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Chen Q, Luo Y, Shen Y, Li X, Yang H, Li J, Wang J, Xiao Y. Fructose corn syrup induces inflammatory injury and obesity by altering gut microbiota and gut microbiota-related arachidonic acid metabolism. J Nutr Biochem 2024; 124:109527. [PMID: 37979711 DOI: 10.1016/j.jnutbio.2023.109527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/27/2023] [Accepted: 11/07/2023] [Indexed: 11/20/2023]
Abstract
Excessive fructose corn syrup (FCS) intake brings a series of health problems. The aim of the present study was to explore the mechanism of FCS-induced metabolic disorders from the perspective of gut microbiota. Mice were fed for 16 weeks with normal or 30% FCS drinking water. Compared to the control group, FCS caused significantly higher fat deposition, hepatic steatosis, liver and intestinal inflammatory damages (P<.05). FCS increased the abundance of Muribaculaceae in vivo and in vitro, which was positively correlated with the indices of metabolic disorders (P<.05). In vivo and in vitro data indicated that FCS enhanced the microbial function involved in pentose phosphate pathway and arachidonic acid metabolism, metabolomics further demonstrated that FCS led to an increase in prostaglandins (the catabolites of arachidonic acid) (P<.05). Our study confirmed that FCS can directly promote gut microbiota to synthesize inflammatory factor prostaglandins, which provides new insights and directions for the treatment of FCS-induced metabolic disorders and inflammation.
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Affiliation(s)
- Qu Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yinmei Luo
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yu Shen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xiaoqiong Li
- Institute of Food Sciences, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Hua Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jinjun Li
- Institute of Food Sciences, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.
| | | | - Yingping Xiao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.
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Manickam S, Rajagopalan VR, Kambale R, Rajasekaran R, Kanagarajan S, Muthurajan R. Plant Metabolomics: Current Initiatives and Future Prospects. Curr Issues Mol Biol 2023; 45:8894-8906. [PMID: 37998735 PMCID: PMC10670879 DOI: 10.3390/cimb45110558] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 10/30/2023] [Accepted: 11/06/2023] [Indexed: 11/25/2023] Open
Abstract
Plant metabolomics is a rapidly advancing field of plant sciences and systems biology. It involves comprehensive analyses of small molecules (metabolites) in plant tissues and cells. These metabolites include a wide range of compounds, such as sugars, amino acids, organic acids, secondary metabolites (e.g., alkaloids and flavonoids), lipids, and more. Metabolomics allows an understanding of the functional roles of specific metabolites in plants' physiology, development, and responses to biotic and abiotic stresses. It can lead to the identification of metabolites linked with specific traits or functions. Plant metabolic networks and pathways can be better understood with the help of metabolomics. Researchers can determine how plants react to environmental cues or genetic modifications by examining how metabolite profiles change under various crop stages. Metabolomics plays a major role in crop improvement and biotechnology. Integrating metabolomics data with other omics data (genomics, transcriptomics, and proteomics) provides a more comprehensive perspective of plant biology. This systems biology approach enables researchers to understand the complex interactions within organisms.
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Affiliation(s)
- Sudha Manickam
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India; (S.M.); (V.R.R.); (R.K.); (R.R.)
| | - Veera Ranjani Rajagopalan
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India; (S.M.); (V.R.R.); (R.K.); (R.R.)
| | - Rohit Kambale
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India; (S.M.); (V.R.R.); (R.K.); (R.R.)
| | - Raghu Rajasekaran
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India; (S.M.); (V.R.R.); (R.K.); (R.R.)
| | - Selvaraju Kanagarajan
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 190, 234 22 Lomma, Sweden
| | - Raveendran Muthurajan
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India; (S.M.); (V.R.R.); (R.K.); (R.R.)
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Ran F, Yuan Y, Bai X, Li C, Li J, Chen H. Carbon and nitrogen metabolism affects kentucky bluegrass rhizome expansion. BMC PLANT BIOLOGY 2023; 23:221. [PMID: 37101108 PMCID: PMC10131326 DOI: 10.1186/s12870-023-04230-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 04/15/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Rhizome is vital for carbon and nitrogen metabolism of the whole plant. However, the effect of carbon and nitrogen in the rhizome on rhizome expansion remains unclear. RESULTS Three wild Kentucky bluegrass (Poa pratensis L.) germplasms with different rhizome expansion capacity (strong expansion capacity, 'YZ'; medium expansion capacity, 'WY'; and weak expansion capacity, 'AD') were planted in the field and the rhizomes number, tiller number, rhizome dry weight, physiological indicators and enzyme activity associated carbon and nitrogen metabolisms were measured. Liquid chromatography coupled to mass spectrometry (LC-MS) was utilized to analyze the metabolomic of the rhizomes. The results showed that the rhizome and tiller numbers of the YZ were 3.26 and 2.69-fold of that of the AD, respectively. The aboveground dry weight of the YZ was the greatest among all three germplasms. Contents of soluble sugar, starch, sucrose, NO3--N, and free amino acid were significantly higher in rhizomes of the YZ than those of the WY and AD (P < 0.05). The activities of glutamine synthetase (GS), glutamate dehydrogenase (GDH) and sucrose phosphate synthase (SPS) of the YZ were the highest among all three germplasm, with values of 17.73 A·g- 1 h- 1, 5.96 µmol·g- 1 min- 1, and 11.35 mg·g- 1 h- 1, respectively. Metabolomics analyses revealed that a total of 28 differentially expressed metabolites (DEMs) were up-regulated, and 25 DEMs were down-regulated in both comparison groups (AD vs. YZ group and WY vs. YZ group). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis demonstrated that metabolites related to histidine metabolism, tyrosine metabolism, tryptophan metabolism, and phenylalanine metabolism were associated with rhizomes carbon and nitrogen metabolism. CONCLUSIONS Overall, the results suggest that soluble sugar, starch, sucrose, NO3--N, and free amino acid in rhizome are important to and promote rhizome expansion in Kentucky bluegrass, while tryptamine, 3-methylhistidine, 3-indoleacetonitrile, indole, and histamine may be key metabolites in promoting carbon and nitrogen metabolism of rhizome.
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Affiliation(s)
- Fu Ran
- College of Grassland Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yajuan Yuan
- College of Grassland Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Xiaoming Bai
- College of Grassland Science, Gansu Agricultural University, Lanzhou, 730070, China.
- Key Laboratory of Grassland Ecosystem, Gansu Agricultural University, Lanzhou, 730070, China.
| | - Changning Li
- College of Grassland Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Juanxia Li
- College of Grassland Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Hui Chen
- College of Grassland Science, Gansu Agricultural University, Lanzhou, 730070, China
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Bornhofen E, Fè D, Nagy I, Lenk I, Greve M, Didion T, Jensen CS, Asp T, Janss L. Genetic architecture of inter-specific and -generic grass hybrids by network analysis on multi-omics data. BMC Genomics 2023; 24:213. [PMID: 37095447 PMCID: PMC10127077 DOI: 10.1186/s12864-023-09292-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 04/02/2023] [Indexed: 04/26/2023] Open
Abstract
BACKGROUND Understanding the mechanisms underlining forage production and its biomass nutritive quality at the omics level is crucial for boosting the output of high-quality dry matter per unit of land. Despite the advent of multiple omics integration for the study of biological systems in major crops, investigations on forage species are still scarce. RESULTS Our results identified substantial changes in gene co-expression and metabolite-metabolite network topologies as a result of genetic perturbation by hybridizing L. perenne with another species within the genus (L. multiflorum) relative to across genera (F. pratensis). However, conserved hub genes and hub metabolomic features were detected between pedigree classes, some of which were highly heritable and displayed one or more significant edges with agronomic traits in a weighted omics-phenotype network. In spite of tagging relevant biological molecules as, for example, the light-induced rice 1 (LIR1), hub features were not necessarily better explanatory variables for omics-assisted prediction than features stochastically sampled and all available regressors. CONCLUSIONS The utilization of computational techniques for the reconstruction of co-expression networks facilitates the identification of key omic features that serve as central nodes and demonstrate correlation with the manifestation of observed traits. Our results also indicate a robust association between early multi-omic traits measured in a greenhouse setting and phenotypic traits evaluated under field conditions.
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Affiliation(s)
- Elesandro Bornhofen
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark.
| | - Dario Fè
- Research Division, DLF Seeds A/S, Store Heddinge, Denmark
| | - Istvan Nagy
- Center for Quantitative Genetics and Genomics, Aarhus University, Slagelse, Denmark
| | - Ingo Lenk
- Research Division, DLF Seeds A/S, Store Heddinge, Denmark
| | - Morten Greve
- Research Division, DLF Seeds A/S, Store Heddinge, Denmark
| | - Thomas Didion
- Research Division, DLF Seeds A/S, Store Heddinge, Denmark
| | | | - Torben Asp
- Center for Quantitative Genetics and Genomics, Aarhus University, Slagelse, Denmark
| | - Luc Janss
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark.
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Hanif S, Bilal M, Nasreen S, Latif M, Zia M. Indole-3-acetic acid (IAA) doping on the surface of CuO-NPs reduces the toxic effects of NPs on Lactuca sativa. J Biotechnol 2023; 367:53-61. [PMID: 36990354 DOI: 10.1016/j.jbiotec.2023.03.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/27/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023]
Abstract
CuO Nanoparticles (CuO NPs) retard the plant growth but at appropriate concentration boosts shoot growth and therefore may function as nano-carrier or nano-fertilizer. To overcome the toxic effects, NPs can be capped with plant growth regulators. In this work, CuO-NPs (30 nm) were synthesized as the carrier and capped with indole-3-acetic acid (IAA) to generate CuO-IAA NPs (30.4 nm) as toxicity mitigant molecules. Seedlings of dicots, Lactuca sativa L. (Lettuce) were exposed to 5, 10 mg Kg-1/ of NPs in the soil to analyze shoot length, fresh and dry weight of shoots, phytochemicals, and antioxidant response. Toxicity to shoot length was recorded at higher concentrations of CuO-NPs, however, a reduction in toxicity was observed for CuO-IAA nanocomposite. Concentration-dependent decrease in the biomass of plants was also observed at higher concentrations of CuO-NPs (10 mg/kg). The antioxidative phytochemicals (phenolics and flavonoids) and antioxidative response increased in plants when exposed to CuO-NPs. However, the presence of CuO-IAA NPs combats the toxic response and a significant decrease in non-enzymatic antioxidants and total antioxidative response and total reducing power potential was observed. The results demonstrate that CuO-NPs can be used as a carrier of hormones for the enhancement of plant biomass and IAA on the surface of NPs reduces the toxic effects on NPs.
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Affiliation(s)
- Saad Hanif
- Department of Biotechnology, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Muhammad Bilal
- Department of Biotechnology, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Syeda Nasreen
- Ibadat International University, Islamabad 44000, Pakistan
| | - Muhammad Latif
- Centre for Genetics and Inherited Diseases (CGID), Taibah University, Madinah, Saudi Arabia; Department of Biochemistry and Molecular Medicine, College of Medicine, Taibah University, Madinah, Saudi Arabia.
| | - Muhammad Zia
- Department of Biotechnology, Quaid-i-Azam University, Islamabad 45320, Pakistan.
