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Contador CA, Liu A, Ng MS, Ku YS, Chan SHJ, Lam HM. Contextualized Metabolic Modelling Revealed Factors Affecting Isoflavone Accumulation in Soybean Seeds. PLANT, CELL & ENVIRONMENT 2024. [PMID: 39292176 DOI: 10.1111/pce.15140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 06/05/2024] [Accepted: 08/20/2024] [Indexed: 09/19/2024]
Abstract
Isoflavones, secondary metabolites with numerous health benefits, are predominantly found in legume seeds, especially soybean; however, their contents in domesticated soybean seeds are highly variable. Wild soybeans are known for higher seed isoflavone contents than cultivars. Here we used experimental and modelling approaches on wild soybean (W05) and cultivated soybean (C08) to delineate factors influencing isoflavone accumulation. We found imported nutrients were converted into storage compounds, with isoflavone accumulation in W05 seeds being faster than in C08 ones. The isoflavone accumulation during seed development was simulated using context-specific cotyledon metabolic models of four developmental stages on cultivar C08, and the metabolic burden imposed by increasing biomass was evaluated. Trade-off analyses between biomass and isoflavone suggest that high biomass requirement in cultivars could limit the reallocation of resources for secondary metabolite production. Isoflavone production in mature seeds was also influenced by biomass compositions. Seeds with higher carbohydrate contents favour isoflavone production, while those with highest protein and oil contents had lowest isoflavone contents. Although seeds could synthesize isoflavones on their own, the predicted fluxes from biosynthesis alone were lower than the empirical levels. Shadow price analyses indicated that isoflavone accumulation depended on both intrinsic biosynthesis and direct contribution from the plant.
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Affiliation(s)
- Carolina A Contador
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Ailin Liu
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Ming-Sin Ng
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Yee-Shan Ku
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Siu H J Chan
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, Colorado, USA
| | - Hon-Ming Lam
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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Hu Y, Ruan Y, Zhao XL, Jiang F, Liu D, Zhu Q, Zhang QY, Yang QY. PCMD: A multilevel comparison database of intra- and cross-species metabolic profiling in 530 plant species. PLANT COMMUNICATIONS 2024:101038. [PMID: 38993115 DOI: 10.1016/j.xplc.2024.101038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 06/19/2024] [Accepted: 07/08/2024] [Indexed: 07/13/2024]
Abstract
Comparative metabolomics plays a crucial role in investigating gene function, exploring metabolite evolution, and accelerating crop genetic improvement. However, a systematic platform for intra- and cross-species comparison of metabolites is currently lacking. Here, we report the Plant Comparative Metabolome Database (PCMD; http://yanglab.hzau.edu.cn/PCMD), a multilevel comparison database based on predicted metabolic profiles of 530 plant species. The PCMD serves as a platform for comparing metabolite characteristics at various levels, including species, metabolites, pathways, and biological taxonomy. The database also provides a number of user-friendly online tools, such as species comparison, metabolite enrichment, and ID conversion, enabling users to perform comparisons and enrichment analyses of metabolites across different species. In addition, the PCMD establishes a unified system based on existing metabolite-related databases by standardizing metabolite numbering. The PCMD is the most species-rich comparative plant metabolomics database currently available, and a case study demonstrates its ability to provide new insights into plant metabolic diversity.
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Affiliation(s)
- Yue Hu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Yao Ruan
- Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Xin-Le Zhao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Feng Jiang
- Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Dongxu Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiang Zhu
- Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Qing-Ye Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
| | - Qing-Yong Yang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China; Yazhouwan National Laboratory, Sanya 572024, China.
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Wang B, Bu Y, Zhang G, Liu N, Feng Z, Gong Y. Comparative transcriptome analysis of vegetable soybean grain discloses genes essential for grain quality. BMC PLANT BIOLOGY 2024; 24:491. [PMID: 38825702 PMCID: PMC11145879 DOI: 10.1186/s12870-024-05214-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 05/29/2024] [Indexed: 06/04/2024]
Abstract
BACKGROUND Vegetable soybean is an important vegetable crop in world. Seed size and soluble sugar content are considered crucial indicators of quality in vegetable soybean, and there is a lack of clarity on the molecular basis of grain quality in vegetable soybean. RESULTS In this context, we performed a comprehensive comparative transcriptome analysis of seeds between a high-sucrose content and large-grain variety (Zhenong 6, ZN6) and a low-sucrose content and small-grain variety (Williams 82, W82) at three developmental stages, i.e. stage R5 (Beginning Seed), stage R6 (Full Seed), and stage R7 (Beginning Maturity). The transcriptome analysis showed that 17,107 and 13,571 differentially expressed genes (DEGs) were identified in ZN6 at R6 (vs. R5) and R7 (vs. R6), respectively, whereas 16,203 and 16,032 were detected in W82. Gene expression pattern and DEGs functional enrichment proposed genotype-specific biological processes during seed development. The genes participating in soluble sugar biosynthesis such as FKGP were overexpressed in ZN6, whereas those responsible for lipid and protein metabolism such as ALDH3 were more enhanced in W82, exhibiting different dry material accumulation between two genotypes. Furthermore, hormone-associated transcriptional factors involved in seed size regulation such as BEH4 were overrepresented in ZN6, exhibiting different seed size regulation processes between two genotypes. CONCLUSIONS Herein, we not only discovered the differential expression of genes encoding metabolic enzymes involved in seed composition, but also identified a type of hormone-associated transcriptional factors overexpressed in ZN6, which may regulate seed size and soluble content. This study provides new insights into the underlying causes of differences in the soybean metabolites and appearance, and suggests that genetic data can be used to improve its appearance and textural quality.
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Affiliation(s)
- Bin Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, 198, Shiqiao Rd, Hangzhou, 310021, Zhejiang, China.
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China of Ministry of Agriculture and Rural Affairs, 198, Shiqiao Rd, Hangzhou, 310021, Zhejiang, China.
| | - Yuanpeng Bu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, 198, Shiqiao Rd, Hangzhou, 310021, Zhejiang, China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China of Ministry of Agriculture and Rural Affairs, 198, Shiqiao Rd, Hangzhou, 310021, Zhejiang, China
| | - Guwen Zhang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, 198, Shiqiao Rd, Hangzhou, 310021, Zhejiang, China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China of Ministry of Agriculture and Rural Affairs, 198, Shiqiao Rd, Hangzhou, 310021, Zhejiang, China
| | - Na Liu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, 198, Shiqiao Rd, Hangzhou, 310021, Zhejiang, China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China of Ministry of Agriculture and Rural Affairs, 198, Shiqiao Rd, Hangzhou, 310021, Zhejiang, China
| | - Zhijuan Feng
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, 198, Shiqiao Rd, Hangzhou, 310021, Zhejiang, China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China of Ministry of Agriculture and Rural Affairs, 198, Shiqiao Rd, Hangzhou, 310021, Zhejiang, China
| | - Yaming Gong
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, 198, Shiqiao Rd, Hangzhou, 310021, Zhejiang, China.
