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Yin B, Jia J, Sun X, Hu X, Ao M, Liu W, Tian Z, Liu H, Li D, Tian W, Hao Y, Xia X, Sade N, Brotman Y, Fernie AR, Chen J, He Z, Chen W. Dynamic metabolite QTL analyses provide novel biochemical insights into kernel development and nutritional quality improvement in common wheat. PLANT COMMUNICATIONS 2024; 5:100792. [PMID: 38173227 PMCID: PMC11121174 DOI: 10.1016/j.xplc.2024.100792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 12/20/2023] [Accepted: 01/01/2024] [Indexed: 01/05/2024]
Abstract
Despite recent advances in crop metabolomics, the genetic control and molecular basis of the wheat kernel metabolome at different developmental stages remain largely unknown. Here, we performed widely targeted metabolite profiling of kernels from three developmental stages (grain-filling kernels [FKs], mature kernels [MKs], and germinating kernels [GKs]) using a population of 159 recombinant inbred lines. We detected 625 annotated metabolites and mapped 3173, 3143, and 2644 metabolite quantitative trait loci (mQTLs) in FKs, MKs, and GKs, respectively. Only 52 mQTLs were mapped at all three stages, indicating the high stage specificity of the wheat kernel metabolome. Four candidate genes were functionally validated by in vitro enzymatic reactions and/or transgenic approaches in wheat, three of which mediated the tricin metabolic pathway. Metabolite flux efficiencies within the tricin pathway were evaluated, and superior candidate haplotypes were identified, comprehensively delineating the tricin metabolism pathway in wheat. Finally, additional wheat metabolic pathways were re-constructed by updating them to incorporate the 177 candidate genes identified in this study. Our work provides new information on variations in the wheat kernel metabolome and important molecular resources for improvement of wheat nutritional quality.
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Affiliation(s)
- Bo Yin
- 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
| | - Xu Sun
- 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
| | - 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
| | - 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
| | - 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
| | - 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
| | - Xianchun Xia
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Nir Sade
- School of Plant Sciences and Food Security, The Institute for Cereal Crops Improvement, Tel Aviv University, Tel Aviv 69978, Israel
| | - Yariv Brotman
- School of Plant Sciences and Food Security, The Institute for Cereal Crops Improvement, Tel Aviv University, Tel Aviv 69978, Israel
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Jie 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; Yazhouwan National Laboratory, Sanya 572025, China.
| | - Zhonghu He
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 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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Kim S, Lee E, Lee J, An YJ, Oh E, Kim JI, Kim SW, Kim MY, Lee MH, Cho KS. Identification of QTLs and allelic effect controlling lignan content in sesame ( Sesamum indicum L.) using QTL-seq approach. Front Genet 2023; 14:1289793. [PMID: 38148976 PMCID: PMC10750367 DOI: 10.3389/fgene.2023.1289793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 11/27/2023] [Indexed: 12/28/2023] Open
Abstract
Sesame (Sesamum indicum L.), an oilseed crop, is gaining worldwide recognition for its healthy functional ingredients as consumption increases. The content of lignans, known for their antioxidant and anti-inflammatory effects, is a key agronomic trait that determines the industrialization of sesame. However, the study of the genetics and physiology of lignans in sesame is challenging, as they are influenced by multiple genes and environmental factors, therefore, the understanding of gene function and synthetic pathways related to lignan in sesame is still limited. To address these knowledge gaps, we conducted genetic analyses using F7 recombinant inbred line (RIL) populations derived from Goenbaek and Gomazou as low and high lignin content variants, respectively. Using the QTL-seq approach, we identified three loci, qLignan1-1, qLignan6-1, and qLignan11-1, that control lignan content, specifically sesamin and sesamolin. The allelic effect between loci was evaluated using the RIL population. qLignan6-1 had an additive effect that increased lignan content when combined with the other two loci, suggesting that it could be an important factor in gene pyramiding for the development of high-lignan varieties. This study not only highlights the value of sesame lignan, but also provides valuable insights for the development of high-lignan varieties through the use of DNA markers in breeding strategies. Overall, this research contributes to our understanding of the importance of sesame oil and facilitates progress in sesame breeding for improved lignan content.
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Affiliation(s)
- Sungup Kim
- Upland Crop Breeding Research Division, Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang, Republic of Korea
| | - Eunsoo Lee
- Upland Crop Breeding Research Division, Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang, Republic of Korea
| | - Jeongeun Lee
- Upland Crop Breeding Research Division, Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang, Republic of Korea
| | - Yeon Ju An
- Upland Crop Breeding Research Division, Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang, Republic of Korea
| | - Eunyoung Oh
- Upland Crop Breeding Research Division, Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang, Republic of Korea
| | - Jung In Kim
- Upland Crop Breeding Research Division, Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang, Republic of Korea
| | - Sang Woo Kim
- Upland Crop Breeding Research Division, Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang, Republic of Korea
| | - Min Young Kim
- Upland Crop Breeding Research Division, Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang, Republic of Korea
| | - Myoung Hee Lee
- Upland Crop Breeding Research Division, Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang, Republic of Korea
| | - Kwang-Soo Cho
- Central Crop Breeding Research Division, Department of Central Area Crop Science, National Institute of Crop Science, Rural Development Administration, Suwon, Republic of Korea
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Doddaraju P, Dharmappa PM, Thiagarayaselvam A, Vijayaraghavareddy P, Bheemanahalli R, Basavaraddi PA, Malagondanahalli MKV, Kambalimath S, Thulasiram HV, Sreeman SM. Comprehensive analysis of physiological and metabolomic responses to drought reveals specific modulation of acquired tolerance mechanisms in rice. PHYSIOLOGIA PLANTARUM 2023; 175:e13917. [PMID: 37087573 DOI: 10.1111/ppl.13917] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 03/16/2023] [Accepted: 04/19/2023] [Indexed: 05/03/2023]
Abstract
Mild stresses induce "acquired tolerance traits" (ATTs) that provide tolerance when stress becomes severe. Here, we identified the genetic variability in ATTs among a panel of rice germplasm accessions and demonstrated their relevance in protecting growth and productivity under water-limited conditions. Diverse approaches, including physiological screens, association mapping and metabolomics, were adopted and revealed 43 significant marker-trait associations. Nontargeted metabolomic profiling of contrasting genotypes revealed 26 "tolerance-related-induced" primary and secondary metabolites in the tolerant genotypes (AC-39000 and AC-39020) compared to the susceptible one (BPT-5204) under water-limited condition. Metabolites that help maintain cellular functions, especially Calvin cycle processes, significantly accumulated more in tolerant genotypes, which resulted in superior photosynthetic capacity and hence water use efficiency. Upregulation of the glutathione cycle intermediates explains the ROS homeostasis among the tolerant genotypes, maintaining spikelet fertility, and grain yield under stress. Bioinformatic dissection of a major effect quantitative trait locus on chromosome 8 revealed genes controlling metabolic pathways leading to the production of osmolites and antioxidants, such as GABA and raffinose. The study also led to the identification of specific trait donor genotypes that can be effectively used in translational crop improvement activities.
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Affiliation(s)
- Pushpa Doddaraju
- Department of Crop Physiology, University of Agricultural Sciences, Bengaluru, India
| | - Prathibha M Dharmappa
- Department of Crop Physiology, University of Agricultural Sciences, Bengaluru, India
- ICAR-Indian Institute of Horticulture Research, Bengaluru, India
| | | | | | - Raju Bheemanahalli
- Department of Crop Physiology, University of Agricultural Sciences, Bengaluru, India
- Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, Mississippi, USA
| | - Priyanka A Basavaraddi
- Department of Crop Physiology, University of Agricultural Sciences, Bengaluru, India
- Department of Crop and Forest Sciences, University of Lleida, Lleida, Spain
| | | | - Sumanth Kambalimath
- Department of Crop Physiology, University of Agricultural Sciences, Bengaluru, India
| | | | - Sheshshayee M Sreeman
- Department of Crop Physiology, University of Agricultural Sciences, Bengaluru, India
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Understanding ayahuasca effects in major depressive disorder treatment through in vitro metabolomics and bioinformatics. Anal Bioanal Chem 2023:10.1007/s00216-023-04556-3. [PMID: 36717401 DOI: 10.1007/s00216-023-04556-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/27/2022] [Accepted: 01/19/2023] [Indexed: 02/01/2023]
Abstract
Emerging insights from metabolomic-based studies of major depression disorder (MDD) are mainly related to biochemical processes such as energy or oxidative stress, in addition to neurotransmission linked to specific metabolite intermediates. Hub metabolites represent nodes in the biochemical network playing a critical role in integrating the information flow in cells between metabolism and signaling pathways. Limited technical-scientific studies have been conducted to understand the effects of ayahuasca (Aya) administration in the metabolism considering MDD molecular context. Therefore, this work aims to investigate an in vitro primary astrocyte model by untargeted metabolomics of two cellular subfractions: secretome and intracellular content after pre-defined Aya treatments, based on DMT concentration. Mass spectrometry (MS)-based metabolomics data revealed significant hub metabolites, which were used to predict biochemical pathway alterations. Branched-chain amino acid (BCAA) metabolism, and vitamin B6 and B3 metabolism were associated to Aya treatment, as "housekeeping" pathways. Dopamine synthesis was overrepresented in the network results when considering the lowest tested DMT concentration (1 µmol L-1). Building reaction networks containing significant and differential metabolites, such as nicotinamide, L-DOPA, and L-leucine, is a useful approach to guide on dose decision and pathway selection in further analytical and molecular studies.
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Wang H, Sun R, Xu N, Wang X, Bao M, Li X, Li J, Lin A, Feng J. Untargeted metabolomics of the cochleae from two laryngeally echolocating bats. Front Mol Biosci 2023; 10:1171366. [PMID: 37152899 PMCID: PMC10154556 DOI: 10.3389/fmolb.2023.1171366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 04/06/2023] [Indexed: 05/09/2023] Open
Abstract
High-frequency hearing is regarded as one of the most functionally important traits in laryngeally echolocating bats. Abundant candidate hearing-related genes have been identified to be the important genetic bases underlying high-frequency hearing for laryngeally echolocating bats, however, extensive metabolites presented in the cochleae have not been studied. In this study, we identified 4,717 annotated metabolites in the cochleae of two typical laryngeally echolocating bats using the liquid chromatography-mass spectroscopy technology, metabolites classified as amino acids, peptides, and fatty acid esters were identified as the most abundant in the cochleae of these two echolocating bat species, Rhinolophus sinicus and Vespertilio sinensis. Furthermore, 357 metabolites were identified as significant differentially accumulated (adjusted p-value <0.05) in the cochleae of these two bat species with distinct echolocating dominant frequencies. Downstream KEGG enrichment analyses indicated that multiple biological processes, including signaling pathways, nervous system, and metabolic process, were putatively different in the cochleae of R. sinicus and V. sinensis. For the first time, this study investigated the extensive metabolites and associated biological pathways in the cochleae of two laryngeal echolocating bats and expanded our knowledge of the metabolic molecular bases underlying high-frequency hearing in the cochleae of echolocating bats.
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Affiliation(s)
- Hui Wang
- College of Life Science, Jilin Agricultural University, Changchun, China
- *Correspondence: Hui Wang, ; Jiang Feng,
| | - Ruyi Sun
- College of Life Science, Jilin Agricultural University, Changchun, China
| | - Ningning Xu
- College of Life Science, Jilin Agricultural University, Changchun, China
| | - Xue Wang
- College of Life Science, Jilin Agricultural University, Changchun, China
| | - Mingyue Bao
- College of Life Science, Jilin Agricultural University, Changchun, China
| | - Xin Li
- College of Life Science, Jilin Agricultural University, Changchun, China
| | - Jiqian Li
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Aiqing Lin
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Jiang Feng
- College of Life Science, Jilin Agricultural University, Changchun, China
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
- *Correspondence: Hui Wang, ; Jiang Feng,
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González-Rodríguez T, Pérez-Limón S, Peniche-Pavía H, Rellán-Álvarez R, Sawers RJH, Winkler R. Genetic mapping of maize metabolites using high-throughput mass profiling. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 326:111530. [PMID: 36368482 DOI: 10.1016/j.plantsci.2022.111530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 11/02/2022] [Indexed: 06/16/2023]
Abstract
Plant metabolites are the basis of human nutrition and have biological relevance in ecology. Farmers selected plants with favorable characteristics since prehistoric times and improved the cultivars, but without knowledge of underlying mechanisms. Understanding the genetic basis of metabolite production can facilitate the successful breeding of plants with augmented nutritional value. To identify genetic factors related to the metabolic composition in maize, we generated mass profiles of 198 recombinant inbred lines (RILs) and their parents (B73 and Mo17) using direct-injection electrospray ionization mass spectrometry (DLI-ESI MS). Mass profiling allowed the correct clustering of samples according to genotype. We quantified 71 mass features from grains and 236 mass features from leaf extracts. For the corresponding ions, we identified tissue-specific metabolic 'Quantitative Trait Loci' (mQTLs) distributed across the maize genome. These genetic regions could regulate multiple metabolite biosynthesis pathways. Our findings demonstrate that DLI-ESI MS has sufficient analytical resolution to map mQTLs. These identified genetic loci will be helpful in metabolite-focused maize breeding. Mass profiling is a powerful tool for detecting mQTLs in maize and enables the high-throughput screening of loci responsible for metabolite biosynthesis.
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Affiliation(s)
- Tzitziki González-Rodríguez
- Center for Research and Advanced Studies (CINVESTAV) Irapuato, Department of Biotechnology and Biochemistry, Mexico
| | - Sergio Pérez-Limón
- The Pennsylvania State University, Department of Plant Science, State College, PA, USA
| | - Héctor Peniche-Pavía
- Center for Research and Advanced Studies (CINVESTAV) Irapuato, Department of Biotechnology and Biochemistry, Mexico
| | - Rubén Rellán-Álvarez
- North Carolina State University, Department of Molecular and Structural Biochemistry, USA; Unidad de Genómica Avanzada (UGA) - Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Km. 9.6 Libramiento Norte Carr. Irapuato-León, 36824 Irapuato Gto, Mexico
| | - Ruairidh J H Sawers
- The Pennsylvania State University, Department of Plant Science, State College, PA, USA; Unidad de Genómica Avanzada (UGA) - Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Km. 9.6 Libramiento Norte Carr. Irapuato-León, 36824 Irapuato Gto, Mexico
| | - Robert Winkler
- Center for Research and Advanced Studies (CINVESTAV) Irapuato, Department of Biotechnology and Biochemistry, Mexico; Unidad de Genómica Avanzada (UGA) - Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Km. 9.6 Libramiento Norte Carr. Irapuato-León, 36824 Irapuato Gto, Mexico.
