene mining using forward genetics in hexaploid wheat. The resultant candidate gene list contains vast molecular resources for decoding the genetic architecture of complex traits and identifying valuable breeding targets and will ultimately aid in achieving wheat crop improvement.
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Affiliation(s)
- Anting Zhu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Mengmeng Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Zhitao Tian
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Wei Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xin Hu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Min Ao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Jingqi Jia
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Taotao Shi
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Hongbo Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Dongqin Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Hailiang Mao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Handong Su
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Wenhao Yan
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Qiang Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Caixia Lan
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Department of Root Biology and Symbiosis, Potsdam-Golm 14476, Germany
| | - Wei Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
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Tian Z, Hu X, Xu Y, Liu M, Liu H, Li D, Hu L, Wei G, Chen W. PMhub 1.0: a comprehensive plant metabolome database. Nucleic Acids Res 2024; 52:D1579-D1587. [PMID: 37819039 PMCID: PMC10767808 DOI: 10.1093/nar/gkad811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/12/2023] [Accepted: 09/20/2023] [Indexed: 10/13/2023] Open
Abstract
The Plant Metabolome Hub (PMhub), available at https://pmhub.org.cn, is a valuable resource designed to provide scientists with comprehensive information on plant metabolites. It offers extensive details about their reference spectra, genetic foundations, chemical reactions, metabolic pathways and biological functions. The PMhub contains chemical data for 188 837 plant metabolites gathered from various sources, with 1 467 041 standard/in-silico high-resolution tandem mass-spectrometry (HRMS/MS) spectra corresponding to these metabolites. Beyond its extensive literature-derived data, PMhub also boasts a sizable collection of experimental metabolites; it contains 144 366 detected features in 10 typical plant species, with 16 423 successfully annotated by using standard/in-silico HRMS/MS data, this collection is further supplemented with thousands of features gathered from reference metabolites. For each metabolite, the PMhub enables the reconstructed of a simulated network based on structural similarities and existing metabolic pathways. Unlike previous plant-specific metabolome databases, PMhub not only contains a vast amount of metabolic data but also assembles the corresponding genomic and/or transcriptomic information, incorporating multiple methods for the comprehensive genetic analysis of metabolites. To validate the practicality, we verified a synthetic pathway for N-p-coumaroyltyramine by in vitro enzymatic activity experiments. In summary, the robust functionality provided by the PMhub will make it an indispensable tool for studying plant metabolomics.
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Affiliation(s)
- Zhitao Tian
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xin Hu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Yingying Xu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Mengmeng Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Hongbo Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Dongqin Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Lisong Hu
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, Hainan 571533, China
| | - Guozhu Wei
- BioBioPha Co., Ltd., Kunming 650201, China
| | - Wei Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
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