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China of Ministry of Agriculture and Rural Affairs, 198, Shiqiao Rd, Hangzhou, 310021, Zhejiang, China.
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Kefale H, Segla Koffi Dossou S, Li F, Jiang N, Zhou R, Wang L, Zhang Y, Li D, You J, Wang L. Widely targeted metabolic profiling provides insights into variations in bioactive compounds and antioxidant activity of sesame, soybean, peanut, and perilla. Food Res Int 2023; 174:113586. [PMID: 37986527 DOI: 10.1016/j.foodres.2023.113586] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/11/2023] [Accepted: 10/13/2023] [Indexed: 11/22/2023]
Abstract
Oilseeds are important sources of diversified nutraceuticals with marked health attributes. Thus, a better understanding of metabolome differences between common oilseeds will be conducive to the food pharmacy. This study aimed to compare the metabolite profiles and antioxidant activity of sesame, soybean, peanut, and perilla seeds and reveal the variation in bioactive compounds. LC-MS-based widely targeted metabolic profiling identified a total of 975 metabolites, of which 753 were common to the four crops. Multivariate analyses unveiled a crop-specific accumulation of metabolites, with 298-388 DAMs (differentially accumulated metabolites) identified. Amino acid metabolism, phenylpropanoid biosynthesis, flavonoid biosynthesis, and lipid metabolism were the most differentially regulated pathways. Furthermore, we revealed the variation in the relative content of 48, 20, 18, 9, 18, 11, and 6 differentially accumulated bioactive flavonoids, phenolic acids, amino acids, vitamins, terpenoids, alkaloids, and coumarins, respectively. Most of the flavonoids accumulated highly in soybean, followed by perilla. Sesame exhibited a better amino acid profile than other oilseeds. DPPH and FRAP assays showed that the antioxidant activity of perilla seed extracts was the highest, followed by soybean, peanut, and sesame. Our results provide data support for the comprehensive use of sesame, perilla, soybean, and peanut seeds in food, and pharmaceutical industries.
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Affiliation(s)
- Habtamu Kefale
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China; Department of Plant Science, College of Agriculture & Natural Resources, Debre Markos University, Ethiopia
| | - Senouwa Segla Koffi Dossou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Feng Li
- Amway (China) Botanical R&D Center, Wuxi 214115, China
| | - Nanjun Jiang
- Amway (China) Botanical R&D Center, Wuxi 214115, China
| | - Rong Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Lei Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Yanxin Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Donghua Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Jun You
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
| | - Linhai Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
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Liao Y, Chen Z, Yang Y, Shen D, Chai S, Ma Y, Ge R, Wang X, Wang S, Liu S. Antibiotic intervention exacerbated oxidative stress and inflammatory responses in SD rats under hypobaric hypoxia exposure. Free Radic Biol Med 2023; 209:70-83. [PMID: 37806597 DOI: 10.1016/j.freeradbiomed.2023.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/28/2023] [Accepted: 10/03/2023] [Indexed: 10/10/2023]
Abstract
The gut microbiota plays a crucial role in maintaining host nutrition, metabolism, and immune homeostasis, particularly in extreme environmental conditions. However, the regulatory mechanisms of the gut microbiota in animal organisms hypobaric hypoxia exposure require further study. We conducted a research by comparing SD rats treated with an antibiotic (ABX) cocktail and untreated SD rats that were housed in a low-pressure oxygen chamber (simulating low pressure and hypoxic environment at 6000 m altitude) for 30 days. After the experiment, blood, feces, and lung tissues from SD rats were collected for analysis of blood, 16S rRNA amplicon sequencing, and non-targeted metabolomics. The results demonstrated that the antibiotic cocktail-treated SD rats exhibited elevated counts of neutrophil (Neu) and monocyte (Mon) cells, an enrichment of sulfate-reducing bacteria (SBC), reduced levels of glutathione, and accumulated phospholipid compounds. Notably, the accumulation of phospholipid compounds, particularly lysophosphatidic acid (LPA), lipopolysaccharide (LPS), and lysophosphatidylcholine (LPC), along with the aforementioned changes, contributed to heightened oxidative stress and inflammation in the organism. In addition, we explored the resistance mechanisms of SD rats in low-oxygen and low-pressure environments and found that increasing the quantity of the Prevotellaceae and related beneficial bacteria (especially Lactobacillus) could reduce oxidative stress and inflammation. These findings offer valuable insights into enhancing the adaptability of low-altitude animals under hypobaric hypoxia exposure.
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Affiliation(s)
- Yang Liao
- College of Animal Husbandry and Veterinary Sciences, Qinghai University, Xining, 810016, China
| | - Zheng Chen
- College of Animal Husbandry and Veterinary Sciences, Qinghai University, Xining, 810016, China
| | - Yingkui Yang
- College of Animal Husbandry and Veterinary Sciences, Qinghai University, Xining, 810016, China
| | - Di Shen
- College of Animal Husbandry and Veterinary Sciences, Qinghai University, Xining, 810016, China
| | - Shatuo Chai
- College of Animal Husbandry and Veterinary Sciences, Qinghai University, Xining, 810016, China
| | - Yan Ma
- Research Center for High Altitude Medicine, Medical College of Qinghai University, Xining, 810001, China
| | - Rili Ge
- Research Center for High Altitude Medicine, Medical College of Qinghai University, Xining, 810001, China
| | - Xun Wang
- College of Animal Husbandry and Veterinary Sciences, Qinghai University, Xining, 810016, China
| | - Shuxiang Wang
- College of Animal Husbandry and Veterinary Sciences, Qinghai University, Xining, 810016, China.
| | - Shujie Liu
- College of Animal Husbandry and Veterinary Sciences, Qinghai University, Xining, 810016, China.