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Pranneshraj V, Sangha MK, Djalovic I, Miladinovic J, Djanaguiraman M. Lipidomics-Assisted GWAS (lGWAS) Approach for Improving High-Temperature Stress Tolerance of Crops. Int J Mol Sci 2022; 23:ijms23169389. [PMID: 36012660 PMCID: PMC9409476 DOI: 10.3390/ijms23169389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/08/2022] [Accepted: 08/12/2022] [Indexed: 11/25/2022] Open
Abstract
High-temperature stress (HT) over crop productivity is an important environmental factor demanding more attention as recent global warming trends are alarming and pose a potential threat to crop production. According to the Sixth IPCC report, future years will have longer warm seasons and frequent heat waves. Thus, the need arises to develop HT-tolerant genotypes that can be used to breed high-yielding crops. Several physiological, biochemical, and molecular alterations are orchestrated in providing HT tolerance to a genotype. One mechanism to counter HT is overcoming high-temperature-induced membrane superfluidity and structural disorganizations. Several HT lipidomic studies on different genotypes have indicated the potential involvement of membrane lipid remodelling in providing HT tolerance. Advances in high-throughput analytical techniques such as tandem mass spectrometry have paved the way for large-scale identification and quantification of the enormously diverse lipid molecules in a single run. Physiological trait-based breeding has been employed so far to identify and select HT tolerant genotypes but has several disadvantages, such as the genotype-phenotype gap affecting the efficiency of identifying the underlying genetic association. Tolerant genotypes maintain a high photosynthetic rate, stable membranes, and membrane-associated mechanisms. In this context, studying the HT-induced membrane lipid remodelling, resultant of several up-/down-regulations of genes and post-translational modifications, will aid in identifying potential lipid biomarkers for HT tolerance/susceptibility. The identified lipid biomarkers (LIPIDOTYPE) can thus be considered an intermediate phenotype, bridging the gap between genotype–phenotype (genotype–LIPIDOTYPE–phenotype). Recent works integrating metabolomics with quantitative genetic studies such as GWAS (mGWAS) have provided close associations between genotype, metabolites, and stress-tolerant phenotypes. This review has been sculpted to provide a potential workflow that combines MS-based lipidomics and the robust GWAS (lipidomics assisted GWAS-lGWAS) to identify membrane lipid remodelling related genes and associations which can be used to develop HS tolerant genotypes with enhanced membrane thermostability (MTS) and heat stable photosynthesis (HP).
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Affiliation(s)
- Velumani Pranneshraj
- Department of Biochemistry, Punjab Agricultural University, Ludhiana 141004, India
| | - Manjeet Kaur Sangha
- Department of Biochemistry, Punjab Agricultural University, Ludhiana 141004, India
| | - Ivica Djalovic
- Institute of Field and Vegetable Crops, National Institute of the Republic of Serbia, Maxim Gorki 30, 21000 Novi Sad, Serbia
- Correspondence: (I.D.); (M.D.)
| | - Jegor Miladinovic
- Institute of Field and Vegetable Crops, National Institute of the Republic of Serbia, Maxim Gorki 30, 21000 Novi Sad, Serbia
| | - Maduraimuthu Djanaguiraman
- Department of Crop Physiology, Tamil Nadu Agricultural University, Coimbatore 641003, India
- Correspondence: (I.D.); (M.D.)
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Melandri G, Monteverde E, Riewe D, AbdElgawad H, McCouch SR, Bouwmeester H. Can biochemical traits bridge the gap between genomics and plant performance? A study in rice under drought. PLANT PHYSIOLOGY 2022; 189:1139-1152. [PMID: 35166848 PMCID: PMC9157150 DOI: 10.1093/plphys/kiac053] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 01/17/2022] [Indexed: 05/13/2023]
Abstract
The possibility of introducing metabolic/biochemical phenotyping to complement genomics-based predictions in breeding pipelines has been considered for years. Here we examine to what extent and under what environmental conditions metabolic/biochemical traits can effectively contribute to understanding and predicting plant performance. In this study, multivariable statistical models based on flag leaf central metabolism and oxidative stress status were used to predict grain yield (GY) performance for 271 indica rice (Oryza sativa) accessions grown in the field under well-watered and reproductive stage drought conditions. The resulting models displayed significantly higher predictability than multivariable models based on genomic data for the prediction of GY under drought (Q2 = 0.54-0.56 versus 0.35) and for stress-induced GY loss (Q2 = 0.59-0.64 versus 0.03-0.06). Models based on the combined datasets showed predictabilities similar to metabolic/biochemical-based models alone. In contrast to genetic markers, models with enzyme activities and metabolite values also quantitatively integrated the effect of physiological differences such as plant height on GY. The models highlighted antioxidant enzymes of the ascorbate-glutathione cycle and a lipid oxidation stress marker as important predictors of rice GY stability under drought at the reproductive stage, and these stress-related variables were more predictive than leaf central metabolites. These findings provide evidence that metabolic/biochemical traits can integrate dynamic cellular and physiological responses to the environment and can help bridge the gap between the genome and the phenome of crops as predictors of GY performance under drought.
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Affiliation(s)
- Giovanni Melandri
- Laboratory of Plant Physiology, Wageningen University and Research, Wageningen, the Netherlands
- School of Integrative Plant Sciences, Plant Breeding and Genetics Section, Cornell University, Ithaca, New York, USA
| | - Eliana Monteverde
- School of Integrative Plant Sciences, Plant Breeding and Genetics Section, Cornell University, Ithaca, New York, USA
- Departamento de Biología Vegetal, Facultad de Agronomía, Laboratorio de Evolución y Domesticación de las Plantas, Universidad de La República, Montevideo, Uruguay
| | - David Riewe
- Julius Kühn-Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Ecological Chemistry, Plant Analysis and Stored Product Protection, Berlin, Germany
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Hamada AbdElgawad
- Laboratory for Integrated Molecular Plant Physiology Research, University of Antwerp, Antwerp, Belgium
- Department of Botany, Faculty of Science, Beni-Suef University, Beni Suef, Egypt
| | - Susan R McCouch
- School of Integrative Plant Sciences, Plant Breeding and Genetics Section, Cornell University, Ithaca, New York, USA
| | - Harro Bouwmeester
- Laboratory of Plant Physiology, Wageningen University and Research, Wageningen, the Netherlands
- Plant Hormone Biology group, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
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9
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Reddy K, Stander MA, Stafford GI, Makunga NP. Mass Spectrometry Metabolomics and Feature-Based Molecular Networking Reveals Population-Specific Chemistry in Some Species of the Sceletium Genus. Front Nutr 2022; 9:819753. [PMID: 35425789 PMCID: PMC9001948 DOI: 10.3389/fnut.2022.819753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/02/2022] [Indexed: 11/21/2022] Open
Abstract
The Sceletium genus has been of medicinal importance in southern Africa for millennia and Sceletium tortuosum (Aizoaceae), one of eight species in the genus has gained pharmaceutical importance as an anxiolytic and anti-depressant due to the presence of mesembrine alkaloids. S. tortuosum is used for the manufacture of herbal teas, dietary supplements and other phytopharmaceutical products. This study aimed to provide a metabolomic characterization of S. tortuosum and its sister species as these are not easy to distinguish using morphology alone. Plant samples were thus collected from various locations in the succulent Karoo (South Africa) and analyzed through liquid chromatography-mass spectrometry (LC-MS), using MSE fragmentation as a putative tool for chemical identities. Metabolomics-based analyses in combination with molecular networking were able to distinguish between the four species of Sceletium based on the presence of 4-(3,4-dimethyoxyphenyl)-4-[2-acetylmethlamino)ethyl]cyclohexanone (m/z 334.2020; RT 6.60 min), mesembrine (m/z 290.1757; RT 5.10 min) and 4'-O-demethylmesembrenol (m/z 276.1597; RT 4.17 min). Metabolomic profiles varied according to the different localities and metabolites occurred at variable quantitative levels in Sceletium ecotypes. Molecular networking provided the added advantage of being able to observe mesembrine alkaloid isomers and coeluting metabolites (from the joubertiamine group) that were difficult to discern without this application. By combining high-throughput metabolomics together with global and feature based-molecular networking, a powerful metabolite profiling platform that is able to discern chemical patterns within and between populations was established. These techniques were able to reveal chemotaxonomic relationships and allowed for the discovery of chemical markers that may be used as part of monitoring protocols during the manufacture of phytopharmaceutical and dietary products based on Sceletium.
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Affiliation(s)
- Kaylan Reddy
- Department of Botany and Zoology, Faculty of Natural Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Marietjie A. Stander
- Department of Biochemistry, Faculty of Natural Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Gary I. Stafford
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - Nokwanda P. Makunga
- Department of Botany and Zoology, Faculty of Natural Sciences, Stellenbosch University, Stellenbosch, South Africa
- *Correspondence: Nokwanda P. Makunga
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Wu J, Gao T, Zhao L, Bao H, Yu C, Hu J, Ma F. Investigating Phragmites australis response to copper exposure using physiologic, Fourier Transform Infrared and metabolomic approaches. FUNCTIONAL PLANT BIOLOGY : FPB 2022; 49:365-381. [PMID: 35290177 DOI: 10.1071/fp21258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 01/19/2022] [Indexed: 06/14/2023]
Abstract
Phragmites australis (Cav.) Trin. ex Steud is a landscape plant with resistance to heavy metals that has significance in phytoremediation. However, little is known about the metabolomic background of the heavy metal resistance mechanisms of Phragmites . We studied copper stress on Phragmites and monitored physiological indicators such as malondialdehyde (MDA) and electrolyte leakage (EL). In addition, Fourier Transform Infrared (FTIR) was used to study the related chemical composition in the roots, stems, and leaves under copper stress. Furthermore, LC-MS technology was used to analyse the plants metabolic profile. Results showed that increased copper concentration in Phragmites led to the accumulation of MDA and EL. FTIR spectrum detected the presence of O-H and C=O stretching. O-H stretching was related to the presence of flavonoids, while C=O stretching reflected the presence of protein amide I. The latter was related to the change of amino acid composition. Both flavonoids and amino acids are regarded as contributors to the antioxidant of Phragmites under copper stress. Metabolomics analysis revealed that arginine and ayarin were accumulated and Phragmites leaves responded to copper stress with changes in the pool size of arginine and ayarin. It is speculated that they could improve resistance. Arginine is accumulated through two pathways: the citrulline decomposition and conversion pathway; and the circular pathway composed of ornithine, citrulline, l -argininosuccinate and arginine. Ayarin is synthesised through the quercetin methylation pathway. This study elucidates the antioxidant mechanisms for enhancing its resistance to heavy metal stress, thus improving of phytoremediation efficiency.
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Affiliation(s)
- Jieting Wu
- School of Environmental Science, Liaoning University, Shenyang 110036, People's Republic of China
| | - Tian Gao
- School of Environmental Science, Liaoning University, Shenyang 110036, People's Republic of China
| | - Lei Zhao
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, People's Republic of China
| | - Hongxu Bao
- School of Environmental Science, Liaoning University, Shenyang 110036, People's Republic of China
| | - Chang Yu
- School of Environmental Science, Liaoning University, Shenyang 110036, People's Republic of China
| | - Jianing Hu
- Dalian Neusoft University of Information, Dalian 116032, People's Republic of China
| | - Fang Ma
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, People's Republic of China
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11
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Melandri G, Thorp KR, Broeckling C, Thompson AL, Hinze L, Pauli D. Assessing Drought and Heat Stress-Induced Changes in the Cotton Leaf Metabolome and Their Relationship With Hyperspectral Reflectance. FRONTIERS IN PLANT SCIENCE 2021; 12:751868. [PMID: 34745185 PMCID: PMC8569624 DOI: 10.3389/fpls.2021.751868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 09/30/2021] [Indexed: 06/13/2023]
Abstract
The study of phenotypes that reveal mechanisms of adaptation to drought and heat stress is crucial for the development of climate resilient crops in the face of climate uncertainty. The leaf metabolome effectively summarizes stress-driven perturbations of the plant physiological status and represents an intermediate phenotype that bridges the plant genome and phenome. The objective of this study was to analyze the effect of water deficit and heat stress on the leaf metabolome of 22 genetically diverse accessions of upland cotton grown in the Arizona low desert over two consecutive years. Results revealed that membrane lipid remodeling was the main leaf mechanism of adaptation to drought. The magnitude of metabolic adaptations to drought, which had an impact on fiber traits, was found to be quantitatively and qualitatively associated with different stress severity levels during the two years of the field trial. Leaf-level hyperspectral reflectance data were also used to predict the leaf metabolite profiles of the cotton accessions. Multivariate statistical models using hyperspectral data accurately estimated (R 2 > 0.7 in ∼34% of the metabolites) and predicted (Q 2 > 0.5 in 15-25% of the metabolites) many leaf metabolites. Predicted values of metabolites could efficiently discriminate stressed and non-stressed samples and reveal which regions of the reflectance spectrum were the most informative for predictions. Combined together, these findings suggest that hyperspectral sensors can be used for the rapid, non-destructive estimation of leaf metabolites, which can summarize the plant physiological status.
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Affiliation(s)
- Giovanni Melandri
- School of Plant Sciences, University of Arizona, Tucson, AZ, United States
| | - Kelly R. Thorp
- United States Department of Agriculture-Agricultural Research Service, Arid Land Agricultural Research Center, Maricopa, AZ, United States
| | - Corey Broeckling
- Analytical Resources Core: Bioanalysis and Omics Center, Colorado State University, Fort Collins, CO, United States
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, United States
| | - Alison L. Thompson
- United States Department of Agriculture-Agricultural Research Service, Arid Land Agricultural Research Center, Maricopa, AZ, United States
| | - Lori Hinze
- United States Department of Agriculture-Agricultural Research Service, Southern Plains Agricultural Research Center, College Station, TX, United States
| | - Duke Pauli
- School of Plant Sciences, University of Arizona, Tucson, AZ, United States
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12
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Wei W, Li S, Wang Y, Wang B, Fan G, Zeng Q, Zhao F, Xu C, Zhang X, Tang T, Feng X, Shi J, Shi G, Zhang W, Song G, Li H, Wang F, Zhang Y, Li X, Wang D, Zhang W, Pei J, Wang X, Zhao Z. Metabolome-Based Genome-Wide Association Study Provides Genetic Insights Into the Natural Variation of Foxtail Millet. FRONTIERS IN PLANT SCIENCE 2021; 12:665530. [PMID: 34386024 PMCID: PMC8353534 DOI: 10.3389/fpls.2021.665530] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 05/20/2021] [Indexed: 05/23/2023]
Abstract
The plant metabolome is considered as a bridge between the genome and the phenome and is essential for the interaction between plant growth and the plant environment. Here, we used the liquid chromatography-tandem mass spectrometry method to perform a widely targeted metabolomics analysis of 150 millet germplasm and simultaneous identification and quantification of 330 annotated metabolites. Comparing the metabolic content of different millets revealed significant natural variation of both primary and secondary metabolites, including flavonoids, phenolamides, hydroxycinnamoyl derivatives, nucleotides, and lipids, in the millets from India and the north and south of China; among them, some of the flavonoids are the most prominent. A total of 2.2 TB sequence data were obtained by sequencing 150 accessions of foxtail millet using the Illumina platform. Further digging into the genetic basis of metabolites by mGWAS analysis found that cyanidin 3-O-glucoside and quercetin O-acetylhexside are concentratedly located at 43.55 Mb on chromosome 5 and 26.9 Mb on chromosome 7, and two Lc were mined as candidate genes, respectively. However, the signals of luteolin 7-O-glucoside and kaempferol 3-O-glucoside were also detected at 14.36 Mb on chromosome 3, and five glycosyltransferase genes on this loci were deemed to regulate their content. Our work is the first research to use mGWAS in millet, and it paves the way for future dissection of complex physiological traits in millet.