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Application of hyperspectral imaging assisted with integrated deep learning approaches in identifying geographical origins and predicting nutrient contents of Coix seeds. Food Chem 2023; 404:134503. [DOI: 10.1016/j.foodchem.2022.134503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 09/28/2022] [Accepted: 10/01/2022] [Indexed: 11/06/2022]
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β-Cyclocitral-Mediated Metabolic Changes Optimize Growth and Defense Responses in Solanum lycopersicum L. Metabolites 2023; 13:metabo13030329. [PMID: 36984769 PMCID: PMC10053473 DOI: 10.3390/metabo13030329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 02/14/2023] [Accepted: 02/18/2023] [Indexed: 02/25/2023] Open
Abstract
β-cyclocitral (βCC) is one of the significant oxidative products of β-carotene. It primes plants for multiple stress acclimation without compromising plant growth. Metabolic reorganization is necessary to maintain a balance between growth and defense. However, the βCC-mediated changes in a plant’s metabolic network are unknown. Here, we demonstrate how βCC-induced metabolic changes enable Solanum lycopersicum L. (tomato) plants to promote defense and maintain growth under stress. An analysis of early (0–240 min) and late (72 h) changes in the tomato metabolome after βCC-treatment using liquid chromatography and tandem mass spectrometry identified 57 compounds. A principal coordinate analysis suggested that βCC treatment significantly changes the metabolite profile. A variable importance in projection (VIP) analysis revealed 16 and 19 discriminant metabolites from early and late samples, respectively (VIP ≥ 1.0). Upregulated metabolites were mainly amino acids and phytophenols. Pathway enrichment analysis showed that βCC treatment influenced amino acid metabolism at early and later times; however, phenylpropanoid and isoquinoline biosynthesis were influenced only at the later time. A 66.6% similarity in the upregulated metabolites of βCC- and simulated-herbivory-treated plants confirmed βCC’s role against herbivores. We conclude that βCC steers a temporal separation in amino acids and defense metabolite accumulation that optimizes resource allocation to growth and defense.
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Calabrese V, Schmitz-Afonso I, Riah-Anglet W, Trinsoutrot-Gattin I, Pawlak B, Afonso C. Direct introduction MALDI FTICR MS based on dried droplet deposition applied to non-targeted metabolomics on Pisum Sativum root exudates. Talanta 2023; 253:123901. [PMID: 36088848 DOI: 10.1016/j.talanta.2022.123901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 12/13/2022]
Abstract
Non-targeted metabolomic approaches based on direct introduction (DI) through a soft ionization source are nowadays used for large-scale analysis and wide cover-up of metabolites in complex matrices. When coupled with ultra-high-resolution Fourier-Transform ion cyclotron resonance (FTICR MS), DI is generally performed through electrospray (ESI), which, despite the great analytical throughput, can suffer of matrix effects due to residual salts or charge competitors. In alternative, matrix assisted laser desorption ionization (MALDI) coupled with FTICR MS offers relatively high salt tolerance but it is mainly used for imaging of small molecule within biological tissues. In this study, we report a systematic evaluation on the performance of direct introduction ESI and MALDI coupled with FTICR MS applied to the analysis of root exudates (RE), a complex mixture of metabolites released from plant root tips and containing a relatively high salt concentration. Classic dried droplet deposition followed by screening of best matrices and ratio allowed the selection of high ranked conditions for non-targeted metabolomics on RE. Optimization of MALDI parameters led to improved reproducibility and precision. A RE desalted sample was used for comparison on ionization efficiency of the two sources and ion enhancement at high salinity was highlighted in MALDI by spiking desalted solution with inorganic salts. Application of a true lyophilized RE sample exhibited the complementarity of the two sources and the ability of MALDI in the detection of undisclosed metabolites suffering of matrix effects in ESI mode.
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Affiliation(s)
- Valentina Calabrese
- Normandie Univ, COBRA, UMR 6014 and FR 3038, Université de Rouen, INSA de Rouen, CNRS, IRCOF, 1 Rue Tesnières, 76821, Mont-Saint-Aignan, Cedex, France
| | - Isabelle Schmitz-Afonso
- Normandie Univ, COBRA, UMR 6014 and FR 3038, Université de Rouen, INSA de Rouen, CNRS, IRCOF, 1 Rue Tesnières, 76821, Mont-Saint-Aignan, Cedex, France.
| | - Wassila Riah-Anglet
- UniLaSalle, AGHYLE Research Unit UP 2018.C101, Rouen Team, 76134 Mont-Saint Aignan, SFR Normandie Végétal FED 4277, 76000, Rouen, France
| | - Isabelle Trinsoutrot-Gattin
- UniLaSalle, AGHYLE Research Unit UP 2018.C101, Rouen Team, 76134 Mont-Saint Aignan, SFR Normandie Végétal FED 4277, 76000, Rouen, France
| | - Barbara Pawlak
- Laboratoire GlycoMEV UR 4358, Université de Rouen Normandie, SFR Normandie Végétal FED 4277, 76000, Rouen, France
| | - Carlos Afonso
- Normandie Univ, COBRA, UMR 6014 and FR 3038, Université de Rouen, INSA de Rouen, CNRS, IRCOF, 1 Rue Tesnières, 76821, Mont-Saint-Aignan, Cedex, France
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Song G, Lu Y, Wang Y, Nie C, Xu M, Wang L, Bai Y. Analysis of metabolic differences in maize in different growth stages under nitrogen stress based on UPLC-QTOF-MS. FRONTIERS IN PLANT SCIENCE 2023; 14:1141232. [PMID: 37077647 PMCID: PMC10106645 DOI: 10.3389/fpls.2023.1141232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 03/20/2023] [Indexed: 05/03/2023]
Abstract
Introduction Maize has a high demand for nitrogen during the growth period. The study of metabolic changes in maize can provide a theoretical basis for rational nitrogen nutrition regulation. Methods In order to investigate the changes of different metabolites and their metabolic pathways in maize leaves under nitrogen stress, we used ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS) for metabolomic analysis of maize leaves under different nitrogen treatments at three critical growth stages (V4, V12 and R1) in a pot experiment under natural conditions. Results and discussion The results showed that nitrogen stress significantly affected sugar metabolism and nitrogen metabolism, and affected carbon and nitrogen balance, and the effects of stress on maize leaves metabolism increased with the growth process. Metabolic pathways such as the TCA cycle and starch and sucrose metabolism were mainly affected at the seeding stage (V4). The stress response to nitrogen deficiency also showed significant upregulation of flavonoids such as luteolin and astragalin during the booting stage (V12) and anthesis-silking stage (R1). During R1 stage, the synthesis of tryptophan and phenylalanine and the degradation of lysine were significantly affected. Compared with nitrogen stress, the metabolic synthesis of key amino acids and jasmonic acid were intensified and the TCA cycle was promoted under nitrogen sufficiency conditions. This study initially revealed that the response mechanism of maize to nitrogen stress at the metabolic level.
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Liu X, Li Y, Micallef SA. Developmentally related and drought-induced shifts in the kale metabolome limited Salmonella enterica association, providing novel insights to enhance food safety. Food Microbiol 2022; 108:104113. [DOI: 10.1016/j.fm.2022.104113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/22/2022] [Accepted: 08/07/2022] [Indexed: 11/27/2022]
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Mishra AK, Sudalaimuthuasari N, Hazzouri KM, Saeed EE, Shah I, Amiri KMA. Tapping into Plant-Microbiome Interactions through the Lens of Multi-Omics Techniques. Cells 2022; 11:3254. [PMID: 36291121 PMCID: PMC9600287 DOI: 10.3390/cells11203254] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 10/21/2023] Open
Abstract
This review highlights the pivotal role of root exudates in the rhizosphere, especially the interactions between plants and microbes and between plants and plants. Root exudates determine soil nutrient mobilization, plant nutritional status, and the communication of plant roots with microbes. Root exudates contain diverse specialized signaling metabolites (primary and secondary). The spatial behavior of these metabolites around the root zone strongly influences rhizosphere microorganisms through an intimate compatible interaction, thereby regulating complex biological and ecological mechanisms. In this context, we reviewed the current understanding of the biological phenomenon of allelopathy, which is mediated by phytotoxic compounds (called allelochemicals) released by plants into the soil that affect the growth, survival, development, ecological infestation, and intensification of other plant species and microbes in natural communities or agricultural systems. Advances in next-generation sequencing (NGS), such as metagenomics and metatranscriptomics, have opened the possibility of better understanding the effects of secreted metabolites on the composition and activity of root-associated microbial communities. Nevertheless, understanding the role of secretory metabolites in microbiome manipulation can assist in designing next-generation microbial inoculants for targeted disease mitigation and improved plant growth using the synthetic microbial communities (SynComs) tool. Besides a discussion on different approaches, we highlighted the advantages of conjugation of metabolomic approaches with genetic design (metabolite-based genome-wide association studies) in dissecting metabolome diversity and understanding the genetic components of metabolite accumulation. Recent advances in the field of metabolomics have expedited comprehensive and rapid profiling and discovery of novel bioactive compounds in root exudates. In this context, we discussed the expanding array of metabolomics platforms for metabolome profiling and their integration with multivariate data analysis, which is crucial to explore the biosynthesis pathway, as well as the regulation of associated pathways at the gene, transcript, and protein levels, and finally their role in determining and shaping the rhizomicrobiome.
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Affiliation(s)
- Ajay Kumar Mishra
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Naganeeswaran Sudalaimuthuasari
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Khaled M. Hazzouri
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Esam Eldin Saeed
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Iltaf Shah
- Department of Chemistry (Biochemistry), College of Science, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Khaled M. A. Amiri
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
- Department of Biology, College of Science, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
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Singh DP, Bisen MS, Shukla R, Prabha R, Maurya S, Reddy YS, Singh PM, Rai N, Chaubey T, Chaturvedi KK, Srivastava S, Farooqi MS, Gupta VK, Sarma BK, Rai A, Behera TK. Metabolomics-Driven Mining of Metabolite Resources: Applications and Prospects for Improving Vegetable Crops. Int J Mol Sci 2022; 23:ijms232012062. [PMID: 36292920 PMCID: PMC9603451 DOI: 10.3390/ijms232012062] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/13/2022] [Accepted: 09/23/2022] [Indexed: 11/16/2022] Open
Abstract
Vegetable crops possess a prominent nutri-metabolite pool that not only contributes to the crop performance in the fields, but also offers nutritional security for humans. In the pursuit of identifying, quantifying and functionally characterizing the cellular metabolome pool, biomolecule separation technologies, data acquisition platforms, chemical libraries, bioinformatics tools, databases and visualization techniques have come to play significant role. High-throughput metabolomics unravels structurally diverse nutrition-rich metabolites and their entangled interactions in vegetable plants. It has helped to link identified phytometabolites with unique phenotypic traits, nutri-functional characters, defense mechanisms and crop productivity. In this study, we explore mining diverse metabolites, localizing cellular metabolic pathways, classifying functional biomolecules and establishing linkages between metabolic fluxes and genomic regulations, using comprehensive metabolomics deciphers of the plant’s performance in the environment. We discuss exemplary reports covering the implications of metabolomics, addressing metabolic changes in vegetable plants during crop domestication, stage-dependent growth, fruit development, nutri-metabolic capabilities, climatic impacts, plant-microbe-pest interactions and anthropogenic activities. Efforts leading to identify biomarker metabolites, candidate proteins and the genes responsible for plant health, defense mechanisms and nutri-rich crop produce are documented. With the insights on metabolite-QTL (mQTL) driven genetic architecture, molecular breeding in vegetable crops can be revolutionized for developing better nutritional capabilities, improved tolerance against diseases/pests and enhanced climate resilience in plants.