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Lippolis A, Roland WSU, Bocova O, Pouvreau L, Trindade LM. The challenge of breeding for reduced off-flavor in faba bean ingredients. FRONTIERS IN PLANT SCIENCE 2023; 14:1286803. [PMID: 37965015 PMCID: PMC10642941 DOI: 10.3389/fpls.2023.1286803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/17/2023] [Indexed: 11/16/2023]
Abstract
The growing interest in plant protein sources, such as pulses, is driven by the necessity for sustainable food production and climate change mitigation strategies. Faba bean (Vicia faba L.) is a promising protein crop for temperate climates, owing to its remarkable yield potential (up to 8 tonnes ha-1 in favourable growing conditions) and high protein content (~29% dry matter basis). Nevertheless, the adoption of faba bean protein in plant-based products that aim to resemble animal-derived counterparts is hindered by its distinctive taste and aroma, regarded as "off-flavors". In this review, we propose to introduce off-flavor as a trait in breeding programs by identifying molecules involved in sensory perception and defining key breeding targets. We discuss the role of lipid oxidation in producing volatile and non-volatile compounds responsible for the beany aroma and bitter taste, respectively. We further investigate the contribution of saponin, tannin, and other polyphenols to bitterness and astringency. To develop faba bean varieties with diminished off-flavors, we suggest targeting genes to reduce lipid oxidation, such as lipoxygenases (lox) and fatty acid desaturases (fad), and genes involved in phenylpropanoid and saponin biosynthesis, such as zero-tannin (zt), chalcone isomerase (chi), chalcone synthase (chs), β-amyrin (bas1). Additionally, we address potential challenges, including the need for high-throughput phenotyping and possible limitations that could arise during the genetic improvement process. The breeding approach can facilitate the use of faba bean protein in plant-based food such as meat and dairy analogues more extensively, fostering a transition toward more sustainable and climate-resilient diets.
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Affiliation(s)
- Antonio Lippolis
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
| | - Wibke S. U. Roland
- Wageningen Food & Biobased Research, Wageningen University & Research, Wageningen, Netherlands
| | - Ornela Bocova
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
| | - Laurice Pouvreau
- Wageningen Food & Biobased Research, Wageningen University & Research, Wageningen, Netherlands
| | - Luisa M. Trindade
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
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7
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Wang W, Zheng Z, Chen J, Duan T, He H, Tang S. Characterization of metabolite landscape distinguishes wild from cultivated Polygonati Rhizomes by UHPLC-Q-TOF-MS untargeted metabolomics. FOOD BIOSCI 2023. [DOI: 10.1016/j.fbio.2023.102574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
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8
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Untargeted and targeted metabolomics identify metabolite biomarkers for Salmonella enteritidis in chicken meat. Food Chem 2023; 409:135294. [PMID: 36592604 DOI: 10.1016/j.foodchem.2022.135294] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 12/07/2022] [Accepted: 12/20/2022] [Indexed: 12/25/2022]
Abstract
Salmonella Enteritidis easily contaminate chicken during slaughtering, processing, transportation, and sales, which seriously endangers human health. This study aimed to identify metabolite biomarkers for Salmonella Enteritidis contamination in chicken meat. UPLC-Q-Orbitrap MS untargeted metabolomics analysis identified 441 and 240 confidently metabolites in positive and negative ion mode, respectively. Thirty metabolites were defined as potential biomarkers for Salmonella enteritidis contamination in chicken meat. UPLC-QQQ-MS based targeted metabolomics was used to quantitatively analyze candidate metabolite biomarkers in Salmonella enteritidis contaminated and fresh chicken samples. A total of 10 candidate metabolite biomarkers were confirmed in the validation set, among which acetylcholine, l-Methionine, l-Proline, l-Valine, and l-Norleucine were identified as biomarkers for Salmonella Enteritidis contamination in chicken. The combined receiver operating characteristic curve analysis of the five biomarkers achieved an AUC of 0.956, indicating their high sensitivity and specificity in predicting Salmonella Enteritidis in raw chicken. In conclusion, the present study identified five metabolite biomarkers for Salmonella enteritidis in raw chicken. These results provide a potential theoretical basis for developing Salmonella Enteritidis detection methods in raw chicken.
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9
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Bao G, Mu L, Wang Y. Effect of Different Accumulative Temperate Zones in Heilongjiang on Glycine Soja Metabolites as Analyzed by Non-Target Metabolomics. Molecules 2023; 28:molecules28083296. [PMID: 37110529 PMCID: PMC10143369 DOI: 10.3390/molecules28083296] [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: 03/04/2023] [Revised: 03/25/2023] [Accepted: 04/03/2023] [Indexed: 04/29/2023] Open
Abstract
To study the effect of growth temperature on the nutritional components and metabolites of the wild soybean (Glycine soja), we analyzed the nutritional components and metabolic gases of the wild soybean in six accumulated temperature regions of the Heilongjiang Province, China, by gas chromatography-time-of-flight mass spectrometry (GC-TOF-MS). A total of 430 metabolites, including organic acids, organic oxides, and lipids, were identified and analyzed using multivariate statistical analysis, orthogonal partial least squares discriminant analysis, principal component analysis, and cluster analysis. Eighty-seven metabolites significantly differed in the sixth accumulated temperature region compared with the other five accumulated temperature regions. The 40 metabolites (such as threonine (Thr) and lysine (Lys)) were found to be elevated in soybeans from the sixth accumulated temperature zone compared with the other five accumulated temperature zones. Through analyzing the metabolic pathways of these metabolites, amino acid metabolism had the greatest influence on wild soybean quality. The results of the amino acid analysis were consistent with those of the GC-TOF-MS and showed that amino acids in wild soybeans from the sixth accumulated temperature zone significantly differed from those of the other zones. Threonine and lysine were the main substances driving these differences. The growth temperature affected the type and concentrations of metabolites in wild soybeans, and the GC-TOF-MS analysis of the effect of growth temperature on wild soybean metabolites was shown to be feasible.
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Affiliation(s)
- Guofeng Bao
- College of Forestry, Northeast Forestry University, Harbin 150040, China
- National Coarse Cereals Engineering Research Center, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Liqiang Mu
- College of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Ying Wang
- National Coarse Cereals Engineering Research Center, Heilongjiang Bayi Agricultural University, Daqing 163319, China
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10
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Duan Z, Li Q, Wang H, He X, Zhang M. Genetic regulatory networks of soybean seed size, oil and protein contents. FRONTIERS IN PLANT SCIENCE 2023; 14:1160418. [PMID: 36959925 PMCID: PMC10028097 DOI: 10.3389/fpls.2023.1160418] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 02/24/2023] [Indexed: 06/18/2023]
Abstract
As a leading oilseed crop that supplies plant oil and protein for daily human life, increasing yield and improving nutritional quality (high oil or protein) are the top two fundamental goals of soybean breeding. Seed size is one of the most critical factors determining soybean yield. Seed size, oil and protein contents are complex quantitative traits governed by genetic and environmental factors during seed development. The composition and quantity of seed storage reserves directly affect seed size. In general, oil and protein make up almost 60% of the total storage of soybean seed. Therefore, soybean's seed size, oil, or protein content are highly correlated agronomical traits. Increasing seed size helps increase soybean yield and probably improves seed quality. Similarly, rising oil and protein contents improves the soybean's nutritional quality and will likely increase soybean yield. Due to the importance of these three seed traits in soybean breeding, extensive studies have been conducted on their underlying quantitative trait locus (QTLs) or genes and the dissection of their molecular regulatory pathways. This review summarized the progress in functional genome controlling soybean seed size, oil and protein contents in recent decades, and presented the challenges and prospects for developing high-yield soybean cultivars with high oil or protein content. In the end, we hope this review will be helpful to the improvement of soybean yield and quality in the future breeding process.