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Affiliation(s)
- Wei Wei
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Shuangdong Li
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Yixiang Wang
- Wuhan Metware Biotechnology Co., Ltd., Wuhan, China
| | - Bin Wang
- Wuhan Metware Biotechnology Co., Ltd., Wuhan, China
| | - Guangyu Fan
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Qisen Zeng
- Wuhan Metware Biotechnology Co., Ltd., Wuhan, China
| | - Fang Zhao
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Congping Xu
- Wuhan Metware Biotechnology Co., Ltd., Wuhan, China
| | - Xiaolei Zhang
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Tang Tang
- Wuhan Metware Biotechnology Co., Ltd., Wuhan, China
| | - Xiaolei Feng
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Jian Shi
- Wuhan Metware Biotechnology Co., Ltd., Wuhan, China
| | - Gaolei Shi
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Weiqin Zhang
- Wuhan Metware Biotechnology Co., Ltd., Wuhan, China
| | - Guoliang Song
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Huan Li
- Wuhan Metware Biotechnology Co., Ltd., Wuhan, China
| | - Feng Wang
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Yali Zhang
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Xinru Li
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Dequan Wang
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Wenying Zhang
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Jingjing Pei
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Xiaoming Wang
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Zhihai Zhao
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
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13
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De Vega JJ, Peel N, Purdy SJ, Hawkins S, Donnison L, Dyer S, Farrar K. Differential expression of starch and sucrose metabolic genes linked to varying biomass yield in Miscanthus hybrids. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:98. [PMID: 33874976 PMCID: PMC8056674 DOI: 10.1186/s13068-021-01948-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 04/07/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Miscanthus is a commercial lignocellulosic biomass crop owing to its high biomass productivity and low chemical input requirements. Within an interspecific Miscanthus cross, progeny with high biomass yield were shown to have low concentrations of starch and sucrose but high concentrations of fructose. We performed a transcriptional RNA-seq analysis between selected Miscanthus hybrids with contrasting values for these phenotypes to clarify how these phenotypes are genetically controlled. RESULTS We observed that genes directly involved in the synthesis and degradation of starch and sucrose were down-regulated in high-yielding Miscanthus hybrids. At the same time, glycolysis and export of triose phosphates were up-regulated in high-yielding Miscanthus hybrids. These differentially expressed genes and biological functions were regulated by a well-connected network of less than 25 co-regulated transcription factors. CONCLUSIONS Our results evidence a direct relationship between high expression of essential enzymatic genes in the starch and sucrose pathways and co-expression with their transcriptional regulators, with high starch concentrations and lower biomass production. The strong interconnectivity between gene expression and regulators, chemotype and agronomic traits opens the door to use the expression of well-characterised genes associated with carbohydrate metabolism, particularly in the starch and sucrose pathway, for the early selection of high biomass-yielding genotypes from large Miscanthus populations.
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Affiliation(s)
| | - Ned Peel
- Earlham Institute, Norwich, NR4 7UZ, UK
| | - Sarah J Purdy
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, SY23 3EE, UK
- NSW Department of Primary Industries, Chief Scientist's Branch, Locked Bag 21, Orange, NSW, 2800, Australia
| | - Sarah Hawkins
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, SY23 3EE, UK
| | - Lain Donnison
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, SY23 3EE, UK
| | - Sarah Dyer
- Earlham Institute, Norwich, NR4 7UZ, UK
- NIAB, Cambridge, CB3 0LE, UK
| | - Kerrie Farrar
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, SY23 3EE, UK.
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14
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Ahmad MZ, Zhang Y, Zeng X, Li P, Wang X, Benedito VA, Zhao J. Isoflavone malonyl-CoA acyltransferase GmMaT2 is involved in nodulation of soybean by modifying synthesis and secretion of isoflavones. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:1349-1369. [PMID: 33130852 DOI: 10.1093/jxb/eraa511] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/26/2020] [Indexed: 05/20/2023]
Abstract
Malonyl-CoA:flavonoid acyltransferases (MaTs) modify isoflavones, but only a few have been characterized for activity and assigned to specific physiological processes. Legume roots exude isoflavone malonates into the rhizosphere, where they are hydrolyzed into isoflavone aglycones. Soybean GmMaT2 was highly expressed in seeds, root hairs, and nodules. GmMaT2 and GmMaT4 recombinant enzymes used isoflavone 7-O-glucosides as acceptors and malonyl-CoA as an acyl donor to generate isoflavone glucoside malonates. GmMaT2 had higher activity towards isoflavone glucosides than GmMaT4. Overexpression in hairy roots of GmMaT2 and GmMaT4 produced more malonyldaidzin, malonylgenistin, and malonylglycitin, and resulted in more nodules than control. However, only GmMaT2 knockdown (KD) hairy roots showed reduced levels of malonyldaidzin, malonylgenistin, and malonylglycitin, and, likewise, reduced nodule numbers. These were consistent with the up-regulation of only GmMaT2 by rhizobial infection, and higher expression levels of early nodulation genes in GmMaT2- and GmMaT4-overexpressing roots, but lower only in GmMaT2-KD roots compared with control roots. Higher malonyl isoflavonoid levels in transgenic hairy roots were associated with higher levels of isoflavones in root exudates and more nodules, and vice versa. We suggest that GmMaT2 participates in soybean nodulation by catalyzing isoflavone malonylation and affecting malonyl isoflavone secretion for activation of Nod factor and nodulation.
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Affiliation(s)
- Muhammad Zulfiqar Ahmad
- State Key Laboratory of Tea Plant Biology and Utilization, College of Tea and Food Science and Technology, Anhui Agricultural University, Hefei, China
| | - Yanrui Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, College of Tea and Food Science and Technology, Anhui Agricultural University, Hefei, China
| | - Xiangsheng Zeng
- College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Penghui Li
- State Key Laboratory of Tea Plant Biology and Utilization, College of Tea and Food Science and Technology, Anhui Agricultural University, Hefei, China
| | - Xiaobo Wang
- College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Vagner A Benedito
- Division of Plant & Soil Sciences, West Virginia University, Morgantown, WV, USA
| | - Jian Zhao
- State Key Laboratory of Tea Plant Biology and Utilization, College of Tea and Food Science and Technology, Anhui Agricultural University, Hefei, China
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15
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Chen J, Hu X, Shi T, Yin H, Sun D, Hao Y, Xia X, Luo J, Fernie AR, He Z, Chen W. Metabolite-based genome-wide association study enables dissection of the flavonoid decoration pathway of wheat kernels. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1722-1735. [PMID: 31930656 PMCID: PMC7336285 DOI: 10.1111/pbi.13335] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 12/29/2019] [Indexed: 05/02/2023]
Abstract
The marriage of metabolomic approaches with genetic design has proven a powerful tool in dissecting diversity in the metabolome and has additionally enhanced our understanding of complex traits. That said, such studies have rarely been carried out in wheat. In this study, we detected 805 metabolites from wheat kernels and profiled their relative contents among 182 wheat accessions, conducting a metabolite-based genome-wide association study (mGWAS) utilizing 14 646 previously described polymorphic SNP markers. A total of 1098 mGWAS associations were detected with large effects, within which 26 candidate genes were tentatively designated for 42 loci. Enzymatic assay of two candidates indicated they could catalyse glucosylation and subsequent malonylation of various flavonoids and thereby the major flavonoid decoration pathway of wheat kernel was dissected. Moreover, numerous high-confidence genes associated with metabolite contents have been provided, as well as more subdivided metabolite networks which are yet to be explored within our data. These combined efforts presented the first step towards realizing metabolomics-associated breeding of wheat.
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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 UniversityWuhanChina
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Xin Hu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Taotao Shi
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Huanran Yin
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Dongfa Sun
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Yuanfeng Hao
- National Wheat Improvement CenterInstitute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Xianchun Xia
- National Wheat Improvement CenterInstitute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Jie Luo
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina
| | | | - Zhonghu He
- National Wheat Improvement CenterInstitute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Wei Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
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16
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Deng M, Zhang X, Luo J, Liu H, Wen W, Luo H, Yan J, Xiao Y. Metabolomics analysis reveals differences in evolution between maize and rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1710-1722. [PMID: 32445406 DOI: 10.1111/tpj.14856] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 05/12/2020] [Indexed: 06/11/2023]
Abstract
Metabolites are the intermediate and final products of metabolism, which play essential roles in plant growth, evolution and adaptation to changing climates. However, it is unclear how evolution contributes to metabolic variation in plants. Here, we investigated the metabolomics data from leaf and seed tissues in maize and rice. Using principal components analysis based on leaf metabolites but not seed metabolites, metabolomics data could be clearly separated for rice Indica and Japonica accessions, while two maize subgroups, temperate and tropical, showed more visible admixture. Rice and maize seed exhibited significant interspecific differences in metabolic variation, while within rice, leaf and seed displayed similar metabolic variations. Among 10 metabolic categories, flavonoids had higher variation in maize than rice, indicating flavonoids are a key constituent of interspecific metabolic divergence. Interestingly, metabolic regulation was also found to be reshaped dramatically from positive to negative correlations, indicative of the differential evolutionary processes in maize and rice. Moreover, perhaps due to this divergence significantly more metabolic interactions were identified in rice than maize. Furthermore, in rice, the leaf was found to harbor much more intense metabolic interactions than the seed. Our result suggests that metabolomes are valuable for tracking evolutionary history, thereby complementing and extending genomic insights concerning which features are responsible for interspecific differentiation in maize and rice.
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Affiliation(s)
- Min Deng
- College of Agronomy, Hunan Agricultural University, Changsha, Hunan, 410128, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xuehai Zhang
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Jingyun Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Haijun Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Weiwei Wen
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, China
| | - Hongbing Luo
- College of Agronomy, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yingjie Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
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17
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Muthuramalingam P, Jeyasri R, Selvaraj A, Pandian SK, Ramesh M. Integrated transcriptomic and metabolomic analyses of glutamine metabolism genes unveil key players in Oryza sativa (L.) to ameliorate the unique and combined abiotic stress tolerance. Int J Biol Macromol 2020; 164:222-231. [PMID: 32682969 DOI: 10.1016/j.ijbiomac.2020.07.143] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/13/2020] [Accepted: 07/13/2020] [Indexed: 10/23/2022]
Abstract
Plants can be considered to biosynthesize the specialized metabolites to adapt to various environmental stressors mainly on abiotic stresses (AbS). Among specialized metabolites, glutamine (Gln) is an essential plant metabolite to achieve sustainable plant growth, yield and food security. In this pilot study, swe employed computational metabolomics genome wide association survey (cmGWAS) of Gln metabolite profiling in Oryza sativa, targeting at the identification of abiotic stress responsible (AbSR) - Gln metabolite producing genes (GlnMPG). Identified 5 AbSR-GlnMPG alter the metabolite levels and play a predominant role in delineating the physiological significance of rice. These genes were systematically analysed for their biological features via OryzaCyc. Spatio-temporal and plant hormonal expression pattern of AbSR-GlnMPG was analysed and their differential expression profiling were noted in 48 different tissues and hormones, respectively. Furthermore, comparative ideogram of these genes revealed the chromosomal synteny with C4 grass genomes. Molecular crosstalks of these proteins, unravelled the various metabolic interaction. The systems expression profiling of AbSR-GlnMPG will lead to unravel the metabolite signaling and putative responses in multiple AbS. On the whole, this holistic study provides deeper insights on biomolecular features of AbSR-GlnMPG, which could be analysed further to decipher their functional metabolisms in AbS dynamism.
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Affiliation(s)
- Pandiyan Muthuramalingam
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630003, Tamil Nadu, India; Department of Systems Biology, Science Research Centre, Yonsei University, Seoul 03722, South Korea
| | - Rajendran Jeyasri
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630003, Tamil Nadu, India
| | - Anthonymuthu Selvaraj
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630003, Tamil Nadu, India
| | | | - Manikandan Ramesh
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630003, Tamil Nadu, India.
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18
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Weckwerth W, Ghatak A, Bellaire A, Chaturvedi P, Varshney RK. PANOMICS meets germplasm. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1507-1525. [PMID: 32163658 PMCID: PMC7292548 DOI: 10.1111/pbi.13372] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 02/17/2020] [Accepted: 02/26/2020] [Indexed: 05/14/2023]
Abstract
Genotyping-by-sequencing has enabled approaches for genomic selection to improve yield, stress resistance and nutritional value. More and more resource studies are emerging providing 1000 and more genotypes and millions of SNPs for one species covering a hitherto inaccessible intraspecific genetic variation. The larger the databases are growing, the better statistical approaches for genomic selection will be available. However, there are clear limitations on the statistical but also on the biological part. Intraspecific genetic variation is able to explain a high proportion of the phenotypes, but a large part of phenotypic plasticity also stems from environmentally driven transcriptional, post-transcriptional, translational, post-translational, epigenetic and metabolic regulation. Moreover, regulation of the same gene can have different phenotypic outputs in different environments. Consequently, to explain and understand environment-dependent phenotypic plasticity based on the available genotype variation we have to integrate the analysis of further molecular levels reflecting the complete information flow from the gene to metabolism to phenotype. Interestingly, metabolomics platforms are already more cost-effective than NGS platforms and are decisive for the prediction of nutritional value or stress resistance. Here, we propose three fundamental pillars for future breeding strategies in the framework of Green Systems Biology: (i) combining genome selection with environment-dependent PANOMICS analysis and deep learning to improve prediction accuracy for marker-dependent trait performance; (ii) PANOMICS resolution at subtissue, cellular and subcellular level provides information about fundamental functions of selected markers; (iii) combining PANOMICS with genome editing and speed breeding tools to accelerate and enhance large-scale functional validation of trait-specific precision breeding.