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Affiliation(s)
- Dhananjaya Pratap Singh
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
- Correspondence:
| | - Mansi Singh Bisen
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
| | - Renu Shukla
- Indian Council of Agricultural Research (ICAR), Krishi Bhawan, Dr. Rajendra Prasad Road, New Delhi 110001, India
| | - Ratna Prabha
- ICAR-Indian Agricultural Statistics Research Institute, Centre for Agricultural Bioinformatics, Library Avenue, Pusa, New Delhi 110012, India
| | - Sudarshan Maurya
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
| | - Yesaru S. Reddy
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
| | - Prabhakar Mohan Singh
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
| | - Nagendra Rai
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
| | - Tribhuwan Chaubey
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
| | - Krishna Kumar Chaturvedi
- ICAR-Indian Agricultural Statistics Research Institute, Centre for Agricultural Bioinformatics, Library Avenue, Pusa, New Delhi 110012, India
| | - Sudhir Srivastava
- ICAR-Indian Agricultural Statistics Research Institute, Centre for Agricultural Bioinformatics, Library Avenue, Pusa, New Delhi 110012, India
| | - Mohammad Samir Farooqi
- ICAR-Indian Agricultural Statistics Research Institute, Centre for Agricultural Bioinformatics, Library Avenue, Pusa, New Delhi 110012, India
| | - Vijai Kumar Gupta
- Biorefining and Advanced Materials Research Centre, Scotland’s Rural College, Kings Buildings, West Mains Road, Edinburgh EH9 3JG, UK
| | - Birinchi K. Sarma
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Anil Rai
- ICAR-Indian Agricultural Statistics Research Institute, Centre for Agricultural Bioinformatics, Library Avenue, Pusa, New Delhi 110012, India
| | - Tusar Kanti Behera
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
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13
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Tang Q, Song Q, Ni X, Shi Z, Chen G, Zhu X. An integrated isotopic labeling and freeze sampling apparatus (ILSA) to support sampling leaf metabolomics at a centi-second scale. PLANT METHODS 2022; 18:97. [PMID: 35907895 PMCID: PMC9338585 DOI: 10.1186/s13007-022-00926-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 07/14/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Photosynthesis close interacts with respiration and nitrogen assimilation, which determine the photosynthetic efficiency of a leaf. Accurately quantifying the metabolic fluxes in photosynthesis, respiration and nitrogen assimilation benefit the design of photosynthetic efficiency improvement. To accurately estimate metabolic fluxes, time-series data including leaf metabolism and isotopic abundance changes should be collected under precisely controlled environments. But for isotopic labelled leaves under defined environments the, time cost of manually sampling usually longer than the turnover time of several intermediates in photosynthetic metabolism. In this case, the metabolic or physiological status of leaf sample would change during the sampling, and the accuracy of metabolomics data could be compromised. RESULTS Here we developed an integrated isotopic labeling and freeze sampling apparatus (ILSA), which could finish freeze sampling automatically in 0.05 s. ILSA can not only be used for sampling of photosynthetic metabolism measurement, but also suit for leaf isotopic labeling experiments under controlled environments ([CO2] and light). Combined with HPLC-MS/MS as the metabolic measurement method, we demonstrated: (1) how pool-size of photosynthetic metabolites change in dark-accumulated rice leaf, and (2) variation in photosynthetic metabolic flux between rice and Arabidopsis thaliana. CONCLUSIONS The development of ILSA supports the photosynthetic research on metabolism and metabolic flux analysis and provides a new tool for the study of leaf physiology.
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Affiliation(s)
- Qiming Tang
- National Key Laboratory for Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qingfeng Song
- National Key Laboratory for Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Xiaoxiang Ni
- National Key Laboratory for Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zai Shi
- National Key Laboratory for Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Genyun Chen
- National Key Laboratory for Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xinguang Zhu
- National Key Laboratory for Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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14
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Determination of the chemical compounds of Shuchazao tea flowers at different developmental stages and in young shoots using 1H NMR-based metabolomics. MONATSHEFTE FUR CHEMIE 2022. [DOI: 10.1007/s00706-022-02928-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
AbstractThe chemical compounds in tea leaves have been extensively explored in recent decades. However, the compounds in tea flowers have not been fully investigated. In present study, the main chemical compounds in tea flowers were identified at four developmental stages using non-targeted metabonomics based on proton nuclear magnetic resonance (1H NMR) and an automatic amino acid analyzer, and compared with those in young tea shoots. The results showed significant differences in catechins, sugars, organic acids and amino acids between tea flowers and young shoots. The concentrations of epigallocatechin gallate, epigallocatechin, epicatechin, and caffeine were significantly lower (p < 0.01) and sugar content significantly higher (p < 0.01) in flowers than in young shoots. Caffeine and β-glucose gradually decreased and sucrose constantly increased during flower development; α-glucose and fructose were most concentrated in the white bud and then decreased with flower development. Tea flowers contained more succinic acid, citric acid, and chlorogenic acid but less quinic acid and malic acid than young shoots. Both tea flowers and young tea shoots contained 20 common amino acids, including 7 essential ones. The concentration of amino acids was highest in the white bud (27.66 mg/g); young tea shoots contained significantly more L-theanine than tea flowers (p < 0.01). Our data indicate that the different stages of tea flowers have a set of characteristic chemical compounds and are potentially useful for functional foods.
Graphical abstract
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15
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Raza A. Metabolomics: a systems biology approach for enhancing heat stress tolerance in plants. PLANT CELL REPORTS 2022; 41:741-763. [PMID: 33251564 DOI: 10.1007/s00299-020-02635-8] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 11/09/2020] [Indexed: 05/22/2023]
Abstract
Comprehensive metabolomic investigations provide a large set of stress-related metabolites and metabolic pathways, advancing crops under heat stress conditions. Metabolomics-assisted breeding, including mQTL and mGWAS boosted our understanding of improving numerous quantitative traits under heat stress. During the past decade, metabolomics has emerged as a fascinating scientific field that includes documentation, evaluation of metabolites, and chemical methods for cell monitoring programs in numerous plant species. A comprehensive metabolome profiling allowed the investigator to handle the comprehensive data groups of metabolites and the equivalent metabolic pathways in an extraordinary manner. Metabolomics, together with transcriptomics, plays an influential role in discovering connections between stress and genes/metabolite, phenotyping, and biomarkers documentation. Further, it helps to decode several metabolic systems connected with heat stress (HS) tolerance in plants. Heat stress is a critical environmental factor that is globally affecting the growth and productivity of plants. Thus, there is an urgent need to exploit modern breeding and biotechnological tools like metabolomics to develop cultivars with improved HS tolerance. Several studies have reported that amino acids, carbohydrates, nitrogen metabolisms, etc. and metabolites involved in the biosynthesis and catalyzing actions play a game-changing role in HS response and help plants to cope with the HS. The use of metabolomics-assisted breeding (MAB) allows a well-organized transmission of higher yield and HS tolerance at the metabolome level with specific properties. Progressive metabolomics systematic techniques have accelerated metabolic profiling. Nonetheless, continuous developments in bioinformatics, statistical tools, and databases are allowing us to produce ever-progressing, comprehensive insights into the biochemical configuration of plants and by what means this is inclined by genetic and environmental cues. Currently, assimilating metabolomics with post-genomic platforms has allowed a significant division of genetic-phenotypic connotation in several plant species. This review highlights the potential of a state-of-the-art plant metabolomics approach for the improvement of crops under HS. The development of plants with specific properties using integrated omics (metabolomics and transcriptomics) and MAB can provide new directions for future research to enhance HS tolerance in plants to achieve a goal of "zero hunger".
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Affiliation(s)
- Ali Raza
- Key Lab of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan, 430062, China.
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16
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Liu J, Zhang L, Huang L, Yang T, Ma J, Yu T, Zhu W, Zhang Z, Tang J. Uncovering the Gene Regulatory Network of Maize Hybrid ZD309 under Heat Stress by Transcriptomic and Metabolomic Analysis. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11050677. [PMID: 35270147 PMCID: PMC8912342 DOI: 10.3390/plants11050677] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 02/25/2022] [Accepted: 02/28/2022] [Indexed: 05/21/2023]
Abstract
Maize is an important cereal crop but is sensitive to heat stress, which significantly restricts its grain yield. To explore the molecular mechanism of maize heat tolerance, a heat-tolerant hybrid ZD309 and its parental lines (H39_1 and M189) were subjected to heat stress, followed by transcriptomic and metabolomic analyses. After six-day-heat treatment, the growth of ZD309 and its parental lines were suppressed, showing dwarf stature and rolled leaf compared with the control plants. ZD309 exhibited vigorous growth; however, M189 displayed superior heat tolerance. By transcriptomic and metabolomic analysis, hundreds to thousands of differentially expressed genes (DEGs) and metabolites (DEMs) were identified. Notably, the female parent H39 shares more DEGs and DEMs with the hybrid ZD309, indicating more genetic gain derived from the female instead of the male. A total of 299 heat shock genes detected among three genotypes were greatly aggregated in sugar transmembrane transporter activity, plasma membrane, photosynthesis, protein processing in the endoplasmic reticulum, cysteine, and methionine metabolism. A total of 150 heat-responsive metabolites detected among three genotypes were highly accumulated, including jasmonic acid, amino acids, sugar, flavonoids, coumarin, and organic acids. Integrating transcriptomic and metabolomic assays revealed that plant hormone signal transduction, cysteine, and methionine metabolism, and α-linolenic acid metabolism play crucial roles in heat tolerance in maize. Our research will be facilitated to identify essential heat tolerance genes in maize, thereby contributing to breeding heat resistance maize varieties.
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Affiliation(s)
- Jingbao Liu
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (J.L.); (L.Z.); (L.H.); (J.M.); (T.Y.); (W.Z.)
| | - Linna Zhang
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (J.L.); (L.Z.); (L.H.); (J.M.); (T.Y.); (W.Z.)
| | - Lu Huang
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (J.L.); (L.Z.); (L.H.); (J.M.); (T.Y.); (W.Z.)
| | - Tianxiao Yang
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32611, USA;
| | - Juan Ma
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (J.L.); (L.Z.); (L.H.); (J.M.); (T.Y.); (W.Z.)
| | - Ting Yu
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (J.L.); (L.Z.); (L.H.); (J.M.); (T.Y.); (W.Z.)
| | - Weihong Zhu
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (J.L.); (L.Z.); (L.H.); (J.M.); (T.Y.); (W.Z.)
| | - Zhanhui Zhang
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (J.L.); (L.Z.); (L.H.); (J.M.); (T.Y.); (W.Z.)
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
- Correspondence: (Z.Z.); (J.T.)
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
- Correspondence: (Z.Z.); (J.T.)