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Affiliation(s)
- Zongbiao Duan
- Hainan Yazhou Bay Seed Laboratory, Sanya, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Qing Li
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Hong Wang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Xuemei He
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Min Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
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11
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Li Y, Liu F, Sun S, Xiang Y, Jiang X, He J. Metabolome of flue-cured tobacco is significantly affected by the presence of leaf stem. BMC PLANT BIOLOGY 2023; 23:89. [PMID: 36782114 PMCID: PMC9926566 DOI: 10.1186/s12870-023-04093-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Leaves of tobacco (Nicotiana tabacum L.) are flue-cured to use as a key industrial supply in various parts of the world. The quality of tobacco leaves is dependent on chemical components and their proportions. Generally, the stem attached to tobacco leaf is detached before curing. However, the leaf stem remains green for an extended period of time (as compared to leaf) during flue-curing. Hence, it is expected to affect the quality of tobacco's final product. RESULTS To understand the impact of the green stem of leaf on the metabolome of flue-cured tobacco, we employed a broad targeted metabolomics approach. We selected two tobacco cultivars (Yun87 and K326) and cultivated them in five geographic locations in China. For flue-curing, leaves were harvested without a stem (L) or with an attached stem (SPL). After metabolome analysis, a total of 1027 metabolites were annotated in these samples. A variable number of metabolites were differentially accumulated between both types of leaves (depending on geographic location or cultivar) representing an influence of environment or genotype. Interestingly, only 68 metabolites were differentially accumulated between L and SPL samples irrespective of the cultivar or geographic location. These differentially accumulated metabolites belonged to major groups of primary and secondary metabolites. We have discussed the importance of identified metabolites in terms of carbon, nitrogen, and polyphenolic metabolism. CONCLUSION The present research is the first comprehensive description of several metabolites in tobacco leaves related to the contribution of leaf stem. The current study opens novel prospects for investigating the potential of such metabolites in improving the quality of flue-cured tobacco.
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Affiliation(s)
- Yingxue Li
- Technology Center, China Tobacco Hubei Industrial Co., LTD, Wuhan, 430040, Hubei, China
| | - Fengfeng Liu
- Technology Center, China Tobacco Hubei Industrial Co., LTD, Wuhan, 430040, Hubei, China
| | - Shubin Sun
- Xiangyang Cigarette Factory, China Tobacco Hubei Industrial Co., LTD, Xiangyang, 441000, Hubei, China
| | - Yu Xiang
- Enshi Cigarette Factory, China Tobacco Hubei Industrial Co., LTD, Enshi, 445000, Hubei, China
| | - Xuebin Jiang
- Technology Center, China Tobacco Hubei Industrial Co., LTD, Wuhan, 430040, Hubei, China
| | - Jiewang He
- Technology Center, China Tobacco Hubei Industrial Co., LTD, Wuhan, 430040, Hubei, China.
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12
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Benkeblia N. Gas chromatography-mass spectrometry and liquid chromatography-mass spectrometry metabolomics platforms: Tools for plant oligosaccharides analysis. CARBOHYDRATE POLYMER TECHNOLOGIES AND APPLICATIONS 2023. [DOI: 10.1016/j.carpta.2023.100304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023] Open
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13
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Guo B, Sun L, Jiang S, Ren H, Sun R, Wei Z, Hong H, Luan X, Wang J, Wang X, Xu D, Li W, Guo C, Qiu LJ. Soybean genetic resources contributing to sustainable protein production. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:4095-4121. [PMID: 36239765 PMCID: PMC9561314 DOI: 10.1007/s00122-022-04222-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 09/10/2022] [Indexed: 06/12/2023]
Abstract
KEY MESSAGE Genetic resources contributes to the sustainable protein production in soybean. Soybean is an important crop for food, oil, and forage and is the main source of edible vegetable oil and vegetable protein. It plays an important role in maintaining balanced dietary nutrients for human health. The soybean protein content is a quantitative trait mainly controlled by gene additive effects and is usually negatively correlated with agronomic traits such as the oil content and yield. The selection of soybean varieties with high protein content and high yield to secure sustainable protein production is one of the difficulties in soybean breeding. The abundant genetic variation of soybean germplasm resources is the basis for overcoming the obstacles in breeding for soybean varieties with high yield and high protein content. Soybean has been cultivated for more than 5000 years and has spread from China to other parts of the world. The rich genetic resources play an important role in promoting the sustainable production of soybean protein worldwide. In this paper, the origin and spread of soybean and the current status of soybean production are reviewed; the genetic characteristics of soybean protein and the distribution of resources are expounded based on phenotypes; the discovery of soybean seed protein-related genes as well as transcriptomic, metabolomic, and proteomic studies in soybean are elaborated; the creation and utilization of high-protein germplasm resources are introduced; and the prospect of high-protein soybean breeding is described.
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Affiliation(s)
- Bingfu Guo
- Nanchang Branch of National Center of Oil crops Improvement, Jiangxi Province Key Laboratory of Oil crops Biology, Crops Research Institute of Jiangxi Academy of Agricultural Sciences, Nanchang, China
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) and MOA KeyLab of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liping Sun
- Nanchang Branch of National Center of Oil crops Improvement, Jiangxi Province Key Laboratory of Oil crops Biology, Crops Research Institute of Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - Siqi Jiang
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding, College of Life Science and Technology, Harbin Normal University, Harbin, China
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) and MOA KeyLab of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Honglei Ren
- Soybean Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Rujian Sun
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) and MOA KeyLab of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhongyan Wei
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) and MOA KeyLab of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huilong Hong
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) and MOA KeyLab of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Soybean Research Institute, Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agriculture University, Harbin, China
| | - Xiaoyan Luan
- Soybean Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Jun Wang
- College of Agriculture, Yangtze University, Jingzhou, China
| | - Xiaobo Wang
- School of Agronomy, Anhui Agricultural University, Hefei, China
| | - Donghe Xu
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences, Tsukuba, Japan
| | - Wenbin Li
- Soybean Research Institute, Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agriculture University, Harbin, China
| | - Changhong Guo
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding, College of Life Science and Technology, Harbin Normal University, Harbin, China
| | - Li-Juan Qiu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) and MOA KeyLab of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China.