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Affiliation(s)
- Wolfram Weckwerth
- Molecular Systems Biology (MOSYS)Department of Functional and Evolutionary EcologyFaculty of Life SciencesUniversity of ViennaViennaAustria
- Vienna Metabolomics Center (VIME)University of ViennaViennaAustria
| | - Arindam Ghatak
- Molecular Systems Biology (MOSYS)Department of Functional and Evolutionary EcologyFaculty of Life SciencesUniversity of ViennaViennaAustria
| | - Anke Bellaire
- Molecular Systems Biology (MOSYS)Department of Functional and Evolutionary EcologyFaculty of Life SciencesUniversity of ViennaViennaAustria
| | - Palak Chaturvedi
- Molecular Systems Biology (MOSYS)Department of Functional and Evolutionary EcologyFaculty of Life SciencesUniversity of ViennaViennaAustria
| | - Rajeev K. Varshney
- Center of Excellence in Genomics & Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadTelanganaIndia
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19
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Cheong BE, Onyemaobi O, Wing Ho Ho W, Biddulph TB, Rupasinghe TWT, Roessner U, Dolferus R. Phenotyping the Chilling and Freezing Responses of Young Microspore Stage Wheat Spikes Using Targeted Metabolome and Lipidome Profiling. Cells 2020; 9:cells9051309. [PMID: 32466096 PMCID: PMC7291281 DOI: 10.3390/cells9051309] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/16/2020] [Accepted: 05/20/2020] [Indexed: 12/22/2022] Open
Abstract
Chilling and frost conditions impose major yield restraints to wheat crops in Australia and other temperate climate regions. Unpredictability and variability of field frost events are major impediments for cold tolerance breeding. Metabolome and lipidome profiling were used to compare the cold response in spikes of cold-tolerant Young and sensitive variety Wyalkatchem at the young microspore (YM) stage of pollen development. We aimed to identify metabolite markers that can reliably distinguish cold-tolerant and sensitive wheat varieties for future cold-tolerance phenotyping applications. We scored changes in spike metabolites and lipids for both varieties during cold acclimation after initial and prolonged exposure to combined chilling and freezing cycles (1 and 4 days, respectively) using controlled environment conditions. The two contrasting wheat varieties showed qualitative and quantitative differences in primary metabolites involved in osmoprotection, but differences in lipid accumulation most distinctively separated the cold response of the two wheat lines. These results resemble what we previously observed in flag leaves of the same two wheat varieties. The fact that this response occurs in tissue types with very different functions indicates that chilling and freezing tolerance in these wheat lines is associated with re-modelling of membrane lipid composition to maintain membrane fluidity.
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Affiliation(s)
- Bo Eng Cheong
- School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia; (B.E.C.); (W.W.H.H.); (T.W.T.R.); (U.R.)
| | - Olive Onyemaobi
- CSIRO Agriculture & Food, GPO Box 1700, Canberra, ACT 2601, Australia;
| | - William Wing Ho Ho
- School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia; (B.E.C.); (W.W.H.H.); (T.W.T.R.); (U.R.)
| | - Thomas Ben Biddulph
- Department of Primary Industries and Regional Development, 3 Baron Hay Court, South Perth, WA 6151, Australia;
| | - Thusitha W. T. Rupasinghe
- School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia; (B.E.C.); (W.W.H.H.); (T.W.T.R.); (U.R.)
| | - Ute Roessner
- School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia; (B.E.C.); (W.W.H.H.); (T.W.T.R.); (U.R.)
| | - Rudy Dolferus
- CSIRO Agriculture & Food, GPO Box 1700, Canberra, ACT 2601, Australia;
- Correspondence: ; Tel.: +61-2-6246 5010
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Valentino G, Graziani V, D’Abrosca B, Pacifico S, Fiorentino A, Scognamiglio M. NMR-Based Plant Metabolomics in Nutraceutical Research: An Overview. Molecules 2020; 25:E1444. [PMID: 32210071 PMCID: PMC7145309 DOI: 10.3390/molecules25061444] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/15/2020] [Accepted: 03/20/2020] [Indexed: 12/13/2022] Open
Abstract
Few topics are able to channel the interest of researchers, the public, and industries, like nutraceuticals. The ever-increasing demand of new compounds or new sources of known active compounds, along with the need of a better knowledge about their effectiveness, mode of action, safety, etc., led to a significant effort towards the development of analytical approaches able to answer the many questions related to this topic. Therefore, the application of cutting edges approaches to this area has been observed. Among these approaches, metabolomics is a key player. Herewith, the applications of NMR-based metabolomics to nutraceutical research are discussed: after a brief overview of the analytical workflow, the use of NMR-based metabolomics to the search for new compounds or new sources of known nutraceuticals are reviewed. Then, possible applications for quality control and nutraceutical optimization are suggested. Finally, the use of NMR-based metabolomics to study the impact of nutraceuticals on human metabolism is discussed.
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Affiliation(s)
- Giovanna Valentino
- Dipartimento di Scienze e Tecnologie Ambientali Biologiche e Farmaceutiche-DiSTABiF, Università degli Studi della Campania Luigi Vanvitelli, via Vivaldi 43, I-81100 Caserta, Italy; (G.V.); (B.D.); (S.P.)
| | - Vittoria Graziani
- Department of Microbiology, Tumor and Cell Biology (MTC), Biomedicum B7, Karolinska Institutet, 17165 Stockholm, Sweden;
| | - Brigida D’Abrosca
- Dipartimento di Scienze e Tecnologie Ambientali Biologiche e Farmaceutiche-DiSTABiF, Università degli Studi della Campania Luigi Vanvitelli, via Vivaldi 43, I-81100 Caserta, Italy; (G.V.); (B.D.); (S.P.)
- Dipartimento di Biotecnologia Marina, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Severina Pacifico
- Dipartimento di Scienze e Tecnologie Ambientali Biologiche e Farmaceutiche-DiSTABiF, Università degli Studi della Campania Luigi Vanvitelli, via Vivaldi 43, I-81100 Caserta, Italy; (G.V.); (B.D.); (S.P.)
| | - Antonio Fiorentino
- Dipartimento di Scienze e Tecnologie Ambientali Biologiche e Farmaceutiche-DiSTABiF, Università degli Studi della Campania Luigi Vanvitelli, via Vivaldi 43, I-81100 Caserta, Italy; (G.V.); (B.D.); (S.P.)
- Dipartimento di Biotecnologia Marina, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Monica Scognamiglio
- Dipartimento di Scienze e Tecnologie Ambientali Biologiche e Farmaceutiche-DiSTABiF, Università degli Studi della Campania Luigi Vanvitelli, via Vivaldi 43, I-81100 Caserta, Italy; (G.V.); (B.D.); (S.P.)
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21
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Li K, Wang D, Gong L, Lyu Y, Guo H, Chen W, Jin C, Liu X, Fang C, Luo J. Comparative analysis of metabolome of rice seeds at three developmental stages using a recombinant inbred line population. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:908-922. [PMID: 31355982 PMCID: PMC6899760 DOI: 10.1111/tpj.14482] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 07/13/2019] [Accepted: 07/23/2019] [Indexed: 05/23/2023]
Abstract
Plants are considered an important food and nutrition source for humans. Despite advances in plant seed metabolomics, knowledge about the genetic and molecular bases of rice seed metabolomes at different developmental stages is still limited. Here, using Zhenshan 97 (ZS97) and Minghui 63 (MH63), we performed a widely targeted metabolic profiling in seeds during grain filling, mature seeds and germinating seeds. The diversity between MH63 and ZS97 was characterized in terms of the content of metabolites and the metabolic shifting across developmental stages. Taking advantage of the ultra-high-density genetic map of a population of 210 recombinant inbred lines (RILs) derived from a cross between ZS97 and MH63, we identified 4681 putative metabolic quantitative trait loci (mQTLs) in seeds across the three stages. Further analysis of the mQTLs for the codetected metabolites across the three stages revealed that the genetic regulation of metabolite accumulation was closely related to developmental stage. Using in silico analyses, we characterized 35 candidate genes responsible for 30 structurally identified or annotated compounds, among which LOC_Os07g04970 and LOC_Os06g03990 were identified to be responsible for feruloylserotonin and l-asparagine content variation across populations, respectively. Metabolite-agronomic trait association and colocation between mQTLs and phenotypic quantitative trait loci (pQTLs) revealed the complexity of the metabolite-agronomic trait relationship and the corresponding genetic basis.
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Affiliation(s)
- Kang Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant ResearchHuazhong Agricultural UniversityWuhan430070China
| | - Dehong Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant ResearchHuazhong Agricultural UniversityWuhan430070China
| | - Liang Gong
- The Jackson Laboratory for Genomic MedicineFarmingtonCTUSA
| | - Yuanyuan Lyu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant ResearchHuazhong Agricultural UniversityWuhan430070China
| | - Hao Guo
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant ResearchHuazhong Agricultural UniversityWuhan430070China
| | - Wei Chen
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
| | - Cheng Jin
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant ResearchHuazhong Agricultural UniversityWuhan430070China
| | - Xianqing Liu
- Hainan Key Laboratory for Sustainable Utilization of Tropical BioresourceCollege of Tropical CropsHainan UniversityHaikou570288China
| | - Chuanying Fang
- Hainan Key Laboratory for Sustainable Utilization of Tropical BioresourceCollege of Tropical CropsHainan UniversityHaikou570288China
| | - Jie Luo
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant ResearchHuazhong Agricultural UniversityWuhan430070China
- Hainan Key Laboratory for Sustainable Utilization of Tropical BioresourceCollege of Tropical CropsHainan UniversityHaikou570288China
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22
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Wagner G, Laperche A, Lariagon C, Marnet N, Renault D, Guitton Y, Bouchereau A, Delourme R, Manzanares-Dauleux MJ, Gravot A. Resolution of quantitative resistance to clubroot into QTL-specific metabolic modules. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:5375-5390. [PMID: 31145785 PMCID: PMC6793449 DOI: 10.1093/jxb/erz265] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 05/21/2019] [Indexed: 05/23/2023]
Abstract
Plant disease resistance is often under quantitative genetic control. Thus, in a given interaction, plant cellular responses to infection are influenced by resistance or susceptibility alleles at different loci. In this study, a genetic linkage analysis was used to address the complexity of the metabolic responses of Brassica napus roots to infection by Plasmodiophora brassicae. Metabolome profiling and pathogen quantification in a segregating progeny allowed a comparative mapping of quantitative trait loci (QTLs) involved in resistance and in metabolic adjustments. Distinct metabolic modules were associated with each resistance QTL, suggesting the involvement of different underlying cellular mechanisms. This approach highlighted the possible role of gluconasturtiin and two unknown metabolites in the resistance conferred by two QTLs on chromosomes C03 and C09, respectively. Only two susceptibility biomarkers (glycine and glutathione) were simultaneously linked to the three main resistance QTLs, suggesting the central role of these compounds in the interaction. By contrast, several genotype-specific metabolic responses to infection were genetically unconnected to resistance or susceptibility. Likewise, variations of root sugar profiles, which might have influenced pathogen nutrition, were not found to be related to resistance QTLs. This work illustrates how genetic metabolomics can help to understand plant stress responses and their possible links with disease.
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Affiliation(s)
- Geoffrey Wagner
- IGEPP, Agrocampus Ouest, INRA, Université de Rennes, Le Rheu, France
| | - Anne Laperche
- IGEPP, Agrocampus Ouest, INRA, Université de Rennes, Le Rheu, France
| | | | - Nathalie Marnet
- Plateau de Profilage Métabolique et Métabolomique (P2M2), Centre de Recherche Angers Nantes BIA, INRA, Le Rheu, France
| | - David Renault
- UMR EcoBio, Université de Rennes, CNRS, Rennes, France
| | - Yann Guitton
- LUNAM Université, Oniris, Laboratoire d’Etude des Résidus et Contaminants dans les Aliments (LABERCA), Nantes, France
| | - Alain Bouchereau
- IGEPP, Agrocampus Ouest, INRA, Université de Rennes, Le Rheu, France
| | - Régine Delourme
- IGEPP, Agrocampus Ouest, INRA, Université de Rennes, Le Rheu, France
| | | | - Antoine Gravot
- IGEPP, Agrocampus Ouest, INRA, Université de Rennes, Le Rheu, France
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23
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Hu X, Xie W, Wu C, Xu S. A directed learning strategy integrating multiple omic data improves genomic prediction. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:2011-2020. [PMID: 30950198 PMCID: PMC6737184 DOI: 10.1111/pbi.13117] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 02/04/2019] [Accepted: 03/13/2019] [Indexed: 05/05/2023]
Abstract
Genomic prediction (GP) aims to construct a statistical model for predicting phenotypes using genome-wide markers and is a promising strategy for accelerating molecular plant breeding. However, current progress of phenotype prediction using genomic data alone has reached a bottleneck, and previous studies on transcriptomic and metabolomic predictions ignored genomic information. Here, we designed a novel strategy of GP called multilayered least absolute shrinkage and selection operator (MLLASSO) by integrating multiple omic data into a single model that iteratively learns three layers of genetic features (GFs) supervised by observed transcriptome and metabolome. Significantly, MLLASSO learns higher order information of gene interactions, which enables us to achieve a significant improvement of predictability of yield in rice from 0.1588 (GP alone) to 0.2451 (MLLASSO). In the prediction of the first two layers, some genes were found to be genetically predictable genes (GPGs) as their expressions were accurately predicted with genetic markers. Interestingly, we made three dramatic discoveries for the GPGs: (i) GPGs are good predictors for highly complex traits like yield; (ii) GPGs are mostly eQTL genes (cis or trans); and (iii) trait-related transcriptional factor families are enriched in GPGs. These findings support the notion that learned GFs not only are good predictors for traits but also have specific biological implications regarding regulation of gene expressions. To differentiate the new method from conventional GP models, we called MLLASSO a directed learning strategy supervised by intermediate omic data. This new prediction model appears to be more reliable and more robust than conventional GP models.