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17
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Sytiuk A, Céréghino R, Hamard S, Delarue F, Dorrepaal E, Küttim M, Lamentowicz M, Pourrut B, Robroek BJM, Tuittila E, Jassey VEJ. Biochemical traits enhance the trait concept in
Sphagnum
ecology. OIKOS 2022. [DOI: 10.1111/oik.09119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Anna Sytiuk
- Laboratoire Ecologie Fonctionnelle et Environnement, Univ. Paul Sabatier Toulouse 3, UPS, CNRS Toulouse France
| | - Regis Céréghino
- Laboratoire Ecologie Fonctionnelle et Environnement, Univ. Paul Sabatier Toulouse 3, UPS, CNRS Toulouse France
| | - Samuel Hamard
- Laboratoire Ecologie Fonctionnelle et Environnement, Univ. Paul Sabatier Toulouse 3, UPS, CNRS Toulouse France
| | | | - Ellen Dorrepaal
- Climate Impacts Research Centre, Dept of Ecology and Environmental Science, Umeå Univ. Abisko Sweden
| | - Martin Küttim
- Inst. of Ecology, School of Natural Sciences and Health, Tallinn Univ. Tallinn Estonia
| | - Mariusz Lamentowicz
- Climate Change Ecology Research Unit, Faculty of Geographical and Geological Sciences, Adam Mickiewicz Univ. in Poznań Poznań Poland
| | - Bertrand Pourrut
- Laboratoire Ecologie Fonctionnelle et Environnement, Univ. Paul Sabatier Toulouse 3, UPS, CNRS Toulouse France
| | - Bjorn J. M. Robroek
- Aquatic Ecology&Environmental Biology, Radboud Inst. for Biological and Environmental Sciences, Faculty of Science, Radboud Univ. Nijmegen Nijmegen the Netherlands
| | - Eeva‐Stiina Tuittila
- Biological Sciences, Faculty of Natural and Environmental Sciences, Inst. for Life Sciences, Univ. of Southampton Southampton UK
| | - Vincent E. J. Jassey
- Laboratoire Ecologie Fonctionnelle et Environnement, Univ. Paul Sabatier Toulouse 3, UPS, CNRS Toulouse France
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18
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Ashraf MF, Hou D, Hussain Q, Imran M, Pei J, Ali M, Shehzad A, Anwar M, Noman A, Waseem M, Lin X. Entailing the Next-Generation Sequencing and Metabolome for Sustainable Agriculture by Improving Plant Tolerance. Int J Mol Sci 2022; 23:651. [PMID: 35054836 PMCID: PMC8775971 DOI: 10.3390/ijms23020651] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/23/2021] [Accepted: 12/29/2021] [Indexed: 02/07/2023] Open
Abstract
Crop production is a serious challenge to provide food for the 10 billion individuals forecasted to live across the globe in 2050. The scientists' emphasize establishing an equilibrium among diversity and quality of crops by enhancing yield to fulfill the increasing demand for food supply sustainably. The exploitation of genetic resources using genomics and metabolomics strategies can help generate resilient plants against stressors in the future. The innovation of the next-generation sequencing (NGS) strategies laid the foundation to unveil various plants' genetic potential and help us to understand the domestication process to unmask the genetic potential among wild-type plants to utilize for crop improvement. Nowadays, NGS is generating massive genomic resources using wild-type and domesticated plants grown under normal and harsh environments to explore the stress regulatory factors and determine the key metabolites. Improved food nutritional value is also the key to eradicating malnutrition problems around the globe, which could be attained by employing the knowledge gained through NGS and metabolomics to achieve suitability in crop yield. Advanced technologies can further enhance our understanding in defining the strategy to obtain a specific phenotype of a crop. Integration among bioinformatic tools and molecular techniques, such as marker-assisted, QTLs mapping, creation of reference genome, de novo genome assembly, pan- and/or super-pan-genomes, etc., will boost breeding programs. The current article provides sequential progress in NGS technologies, a broad application of NGS, enhancement of genetic manipulation resources, and understanding the crop response to stress by producing plant metabolites. The NGS and metabolomics utilization in generating stress-tolerant plants/crops without deteriorating a natural ecosystem is considered a sustainable way to improve agriculture production. This highlighted knowledge also provides useful research that explores the suitable resources for agriculture sustainability.
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Affiliation(s)
- Muhammad Furqan Ashraf
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Lin’An, Hangzhou 311300, China; (M.F.A.); (D.H.); (Q.H.); (J.P.)
| | - Dan Hou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Lin’An, Hangzhou 311300, China; (M.F.A.); (D.H.); (Q.H.); (J.P.)
| | - Quaid Hussain
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Lin’An, Hangzhou 311300, China; (M.F.A.); (D.H.); (Q.H.); (J.P.)
| | - Muhammad Imran
- Colleges of Agriculture and Horticulture, South China Agricultural University, Guangzhou 510642, China; (M.I.); (M.W.)
| | - Jialong Pei
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Lin’An, Hangzhou 311300, China; (M.F.A.); (D.H.); (Q.H.); (J.P.)
| | - Mohsin Ali
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China;
| | - Aamar Shehzad
- Maize Research Station, AARI, Faisalabad 38000, Pakistan;
| | - Muhammad Anwar
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China;
| | - Ali Noman
- Department of Botany, Government College University, Faisalabad 38000, Pakistan;
| | - Muhammad Waseem
- Colleges of Agriculture and Horticulture, South China Agricultural University, Guangzhou 510642, China; (M.I.); (M.W.)
| | - Xinchun Lin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Lin’An, Hangzhou 311300, China; (M.F.A.); (D.H.); (Q.H.); (J.P.)
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19
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Large-Scale Non-Targeted Metabolomics Reveals Antioxidant, Nutraceutical and Therapeutic Potentials of Sorghum. Antioxidants (Basel) 2021; 10:antiox10101511. [PMID: 34679645 PMCID: PMC8532915 DOI: 10.3390/antiox10101511] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/17/2021] [Accepted: 09/18/2021] [Indexed: 01/10/2023] Open
Abstract
Sorghum is one of the most important food and feed cereal crops and has been gaining industrial importance in recent years for its biofuel, nutraceutical and antioxidant values. A genetic profile variation study was undertaken for the accumulation of phytochemicals in 61 diverse sorghum accessions differing in their growth habitat and grain color through non-targeted Gas Chromatography–Mass Spectrometry (GC-MS/MS) analysis. Mass Spectrometry–Data Independent AnaLysis (MS-DIAL) and MetaboAnalyst identified 221 metabolites belonging to 27 different phytochemicals. Tropical and temperate sorghums were distinct in their metabolic profiles with minimum overlaps, and 51 different metabolites were crucial in differentiating the two groups. Temperate sorghums had the ability to accumulate more of phenolic acids, phytosterols, flavonoids, carotenoids, and tropical sorghums for stress-related amino acids, sugars and fatty acids. Grain-color-based Partial Least Square–Discriminant Analysis (PLS-DA) analysis identified 94 Variable Importance in Projections (VIP) metabolites containing majority of flavonoids, phenylpropanoids and phytosterols. This study identified two sorghum lines (IS 7748 and IS 14861) with rich amounts of antioxidants (catechins and epicatechins) belonging to the group of condensed tannins that otherwise do not accumulate commonly in sorghum. Out of 13 metabolic pathways identified, flavonoid biosynthesis showed the highest expression. This study provided new opportunities for developing biofortified sorghum with enhanced nutraceutical and therapeutics through molecular breeding and metabolic engineering.
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20
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Ackerman A, Wenndt A, Boyles R. The Sorghum Grain Mold Disease Complex: Pathogens, Host Responses, and the Bioactive Metabolites at Play. FRONTIERS IN PLANT SCIENCE 2021; 12:660171. [PMID: 34122480 PMCID: PMC8192977 DOI: 10.3389/fpls.2021.660171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/21/2021] [Indexed: 06/12/2023]
Abstract
Grain mold is a major concern in sorghum [Sorghum bicolor (L.) Moench] production systems, threatening grain quality, safety, and nutritional value as both human food and livestock feed. The crop's nutritional value, environmental resilience, and economic promise poise sorghum for increased acreage, especially in light of the growing pressures of climate change on global food systems. In order to fully take advantage of this potential, sorghum improvement efforts and production systems must be proactive in managing the sorghum grain mold disease complex, which not only jeopardizes agricultural productivity and profitability, but is also the culprit of harmful mycotoxins that warrant substantial public health concern. The robust scholarly literature from the 1980s to the early 2000s yielded valuable insights and key comprehensive reviews of the grain mold disease complex. Nevertheless, there remains a substantial gap in understanding the complex multi-organismal dynamics that underpin the plant-pathogen interactions involved - a gap that must be filled in order to deliver improved germplasm that is not only capable of withstanding the pressures of climate change, but also wields robust resistance to disease and mycotoxin accumulation. The present review seeks to provide an updated perspective of the sorghum grain mold disease complex, bolstered by recent advances in the understanding of the genetic and the biochemical interactions among the fungal pathogens, their corresponding mycotoxins, and the sorghum host. Critical components of the sorghum grain mold disease complex are summarized in narrative format to consolidate a collection of important concepts: (1) the current state of sorghum grain mold in research and production systems; (2) overview of the individual pathogens that contribute to the grain mold complex; (3) the mycotoxin-producing potential of these pathogens on sorghum and other substrates; and (4) a systems biology approach to the understanding of host responses.
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Affiliation(s)
- Arlyn Ackerman
- Cereal Grains Breeding and Genetics, Pee Dee Research and Education Center, Department of Plant & Environmental Sciences, Clemson University, Florence, SC, United States
| | - Anthony Wenndt
- Plant Pathology and Plant-Microbe Biology, The School of Integrated Plant Sciences, Cornell University, Ithaca, NY, United States
| | - Richard Boyles
- Cereal Grains Breeding and Genetics, Pee Dee Research and Education Center, Department of Plant & Environmental Sciences, Clemson University, Florence, SC, United States
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21
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Drobnitch ST, Comas LH, Flynn N, Ibarra Caballero J, Barton RW, Wenz J, Person T, Bushey J, Jahn CE, Gleason SM. Drought-Induced Root Pressure in Sorghum bicolor. FRONTIERS IN PLANT SCIENCE 2021; 12:571072. [PMID: 33613594 PMCID: PMC7886691 DOI: 10.3389/fpls.2021.571072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 01/08/2021] [Indexed: 05/26/2023]
Abstract
Root pressure, also manifested as profusive sap flowing from cut stems, is a phenomenon in some species that has perplexed biologists for much of the last century. It is associated with increased crop production under drought, but its function and regulation remain largely unknown. In this study, we investigated the initiation, mechanisms, and possible adaptive function of root pressure in six genotypes of Sorghum bicolor during a drought experiment in the greenhouse. We observed that root pressure was induced in plants exposed to drought followed by re-watering but possibly inhibited by 100% re-watering in some genotypes. We found that root pressure in drought stressed and re-watered plants was associated with greater ratio of fine: coarse root length and shoot biomass production, indicating a possible role of root allocation in creating root pressure and adaptive benefit of root pressure for shoot biomass production. Using RNA-Seq, we identified gene transcripts that were up- and down-regulated in plants with root pressure expression, focusing on genes for aquaporins, membrane transporters, and ATPases that could regulate inter- and intra-cellular transport of water and ions to generate positive xylem pressure in root tissue.