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14
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Islam N, Krishnan HB, Natarajan SS. Protein profiling of fast neutron soybean mutant seeds reveals differential accumulation of seed and iron storage proteins. PHYTOCHEMISTRY 2022; 200:113214. [PMID: 35469783 DOI: 10.1016/j.phytochem.2022.113214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 04/18/2022] [Accepted: 04/19/2022] [Indexed: 06/14/2023]
Abstract
A fast neutron (FN) radiated mutant soybean (Glycine max (L.) Merr., Fabaceae) displaying large duplications exhibited an increase in total seed protein content. A tandem mass tag (TMT) based protein profiling of matured seeds resulted in the identification of 4338 proteins. Gene duplication resulted in a significant increase in several seed storage proteins and protease inhibitors. Among the storage proteins, basic 7 S globulin, glycinin G4, and beta-conglycinin showed higher abundance in matured FN mutant seeds in addition to protease inhibitors. A significantly higher abundance of L-ascorbate peroxidases, acid phosphatases, and iron storage proteins was also observed. A higher amount of albumin, sucrose synthase, iron storage, and ascorbate family proteins in the mutant seeds was observed at the mid-stage of seed filling. We anticipate that the duplicated genes might have a cascading effect on the genome constituents, thus, resulting in increased storage and iron-containing protein content in the mutant seeds.
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Affiliation(s)
- Nazrul Islam
- Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, 20705, USA
| | - Hari B Krishnan
- Plant Genetics Research Unit, USDA-ARS, University of Missouri, Columbia, MO, 65211, USA
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15
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Chen Z, Zhong W, Zhou Y, Ji P, Wan Y, Shi S, Yang Z, Gong Y, Mu F, Chen S. Integrative analysis of metabolome and transcriptome reveals the improvements of seed quality in vegetable soybean (Glycine max (L.) Merr.). PHYTOCHEMISTRY 2022; 200:113216. [PMID: 35487251 DOI: 10.1016/j.phytochem.2022.113216] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 06/14/2023]
Abstract
Vegetable soybean is derived from grain soybean. Seeds of vegetable soybean are bigger, sweeter, and have smoother texture and better flavor than those of grain soybean. To better understand the improvements of seed quality in vegetable soybean, comparative metabolome and transcriptome analyses were performed in the developing seeds between grain (Williams 82) and vegetable (Jiaoda 133) soybeans. A total of 299 differential metabolites were identified between two genotypes, with an increase in free amino acids, carbohydrates, sterols, and flavonoids and a decrease in fatty acid in vegetable soybean. Thousands of differentially expressed genes (DEGs) were identified by transcriptome analysis. DEGs were used for weighted gene co-expression network analysis (WGCNA), yielding 16 co-expression modules. The expression patterns of DEGs within these modules were distinct between two genotypes. Functional enrichment analysis revealed that metabolic pathways, including alanine, aspartate and glutamate metabolism, fatty acid degradation, starch and sucrose metabolism, sucrose transport, and flavonoid biosynthesis, were up-regulated, whereas photosynthesis, arginine biosynthesis, arginine and proline metabolism, glycolysis/gluconeogenesis, and fatty acid biosynthesis were down-regulated in vegetable soybean. Reasonably, the alterations of metabolic pathways corresponding to DEGs partly explained the formation of differential metabolites. These findings provide a better understanding of seed development and breeding improvements of vegetable soybean.
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Affiliation(s)
- Zhengjie Chen
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Science, No.159 Huajin Avanue, Qingbaijiang District, Chengdu City, 610300, China.
| | - Wenjuan Zhong
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Science, No.159 Huajin Avanue, Qingbaijiang District, Chengdu City, 610300, China.
| | - Yonghang Zhou
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Science, No.159 Huajin Avanue, Qingbaijiang District, Chengdu City, 610300, China.
| | - Peicheng Ji
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Science, No.159 Huajin Avanue, Qingbaijiang District, Chengdu City, 610300, China.
| | - Yonglu Wan
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Science, No.159 Huajin Avanue, Qingbaijiang District, Chengdu City, 610300, China.
| | - Shengjia Shi
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Science, No.159 Huajin Avanue, Qingbaijiang District, Chengdu City, 610300, China.
| | - Zehu Yang
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Science, No.159 Huajin Avanue, Qingbaijiang District, Chengdu City, 610300, China.
| | - Yiyun Gong
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Science, No.159 Huajin Avanue, Qingbaijiang District, Chengdu City, 610300, China.
| | - Fangsheng Mu
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Science, No.159 Huajin Avanue, Qingbaijiang District, Chengdu City, 610300, China.
| | - Siwei Chen
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Science, No.159 Huajin Avanue, Qingbaijiang District, Chengdu City, 610300, China.
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16
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Application of energy dispersive X-ray fluorescence spectrometry and near-infrared reflectance spectroscopy combined with multivariate statistical analysis for discriminating the geographical origin of soybeans. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.109140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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17
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Cao P, Zhao Y, Wu F, Xin D, Liu C, Wu X, Lv J, Chen Q, Qi Z. Multi-Omics Techniques for Soybean Molecular Breeding. Int J Mol Sci 2022; 23:4994. [PMID: 35563386 PMCID: PMC9099442 DOI: 10.3390/ijms23094994] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 04/22/2022] [Accepted: 04/28/2022] [Indexed: 02/04/2023] Open
Abstract
Soybean is a major crop that provides essential protein and oil for food and feed. Since its origin in China over 5000 years ago, soybean has spread throughout the world, becoming the second most important vegetable oil crop and the primary source of plant protein for global consumption. From early domestication and artificial selection through hybridization and ultimately molecular breeding, the history of soybean breeding parallels major advances in plant science throughout the centuries. Now, rapid progress in plant omics is ushering in a new era of precision design breeding, exemplified by the engineering of elite soybean varieties with specific oil compositions to meet various end-use targets. The assembly of soybean reference genomes, made possible by the development of genome sequencing technology and bioinformatics over the past 20 years, was a great step forward in soybean research. It facilitated advances in soybean transcriptomics, proteomics, metabolomics, and phenomics, all of which paved the way for an integrated approach to molecular breeding in soybean. In this review, we summarize the latest progress in omics research, highlight novel findings made possible by omics techniques, note current drawbacks and areas for further research, and suggest that an efficient multi-omics approach may accelerate soybean breeding in the future. This review will be of interest not only to soybean breeders but also to researchers interested in the use of cutting-edge omics technologies for crop research and improvement.