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Affiliation(s)
- Xuehai Hu
- College of InformaticsAgricultural Bioinformatics Key Laboratory of Hubei ProvinceHuazhong Agricultural UniversityWuhanHubeiChina
- Department of Botany and Plant SciencesUniversity of CaliforniaRiversideCAUSA
| | - Weibo Xie
- College of InformaticsAgricultural Bioinformatics Key Laboratory of Hubei ProvinceHuazhong Agricultural UniversityWuhanHubeiChina
- Department of Botany and Plant SciencesUniversity of CaliforniaRiversideCAUSA
| | - Chengchao Wu
- College of InformaticsAgricultural Bioinformatics Key Laboratory of Hubei ProvinceHuazhong Agricultural UniversityWuhanHubeiChina
| | - Shizhong Xu
- Department of Botany and Plant SciencesUniversity of CaliforniaRiversideCAUSA
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24
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Metabolomic profiles differ among unique genotypes of a threatened Caribbean coral. Sci Rep 2019; 9:6067. [PMID: 30988456 PMCID: PMC6465396 DOI: 10.1038/s41598-019-42434-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 04/01/2019] [Indexed: 11/20/2022] Open
Abstract
Global threats to reefs require urgent efforts to resolve coral attributes that affect survival in a changing environment. Genetically different individuals of the same coral species are known to exhibit different responses to the same environmental conditions. New information on coral physiology, particularly as it relates to genotype, could aid in unraveling mechanisms that facilitate coral survival in the face of stressors. Metabolomic profiling detects a large subset of metabolites in an organism, and, when linked to metabolic pathways, can provide a snapshot of an organism’s physiological state. Identifying metabolites associated with desirable, genotype-specific traits could improve coral selection for restoration and other interventions. A key step toward this goal is determining whether intraspecific variation in coral metabolite profiles can be detected for species of interest, however little information exists to illustrate such differences. To address this gap, we applied untargeted 1H-NMR and LC-MS metabolomic profiling to three genotypes of the threatened coral Acropora cervicornis. Both methods revealed distinct metabolite “fingerprints” for each genotype examined. A number of metabolites driving separation among genotypes were identified or putatively annotated. Pathway analysis suggested differences in protein synthesis among genotypes. For the first time, these data illustrate intraspecific variation in metabolomic profiles for corals in a common garden. Our results contribute to the growing body of work on coral metabolomics and suggest future work could identify specific links between phenotype and metabolite profile in corals.
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25
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Kooke R, Morgado L, Becker F, van Eekelen H, Hazarika R, Zheng Q, de Vos RCH, Johannes F, Keurentjes JJB. Epigenetic mapping of the Arabidopsis metabolome reveals mediators of the epigenotype-phenotype map. Genome Res 2018; 29:96-106. [PMID: 30504416 PMCID: PMC6314165 DOI: 10.1101/gr.232371.117] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 11/27/2018] [Indexed: 11/24/2022]
Abstract
Identifying the sources of natural variation underlying metabolic differences between plants will enable a better understanding of plant metabolism and provide insights into the regulatory networks that govern plant growth and morphology. So far, however, the contribution of epigenetic variation to metabolic diversity has been largely ignored. In the present study, we utilized a panel of Arabidopsis thaliana epigenetic recombinant inbred lines (epiRILs) to assess the impact of epigenetic variation on the metabolic composition. Thirty epigenetic QTL (QTLepi) were detected, which partly overlap with QTLepi linked to growth and morphology. In an effort to identify causal candidate genes in the QTLepi regions and their putative trans-targets, we performed in silico small RNA and qPCR analyses. Differentially expressed genes were further studied by phenotypic and metabolic analyses of knockout mutants. Three genes were detected that recapitulated the detected QTLepi effects, providing evidence for epigenetic regulation in cis and in trans. These results indicate that epigenetic mechanisms impact metabolic diversity, possibly via small RNAs, and thus aid in further disentangling the complex epigenotype-phenotype map.
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Affiliation(s)
- Rik Kooke
- Laboratory of Genetics, Wageningen University and Research, 6708 PB Wageningen, The Netherlands.,Laboratory of Biometris, Wageningen University and Research, 6708 PB Wageningen, The Netherlands.,Centre for Biosystems Genomics, 6708 PB Wageningen, The Netherlands
| | - Lionel Morgado
- Groningen Bioinformatics Centre, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Frank Becker
- Laboratory of Genetics, Wageningen University and Research, 6708 PB Wageningen, The Netherlands
| | - Henriëtte van Eekelen
- Business Unit Bioscience, Wageningen Plant Research, 6708 PB Wageningen, The Netherlands
| | - Rashmi Hazarika
- Institute for Advanced Study, Technical University of Munich, 85748 Garching, Germany
| | - Qunfeng Zheng
- Business Unit Bioscience, Wageningen Plant Research, 6708 PB Wageningen, The Netherlands.,Tea Research Institute, Chinese Academy of Agricultural Sciences, 310008 Hangzhou, P.R. China
| | - Ric C H de Vos
- Centre for Biosystems Genomics, 6708 PB Wageningen, The Netherlands.,Business Unit Bioscience, Wageningen Plant Research, 6708 PB Wageningen, The Netherlands.,Netherlands Metabolomics Centre, 2333 CC Leiden, The Netherlands
| | - Frank Johannes
- Institute for Advanced Study, Technical University of Munich, 85748 Garching, Germany.,Population Epigenetics and Epigenomics, Department of Plant Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Joost J B Keurentjes
- Laboratory of Genetics, Wageningen University and Research, 6708 PB Wageningen, The Netherlands.,Centre for Biosystems Genomics, 6708 PB Wageningen, The Netherlands
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26
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Kawade K, Li Y, Koga H, Sawada Y, Okamoto M, Kuwahara A, Tsukaya H, Hirai MY. The cytochrome P450 CYP77A4 is involved in auxin-mediated patterning of the Arabidopsis thaliana embryo. Development 2018; 145:145/17/dev168369. [PMID: 30213790 DOI: 10.1242/dev.168369] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 07/30/2018] [Indexed: 12/30/2022]
Abstract
Metabolism often plays an important role in developmental control, in addition to supporting basal physiological requirements. However, our understanding of this interaction remains limited. Here, we performed quantitative phenome analysis of Arabidopsis thaliana cytochrome P450 mutants to identify a novel interaction between development and metabolism. We found that cyp77a4 mutants exhibit specific defects in cotyledon development, including asymmetric positioning and cup-shaped morphology, which could be rescued by introducing the CYP77A4 gene. Microscopy revealed that the abnormal patterning was detected at least from the 8-cell stage of the cyp77a4 embryos. We next analysed auxin distribution in mutant embryos, as the phenotypes resembled those of auxin-related mutants. We found that the auxin response pattern was severely perturbed in the cyp77a4 embryos owing to an aberrant distribution of the auxin efflux carrier PIN1. CYP77A4 intracellularly localised to the endoplasmic reticulum, which is consistent with the notion that this enzyme acts as an epoxidase of unsaturated fatty acids in the microsomal fraction. We propose that the CYP77A4-dependent metabolic pathway is an essential element for the establishment of polarity in plant embryos.
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Affiliation(s)
- Kensuke Kawade
- Okazaki Institute for Integrative Bioscience, 5-1, Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan .,National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki, Aichi 444-8585, Japan.,Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), 38 Nishigonaka, Myodaiji, Okazaki, Aichi 444-8585, Japan.,RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Yimeng Li
- RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Hiroyuki Koga
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yuji Sawada
- RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Mami Okamoto
- RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Ayuko Kuwahara
- RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Hirokazu Tsukaya
- Okazaki Institute for Integrative Bioscience, 5-1, Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan.,Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masami Yokota Hirai
- RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
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27
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Zhao L, Huang Y, Paglia K, Vaniya A, Wancewicz B, Keller AA. Metabolomics Reveals the Molecular Mechanisms of Copper Induced Cucumber Leaf ( Cucumis sativus) Senescence. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:7092-7100. [PMID: 29792813 DOI: 10.1021/acs.est.8b00742] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Excess copper may disturb plant photosynthesis and induce leaf senescence. The underlying toxicity mechanism is not well understood. Here, 3-week-old cucumber plants were foliar exposed to different copper concentrations (10, 100, and 500 mg/L) for a final dose of 0.21, 2.1, and 10 mg/plant, using CuSO4 as the Cu ion source for 7 days, three times per day. Metabolomics quantified 149 primary and 79 secondary metabolites. A number of intermediates of the tricarboxylic acid (TCA) cycle were significantly down-regulated 1.4-2.4 fold, indicating a perturbed carbohydrate metabolism. Ascorbate and aldarate metabolism and shikimate-phenylpropanoid biosynthesis (antioxidant and defense related pathways) were perturbed by excess copper. These metabolic responses occur even at the lowest copper dose considered although no phenotype changes were observed at this dose. High copper dose resulted in a 2-fold increase in phytol, a degradation product of chlorophyll. Polyphenol metabolomics revealed that some flavonoids were down-regulated, while the nonflavonoid 4-hydroxycinnamic acid and trans-2-hydroxycinnamic acid were significantly up-regulated 4- and 26-fold compared to the control. This study enhances current understanding of copper toxicity to plants and demonstrates that metabolomics profiling provides a more comprehensive view of plant responses to stressors, which can be applied to other plant species and contaminants.
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Affiliation(s)
- Lijuan Zhao
- Key Laboratory of Pollution Control and Resource Reuse, School of Environment , Nanjing University , Nanjing , Jiangsu 210023 , China
| | - Yuxiong Huang
- Bren School of Environmental Science & Management , University of California , Santa Barbara , California 93106-5131 , United States
- University of California , Center for Environmental Implications of Nanotechnology , Santa Barbara , California 93106 , United States
| | - Kelly Paglia
- UC Davis Genome Center-Metabolomics , University of California Davis , 451 Health Sciences Drive , Davis , California 95616 , United States
| | - Arpana Vaniya
- UC Davis Genome Center-Metabolomics , University of California Davis , 451 Health Sciences Drive , Davis , California 95616 , United States
| | - Benjamin Wancewicz
- UC Davis Genome Center-Metabolomics , University of California Davis , 451 Health Sciences Drive , Davis , California 95616 , United States
| | - Arturo A Keller
- Bren School of Environmental Science & Management , University of California , Santa Barbara , California 93106-5131 , United States
- University of California , Center for Environmental Implications of Nanotechnology , Santa Barbara , California 93106 , United States
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28
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Global analysis of threonine metabolism genes unravel key players in rice to improve the abiotic stress tolerance. Sci Rep 2018; 8:9270. [PMID: 29915249 PMCID: PMC6006157 DOI: 10.1038/s41598-018-27703-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 06/08/2018] [Indexed: 12/13/2022] Open
Abstract
The diversity in plant metabolites with improved phytonutrients is essential to achieve global food security and sustainable crop yield. Our study using computational metabolomics genome wide association study (cmGWAS) reports on a comprehensive profiling of threonine (Thr) metabolite in rice. Sixteen abiotic stress responsive (AbSR) – Thr metabolite producing genes (ThrMPG), modulate metabolite levels and play a significant role determining both physiological and nutritional importance of rice. These AbSR-ThrMPG were computationally analysed for their protein properties using OryzaCyc through plant metabolic network analyser. A total of 1373 and 1028 SNPs were involved in complex traits and genomic variations. Comparative mapping of AbSR-ThrMPG revealed the chromosomal colinearity with C4 grass species. Further, computational expression pattern of these genes predicted a differential expression profiling in diverse developmental tissues. Protein interaction of protein coding gene sequences revealed that the abiotic stresses (AbS) are multigenic in nature. In silico expression of AbSR-ThrMPG determined the putative involvement in response to individual AbS. This is the first comprehensive genome wide study reporting on AbSR –ThrMPG analysis in rice. The results of this study provide a pivotal resource for further functional investigation of these key genes in the vital areas of manipulating AbS signaling in rice improvement.
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29
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Klopsch R, Witzel K, Artemyeva A, Ruppel S, Hanschen FS. Genotypic Variation of Glucosinolates and Their Breakdown Products in Leaves of Brassica rapa. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:5481-5490. [PMID: 29746112 DOI: 10.1021/acs.jafc.8b01038] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
An in-depth glucosinolate (GLS) profiling was performed on a core collection of 91 Brassica rapa accessions, representing diverse morphotypes of heterogeneous geographical origin, to better understand the natural variation in GLS accumulation and GLS breakdown product formation. Leaves of the 91 B. rapa accessions were analyzed for their GLS composition by UHPLC-DAD and the corresponding breakdown products by GC-MS. Fifteen different GLSs were identified, and aliphatic GLSs prevailed regarding diversity and concentration. Twenty-three GLS breakdown products were identified, among them nine isothiocyanates, ten nitriles, and four epithionitriles. Epithionitriles were the prevailing breakdown products due to the high abundance of alkenyl GLSs. The large scale data set allowed the identification of correlations in abundance of specific GLSs or of GLS breakdown products. Discriminant function analysis identified subspecies with high levels of similarity in the acquired metabolite profiles. In general, the five main subspecies grouped significantly in terms of their GLS profiles.
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Affiliation(s)
- Rebecca Klopsch
- Leibniz Institute of Vegetable and Ornamental Crops, Theodor-Echtermeyer-Weg 1 , 14979 Großbeeren , Germany
| | - Katja Witzel
- Leibniz Institute of Vegetable and Ornamental Crops, Theodor-Echtermeyer-Weg 1 , 14979 Großbeeren , Germany
| | - Anna Artemyeva
- N.I.Vavilov Institute of Plant Genetic Resources, Bolshaya Morskaya Street 42-44 , 190000 St. Petersburg , Russia
- Agrophysical Research Institute, Grazhdanskiy prospect 14 , 195220 St. Petersburg , Russia
| | - Silke Ruppel
- Leibniz Institute of Vegetable and Ornamental Crops, Theodor-Echtermeyer-Weg 1 , 14979 Großbeeren , Germany
| | - Franziska S Hanschen
- Leibniz Institute of Vegetable and Ornamental Crops, Theodor-Echtermeyer-Weg 1 , 14979 Großbeeren , Germany
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Wen W, Jin M, Li K, Liu H, Xiao Y, Zhao M, Alseekh S, Li W, de Abreu E Lima F, Brotman Y, Willmitzer L, Fernie AR, Yan J. An integrated multi-layered analysis of the metabolic networks of different tissues uncovers key genetic components of primary metabolism in maize. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:1116-1128. [PMID: 29381266 DOI: 10.1111/tpj.13835] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 12/20/2017] [Accepted: 01/08/2018] [Indexed: 06/07/2023]
Abstract
Primary metabolism plays a pivotal role in normal plant growth, development and reproduction. As maize is a major crop worldwide, the primary metabolites produced by maize plants are of immense importance from both calorific and nutritional perspectives. Here a genome-wide association study (GWAS) of 61 primary metabolites using a maize association panel containing 513 inbred lines identified 153 significant loci associated with the level of these metabolites in four independent tissues. The genome-wide expression level of 760 genes was also linked with metabolite levels within the same tissue. On average, the genetic variants at each locus or transcriptional variance of each gene identified here were estimated to have a minor effect (4.4-7.8%) on primary metabolic variation. Thirty-six loci or genes were prioritized as being worthy of future investigation, either with regard to functional characterization or for their utility for genetic improvement. This target list includes the well-known opaque 2 (O2) and lkr/sdh genes as well as many less well-characterized genes. During our investigation of these 36 loci, we analyzed the genetic components and variations underlying the trehalose, aspartate and aromatic amino acid pathways, thereby functionally characterizing four genes involved in primary metabolism in maize.