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Affiliation(s)
- Sarah Tepler Drobnitch
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, United States
| | - Louise H. Comas
- Water Management Research Unit, Agricultural Research Service, USDA, Ft. Collins, CO, United States
| | - Nora Flynn
- Water Management Research Unit, Agricultural Research Service, USDA, Ft. Collins, CO, United States
| | - Jorge Ibarra Caballero
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, United States
| | - Ryan W. Barton
- Water Management Research Unit, Agricultural Research Service, USDA, Ft. Collins, CO, United States
| | - Joshua Wenz
- Water Management Research Unit, Agricultural Research Service, USDA, Ft. Collins, CO, United States
| | - Taylor Person
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, United States
| | - Julie Bushey
- Water Management Research Unit, Agricultural Research Service, USDA, Ft. Collins, CO, United States
| | - Courtney E. Jahn
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, United States
| | - Sean M. Gleason
- Water Management Research Unit, Agricultural Research Service, USDA, Ft. Collins, CO, United States
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22
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Martins MCM, Mafra V, Monte-Bello CC, Caldana C. The Contribution of Metabolomics to Systems Biology: Current Applications Bridging Genotype and Phenotype in Plant Science. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1346:91-105. [DOI: 10.1007/978-3-030-80352-0_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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23
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Promoting Human Nutrition and Health through Plant Metabolomics: Current Status and Challenges. BIOLOGY 2020; 10:biology10010020. [PMID: 33396370 PMCID: PMC7823625 DOI: 10.3390/biology10010020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/22/2020] [Accepted: 12/28/2020] [Indexed: 12/14/2022]
Abstract
Simple Summary This review summarizes the status, applications, and challenges of plant metabolomics in the context of crop breeding, food quality and safety, and human nutrition and health. It also highlights the importance of plant metabolomics in elucidating biochemical and genetic bases of traits associated with nutritive and healthy beneficial foods and other plant products to secure food supply, to ensure food quality, to protect humans from malnutrition and other diseases. Meanwhile, this review calls for comprehensive collaborations to accelerate relevant researches and applications in the context of human nutrition and health. Abstract Plant metabolomics plays important roles in both basic and applied studies regarding all aspects of plant development and stress responses. With the improvement of living standards, people need high quality and safe food supplies. Thus, understanding the pathways involved in the biosynthesis of nutritionally and healthily associated metabolites in plants and the responses to plant-derived biohazards in humans is of equal importance to meet people’s needs. For each, metabolomics has a vital role to play, which is discussed in detail in this review. In addition, the core elements of plant metabolomics are highlighted, researches on metabolomics-based crop improvement for nutrition and safety are summarized, metabolomics studies on plant natural products including traditional Chinese medicine (TCM) for health promotion are briefly presented. Challenges are discussed and future perspectives of metabolomics as one of the most important tools to promote human nutrition and health are proposed.
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Anthony BM, Chaparro JM, Prenni JE, Minas IS. Early metabolic priming under differing carbon sufficiency conditions influences peach fruit quality development. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 157:416-431. [PMID: 33202321 DOI: 10.1016/j.plaphy.2020.11.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 11/04/2020] [Indexed: 06/11/2023]
Abstract
Crop load management is an important preharvest factor to balance yield, quality, and maturation in peach. However, few studies have addressed how preharvest factors impact metabolism on fruit of equal maturity. An experiment was conducted to understand how carbon competition impacts fruit internal quality and metabolism in 'Cresthaven' peach trees by imposing distinct thinning severities. Fruit quality was evaluated at three developmental stages (S2, S3, S4), while controlling for equal maturity using non-destructive visual to near-infrared spectroscopy. Non-targeted metabolite profiling was used to characterize fruit at each developmental stage from trees that were unthinned (carbon starvation) or thinned (carbon sufficiency). Carbon sufficiency resulted in significantly higher fruit dry matter content and soluble solids concentration at harvest when compared to the carbon starved, underscoring the true impact of carbon manipulation on fruit quality. Significant differences in the fruit metabolome between treatments were observed at S2 when phenotypes were similar, while less differences were observed at S4 when the carbon sufficient fruit exhibited a superior phenotype. This suggests a potential metabolic priming effect on fruit quality when carbon is sufficiently supplied during early fruit growth and development. In particular, elevated levels of catechin may suggest a link between secondary/primary metabolism and fruit quality development.
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Affiliation(s)
- Brendon M Anthony
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, 80523, USA
| | - Jacqueline M Chaparro
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, 80523, USA
| | - Jessica E Prenni
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, 80523, USA
| | - Ioannis S Minas
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, 80523, USA.
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25
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Metabolomics: A Tool for Cultivar Phenotyping and Investigation of Grain Crops. AGRONOMY-BASEL 2020. [DOI: 10.3390/agronomy10060831] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The quality of plants is often enhanced for diverse purposes such as improved resistance to environmental pressures, better taste, and higher yields. Considering the world’s dependence on plants (nutrition, medicine, or biofuel), developing new cultivars with superior characteristics is of great importance. As part of the ‘omics’ approaches, metabolomics has been employed to investigate the large number of metabolites present in plant systems under well-defined environmental conditions. Recent advances in the metabolomics field have greatly expanded our understanding of plant metabolism, largely driven by potential application to agricultural systems. The current review presents the workflow for plant metabolome analyses, current knowledge, and future directions of such research as determinants of cultivar phenotypes. Furthermore, the value of metabolome analyses in contemporary crop science is illustrated. Here, metabolomics has provided valuable information in research on grain crops and identified significant biomarkers under different conditions and/or stressors. Moreover, the value of metabolomics has been redefined from simple biomarker identification to a tool for discovering active drivers involved in biological processes. We illustrate and conclude that the rapid advances in metabolomics are driving an explosion of information that will advance modern breeding approaches for grain crops and address problems associated with crop productivity and sustainable agriculture.
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26
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Mutale-Joan C, Redouane B, Najib E, Yassine K, Lyamlouli K, Laila S, Zeroual Y, Hicham EA. Screening of microalgae liquid extracts for their bio stimulant properties on plant growth, nutrient uptake and metabolite profile of Solanum lycopersicum L. Sci Rep 2020; 10:2820. [PMID: 32071360 PMCID: PMC7028939 DOI: 10.1038/s41598-020-59840-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 02/04/2020] [Indexed: 12/27/2022] Open
Abstract
The present study investigates the biostimulant effects of 18 Crude Bio-Extracts (CBEs) obtained from Microalgae and Cyanobacteria on tomato plant growth, chlorophyll content, nutrient uptake and metabolite profile. Significant root and shoot length improvement (112.65%, 53.70%); was recorded at treatment with Aphanothece sp and C. ellipsoidea CBEs respectively. Meanwhile, the highest root and shoot dry weight (DW) (34.81%, 58.69%) were obtained at treatment with Aphanothece sp. The latter also displayed the maximum uptake of Nitrogen, phosphorus and potassium, which increased by 185.17%, 119.36% and 78.04% respectively compared with non-treated plants. Principal Component Analysis (PCA) confirmed that Phosphorus and Potassium levels in roots were closely related to enhanced Root length, whereas Nitrogen and chlorophyll b were closely related to Shoot and root DW. Additionally, Gas Chromatography-mass spectrometry (GC-MS) indicated that treatment with CBEs, induced the production of a vast array of metabolites. Treated plants recorded higher accumulation of palmitic and stearic acids, which could indicate a stimulation in de novo Lipid synthesis. CBEs also triggered the accumulation of pyridine-3-carboxamide (an amide active form of vitamin B3) and Linolenic acid; one of the key precursors in the biosynthetic pathway leading to plant jasmonates. Our results are a first step towards understanding the effects of microalgal extracts on plant physiology and biochemical pathways. Further investigations on biochemical fractionation of microalgal extracts and agronomic tests of their purified bioactive compounds could be a useful principal novelty for in-depth study of CBE action mechanisms. Other useful tools include; Comparative hormone profiling of treated and non-treated plants accompanied with combined High-Throughput Plant Phenotyping, transcriptomics and metabolomics analysis.
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Affiliation(s)
- Chanda Mutale-Joan
- Green Biotechnology laboratory, Moroccan Foundation for Advanced Science, Innovation & Research (MASCIR), Rabat Design Center Rue Mohamed Al Jazouli - Madinat Al Irfane Rabat 10 100, Rabat, Morocco
- Microbiology and Molecular Biology Team, Center of Plant and Microbial Biotechnology, Biodiversity and Environment. Faculty of Sciences, Mohammed V University of Rabat, Avenue Ibn Battouta, BP 1014, Rabat, 10000, Morocco
| | - Benhima Redouane
- Green Biotechnology laboratory, Moroccan Foundation for Advanced Science, Innovation & Research (MASCIR), Rabat Design Center Rue Mohamed Al Jazouli - Madinat Al Irfane Rabat 10 100, Rabat, Morocco
| | - Elmernissi Najib
- Green Biotechnology laboratory, Moroccan Foundation for Advanced Science, Innovation & Research (MASCIR), Rabat Design Center Rue Mohamed Al Jazouli - Madinat Al Irfane Rabat 10 100, Rabat, Morocco
| | - Kasmi Yassine
- Green Biotechnology laboratory, Moroccan Foundation for Advanced Science, Innovation & Research (MASCIR), Rabat Design Center Rue Mohamed Al Jazouli - Madinat Al Irfane Rabat 10 100, Rabat, Morocco
| | - Karim Lyamlouli
- AgBSprogram UM6P University Jorflasfar Morocco, Rabat, Morocco
| | - Sbabou Laila
- Microbiology and Molecular Biology Team, Center of Plant and Microbial Biotechnology, Biodiversity and Environment. Faculty of Sciences, Mohammed V University of Rabat, Avenue Ibn Battouta, BP 1014, Rabat, 10000, Morocco
| | - Youssef Zeroual
- AgBSprogram UM6P University Jorflasfar Morocco, Rabat, Morocco
| | - El Arroussi Hicham
- Green Biotechnology laboratory, Moroccan Foundation for Advanced Science, Innovation & Research (MASCIR), Rabat Design Center Rue Mohamed Al Jazouli - Madinat Al Irfane Rabat 10 100, Rabat, Morocco.
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27
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Sedlacko EM, Jahn CE, Heuberger AL, Sindt NM, Miller HM, Borch T, Blaine AC, Cath TY, Higgins CP. Potential for Beneficial Reuse of Oil and Gas-Derived Produced Water in Agriculture: Physiological and Morphological Responses in Spring Wheat (Triticum aestivum). ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2019; 38:1756-1769. [PMID: 31017691 DOI: 10.1002/etc.4449] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/15/2019] [Accepted: 04/19/2019] [Indexed: 05/23/2023]
Abstract
Produced water (PW) from oil and gas operations is considered a potential resource for food crop irrigation because of increasing water scarcity in dryland agriculture. However, efforts to employ PW for agriculture have been met with limited success. A greenhouse study was performed to evaluate the effects of PW on physiological and morphological traits of spring wheat (Triticum aestivum). Plants were irrigated with water treatments containing 10 and 50% PW (PW10 and PW50, respectively) and compared to a matching 50% salinity (NaCl50) and 100% tap water controls. Compared to controls, plants watered with PW10 and PW50 exhibited developmental arrest and reductions in aboveground and belowground biomass, photosynthetic efficiency, and reproductive growth. Decreases in grain yield ranged from 70 to 100% in plants irrigated with PW compared to the tap water control. Importantly, the PW10 and NaCl50 treatments were comparable for morphophysiological effects, even though NaCl50 contained 5 times the total dissolved solids, suggesting that constituents other than NaCl in PW contributed to plant stress. These findings indicate that despite discharge and reuse requirements focused on total dissolved solids, salinity stress may not be the primary factor affecting crop health. The results of the present study are informative for developing guidelines for the use of PW in agriculture to ensure minimal effects on crop morphology and physiology. Environ Toxicol Chem 2019;38:1756-1769. © 2019 SETAC.