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Affiliation(s)
- Pan Cao
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (P.C.); (Y.Z.); (F.W.); (D.X.); (C.L.)
| | - Ying Zhao
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (P.C.); (Y.Z.); (F.W.); (D.X.); (C.L.)
| | - Fengjiao Wu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (P.C.); (Y.Z.); (F.W.); (D.X.); (C.L.)
| | - Dawei Xin
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (P.C.); (Y.Z.); (F.W.); (D.X.); (C.L.)
| | - Chunyan Liu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (P.C.); (Y.Z.); (F.W.); (D.X.); (C.L.)
| | - Xiaoxia Wu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (P.C.); (Y.Z.); (F.W.); (D.X.); (C.L.)
| | - Jian Lv
- Department of Innovation, Syngenta Biotechnology China, Beijing 102206, China
| | - Qingshan Chen
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (P.C.); (Y.Z.); (F.W.); (D.X.); (C.L.)
| | - Zhaoming Qi
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (P.C.); (Y.Z.); (F.W.); (D.X.); (C.L.)
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18
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Discrimination of the Geographical Origin of Soybeans Using NMR-Based Metabolomics. Foods 2021; 10:foods10020435. [PMID: 33671190 PMCID: PMC7922469 DOI: 10.3390/foods10020435] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/10/2021] [Accepted: 02/12/2021] [Indexed: 02/01/2023] Open
Abstract
With the increase in soybean trade between countries, the intentional mislabeling of the origin of soybeans has become a serious problem worldwide. In this study, metabolic profiling of soybeans from the Republic of Korea and China was performed by nuclear magnetic resonance (NMR) spectroscopy coupled with multivariate statistical analysis to predict the geographical origin of soybeans. The optimal orthogonal partial least squares-discriminant analysis (OPLS-DA) model was obtained using total area normalization and unit variance (UV) scaling, without applying the variable influences on projection (VIP) cut-off value, resulting in 96.9% sensitivity, 94.4% specificity, and 95.6% accuracy in the leave-one-out cross validation (LOO-CV) test for discriminating between Korean and Chinese soybeans. Soybeans from the northeastern, middle, and southern regions of China were successfully differentiated by standardized area normalization and UV scaling with a VIP cut-off value of 1.0, resulting in 100% sensitivity, 91.7%–100% specificity, and 94.4%–100% accuracy in a LOO-CV test. The methods employed in this study can be used to obtain essential information for the authentication of soybean samples from diverse geographical locations in future studies.
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19
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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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20
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Ren RJ, Wang P, Wang LN, Su JP, Sun LJ, Sun Y, Chen DF, Chen XW. Os4BGlu14, a monolignol β-Glucosidase, negatively affects seed longevity by influencing primary metabolism in rice. PLANT MOLECULAR BIOLOGY 2020; 104:513-527. [PMID: 32833149 DOI: 10.1007/s11103-020-01056-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 08/15/2020] [Indexed: 05/10/2023]
Abstract
Os4BGlu14, a monolignol β-glucosidase, plays a negative role in seed longevity by affecting primary metabolism during seed development and aging. Seed longevity is a crucial trait in agriculture and in the conservation of germplasm resources. β-Glucosidases (BGlus) are multifunctional enzymes that affect plant growth and their adaptation to the environment. The function of rice BGlus in seed longevity, however, remains unknown. We report here that Os4BGlu14, a rice β-Glucosidase, negatively affected seed longevity during accelerated aging. Os4BGlu14 was highly expressed in rice embryos and induced by accelerated aging. Compared to the wild type, rice lines overexpressing Os4BGlu14 had significantly greater grain length, but smaller grain width and thickness. Overexpressing (OE) lines also showed lower starch but higher glucose contents. After accelerated aging treatment, OE lines displayed a significantly lower germination percentage than the wild type. Additionally, these lines had higher lignin accumulation before and after accelerated aging. Metabolome analysis detected 217 metabolites in untreated and aged rice seeds. Comparison of the differential metabolites between WT and OE5 revealed that ten key metabolites, four of which (e.g., uridine 5'-diphosphoglucose-glucose, UDPG) were increased, while the other six (e.g., γ-aminobutyric acid and methionine) were decreased, might be the crucial factors that lead to seed deterioration. Further analysis confirmed higher UDPG levels and more severe programmed cell death in OE lines than in the wild type. Furthermore, OE lines presented a lower germination rate after abscisic acid and paclobutrazol treatment during germination, compared to the wild type. Our study provides a basis for understanding the function of Os4BGlu14 in seed longevity in rice.
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Affiliation(s)
- Rui-Juan Ren
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Pei Wang
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Li-Na Wang
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Jing-Ping Su
- Tianjin Crop Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin, 300384, China
| | - Lin-Jing Sun
- Tianjin Crop Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin, 300384, China
| | - Yue Sun
- Tianjin Crop Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin, 300384, China
| | - De-Fu Chen
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China.
| | - Xi-Wen Chen
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China.
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21
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Hepatotoxicity of nutmeg: A pilot study based on metabolomics. Biomed Pharmacother 2020; 131:110780. [PMID: 33152938 DOI: 10.1016/j.biopha.2020.110780] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 09/08/2020] [Accepted: 09/17/2020] [Indexed: 12/22/2022] Open
Abstract
Incidences of abuse and poisoning have been reported for nutmeg, a household spice made from grinding the seed of Myristica fragrans, owing to its hallucinogenic properties. However, there have been no reports on nutmeg hepatotoxicity in relation to dose and duration of exposure. To investigate the hepatotoxicity of different nutmeg exposure durations and doses, male mice were administered daily with normal saline, 1.0 g/kg nutmeg, or 4.0 g/kg nutmeg by intragastrical gavage for either 7 or 14 days (for a total of six treatment groups, n = 6). Body weight of each mouse was monitored daily. Histological analysis of liver tissues was performed using hematoxylin and eosin (H&E) staining to investigate the morphological changes in hepatocytes. Serum aspartate aminotransferase (AST) and alanine aminotransferase (ALT) levels were determined using enzyme-linked immunosorbent assay (ELISA) to investigate liver function. Metabolomics and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed between treatment groups for identifying differential metabolites. Mice in the nutmeg exposure groups exhibited slow growth trends, hepatocyte damage, and significantly elevated serum AST and ALT levels associated with nutmeg dose and exposure duration. Metabolomics and KEGG enrichment pathway analyses also revealed differential levels of some metabolites related to liver function upon nutmeg exposure. Therefore, the present study reasonably speculates that nutmeg exposure may cause liver damage and affect liver function depending on the dose and duration.