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Affiliation(s)
- Weiwei Wen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, China
| | - Min Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Kun Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Haijun Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yingjie Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mingchao Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070, China
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Wenqiang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | | | - Yariv Brotman
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
- Department of Life Sciences, Ben-Gurion University of the Negev, Beersheba, Israel
| | - Lothar Willmitzer
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
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Wu S, Tohge T, Cuadros-Inostroza Á, Tong H, Tenenboim H, Kooke R, Méret M, Keurentjes JB, Nikoloski Z, Fernie AR, Willmitzer L, Brotman Y. Mapping the Arabidopsis Metabolic Landscape by Untargeted Metabolomics at Different Environmental Conditions. MOLECULAR PLANT 2018; 11:118-134. [PMID: 28866081 DOI: 10.1016/j.molp.2017.08.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Revised: 08/16/2017] [Accepted: 08/23/2017] [Indexed: 05/07/2023]
Abstract
Metabolic genome-wide association studies (mGWAS), whereupon metabolite levels are regarded as traits, can help unravel the genetic basis of metabolic networks. A total of 309 Arabidopsis accessions were grown under two independent environmental conditions (control and stress) and subjected to untargeted LC-MS-based metabolomic profiling; levels of the obtained hydrophilic metabolites were used in GWAS. Our two-condition-based GWAS for more than 3000 semi-polar metabolites resulted in the detection of 123 highly resolved metabolite quantitative trait loci (p ≤ 1.0E-08), 24.39% of which were environment-specific. Interestingly, differently from natural variation in Arabidopsis primary metabolites, which tends to be controlled by a large number of small-effect loci, we found several major large-effect loci alongside a vast number of small-effect loci controlling variation of secondary metabolites. The two-condition-based GWAS was followed by integration with network-derived metabolite-transcript correlations using a time-course stress experiment. Through this integrative approach, we selected 70 key candidate associations between structural genes and metabolites, and experimentally validated eight novel associations, two of them showing differential genetic regulation in the two environments studied. We demonstrate the power of combining large-scale untargeted metabolomics-based GWAS with time-course-derived networks both performed under different abiotic environments for identifying metabolite-gene associations, providing novel global insights into the metabolic landscape of Arabidopsis.
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Affiliation(s)
- Si Wu
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Takayuki Tohge
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Álvaro Cuadros-Inostroza
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; MetaSysX GmbH, Am Mühlenberg 11, 14476 Potsdam-Golm, Germany
| | - Hao Tong
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Hezi Tenenboim
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; MetaSysX GmbH, Am Mühlenberg 11, 14476 Potsdam-Golm, Germany
| | - Rik Kooke
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Michaël Méret
- MetaSysX GmbH, Am Mühlenberg 11, 14476 Potsdam-Golm, Germany
| | - Joost B Keurentjes
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Zoran Nikoloski
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Lothar Willmitzer
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Yariv Brotman
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; Department of Life Sciences, Ben Gurion University of the Negev, Beersheva, Israel.
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Nagler M, Nägele T, Gilli C, Fragner L, Korte A, Platzer A, Farlow A, Nordborg M, Weckwerth W. Eco-Metabolomics and Metabolic Modeling: Making the Leap From Model Systems in the Lab to Native Populations in the Field. FRONTIERS IN PLANT SCIENCE 2018; 9:1556. [PMID: 30459786 PMCID: PMC6232504 DOI: 10.3389/fpls.2018.01556] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 10/04/2018] [Indexed: 05/05/2023]
Abstract
Experimental high-throughput analysis of molecular networks is a central approach to characterize the adaptation of plant metabolism to the environment. However, recent studies have demonstrated that it is hardly possible to predict in situ metabolic phenotypes from experiments under controlled conditions, such as growth chambers or greenhouses. This is particularly due to the high molecular variance of in situ samples induced by environmental fluctuations. An approach of functional metabolome interpretation of field samples would be desirable in order to be able to identify and trace back the impact of environmental changes on plant metabolism. To test the applicability of metabolomics studies for a characterization of plant populations in the field, we have identified and analyzed in situ samples of nearby grown natural populations of Arabidopsis thaliana in Austria. A. thaliana is the primary molecular biological model system in plant biology with one of the best functionally annotated genomes representing a reference system for all other plant genome projects. The genomes of these novel natural populations were sequenced and phylogenetically compared to a comprehensive genome database of A. thaliana ecotypes. Experimental results on primary and secondary metabolite profiling and genotypic variation were functionally integrated by a data mining strategy, which combines statistical output of metabolomics data with genome-derived biochemical pathway reconstruction and metabolic modeling. Correlations of biochemical model predictions and population-specific genetic variation indicated varying strategies of metabolic regulation on a population level which enabled the direct comparison, differentiation, and prediction of metabolic adaptation of the same species to different habitats. These differences were most pronounced at organic and amino acid metabolism as well as at the interface of primary and secondary metabolism and allowed for the direct classification of population-specific metabolic phenotypes within geographically contiguous sampling sites.
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Affiliation(s)
- Matthias Nagler
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Thomas Nägele
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
- LMU Munich, Plant Evolutionary Cell Biology, Munich, Germany
| | - Christian Gilli
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Lena Fragner
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Arthur Korte
- Center for Computational and Theoretical Biology, University of Würzburg, Würzburg, Germany
| | - Alexander Platzer
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria
| | - Ashley Farlow
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria
| | - Magnus Nordborg
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
- *Correspondence: Wolfram Weckwerth,
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Ning K, Ding C, Zhu W, Zhang W, Dong Y, Shen Y, Su X. Comparative Metabolomic Analysis of the Cambium Tissue of Non-transgenic and Multi-Gene Transgenic Poplar ( Populus × euramericana 'Guariento'). FRONTIERS IN PLANT SCIENCE 2018; 9:1201. [PMID: 30174679 PMCID: PMC6108131 DOI: 10.3389/fpls.2018.01201] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 07/26/2018] [Indexed: 05/09/2023]
Abstract
Poplar, a model for woody plant research, is the most widely distributed tree species in the world. Metabolites are the basis of phenotypes, allowing an intuitive and effective understanding of biological processes and their mechanisms. However, metabolites in non-transgenic and multi-gene transgenic poplar remains poorly characterized, especially in regards of the influences on quantity and in the analysis of the relative abundance of metabolites after the introduction of multi stress-related genes. In this study, we investigated the cambium metabolomes of one non-transgenic (D5-0) and two multi-gene (vgb, SacB, ERF36, BtCry3A, and OC-I) transgenic lines (D5-20 and D5-21) of hybrid poplar (Populus × euramericana 'Guariento') using both gas chromatography-mass spectrometry (GC-MS) and ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). We aimed to explore the effects of the exogenous genes on metabolite composition and to screen out metabolites with important biological functions. Finally, we identified 239 named metabolites and determined their relative abundance. Among these, 197 metabolites had a different abundance across the three lines. These methabolites spanned nine primary and 44 secondary metabolism pathways. Arginine and glutamate, as substrates and intermediates in nitrogen metabolism, and important in growth and stress-related processes, as well as sucrose, uridine diphosphate glucose, and their derivatives, precursors in cell wall pathways, and catechol, relevant to insect resistance, differed greatly between the genetically modified and non-transgenic poplar. These findings may provide a basis for further study of cambium metabolism, and fully understand metabolites associated with stress response.
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Affiliation(s)
- Kun Ning
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Beijing, China
| | - Changjun Ding
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Beijing, China
| | - Wenxu Zhu
- College of Forestry, Shenyang Agricultural University, Shenyang, China
| | - Weixi Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Beijing, China
| | - Yufeng Dong
- Shandong Provincial Key Laboratory of Forest Tree Genetic Improvement, Shandong Academy of Forestry, Jinan, China
| | - Yingbai Shen
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xiaohua Su
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Beijing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- *Correspondence: Xiaohua Su,
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Nijveen H, Ligterink W, Keurentjes JJB, Loudet O, Long J, Sterken MG, Prins P, Hilhorst HW, de Ridder D, Kammenga JE, Snoek BL. AraQTL - workbench and archive for systems genetics in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:1225-1235. [PMID: 27995664 DOI: 10.1111/tpj.13457] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 11/24/2016] [Accepted: 12/06/2016] [Indexed: 06/06/2023]
Abstract
Genetical genomics studies uncover genome-wide genetic interactions between genes and their transcriptional regulators. High-throughput measurement of gene expression in recombinant inbred line populations has enabled investigation of the genetic architecture of variation in gene expression. This has the potential to enrich our understanding of the molecular mechanisms affected by and underlying natural variation. Moreover, it contributes to the systems biology of natural variation, as a substantial number of experiments have resulted in a valuable amount of interconnectable phenotypic, molecular and genotypic data. A number of genetical genomics studies have been published for Arabidopsis thaliana, uncovering many expression quantitative trait loci (eQTLs). However, these complex data are not easily accessible to the plant research community, leaving most of the valuable genetic interactions unexplored as cross-analysis of these studies is a major effort. We address this problem with AraQTL (http://www.bioinformatics.nl/Ara QTL/), an easily accessible workbench and database for comparative analysis and meta-analysis of all published Arabidopsis eQTL datasets. AraQTL provides a workbench for comparing, re-using and extending upon the results of these experiments. For example, one can easily screen a physical region for specific local eQTLs that could harbour candidate genes for phenotypic QTLs, or detect gene-by-environment interactions by comparing eQTLs under different conditions.
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Affiliation(s)
- Harm Nijveen
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, Wageningen, NL-6708 PB, The Netherlands
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, Wageningen, NL-6708 PB, The Netherlands
| | - Wilco Ligterink
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, Wageningen, NL-6708 PB, The Netherlands
| | - Joost J B Keurentjes
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, Wageningen, NL-6708 PB, The Netherlands
| | - Olivier Loudet
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, 78000, France
| | - Jiao Long
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, Wageningen, NL-6708 PB, The Netherlands
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, Wageningen, NL-6708 PB, The Netherlands
| | - Mark G Sterken
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, Wageningen, NL-6708 PB, The Netherlands
| | - Pjotr Prins
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, 38163, USA
| | - Henk W Hilhorst
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, Wageningen, NL-6708 PB, The Netherlands
| | - Dick de Ridder
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, Wageningen, NL-6708 PB, The Netherlands
| | - Jan E Kammenga
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, Wageningen, NL-6708 PB, The Netherlands
| | - Basten L Snoek
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, Wageningen, NL-6708 PB, The Netherlands
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Kazmi RH, Willems LAJ, Joosen RVL, Khan N, Ligterink W, Hilhorst HWM. Metabolomic analysis of tomato seed germination. Metabolomics 2017; 13:145. [PMID: 29104520 PMCID: PMC5653705 DOI: 10.1007/s11306-017-1284-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 10/13/2017] [Indexed: 01/19/2023]
Abstract
INTRODUCTION Seed germination is inherently related to seed metabolism, which changes throughout its maturation, desiccation and germination processes. The metabolite content of a seed and its ability to germinate are determined by underlying genetic architecture and environmental effects during development. OBJECTIVE This study aimed to assess an integrative approach to explore genetics modulating seed metabolism in different developmental stages and the link between seed metabolic- and germination traits. METHODS We have utilized gas chromatography-time-of-flight/mass spectrometry (GC-TOF/MS) metabolite profiling to characterize tomato seeds during dry and imbibed stages. We describe, for the first time in tomato, the use of a so-called generalized genetical genomics (GGG) model to study the interaction between genetics, environment and seed metabolism using 100 tomato recombinant inbred lines (RILs) derived from a cross between Solanum lycopersicum and Solanum pimpinellifolium. RESULTS QTLs were found for over two-thirds of the metabolites within several QTL hotspots. The transition from dry to 6 h imbibed seeds was associated with programmed metabolic switches. Significant correlations varied among individual metabolites and the obtained clusters were significantly enriched for metabolites involved in specific biochemical pathways. CONCLUSIONS Extensive genetic variation in metabolite abundance was uncovered. Numerous identified genetic regions that coordinate groups of metabolites were detected and these will contain plausible candidate genes. The combined analysis of germination phenotypes and metabolite profiles provides a strong indication for the hypothesis that metabolic composition is related to germination phenotypes and thus to seed performance.
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Affiliation(s)
- Rashid H. Kazmi
- 0000 0001 0791 5666grid.4818.5Wageningen Seed Lab, Lab. of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Leo A. J. Willems
- 0000 0001 0791 5666grid.4818.5Wageningen Seed Lab, Lab. of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Ronny V. L. Joosen
- 0000 0001 0791 5666grid.4818.5Wageningen Seed Lab, Lab. of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Noorullah Khan
- 0000 0001 0791 5666grid.4818.5Wageningen Seed Lab, Lab. of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Wilco Ligterink
- 0000 0001 0791 5666grid.4818.5Wageningen Seed Lab, Lab. of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Henk W. M. Hilhorst
- 0000 0001 0791 5666grid.4818.5Wageningen Seed Lab, Lab. of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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Comparative and parallel genome-wide association studies for metabolic and agronomic traits in cereals. Nat Commun 2016; 7:12767. [PMID: 27698483 PMCID: PMC5059443 DOI: 10.1038/ncomms12767] [Citation(s) in RCA: 154] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 07/29/2016] [Indexed: 01/19/2023] Open
Abstract
The plant metabolome is characterized by extensive diversity and is often regarded as a bridge between genome and phenome. Here we report metabolic and phenotypic genome-wide studies (mGWAS and pGWAS) in rice grain that, in addition to previous metabolic GWAS in rice leaf and maize kernel, show both distinct and overlapping aspects of genetic control of metabolism within and between species. We identify new candidate genes potentially influencing important metabolic and/or morphological traits. We show that the differential genetic architecture of rice metabolism between different tissues is in part determined by tissue specific expression. Using parallel mGWAS and pGWAS we identify new candidate genes potentially responsible for variation in traits such as grain colour and size, and provide evidence of metabotype-phenotype linkage. Our study demonstrates a powerful strategy for interactive functional genomics and metabolomics in plants, especially the cloning of minor QTLs for complex phenotypic traits.
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Xu S, Xu Y, Gong L, Zhang Q. Metabolomic prediction of yield in hybrid rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:219-227. [PMID: 27311694 DOI: 10.1111/tpj.13242] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 06/10/2016] [Accepted: 06/15/2016] [Indexed: 05/18/2023]
Abstract
Rice (Oryza sativa) provides a staple food source for more than 50% of the world's population. An increase in yield can significantly contribute to global food security. Hybrid breeding can potentially help to meet this goal because hybrid rice often shows a considerable increase in yield when compared with pure-bred cultivars. We recently developed a marker-guided prediction method for hybrid yield and showed a substantial increase in yield through genomic hybrid breeding. We now have transcriptomic and metabolomic data as potential resources for prediction. Using six prediction methods, including least absolute shrinkage and selection operator (LASSO), best linear unbiased prediction (BLUP), stochastic search variable selection, partial least squares, and support vector machines using the radial basis function and polynomial kernel function, we found that the predictability of hybrid yield can be further increased using these omic data. LASSO and BLUP are the most efficient methods for yield prediction. For high heritability traits, genomic data remain the most efficient predictors. When metabolomic data are used, the predictability of hybrid yield is almost doubled compared with genomic prediction. Of the 21 945 potential hybrids derived from 210 recombinant inbred lines, selection of the top 10 hybrids predicted from metabolites would lead to a ~30% increase in yield. We hypothesize that each metabolite represents a biologically built-in genetic network for yield; thus, using metabolites for prediction is equivalent to using information integrated from these hidden genetic networks for yield prediction.