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Affiliation(s)
- Erin M Sedlacko
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, Colorado, USA
| | - Courtney E Jahn
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado, USA
| | - Adam L Heuberger
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, Colorado, USA
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Nathan M Sindt
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Hannah M Miller
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Thomas Borch
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Andrea C Blaine
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, Colorado, USA
| | - Tzahi Y Cath
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, Colorado, USA
| | - Christopher P Higgins
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, Colorado, USA
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28
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Pinu FR, Goldansaz SA, Jaine J. Translational Metabolomics: Current Challenges and Future Opportunities. Metabolites 2019; 9:E108. [PMID: 31174372 PMCID: PMC6631405 DOI: 10.3390/metabo9060108] [Citation(s) in RCA: 118] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 06/04/2019] [Accepted: 06/04/2019] [Indexed: 02/06/2023] Open
Abstract
Metabolomics is one of the latest omics technologies that has been applied successfully in many areas of life sciences. Despite being relatively new, a plethora of publications over the years have exploited the opportunities provided through this data and question driven approach. Most importantly, metabolomics studies have produced great breakthroughs in biomarker discovery, identification of novel metabolites and more detailed characterisation of biological pathways in many organisms. However, translation of the research outcomes into clinical tests and user-friendly interfaces has been hindered due to many factors, some of which have been outlined hereafter. This position paper is the summary of discussion on translational metabolomics undertaken during a peer session of the Australian and New Zealand Metabolomics Conference (ANZMET 2018) held in Auckland, New Zealand. Here, we discuss some of the key areas in translational metabolomics including existing challenges and suggested solutions, as well as how to expand the clinical and industrial application of metabolomics. In addition, we share our perspective on how full translational capability of metabolomics research can be explored.
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Affiliation(s)
- Farhana R Pinu
- The New Zealand Institute for Plant and Food Research, Private Bag 92169, Auckland 1142, New Zealand.
| | - Seyed Ali Goldansaz
- Department of Agriculture, Food and Nutritional Sciences, University of Alberta, Edmonton, AB T6G 2P5, Canada.
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
| | - Jacob Jaine
- Analytica Laboratories Ltd., Ruakura Research Centre, Hamilton 3216, New Zealand.
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29
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Subbaraj AK, Huege J, Fraser K, Cao M, Rasmussen S, Faville M, Harrison SJ, Jones CS. A large-scale metabolomics study to harness chemical diversity and explore biochemical mechanisms in ryegrass. Commun Biol 2019; 2:87. [PMID: 30854479 PMCID: PMC6399292 DOI: 10.1038/s42003-019-0289-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 12/20/2018] [Indexed: 12/25/2022] Open
Abstract
Perennial ryegrass (Lolium perenne) is integral to temperate pastoral agriculture, which contributes most of the milk and meat production worldwide. Chemical profiles and diversity of ryegrass offer several opportunities to harness specific traits and elucidate underlying biological mechanisms for forage improvement. We conducted a large-scale metabolomics study of perennial ryegrass comprising 715 genotypes, representing 118 populations from 21 countries. Liquid/gas chromatography-mass spectrometry based targeted and non-targeted techniques were used to analyse fructan oligosaccharides, lipids, fatty acid methyl esters, polar and semi-polar compounds. Fructan diversity across all genotypes was evaluated, high- and low-sugar groups identified, and fructan accumulation mechanisms explored. Metabolites differentiating the two groups were characterised, modules and pathways they represent deduced, and finally, visualisation and interpretation provided in a biological context. We also demonstrate a workflow for large-scale metabolomics studies from raw data through to statistical and pathway analysis. Raw files and metadata are available at the MetaboLights database.
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Affiliation(s)
- Arvind K Subbaraj
- AgResearch Limited, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North, New Zealand.
| | - Jan Huege
- AgResearch Limited, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North, New Zealand
| | - Karl Fraser
- AgResearch Limited, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North, New Zealand
| | - Mingshu Cao
- AgResearch Limited, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North, New Zealand
| | - Susanne Rasmussen
- AgResearch Limited, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North, New Zealand
- Institute of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Marty Faville
- AgResearch Limited, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North, New Zealand
| | - Scott J Harrison
- AgResearch Limited, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North, New Zealand
- PepsiCo, Cork, Ireland
| | - Chris S Jones
- AgResearch Limited, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North, New Zealand
- Feed and Forage Biosciences, International Livestock Research Institute, PO Box 5689, Addis Ababa, Ethiopia
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30
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Luo B, Ma P, Nie Z, Zhang X, He X, Ding X, Feng X, Lu Q, Ren Z, Lin H, Wu Y, Shen Y, Zhang S, Wu L, Liu D, Pan G, Rong T, Gao S. Metabolite profiling and genome-wide association studies reveal response mechanisms of phosphorus deficiency in maize seedling. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:947-969. [PMID: 30472798 PMCID: PMC6850195 DOI: 10.1111/tpj.14160] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 11/05/2018] [Accepted: 11/06/2018] [Indexed: 05/21/2023]
Abstract
Inorganic phosphorus (Pi) is an essential element in numerous metabolic reactions and signaling pathways, but the molecular details of these pathways remain largely unknown. In this study, metabolite profiles of maize (Zea mays L.) leaves and roots were compared between six low-Pi-sensitive lines and six low-Pi-tolerant lines under Pi-sufficient and Pi-deficient conditions to identify pathways and genes associated with the low-Pi stress response. Results showed that under Pi deprivation the concentrations of nucleic acids, organic acids and sugars were increased, but that the concentrations of phosphorylated metabolites, certain amino acids, lipid metabolites and nitrogenous compounds were decreased. The levels of secondary metabolites involved in plant immune reactions, including benzoxazinoids and flavonoids, were significantly different in plants grown under Pi-deficient conditions. Among them, the 11 most stable metabolites showed significant differences under low- and normal-Pi conditions based on the coefficient of variation (CV). Isoleucine and alanine were the most stable metabolites for the identification of Pi-sensitive and Pi-resistant maize inbred lines. With the significant correlation between morphological traits and metabolites, five low-Pi-responding consensus genes associated with morphological traits and simultaneously involved in metabolic pathways were mined by combining metabolites profiles and genome-wide association study (GWAS). The consensus genes induced by Pi deficiency in maize seedlings were also validated by reverse-transcription quantitative polymerase chain reaction (RT-qPCR). Moreover, these genes were further validated in a recombinant inbred line (RIL) population, in which the glucose-6-phosphate-1-epimerase encoding gene mediated yield and correlated traits to phosphorus availability. Together, our results provide a framework for understanding the metabolic processes underlying Pi-deficient responses and give multiple insights into improving the efficiency of Pi use in maize.
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Affiliation(s)
- Bowen Luo
- Maize Research InstituteSichuan Agricultural University611130SichuanChengduChina
| | - Peng Ma
- Maize Research InstituteSichuan Agricultural University611130SichuanChengduChina
| | - Zhi Nie
- Maize Research InstituteSichuan Agricultural University611130SichuanChengduChina
| | - Xiao Zhang
- Maize Research InstituteSichuan Agricultural University611130SichuanChengduChina
| | - Xuan He
- Maize Research InstituteSichuan Agricultural University611130SichuanChengduChina
| | - Xin Ding
- Maize Research InstituteSichuan Agricultural University611130SichuanChengduChina
| | - Xing Feng
- Maize Research InstituteSichuan Agricultural University611130SichuanChengduChina
| | - Quanxiao Lu
- Maize Research InstituteSichuan Agricultural University611130SichuanChengduChina
| | - Zhiyong Ren
- Maize Research InstituteSichuan Agricultural University611130SichuanChengduChina
| | - Haijian Lin
- Maize Research InstituteSichuan Agricultural University611130SichuanChengduChina
| | - Yuanqi Wu
- Maize Research InstituteSichuan Agricultural University611130SichuanChengduChina
| | - Yaou Shen
- Maize Research InstituteSichuan Agricultural University611130SichuanChengduChina
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease ControlSichuanChengduChina
| | - Suzhi Zhang
- Maize Research InstituteSichuan Agricultural University611130SichuanChengduChina
| | - Ling Wu
- Maize Research InstituteSichuan Agricultural University611130SichuanChengduChina
| | - Dan Liu
- Maize Research InstituteSichuan Agricultural University611130SichuanChengduChina
| | - Guangtang Pan
- Maize Research InstituteSichuan Agricultural University611130SichuanChengduChina
| | - Tingzhao Rong
- Maize Research InstituteSichuan Agricultural University611130SichuanChengduChina
| | - Shibin Gao
- Maize Research InstituteSichuan Agricultural University611130SichuanChengduChina
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease ControlSichuanChengduChina
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31
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Sheflin AM, Chiniquy D, Yuan C, Goren E, Kumar I, Braud M, Brutnell T, Eveland AL, Tringe S, Liu P, Kresovich S, Marsh EL, Schachtman DP, Prenni JE. Metabolomics of sorghum roots during nitrogen stress reveals compromised metabolic capacity for salicylic acid biosynthesis. PLANT DIRECT 2019; 3:e00122. [PMID: 31245765 PMCID: PMC6508800 DOI: 10.1002/pld3.122] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 01/31/2019] [Accepted: 02/10/2019] [Indexed: 05/13/2023]
Abstract
Sorghum (Sorghum bicolor [L.] Moench) is the fifth most productive cereal crop worldwide with some hybrids having high biomass yield traits making it promising for sustainable, economical biofuel production. To maximize biofuel feedstock yields, a more complete understanding of metabolic responses to low nitrogen (N) will be useful for incorporation in crop improvement efforts. In this study, 10 diverse sorghum entries (including inbreds and hybrids) were field-grown under low and full N conditions and roots were sampled at two time points for metabolomics and 16S amplicon sequencing. Roots of plants grown under low N showed altered metabolic profiles at both sampling dates including metabolites important in N storage and synthesis of aromatic amino acids. Complementary investigation of the rhizosphere microbiome revealed dominance by a single operational taxonomic unit (OTU) in an early sampling that was taxonomically assigned to the genus Pseudomonas. Abundance of this Pseudomonas OTU was significantly greater under low N in July and was decreased dramatically in September. Correlation of Pseudomonas abundance with root metabolites revealed a strong negative association with the defense hormone salicylic acid (SA) under full N but not under low N, suggesting reduced defense response. Roots from plants with N stress also contained reduced phenylalanine, a precursor for SA, providing further evidence for compromised metabolic capacity for defense response under low N conditions. Our findings suggest that interactions between biotic and abiotic stresses may affect metabolic capacity for plant defense and need to be concurrently prioritized as breeding programs become established for biofuels production on marginal soils.