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22
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Hyeon H, Xu JL, Kim JK, Choi Y. Comparative metabolic profiling of cultivated and wild black soybeans reveals distinct metabolic alterations associated with their domestication. Food Res Int 2020; 134:109290. [PMID: 32517920 DOI: 10.1016/j.foodres.2020.109290] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 04/15/2020] [Accepted: 05/01/2020] [Indexed: 12/26/2022]
Abstract
Generally, cultivated black soybean (CBS) has been used as a major source of various nutrients for humans and animals. To assess the metabolic alterations induced by domestication in soybean, we performed a comprehensive metabolite profiling of 56 soybean varieties, including 28 CBS and 28 wild black soybean (WBS) varieties. A total of 48 metabolites were characterized, including 45 primary and 3 secondary metabolites, from CBS and WBS. The results of principal component analysis and hierarchical cluster analysis (HCA) revealed significant metabolic differences between CBS and WBS that were closely related to metabolic pathways. The results indicate that flavonoids correlated positively with phenylalanine, a precursor for phenylpropanoid biosynthesis; the contents of flavonoids and phenylpropanoids were higher in WBS. Pathway analysis revealed that CBS contained large amounts of TCA cycle intermediates, amino acids, and fatty acids as a result of increased energy metabolism, amino acid metabolism, and seed filling. The projection to latent structure method, using the partial least squares method, was applied to predict the flavonoid content in soybean seed, which indicated that sucrose, threonic acid, citric acid, and fatty acids are important in predicting the antioxidant content of samples. This work will provide important information for designing new soybean cultivars with enhanced nutritional and agricultural traits.
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Affiliation(s)
- Hyejin Hyeon
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Republic of Korea
| | - Jiu Liang Xu
- Natural Product Research Center, Korea Institute of Science and Technology (KIST), Gangneung 25451, Republic of Korea; College of Resources and Environmental Sciences; National Academy of Agriculture Green Development; School of Agriculture Green Development, China Agricultural University, 100193 Beijing, China
| | - Jae Kwang Kim
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Republic of Korea.
| | - Yongsoo Choi
- Natural Product Research Center, Korea Institute of Science and Technology (KIST), Gangneung 25451, Republic of Korea; Department of Biological Chemistry, University of Science and Technology, Youseng-gu, Daejeon 305-350, Republic of Korea.
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23
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Deng M, Zhang X, Luo J, Liu H, Wen W, Luo H, Yan J, Xiao Y. Metabolomics analysis reveals differences in evolution between maize and rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1710-1722. [PMID: 32445406 DOI: 10.1111/tpj.14856] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 05/12/2020] [Indexed: 06/11/2023]
Abstract
Metabolites are the intermediate and final products of metabolism, which play essential roles in plant growth, evolution and adaptation to changing climates. However, it is unclear how evolution contributes to metabolic variation in plants. Here, we investigated the metabolomics data from leaf and seed tissues in maize and rice. Using principal components analysis based on leaf metabolites but not seed metabolites, metabolomics data could be clearly separated for rice Indica and Japonica accessions, while two maize subgroups, temperate and tropical, showed more visible admixture. Rice and maize seed exhibited significant interspecific differences in metabolic variation, while within rice, leaf and seed displayed similar metabolic variations. Among 10 metabolic categories, flavonoids had higher variation in maize than rice, indicating flavonoids are a key constituent of interspecific metabolic divergence. Interestingly, metabolic regulation was also found to be reshaped dramatically from positive to negative correlations, indicative of the differential evolutionary processes in maize and rice. Moreover, perhaps due to this divergence significantly more metabolic interactions were identified in rice than maize. Furthermore, in rice, the leaf was found to harbor much more intense metabolic interactions than the seed. Our result suggests that metabolomes are valuable for tracking evolutionary history, thereby complementing and extending genomic insights concerning which features are responsible for interspecific differentiation in maize and rice.
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Affiliation(s)
- Min Deng
- College of Agronomy, Hunan Agricultural University, Changsha, Hunan, 410128, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xuehai Zhang
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Jingyun Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Haijun Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Weiwei Wen
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, China
| | - Hongbing Luo
- College of Agronomy, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yingjie Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
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Nuraini A, Qosim WA. Effect of Salinity Stress on Shoot <i>Musa acuminata</i> L. Barangan Cultivar <i>in vitro </i>Culture. Pak J Biol Sci 2020; 22:201-205. [PMID: 31930822 DOI: 10.3923/pjbs.2019.201.205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND AND OBJECTIVE Quality banana fruit is significantly related with number and type of metabolite produce. Metabolite production of Musa acuminata L. is effected by abiotic factors such as salinity. So the purpose of this research was to study the effect of plant response under salinity stress and also identified the chemical compound especially phenolic compound. MATERIALS AND METHODS Explants used in this research were shoot of Musa acuminata L., Murashige and Skoog medium, Benzyl amino purine, sugar, agar, sodium chloride. The research was conducted in two stages; stage (1): Developing in vitro culture of shoot of Musa acuminata L. with NaCl treatment i.e., 0, 50, 100, 150 and 200 mM concentration, stage (2): Gas Chromatography Mass Spectrometry (GCMS) analysis on the shoot of in vitro banana plantlets. RESULTS The findings of this study showed that compound content of shoot of banana plantlets were Amine, Ester, Propane, Keton, Alkohol, Phenol, Methyl, Acid and it was observed that Ester (27.515%) was the highest detected compound. CONCLUSION It is concluded that the salinity had affected the plant growth. The analysis showed that the highest compound content of Musa acuminate L. Barangan cultivar was Ester and Phenols.