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Affiliation(s)
- Shizhong Xu
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92507, USA
| | - Yang Xu
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92507, USA
| | - Liang Gong
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Qifa Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
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Castellani GC, Menichetti G, Garagnani P, Giulia Bacalini M, Pirazzini C, Franceschi C, Collino S, Sala C, Remondini D, Giampieri E, Mosca E, Bersanelli M, Vitali S, Valle IFD, Liò P, Milanesi L. Systems medicine of inflammaging. Brief Bioinform 2016; 17:527-40. [PMID: 26307062 PMCID: PMC4870395 DOI: 10.1093/bib/bbv062] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 06/29/2015] [Indexed: 12/30/2022] Open
Abstract
Systems Medicine (SM) can be defined as an extension of Systems Biology (SB) to Clinical-Epidemiological disciplines through a shifting paradigm, starting from a cellular, toward a patient centered framework. According to this vision, the three pillars of SM are Biomedical hypotheses, experimental data, mainly achieved by Omics technologies and tailored computational, statistical and modeling tools. The three SM pillars are highly interconnected, and their balancing is crucial. Despite the great technological progresses producing huge amount of data (Big Data) and impressive computational facilities, the Bio-Medical hypotheses are still of primary importance. A paradigmatic example of unifying Bio-Medical theory is the concept of Inflammaging. This complex phenotype is involved in a large number of pathologies and patho-physiological processes such as aging, age-related diseases and cancer, all sharing a common inflammatory pathogenesis. This Biomedical hypothesis can be mapped into an ecological perspective capable to describe by quantitative and predictive models some experimentally observed features, such as microenvironment, niche partitioning and phenotype propagation. In this article we show how this idea can be supported by computational methods useful to successfully integrate, analyze and model large data sets, combining cross-sectional and longitudinal information on clinical, environmental and omics data of healthy subjects and patients to provide new multidimensional biomarkers capable of distinguishing between different pathological conditions, e.g. healthy versus unhealthy state, physiological versus pathological aging.
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Sun CX, Gao XX, Li MQ, Fu JQ, Zhang YL. Plastic responses in the metabolome and functional traits of maize plants to temperature variations. PLANT BIOLOGY (STUTTGART, GERMANY) 2016; 18:249-61. [PMID: 26280133 DOI: 10.1111/plb.12378] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 08/10/2015] [Indexed: 05/21/2023]
Abstract
Environmentally inducible phenotypic plasticity is a major player in plant responses to climate change. However, metabolic responses and their role in determining the phenotypic plasticity of plants that are subjected to temperature variations remain poorly understood. The metabolomic profiles and metabolite levels in the leaves of three maize inbred lines grown in different temperature conditions were examined with a nuclear magnetic resonance metabolomic technique. The relationship of functional traits to metabolome profiles and the metabolic mechanism underlying temperature variations were then explored. A comparative analysis showed that during heat and cold stress, maize plants shared common plastic responses in biomass accumulation, carbon, nitrogen, sugars, some amino acids and compatible solutes. We also found that the plastic response of maize plants to heat stress was different from that under cold stress, mainly involving biomass allocation, shikimate and its aromatic amino acid derivatives, and other non-polar metabolites. The plastic responsiveness of functional traits of maize lines to temperature variations was low, while the metabolic responsiveness in plasticity was high, indicating that functional and metabolic plasticity may play different roles in maize plant adaptation to temperature variations. A linear regression analysis revealed that the maize lines could adapt to growth temperature variations through the interrelation of plastic responses in the metabolomes and functional traits, such as biomass allocation and the status of carbon and nitrogen. We provide valuable insight into the plastic response strategy of maize plants to temperature variations that will permit the optimisation of crop cultivation in an increasingly variable environment.
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Affiliation(s)
- C X Sun
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - X X Gao
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - M Q Li
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - J Q Fu
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Y L Zhang
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
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Technow F, Messina CD, Totir LR, Cooper M. Integrating Crop Growth Models with Whole Genome Prediction through Approximate Bayesian Computation. PLoS One 2015; 10:e0130855. [PMID: 26121133 PMCID: PMC4488317 DOI: 10.1371/journal.pone.0130855] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 05/25/2015] [Indexed: 11/18/2022] Open
Abstract
Genomic selection, enabled by whole genome prediction (WGP) methods, is revolutionizing plant breeding. Existing WGP methods have been shown to deliver accurate predictions in the most common settings, such as prediction of across environment performance for traits with additive gene effects. However, prediction of traits with non-additive gene effects and prediction of genotype by environment interaction (G×E), continues to be challenging. Previous attempts to increase prediction accuracy for these particularly difficult tasks employed prediction methods that are purely statistical in nature. Augmenting the statistical methods with biological knowledge has been largely overlooked thus far. Crop growth models (CGMs) attempt to represent the impact of functional relationships between plant physiology and the environment in the formation of yield and similar output traits of interest. Thus, they can explain the impact of G×E and certain types of non-additive gene effects on the expressed phenotype. Approximate Bayesian computation (ABC), a novel and powerful computational procedure, allows the incorporation of CGMs directly into the estimation of whole genome marker effects in WGP. Here we provide a proof of concept study for this novel approach and demonstrate its use with synthetic data sets. We show that this novel approach can be considerably more accurate than the benchmark WGP method GBLUP in predicting performance in environments represented in the estimation set as well as in previously unobserved environments for traits determined by non-additive gene effects. We conclude that this proof of concept demonstrates that using ABC for incorporating biological knowledge in the form of CGMs into WGP is a very promising and novel approach to improving prediction accuracy for some of the most challenging scenarios in plant breeding and applied genetics.
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Affiliation(s)
- Frank Technow
- Breeding Technologies, DuPont Pioneer, Johnston, IA, USA
- * E-mail:
| | - Carlos D. Messina
- Trait Characterization & Development, DuPont Pioneer, Johnston, IA, USA
| | - L. Radu Totir
- Breeding Technologies, DuPont Pioneer, Johnston, IA, USA
| | - Mark Cooper
- Trait Characterization & Development, DuPont Pioneer, Johnston, IA, USA
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Joseph B, Corwin JA, Kliebenstein DJ. Genetic variation in the nuclear and organellar genomes modulates stochastic variation in the metabolome, growth, and defense. PLoS Genet 2015; 11:e1004779. [PMID: 25569687 PMCID: PMC4287608 DOI: 10.1371/journal.pgen.1004779] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 09/25/2014] [Indexed: 11/25/2022] Open
Abstract
Recent studies are starting to show that genetic control over stochastic variation is a key evolutionary solution of single celled organisms in the face of unpredictable environments. This has been expanded to show that genetic variation can alter stochastic variation in transcriptional processes within multi-cellular eukaryotes. However, little is known about how genetic diversity can control stochastic variation within more non-cell autonomous phenotypes. Using an Arabidopsis reciprocal RIL population, we showed that there is significant genetic diversity influencing stochastic variation in the plant metabolome, defense chemistry, and growth. This genetic diversity included loci specific for the stochastic variation of each phenotypic class that did not affect the other phenotypic classes or the average phenotype. This suggests that the organism's networks are established so that noise can exist in one phenotypic level like metabolism and not permeate up or down to different phenotypic levels. Further, the genomic variation within the plastid and mitochondria also had significant effects on the stochastic variation of all phenotypic classes. The genetic influence over stochastic variation within the metabolome was highly metabolite specific, with neighboring metabolites in the same metabolic pathway frequently showing different levels of noise. As expected from bet-hedging theory, there was more genetic diversity and a wider range of stochastic variation for defense chemistry than found for primary metabolism. Thus, it is possible to begin dissecting the stochastic variation of whole organismal phenotypes in multi-cellular organisms. Further, there are loci that modulate stochastic variation at different phenotypic levels. Finding the identity of these genes will be key to developing complete models linking genotype to phenotype.
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Affiliation(s)
- Bindu Joseph
- Department of Plant Sciences, University of California, Davis, Davis, California, United States of America
| | - Jason A Corwin
- Department of Plant Sciences, University of California, Davis, Davis, California, United States of America
| | - Daniel J Kliebenstein
- Department of Plant Sciences, University of California, Davis, Davis, California, United States of America; DynaMo Center of Excellence, University of Copenhagen, Frederiksberg, Denmark
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Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Nat Genet 2014; 46:714-21. [PMID: 24908251 DOI: 10.1038/ng.3007] [Citation(s) in RCA: 416] [Impact Index Per Article: 41.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 05/15/2014] [Indexed: 12/21/2022]
Abstract
Plant metabolites are important to world food security in terms of maintaining sustainable yield and providing food with enriched phytonutrients. Here we report comprehensive profiling of 840 metabolites and a further metabolic genome-wide association study based on ∼6.4 million SNPs obtained from 529 diverse accessions of Oryza sativa. We identified hundreds of common variants influencing numerous secondary metabolites with large effects at high resolution. We observed substantial heterogeneity in the natural variation of metabolites and their underlying genetic architectures among different subspecies of rice. Data mining identified 36 candidate genes modulating levels of metabolites that are of potential physiological and nutritional importance. As a proof of concept, we functionally identified or annotated five candidate genes influencing metabolic traits. Our study provides insights into the genetic and biochemical bases of rice metabolome variation and can be used as a powerful complementary tool to classical phenotypic trait mapping for rice improvement.
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Wen F, Cheng X, Liu W, Xuan M, Zhang L, Zhao X, Shan M, Li Y, Teng L, Wang Z, Wang C. Chemical fingerprint and simultaneous determination of alkaloids and flavonoids in aerial parts of genusPeganumindigenous to China based on HPLC-UV: application of analysis on secondary metabolites accumulation. Biomed Chromatogr 2014; 28:1763-73. [DOI: 10.1002/bmc.3218] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 12/10/2013] [Accepted: 03/21/2014] [Indexed: 11/08/2022]
Affiliation(s)
- Fangfang Wen
- The MOE Key Laboratory for Standardization of Chinese Medicines and The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica; Shanghai University of Traditional Chinese Medicine, Shanghai R&D Centre for Standardization of Chinese Medicines; 1200 Cailun Road Shanghai 201203 People's Republic of China
| | - Xuemei Cheng
- The MOE Key Laboratory for Standardization of Chinese Medicines and The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica; Shanghai University of Traditional Chinese Medicine, Shanghai R&D Centre for Standardization of Chinese Medicines; 1200 Cailun Road Shanghai 201203 People's Republic of China
| | - Wei Liu
- The MOE Key Laboratory for Standardization of Chinese Medicines and The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica; Shanghai University of Traditional Chinese Medicine, Shanghai R&D Centre for Standardization of Chinese Medicines; 1200 Cailun Road Shanghai 201203 People's Republic of China
| | - Min Xuan
- The MOE Key Laboratory for Standardization of Chinese Medicines and The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica; Shanghai University of Traditional Chinese Medicine, Shanghai R&D Centre for Standardization of Chinese Medicines; 1200 Cailun Road Shanghai 201203 People's Republic of China
| | - Lei Zhang
- The MOE Key Laboratory for Standardization of Chinese Medicines and The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica; Shanghai University of Traditional Chinese Medicine, Shanghai R&D Centre for Standardization of Chinese Medicines; 1200 Cailun Road Shanghai 201203 People's Republic of China
| | - Xin Zhao
- Department of Pharmaceutical, College of Pharmacy; Xinjiang Medical University; 393 Xinyi Road, Urumqi 830011 Xinjiang People's Republic of China
| | - Meng Shan
- Department of Pharmaceutical, College of Pharmacy; Xinjiang Medical University; 393 Xinyi Road, Urumqi 830011 Xinjiang People's Republic of China
| | - Yan Li
- Department of Pharmaceutical, College of Pharmacy; Xinjiang Medical University; 393 Xinyi Road, Urumqi 830011 Xinjiang People's Republic of China
| | - Liang Teng
- The MOE Key Laboratory for Standardization of Chinese Medicines and The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica; Shanghai University of Traditional Chinese Medicine, Shanghai R&D Centre for Standardization of Chinese Medicines; 1200 Cailun Road Shanghai 201203 People's Republic of China
- Department of Pharmaceutical, College of Pharmacy; Xinjiang Medical University; 393 Xinyi Road, Urumqi 830011 Xinjiang People's Republic of China
| | - Zhengtao Wang
- The MOE Key Laboratory for Standardization of Chinese Medicines and The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica; Shanghai University of Traditional Chinese Medicine, Shanghai R&D Centre for Standardization of Chinese Medicines; 1200 Cailun Road Shanghai 201203 People's Republic of China
| | - Changhong Wang
- The MOE Key Laboratory for Standardization of Chinese Medicines and The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica; Shanghai University of Traditional Chinese Medicine, Shanghai R&D Centre for Standardization of Chinese Medicines; 1200 Cailun Road Shanghai 201203 People's Republic of China
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44
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Heuberger AL, Broeckling CD, Kirkpatrick KR, Prenni JE. Application of nontargeted metabolite profiling to discover novel markers of quality traits in an advanced population of malting barley. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:147-60. [PMID: 24119106 DOI: 10.1111/pbi.12122] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 08/15/2013] [Accepted: 08/20/2013] [Indexed: 05/02/2023]
Abstract
The process of breeding superior varieties for the agricultural industry is lengthy and expensive. Plant metabolites may act as markers of quality traits, potentially expediting the appraisal of experimental lines during breeding. Here, we evaluated the utility of metabolites as markers by assessing metabolic variation influenced by genetic and environmental factors in an advanced breeding setting and in relation to the phenotypic distribution of 20 quality traits. Nontargeted liquid chromatography-mass spectrometry metabolite profiling was performed on barley (Hordeum vulgare L.) grain and malt from 72 advanced malting barley lines grown at two distinct but climatically similar locations, with 2-row and 6-row barley as the main genetic factors. 27 420 molecular features were detected, and the metabolite and quality trait profiles were similarly influenced by genotype and environment; however, malt was more influenced by genotype compared with barley. An O2PLS model characterized molecular features and quality traits that covaried, and 1319 features associated with at least one of 20 quality traits. An indiscriminant MS/MS acquisition and novel data analysis method facilitated the identification of metabolites. The analysis described 216 primary and secondary metabolites that correlated with multiple quality traits and included amines, amino acids, alkaloids, polyphenolics and lipids. The mechanisms governing quality trait-metabolite associations were interpreted based on colocalization to genetic markers and their gene annotations. The results of this study support the hypothesis that metabolism and quality traits are co-influenced by relatively narrow genetic and environmental factors and illustrate the utility of grain metabolites as functional markers of quality traits.