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Affiliation(s)
- Amy M. Sheflin
- Department of Horticulture and Landscape ArchitectureColorado State UniversityFort CollinsColorado
| | - Dawn Chiniquy
- Joint Genome InstituteDepartment of EnergyWalnut CreekCalifornia
| | - Chaohui Yuan
- Bioinformatics & Computational BiologyIowa State UniversityAmesIowa
| | - Emily Goren
- Bioinformatics & Computational BiologyIowa State UniversityAmesIowa
| | | | - Max Braud
- Donald Danforth Plant Science CenterSt. LouisMissouri
| | | | | | - Susannah Tringe
- Joint Genome InstituteDepartment of EnergyWalnut CreekCalifornia
| | - Peng Liu
- Bioinformatics & Computational BiologyIowa State UniversityAmesIowa
| | - Stephen Kresovich
- Plant and Environmental Genetics and Biochemistry DepartmentsClemson UniversityClemsonSouth Carolina
| | - Ellen L. Marsh
- Center for BiotechnologyUniversity of Nebraska‐LincolnLincolnNebraska
| | | | - Jessica E. Prenni
- Department of Horticulture and Landscape ArchitectureColorado State UniversityFort CollinsColorado
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32
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Handakumbura PP, Stanfill B, Rivas-Ubach A, Fortin D, Vogel JP, Jansson C. Metabotyping as a Stopover in Genome-to-Phenome Mapping. Sci Rep 2019; 9:1858. [PMID: 30755686 PMCID: PMC6372633 DOI: 10.1038/s41598-019-38483-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 12/21/2018] [Indexed: 01/01/2023] Open
Abstract
Predicting phenotypic expression from genomic and environmental information is arguably the greatest challenge in today's biology. Being able to survey genomic content, e.g., as single-nucleotide polymorphism data, within a diverse population and predict the phenotypes of external traits, represents the holy grail across genome-informed disciplines, from personal medicine and nutrition to plant breeding. In the present study, we propose a two-step procedure in bridging the genome to phenome gap where external phenotypes are viewed as emergent properties of internal phenotypes, such as molecular profiles, in interaction with the environment. Using biomass accumulation and shoot-root allometry as external traits in diverse genotypes of the model grass Brachypodium distachyon, we established correlative models between genotypes and metabolite profiles (metabotypes) as internal phenotypes, and between metabotypes and external phenotypes under two contrasting watering regimes. Our results demonstrate the potential for employing metabotypes as an integrator in predicting external phenotypes from genomic information.
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Affiliation(s)
- Pubudu P Handakumbura
- The Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Washington, WA, 99352, USA.
| | - Bryan Stanfill
- Advanced Computing, Computing and Analytics Division, PNNL, Richland, WA, 99352, USA
| | - Albert Rivas-Ubach
- The Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Washington, WA, 99352, USA
| | - Dan Fortin
- Advanced Computing, Computing and Analytics Division, PNNL, Richland, WA, 99352, USA
| | - John P Vogel
- US Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, CA, 94598, USA
| | - Christer Jansson
- The Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Washington, WA, 99352, USA.
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33
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Miller SB, Heuberger AL, Broeckling CD, Jahn CE. Non-Targeted Metabolomics Reveals Sorghum Rhizosphere-Associated Exudates are Influenced by the Belowground Interaction of Substrate and Sorghum Genotype. Int J Mol Sci 2019; 20:E431. [PMID: 30669498 PMCID: PMC6358735 DOI: 10.3390/ijms20020431] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 01/12/2019] [Accepted: 01/14/2019] [Indexed: 12/29/2022] Open
Abstract
Root exudation is an important plant process by which roots release small molecules into the rhizosphere that serve in overall plant functioning. Yet, there is a major gap in our knowledge in translating plant root exudation in artificial systems (i.e., hydroponics, sterile media) to crops, specifically for soils expected in field conditions. Sorghum (Sorghum bicolor L. Moench) root exudation was determined using both ultra-performance liquid chromatography and gas chromatography mass spectrometry-based non-targeted metabolomics to evaluate variation in exudate composition of two sorghum genotypes among three substrates (sand, clay, and soil). Above and belowground plant traits were measured to determine the interaction between sorghum genotype and belowground substrate. Plant growth and quantitative exudate composition were found to vary largely by substrate. Two types of changes to rhizosphere metabolites were observed: rhizosphere-enhanced metabolites (REMs) and rhizosphere-abated metabolites (RAMs). More REMs and RAMs were detected in sand and clay substrates compared to the soil substrate. This study demonstrates that belowground substrate influences the root exudate profile in sorghum, and that two sorghum genotypes exuded metabolites at different magnitudes. However, metabolite identification remains a major bottleneck in non-targeted metabolite profiling of the rhizosphere.
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Affiliation(s)
- Sarah B Miller
- Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, USA.
| | - Adam L Heuberger
- Horticulture and Landscape Architecture, Colorado State University, Colorado State University, Fort Collins, CO 80523, USA.
| | - Corey D Broeckling
- Proteomics and Metabolomics Facility, Colorado State University, Colorado State University, Fort Collins, CO 80523, USA.
| | - Courtney E Jahn
- Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, USA.
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34
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Alseekh S, Bermudez L, de Haro LA, Fernie AR, Carrari F. Crop metabolomics: from diagnostics to assisted breeding. Metabolomics 2018; 14:148. [PMID: 30830402 DOI: 10.1007/s11306-018-1446-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/26/2018] [Indexed: 01/02/2023]
Abstract
BACKGROUND Until recently, plant metabolomics have provided a deep understanding on the metabolic regulation in individual plants as experimental units. The application of these techniques to agricultural systems subjected to more complex interactions is a step towards the implementation of translational metabolomics in crop breeding. AIM OF REVIEW We present here a review paper discussing advances in the knowledge reached in the last years derived from the application of metabolomic techniques that evolved from biomarker discovery to improve crop yield and quality. KEY SCIENTIFIC CONCEPTS OF REVIEW Translational metabolomics applied to crop breeding programs.
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Affiliation(s)
- Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Center of Plant System Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Luisa Bermudez
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaria (IB-INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), PO Box 25, B1686WAA, Castelar, Argentina
- Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Luis Alejandro de Haro
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaria (IB-INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), PO Box 25, B1686WAA, Castelar, Argentina
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Ciudad Universitaria, C1428EHA, Buenos Aires, Argentina
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Center of Plant System Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Fernando Carrari
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaria (IB-INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), PO Box 25, B1686WAA, Castelar, Argentina.
- Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina.
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, São Paulo, 05508-090, Brazil.
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Ciudad Universitaria, C1428EHA, Buenos Aires, Argentina.
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Robison FM, Turner MF, Jahn CE, Schwartz HF, Prenni JE, Brick MA, Heuberger AL. Common bean varieties demonstrate differential physiological and metabolic responses to the pathogenic fungus Sclerotinia sclerotiorum. PLANT, CELL & ENVIRONMENT 2018; 41:2141-2154. [PMID: 29476531 DOI: 10.1111/pce.13176] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 02/18/2018] [Accepted: 02/20/2018] [Indexed: 06/08/2023]
Abstract
Plant physiology and metabolism are important components of a plant response to microbial pathogens. Physiological resistance of common bean (Phaseolus vulgaris L.) to the fungal pathogen Sclerotinia sclerotiorum has been established, but the mechanisms of resistance are largely unknown. Here, the physiological and metabolic responses of bean varieties that differ in physiological resistance to S. sclerotiorum are investigated. Upon infection, the resistant bean variety A195 had a unique physiological response that included reduced photosynthesis and maintaining a higher leaf surface pH during infection. Leaf metabolomics was performed on healthy tissue adjacent to the necrotic lesion at 16, 24, and 48 hr post inoculation, and 144 metabolites were detected that varied between A195 and Sacramento following infection. The metabolites that varied in leaves included amines/amino acids, organic acids, phytoalexins, and ureides. The metabolic pathways associated with resistance included amine metabolism, uriede-based nitrogen remobilization, antioxidant production, and bean-specific phytoalexin production. A second experiment was conducted in stems of 13 bean genotypes with varying resistance. Stem resistance was associated with phytoalexin production, but unlike leaf metabolism, lipid changes were associated with susceptibility. Taken together, the data supports a multifaceted, physiometabolic response of common bean to S. sclerotiorum that mediates resistance.
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Affiliation(s)
- Faith M Robison
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Marie F Turner
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, 80523, USA
| | - Courtney E Jahn
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, 80523, USA
| | - Howard F Schwartz
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, 80523, USA
| | - Jessica E Prenni
- Proteomics and Metabolomics Facility, Colorado State University, Fort Collins, CO, 80523, USA
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Mark A Brick
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Adam L Heuberger
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, 80523, USA
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, 80523, USA
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Bettenhausen HM, Barr L, Broeckling CD, Chaparro JM, Holbrook C, Sedin D, Heuberger AL. Influence of malt source on beer chemistry, flavor, and flavor stability. Food Res Int 2018; 113:487-504. [PMID: 30195545 DOI: 10.1016/j.foodres.2018.07.024] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 07/05/2018] [Accepted: 07/14/2018] [Indexed: 01/10/2023]
Abstract
Beverage quality in the brewing industry is heavily influenced by ingredient properties. The contribution of raw ingredients such as yeast and hops to beer flavor is well understood. However, the influence of barley genotype and/or environment on flavor (the malt 'source') is largely unexplored. Here, a study was performed to determine (i) if there are metabolite differences among six commercial malt sources, (ii) if differences in malt chemistry are reflected in the chemistry of the beer, and (iii) if the differences in the beer chemistry impact sensory attributes of beer, through flavor and flavor stability. Six distinct sources of malts (six varieties from three maltsters) were brewed into six beers using a recipe designed to evaluate differences in flavor. Metabolomics and ionomics was used to characterize chemical variation among the six malts and beers using UHPLC- and HILIC-MS (non-volatile metabolites), HS-SPME/GC-MS (beer volatiles), and ICP-MS (malt metals). These analyses detected a total of 5042 compounds in malt, of which 217 were annotated and included amines, amino acids, fatty acids/lipids/fatty acyls, saccharides/glucosides/sugar acids/sugar alcohols, carboxylic acid derivatives, organic acids, phenolics/benzenoids, purines, pyrimidines/pyridines, terpenes, and organosulfurs. A total of 4568 compounds were detected in beer, of which 246 were annotated and included esters, aldehydes, and alcohols. Statistical analysis revealed chemical variation among the six malts (50/217 malt metabolites varied) and beers (150/246). The six beers were evaluated for flavor using a modified descriptive analysis for 45 sensory traits at 0, 4, and 8 weeks of storage at 4 °C. Principal component analysis of the sensory data revealed flavor differences among the six beers at 8 weeks, and the malt-type Full Pint was described as fruity and Meredith as corn chip. The metabolite and sensory data were integrated and revealed associations between flavor profiles in beer and the annotated malt and beer. The fruity or corn chip flavor profiles in beer were associated beer purines/pyrimidines, volatile ketones, amines, and phenolics, and malt lipids, saccharides, phenols, amines, and alkaloids. Taken together, these data support a role of malt source in beer flavor and flavor stability. As a raw ingredient, malting barley genotypes can be evaluated for a contribution to flavor, and this may be a future target for plant breeding, agronomy, and malting efforts to selectively improve flavor, flavor stability, and quality in beer.
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Affiliation(s)
- Harmonie M Bettenhausen
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, USA
| | - Lindsay Barr
- New Belgium Brewing Company, Fort Collins, CO, USA
| | - Corey D Broeckling
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, USA; Proteomics and Metabolomics Facility, Colorado State University, Fort Collins, CO, USA
| | - Jacqueline M Chaparro
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, USA; Proteomics and Metabolomics Facility, Colorado State University, Fort Collins, CO, USA
| | | | - Dana Sedin
- New Belgium Brewing Company, Fort Collins, CO, USA
| | - Adam L Heuberger
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, USA; Department of Soil and Crop Sciences, Fort Collins, CO, USA.