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Affiliation(s)
- Adam L Heuberger
- Proteomics and Metabolomics Facility, Colorado State University, Fort Collins, CO, USA
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Lewis IA, Wacker M, Olszewski KL, Cobbold SA, Baska KS, Tan A, Ferdig MT, Llinás M. Metabolic QTL analysis links chloroquine resistance in Plasmodium falciparum to impaired hemoglobin catabolism. PLoS Genet 2014; 10:e1004085. [PMID: 24391526 PMCID: PMC3879234 DOI: 10.1371/journal.pgen.1004085] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 11/19/2013] [Indexed: 11/29/2022] Open
Abstract
Drug resistant strains of the malaria parasite, Plasmodium falciparum, have rendered chloroquine ineffective throughout much of the world. In parts of Africa and Asia, the coordinated shift from chloroquine to other drugs has resulted in the near disappearance of chloroquine-resistant (CQR) parasites from the population. Currently, there is no molecular explanation for this phenomenon. Herein, we employ metabolic quantitative trait locus mapping (mQTL) to analyze progeny from a genetic cross between chloroquine-susceptible (CQS) and CQR parasites. We identify a family of hemoglobin-derived peptides that are elevated in CQR parasites and show that peptide accumulation, drug resistance, and reduced parasite fitness are all linked in vitro to CQR alleles of the P. falciparum chloroquine resistance transporter (pfcrt). These findings suggest that CQR parasites are less fit because mutations in pfcrt interfere with hemoglobin digestion by the parasite. Moreover, our findings may provide a molecular explanation for the reemergence of CQS parasites in wild populations. Chloroquine was formerly a front line drug in the treatment of malaria. However, drug resistant strains of the malaria parasite have made this drug ineffective in many malaria endemic regions. Surprisingly, the discontinuation of chloroquine therapy has led to the reappearance of drug-sensitive parasites. In this study, we use metabolite quantitative trait locus analysis, parasite genetics, and peptidomics to demonstrate that chloroquine resistance is inherently linked to a defect in the parasite's ability to digest hemoglobin, which is an essential metabolic activity for malaria parasites. This metabolic impairment makes it harder for the drug-resistant parasites to reproduce than genetically-equivalent drug-sensitive parasites, and thus favors selection for drug-sensitive lines when parasites are in direct competition. Given these results, we attribute the re-emergence of chloroquine sensitive parasites in the wild to more efficient hemoglobin digestion.
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Affiliation(s)
- Ian A. Lewis
- Department of Molecular Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Mark Wacker
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Kellen L. Olszewski
- Department of Molecular Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Simon A. Cobbold
- Department of Molecular Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Katelynn S. Baska
- Department of Molecular Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Asako Tan
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Michael T. Ferdig
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
- * E-mail: (MTF); (ML)
| | - Manuel Llinás
- Department of Molecular Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- * E-mail: (MTF); (ML)
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Tomé F, Nägele T, Adamo M, Garg A, Marco-llorca C, Nukarinen E, Pedrotti L, Peviani A, Simeunovic A, Tatkiewicz A, Tomar M, Gamm M. The low energy signaling network. FRONTIERS IN PLANT SCIENCE 2014; 5:353. [PMID: 25101105 PMCID: PMC4102169 DOI: 10.3389/fpls.2014.00353] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 07/02/2014] [Indexed: 05/07/2023]
Abstract
Stress impacts negatively on plant growth and crop productivity, caicultural production worldwide. Throughout their life, plants are often confronted with multiple types of stress that affect overall cellular energy status and activate energy-saving responses. The resulting low energy syndrome (LES) includes transcriptional, translational, and metabolic reprogramming and is essential for stress adaptation. The conserved kinases sucrose-non-fermenting-1-related protein kinase-1 (SnRK1) and target of rapamycin (TOR) play central roles in the regulation of LES in response to stress conditions, affecting cellular processes and leading to growth arrest and metabolic reprogramming. We review the current understanding of how TOR and SnRK1 are involved in regulating the response of plants to low energy conditions. The central role in the regulation of cellular processes, the reprogramming of metabolism, and the phenotypic consequences of these two kinases will be discussed in light of current knowledge and potential future developments.
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Affiliation(s)
- Filipa Tomé
- Bayer CropScience NV, Innovation CenterGhent, Belgium
- *Correspondence: Filipa Tomé, Bayer CropScience NV, Innovation Center, Technologiepark 38, 9052 Zwijnaarde (Ghent), Belgium e-mail:
| | - Thomas Nägele
- Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
| | | | - Abhroop Garg
- Zentrum für Molekularbiologie der Pflanzen, Eberhard Karls Universität TübingenTübingen, Germany
| | - Carles Marco-llorca
- Zentrum für Molekularbiologie der Pflanzen, Eberhard Karls Universität TübingenTübingen, Germany
| | - Ella Nukarinen
- Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
| | - Lorenzo Pedrotti
- Julius-von-Sachs-Institut, Julius-Maximilians-Universität WürzburgWürzburg, Germany
| | - Alessia Peviani
- Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht UniversityUtrecht, Netherlands
| | - Andrea Simeunovic
- Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
| | - Anna Tatkiewicz
- Universidad Politécnica de Madrid–Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de MadridMadrid, Spain
| | - Monika Tomar
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht UniversityUtrecht, Netherlands
| | - Magdalena Gamm
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht UniversityUtrecht, Netherlands
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Pascual L, Xu J, Biais B, Maucourt M, Ballias P, Bernillon S, Deborde C, Jacob D, Desgroux A, Faurobert M, Bouchet JP, Gibon Y, Moing A, Causse M. Deciphering genetic diversity and inheritance of tomato fruit weight and composition through a systems biology approach. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:5737-52. [PMID: 24151307 PMCID: PMC3871826 DOI: 10.1093/jxb/ert349] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Integrative systems biology proposes new approaches to decipher the variation of phenotypic traits. In an effort to link the genetic variation and the physiological and molecular bases of fruit composition, the proteome (424 protein spots), metabolome (26 compounds), enzymatic profile (26 enzymes), and phenotypes of eight tomato accessions, covering the genetic diversity of the species, and four of their F1 hybrids, were characterized at two fruit developmental stages (cell expansion and orange-red). The contents of metabolites varied among the genetic backgrounds, while enzyme profiles were less variable, particularly at the cell expansion stage. Frequent genotype by stage interactions suggested that the trends observed for one accession at a physiological level may change in another accession. In agreement with this, the inheritance modes varied between crosses and stages. Although additivity was predominant, 40% of the traits were non-additively inherited. Relationships among traits revealed associations between different levels of expression and provided information on several key proteins. Notably, the role of frucktokinase, invertase, and cysteine synthase in the variation of metabolites was highlighted. Several stress-related proteins also appeared related to fruit weight differences. These key proteins might be targets for improving metabolite contents of the fruit. This systems biology approach provides better understanding of networks controlling the genetic variation of tomato fruit composition. In addition, the wide data sets generated provide an ideal framework to develop innovative integrated hypothesis and will be highly valuable for the research community.
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Affiliation(s)
- Laura Pascual
- INRA, UR1052, Unité de Génétique et Amélioration des Fruits et Légumes, F-84143 Avignon, France
| | - Jiaxin Xu
- INRA, UR1052, Unité de Génétique et Amélioration des Fruits et Légumes, F-84143 Avignon, France
- Northwest A&F University, College of Horticulture, Yang Ling, Shaanxin 712100, PR China
| | - Benoît Biais
- INRA-UMR 1332 Biologie du Fruit et Pathologie, Centre INRA de Bordeaux, F-33140 Villenave d’Ornon, France
- Université de Bordeaux, UMR1332 Biologie du Fruit et Pathologie, Centre INRA de Bordeaux, F-33140 Villenave d’Ornon, France
| | - Mickaël Maucourt
- Université de Bordeaux, UMR1332 Biologie du Fruit et Pathologie, Centre INRA de Bordeaux, F-33140 Villenave d’Ornon, France
- Metabolome Facility of Bordeaux Functional Genomics Center, IBVM, Centre INRA de Bordeaux, F-33140 Villenave d’Ornon, France
| | | | - Stéphane Bernillon
- INRA-UMR 1332 Biologie du Fruit et Pathologie, Centre INRA de Bordeaux, F-33140 Villenave d’Ornon, France
- Metabolome Facility of Bordeaux Functional Genomics Center, IBVM, Centre INRA de Bordeaux, F-33140 Villenave d’Ornon, France
| | - Catherine Deborde
- INRA-UMR 1332 Biologie du Fruit et Pathologie, Centre INRA de Bordeaux, F-33140 Villenave d’Ornon, France
| | - Daniel Jacob
- INRA-UMR 1332 Biologie du Fruit et Pathologie, Centre INRA de Bordeaux, F-33140 Villenave d’Ornon, France
- Metabolome Facility of Bordeaux Functional Genomics Center, IBVM, Centre INRA de Bordeaux, F-33140 Villenave d’Ornon, France
| | - Aurore Desgroux
- INRA, UR1052, Unité de Génétique et Amélioration des Fruits et Légumes, F-84143 Avignon, France
| | - Mireille Faurobert
- INRA, UR1052, Unité de Génétique et Amélioration des Fruits et Légumes, F-84143 Avignon, France
| | - Jean-Paul Bouchet
- INRA, UR1052, Unité de Génétique et Amélioration des Fruits et Légumes, F-84143 Avignon, France
| | - Yves Gibon
- INRA-UMR 1332 Biologie du Fruit et Pathologie, Centre INRA de Bordeaux, F-33140 Villenave d’Ornon, France
- Metabolome Facility of Bordeaux Functional Genomics Center, IBVM, Centre INRA de Bordeaux, F-33140 Villenave d’Ornon, France
| | - Annick Moing
- INRA-UMR 1332 Biologie du Fruit et Pathologie, Centre INRA de Bordeaux, F-33140 Villenave d’Ornon, France
| | - Mathilde Causse
- INRA, UR1052, Unité de Génétique et Amélioration des Fruits et Légumes, F-84143 Avignon, France
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48
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Systems genetics in "-omics" era: current and future development. Theory Biosci 2012; 132:1-16. [PMID: 23138757 DOI: 10.1007/s12064-012-0168-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Accepted: 10/25/2012] [Indexed: 02/06/2023]
Abstract
The systems genetics is an emerging discipline that integrates high-throughput expression profiling technology and systems biology approaches for revealing the molecular mechanism of complex traits, and will improve our understanding of gene functions in the biochemical pathway and genetic interactions between biological molecules. With the rapid advances of microarray analysis technologies, bioinformatics is extensively used in the studies of gene functions, SNP-SNP genetic interactions, LD block-block interactions, miRNA-mRNA interactions, DNA-protein interactions, protein-protein interactions, and functional mapping for LD blocks. Based on bioinformatics panel, which can integrate "-omics" datasets to extract systems knowledge and useful information for explaining the molecular mechanism of complex traits, systems genetics is all about to enhance our understanding of biological processes. Systems biology has provided systems level recognition of various biological phenomena, and constructed the scientific background for the development of systems genetics. In addition, the next-generation sequencing technology and post-genome wide association studies empower the discovery of new gene and rare variants. The integration of different strategies will help to propose novel hypothesis and perfect the theoretical framework of systems genetics, which will make contribution to the future development of systems genetics, and open up a whole new area of genetics.
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Rasmussen S, Parsons AJ, Jones CS. Metabolomics of forage plants: a review. ANNALS OF BOTANY 2012; 110:1281-90. [PMID: 22351485 PMCID: PMC3478039 DOI: 10.1093/aob/mcs023] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Accepted: 01/12/2012] [Indexed: 05/06/2023]
Abstract
BACKGROUND Forage plant breeding is under increasing pressure to deliver new cultivars with improved yield, quality and persistence to the pastoral industry. New innovations in DNA sequencing technologies mean that quantitative trait loci analysis and marker-assisted selection approaches are becoming faster and cheaper, and are increasingly used in the breeding process with the aim to speed it up and improve its precision. High-throughput phenotyping is currently a major bottle neck and emerging technologies such as metabolomics are being developed to bridge the gap between genotype and phenotype; metabolomics studies on forages are reviewed in this article. SCOPE Major challenges for pasture production arise from the reduced availability of resources, mainly water, nitrogen and phosphorus, and metabolomics studies on metabolic responses to these abiotic stresses in Lolium perenne and Lotus species will be discussed here. Many forage plants can be associated with symbiotic microorganisms such as legumes with nitrogen fixing rhizobia, grasses and legumes with phosphorus-solubilizing arbuscular mycorrhizal fungi, and cool temperate grasses with fungal anti-herbivorous alkaloid-producing Neotyphodium endophytes and metabolomics studies have shown that these associations can significantly affect the metabolic composition of forage plants. The combination of genetics and metabolomics, also known as genetical metabolomics can be a powerful tool to identify genetic regions related to specific metabolites or metabolic profiles, but this approach has not been widely adopted for forages yet, and we argue here that more studies are needed to improve our chances of success in forage breeding. CONCLUSIONS Metabolomics combined with other '-omics' technologies and genome sequencing can be invaluable tools for large-scale geno- and phenotyping of breeding populations, although the implementation of these approaches in forage breeding programmes still lags behind. The majority of studies using metabolomics approaches have been performed with model species or cereals and findings from these studies are not easily translated to forage species. To be most effective these approaches should be accompanied by whole-plant physiology and proof of concept (modelling) studies. Wider considerations of possible consequences of novel traits on the fitness of new cultivars and symbiotic associations need also to be taken into account.
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Affiliation(s)
- Susanne Rasmussen
- AgResearch Limited, Grasslands Research Centre, Tennent Drive, Palmerston North 4442, New Zealand.
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50
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Carreno-Quintero N, Bouwmeester HJ, Keurentjes JJB. Genetic analysis of metabolome-phenotype interactions: from model to crop species. Trends Genet 2012; 29:41-50. [PMID: 23084137 DOI: 10.1016/j.tig.2012.09.006] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Revised: 09/18/2012] [Accepted: 09/20/2012] [Indexed: 10/27/2022]
Abstract
The past decade has seen increased interest from the scientific community, and particularly plant biologists, in integrating metabolic approaches into research aimed at unraveling phenotypic diversity and its underlying genetic variation. Advances in plant metabolomics have enabled large-scale analyses that have identified qualitative and quantitative variation in the metabolic content of various species, and this variation has been linked to genetic factors through genetic-mapping approaches, providing a glimpse of the genetic architecture of the plant metabolome. Parallel analyses of morphological phenotypes and physiological performance characteristics have further enhanced our understanding of the complex molecular mechanisms regulating these quantitative traits. This review aims to illustrate the advantages of including assessments of phenotypic and metabolic diversity in investigations of the genetic basis of complex traits, and the value of this approach in studying agriculturally important crops. We highlight the ground-breaking work on model species and discuss recent achievements in important crop species.
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