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Next generation crop improvement program: Progress and prospect in tea ( Camellia sinensis (L.) O. Kuntze). ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.aasci.2018.02.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Chaparro JM, Holm DG, Broeckling CD, Prenni JE, Heuberger AL. Metabolomics and Ionomics of Potato Tuber Reveals an Influence of Cultivar and Market Class on Human Nutrients and Bioactive Compounds. Front Nutr 2018; 5:36. [PMID: 29876353 PMCID: PMC5974217 DOI: 10.3389/fnut.2018.00036] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 04/19/2018] [Indexed: 01/11/2023] Open
Abstract
Potato (Solanum tuberosum L.) is an important global food crop that contains phytochemicals with demonstrated effects on human health. Understanding sources of chemical variation of potato tuber can inform breeding for improved health attributes of the cooked food. Here, a comprehensive metabolomics (UPLC- and GC-MS) and ionomics (ICP-MS) analysis of raw and cooked potato tuber was performed on 60 unique potato genotypes that span 5 market classes including russet, red, yellow, chip, and specialty potatoes. The analyses detected 2,656 compounds that included known bioactives (43 compounds), nutrients (42), lipids (76), and 23 metals. Most nutrients and bioactives were partially degraded during cooking (44 out of 85; 52%), however genotypes with high quantities of bioactives remained highest in the cooked tuber. Chemical variation was influenced by genotype and market class. Specifically, ~53% of all detected compounds from cooked potato varied among market class and 40% varied by genotype. The most notable metabolite profiles were observed in yellow-flesh potato which had higher levels of carotenoids and specialty potatoes which had the higher levels of chlorogenic acid as compared to the other market classes. Variation in several molecules with known association to health was observed among market classes and included vitamins (e.g., pyridoxal, ~2-fold variation), bioactives (e.g., chlorogenic acid, ~40-fold variation), medicinals (e.g., kukoamines, ~6-fold variation), and minerals (e.g., calcium, iron, molybdenum, ~2-fold variation). Furthermore, more metabolite variation was observed within market class than among market class (e.g., α-tocopherol, ~1-fold variation among market class vs. ~3-fold variation within market class). Taken together, the analysis characterized significant metabolite and mineral variation in raw and cooked potato tuber, and support the potential to breed new cultivars for improved health traits.
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Affiliation(s)
- Jacqueline M. Chaparro
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, United States
- Proteomics and Metabolomics Facility, Colorado State University, Fort Collins, CO, United States
| | - David G. Holm
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, United States
| | - Corey D. Broeckling
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, United States
- Proteomics and Metabolomics Facility, Colorado State University, Fort Collins, CO, United States
| | - Jessica E. Prenni
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, United States
- Proteomics and Metabolomics Facility, Colorado State University, Fort Collins, CO, United States
| | - Adam L. Heuberger
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, United States
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, United States
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Suh DH, Jung ES, Lee GM, Lee CH. Distinguishing Six Edible Berries Based on Metabolic Pathway and Bioactivity Correlations by Non-targeted Metabolite Profiling. FRONTIERS IN PLANT SCIENCE 2018; 9:1462. [PMID: 30333849 PMCID: PMC6175979 DOI: 10.3389/fpls.2018.01462] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 09/13/2018] [Indexed: 05/09/2023]
Abstract
Berries have been used as valuable sources of polyphenols for human health; however, injudicious uses of berries are widespread without regard to the specific metabolite constituent of each berry. We classified 6 different edible berries (honeyberry, blueberry, mandarin melonberry, mulberry, chokeberry, and Korean black raspberry) based on their metabolite distributions in biosynthetic pathways by non-targeted metabolite profiling and bioactive correlation analysis. Principal component analysis revealed a distinct clustering pattern of metabolites for each berry. Metabolic pathway analysis revealed different biosynthetic routes of secondary metabolites in each berry. Mandarin melonberry contains a relatively higher proportion of genistein, genistein glycoside, and genistein-derived isoflavonoids and prenylflavonoids than the other berries. Various anthocyanin glycosides, synthesized from dihydroquercetin and cyanidin, were more abundant in chokeberry and honeyberry, whereas high levels of flavonoid-and anthocyanins-rutinoside forms were observed in Korean black raspberry. The levels of anthocyanins derived from dihydromyricetin were high in blueberry. The highest anti-oxidant activity was observed in chokeberry and Korean black raspberry, which is positively related to the proportional concentration of flavonoids, phenolics, and anthocyanins. The lowest sugar contents were observed in Korean black raspberry, highest acidity in honeyberry, and lowest acidity in mandarin melonberry, which were specific characteristics among the berries. Taken together, biosynthetic pathway and physicochemical characteristics analyses revealed that the different synthesized routes of flavonoids and anthocyanins and associated bio-activities may be distinct features in each berry and explain their phenotypic diversity at the molecular level.
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Affiliation(s)
- Dong Ho Suh
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, South Korea
| | - Eun Sung Jung
- Department of Systems Biotechnology, Konkuk University, Seoul, South Korea
| | - Gyu Min Lee
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, South Korea
| | - Choong Hwan Lee
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, South Korea
- Department of Systems Biotechnology, Konkuk University, Seoul, South Korea
- *Correspondence: Choong Hwan Lee
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Perrier L, Rouan L, Jaffuel S, Clément-Vidal A, Roques S, Soutiras A, Baptiste C, Bastianelli D, Fabre D, Dubois C, Pot D, Luquet D. Plasticity of Sorghum Stem Biomass Accumulation in Response to Water Deficit: A Multiscale Analysis from Internode Tissue to Plant Level. FRONTIERS IN PLANT SCIENCE 2017; 8:1516. [PMID: 28919904 PMCID: PMC5585773 DOI: 10.3389/fpls.2017.01516] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 08/17/2017] [Indexed: 05/20/2023]
Abstract
Sorghum is increasingly used as a biomass crop worldwide. Its genetic diversity provides a large range of stem biochemical composition suitable for various end-uses as bioenergy or forage. Its drought tolerance enables it to reasonably sustain biomass production under water limited conditions. However, drought effect on the accumulation of sorghum stem biomass remains poorly understood which limits progress in crop improvement and management. This study aimed at identifying the morphological, biochemical and histological traits underlying biomass accumulation in the sorghum stem and its plasticity in response to water deficit. Two hybrids (G1, G4) different in stem biochemical composition (G4, more lignified, less sweet) were evaluated during 2 years in the field in Southern France, under two water treatments differentiated during stem elongation (irrigated; 1 month dry-down until an average soil water deficit of -8.85 bars). Plant phenology was observed weekly. At the end of the water treatment and at final harvest, plant height, stem and leaf dry-weight and the size, biochemical composition and tissue histology of internodes at 2-4 positions along the stem were measured. Stem biomass accumulation was significantly reduced by drought (in average 42% at the end of the dry-down). This was due to the reduction of the length, but not diameter, of the internodes expanded during water deficit. These internodes had more soluble sugar but lower lignin and cellulose contents. This was associated with a decrease of the areal proportion of lignified cell wall in internode outer zone whereas the areal proportion of this zone was not affected. All internodes for a given genotype and environment followed a common histochemical dynamics. Hemicellulose content and the areal proportion of inner vs. outer internode tissues were set up early during internode growth and were not drought responsive. G4 exhibited a higher drought sensitivity than G1 for plant height only. At final harvest, the stem dry weight was only 18% lower in water deficit (re-watered) compared to well-watered treatment and internodes growing during re-watering were similar to those on the well-watered plants. These results are being valorized to refine the phenotyping of sorghum diversity panels and breeding populations.
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Kumar R, Bohra A, Pandey AK, Pandey MK, Kumar A. Metabolomics for Plant Improvement: Status and Prospects. FRONTIERS IN PLANT SCIENCE 2017; 8:1302. [PMID: 28824660 PMCID: PMC5545584 DOI: 10.3389/fpls.2017.01302] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 07/11/2017] [Indexed: 05/12/2023]
Abstract
Post-genomics era has witnessed the development of cutting-edge technologies that have offered cost-efficient and high-throughput ways for molecular characterization of the function of a cell or organism. Large-scale metabolite profiling assays have allowed researchers to access the global data sets of metabolites and the corresponding metabolic pathways in an unprecedented way. Recent efforts in metabolomics have been directed to improve the quality along with a major focus on yield related traits. Importantly, an integration of metabolomics with other approaches such as quantitative genetics, transcriptomics and genetic modification has established its immense relevance to plant improvement. An effective combination of these modern approaches guides researchers to pinpoint the functional gene(s) and the characterization of massive metabolites, in order to prioritize the candidate genes for downstream analyses and ultimately, offering trait specific markers to improve commercially important traits. This in turn will improve the ability of a plant breeder by allowing him to make more informed decisions. Given this, the present review captures the significant leads gained in the past decade in the field of plant metabolomics accompanied by a brief discussion on the current contribution and the future scope of metabolomics to accelerate plant improvement.
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Affiliation(s)
- Rakesh Kumar
- Department of Plant Sciences, University of Hyderabad (UoH)Hyderabad, India
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Hyderabad, India
| | - Abhishek Bohra
- Crop Improvement Division, Indian Institute of Pulses Research (IIPR)Kanpur, India
| | - Arun K. Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Hyderabad, India
| | - Manish K. Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Hyderabad, India
| | - Anirudh Kumar
- Department of Botany, Indira Gandhi National Tribal University (IGNTU)Amarkantak, India
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Ma HK, Pineda A, van der Wurff AWG, Raaijmakers C, Bezemer TM. Plant-Soil Feedback Effects on Growth, Defense and Susceptibility to a Soil-Borne Disease in a Cut Flower Crop: Species and Functional Group Effects. FRONTIERS IN PLANT SCIENCE 2017; 8:2127. [PMID: 29312387 PMCID: PMC5742127 DOI: 10.3389/fpls.2017.02127] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 11/30/2017] [Indexed: 05/22/2023]
Abstract
Plants can influence the soil they grow in, and via these changes in the soil they can positively or negatively influence other plants that grow later in this soil, a phenomenon called plant-soil feedback. A fascinating possibility is then to apply positive plant-soil feedback effects in sustainable agriculture to promote plant growth and resistance to pathogens. We grew the cut flower chrysanthemum (Dendranthema X grandiflora) in sterile soil inoculated with soil collected from a grassland that was subsequently conditioned by 37 plant species of three functional groups (grass, forb, legume), and compared it to growth in 100% sterile soil (control). We tested the performance of chrysanthemum by measuring plant growth, and defense (leaf chlorogenic acid concentration) and susceptibility to the oomycete pathogen Pythium ultimum. In presence of Pythium, belowground biomass of chrysanthemum declined but aboveground biomass was not affected compared to non-Pythium inoculated plants. We observed strong differences among species and among functional groups in their plant-soil feedback effects on chrysanthemum. Soil inocula that were conditioned by grasses produced higher chrysanthemum above- and belowground biomass and less leaf yellowness than inocula conditioned by legumes or forbs. Chrysanthemum had lower root/shoot ratios in response to Pythium in soil conditioned by forbs than by grasses. Leaf chlorogenic acid concentrations increased in presence of Pythium and correlated positively with chrysanthemum aboveground biomass. Although chlorogenic acid differed between soil inocula, it did not differ between functional groups. There was no relationship between the phylogenetic distance of the conditioning plant species to chrysanthemum and their plant-soil feedback effects on chrysanthemum. Our study provides novel evidence that plant-soil feedback effects can influence crop health, and shows that plant-soil feedbacks, plant disease susceptibility, and plant aboveground defense compounds are tightly linked. Moreover, we highlight the relevance of considering plant-soil feedbacks in sustainable horticulture, and the larger role of grasses compared to legumes or forbs in this.
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Affiliation(s)
- Hai-Kun Ma
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands
- Section Plant Ecology and Phytochemistry, Institute of Biology, Leiden University, Leiden, Netherlands
- *Correspondence: Hai-Kun Ma,
| | - Ana Pineda
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands
| | | | - Ciska Raaijmakers
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands
| | - T. M. Bezemer
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands
- Section Plant Ecology and Phytochemistry, Institute of Biology, Leiden University, Leiden, Netherlands
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