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Wang J, Zhou P, Shi X, Yang N, Yan L, Zhao Q, Yang C, Guan Y. Primary metabolite contents are correlated with seed protein and oil traits in near-isogenic lines of soybean. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.cj.2019.04.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Zhao GC, Zhang YX, Sun SY, Xie MX, Hu CY, Shi YQ, Shi JX, Li JY. Identification of the biochemical characteristics of developing giant embryo rice grains using non-targeted metabolomics. J Cereal Sci 2019. [DOI: 10.1016/j.jcs.2018.10.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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27
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Khan WA, Hou X, Han K, Khan N, Dong H, Saqib M, Zhang Z, Naseri E, Hu C. Lipidomic study reveals the effect of morphological variation and other metabolite interactions on the lipid composition in various cultivars of Bok choy. Biochem Biophys Res Commun 2018; 506:755-764. [PMID: 29673595 DOI: 10.1016/j.bbrc.2018.04.112] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 04/13/2018] [Indexed: 12/16/2022]
Abstract
Bok choy is an important Brassica vegetable which is also known for its wide range of cultivars that differ in their appearance, leaf color, size and shape. For the purpose to investigate the effect of these phenotypic differences on their lipid composition, seven morphotypes of NHCC (Suzhouqing, Aijaohuang, Wutacai, Yellowrose, Ziluolan, Xiangqingcai and Zicaitai) were selected for this study. For this reason, extensive metabolic approach was adopted which was mainly focused on lipidomics. The overall metabolic position of lipids was determined and the isolated lipid compounds were characterized on the basis of their lipid classes. Moreover, discriminative analysis was applied to monitor the distribution pattern of lipid in different cultivars. Aijiaohuang was the leading cultivar which contained highest lipid levels, whereas least proportion was found in Zicaitai. We proposed that leaf color might have an effect on the lipid composition such as purple cultivars were dominated in glycerophopholipids, light green in fatty acids and dark green were rich in glycerolipids. The level of metabolites differed greatly among different genotypes. Lipid-metabolite interactions revealed the positive correlation of lipids with flavonoid and hydroxycinnamoyl derivatives, whereas negative correlation was noticed in case of phenylamines. This is the first comprehensive study based on lipidomics in order to evaluate the substantial impact of various phenotypes on the metabolic composition of NHCC.
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Affiliation(s)
- Waleed Amjad Khan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Science and Technology/College of Horticulture, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Xilin Hou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Science and Technology/College of Horticulture, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Ke Han
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Science and Technology/College of Horticulture, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Nadeem Khan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Science and Technology/College of Horticulture, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Huijie Dong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Science and Technology/College of Horticulture, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Muhammad Saqib
- Department of Horticulture, Faculty of Agricultural Sciences & Technology, Bahauddin Zakariya University, Multan 60000, Pakistan
| | - Zhishuo Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Science and Technology/College of Horticulture, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Emal Naseri
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Science and Technology/College of Horticulture, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Chunmei Hu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Science and Technology/College of Horticulture, Nanjing Agricultural University, Nanjing 210095, PR China; New Rural Research Institute in Lianyungang, Nanjing Agricultural University, PR China.
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Yan S, Huang W, Gao J, Fu H, Liu J. Comparative metabolomic analysis of seed metabolites associated with seed storability in rice (Oryza sativa L.) during natural aging. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 127:590-598. [PMID: 29729608 DOI: 10.1016/j.plaphy.2018.04.020] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 03/28/2018] [Accepted: 04/19/2018] [Indexed: 05/02/2023]
Abstract
Seed storability is an important trait for crop breeding, however, the mechanism underlying seed storability remains largely unknown. Here, a mass spectrometry-based comparative metabolomic study was performed for rice seeds before and after 24-month natural storage between two hybrid rice cultivars, IIYou 998 (IIY) with low storability and BoYou 998 (BY) with relative high storability. A total of 48 metabolites among 90 metabolite peaks detected were conclusively identified, and most of them are involved in the primary metabolism. During the 24-month storage, 19 metabolites with significant changes in abundance were found in the storage-sensitive IIY seeds, but only 8 in the BY seeds, most of which are free amino acids and soluble sugars. The observed changes of the metabolites in IIY seeds that are consistent with our protoemics results are likely to be involved in its sensitivity to storage. Levels of all identified 18 amino acid-related metabolites and most sugar-related metabolites were significantly higher in IIY seeds both before and after storage. However the level of raffinose was lower in IIY seeds before and after storage, and did not change significantly throughout the storage period in both two cultivars, suggesting its potential role in seed storability. Taken together, these results may help to improve our understanding of seed storability.
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Affiliation(s)
- Shijuan Yan
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Tianhe District, Guangzhou 510640, China.
| | - Wenjie Huang
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Tianhe District, Guangzhou 510640, China.
| | - Jiadong Gao
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Tianhe District, Guangzhou 510640, China.
| | - Hua Fu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Tianhe District, Guangzhou 510640, China.
| | - Jun Liu
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Tianhe District, Guangzhou 510640, China.
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Sun B, Zheng AH, Zhang F, Wei KS, Chen Q, Luo Y, Zhang Y, Wang XR, Lin FC, Yang J, Tang HR. Metabolic profiles of Cuibi-1 and Zhongyan-100 flue-cured tobacco leaves in different growing regions by gas chromatography/mass spectrometry. ROYAL SOCIETY OPEN SCIENCE 2018; 5:180261. [PMID: 29892458 PMCID: PMC5990828 DOI: 10.1098/rsos.180261] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 04/18/2018] [Indexed: 06/08/2023]
Abstract
The metabolic profiles of tobacco leaves of two differential Chinese cultivars from different growing regions were analysed using gas chromatography-mass spectrometry (GC-MS). The results of principal component analysis, partial least-squares discriminant analysis and hierarchical cluster analysis showed significant differences in metabolome among three groups, identified 24 differential metabolites, and analysed the metabolic pathway in which the metabolites were involved. Among them, 13 metabolites were associated with geographical regions, including seven organic and fatty acids, four carbohydrates and two secondary metabolites. Four amino acids and two monosaccharides were associated with cultivars and the remaining five metabolites were associated with both. The relationships among the differential metabolites and the distinct characteristics of environment and cultivar were further discussed. In addition, correlation analysis indicated that most of the differential carbohydrates were negatively correlated with the differential amino acids and organic acids. Taken together, this study demonstrates the metabolite differences between two cultivars in different regions, and highlights the effect of environment and cultivar on tobacco leaf metabolism.
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Affiliation(s)
- Bo Sun
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, People's Republic of China
- Zhengzhou Tobacco Research Institute, Zhengzhou 450001, People's Republic of China
| | - Ai-Hong Zheng
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, People's Republic of China
| | - Fen Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, People's Republic of China
- Zhengzhou Tobacco Research Institute, Zhengzhou 450001, People's Republic of China
| | - Ke-Su Wei
- Guizhou Academy of Tobacco Science, Guiyang 550081, People's Republic of China
| | - Qing Chen
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, People's Republic of China
| | - Ya Luo
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, People's Republic of China
| | - Yong Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, People's Republic of China
| | - Xiao-Rong Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, People's Republic of China
| | - Fu-Cheng Lin
- Zhengzhou Tobacco Research Institute, Zhengzhou 450001, People's Republic of China
| | - Jun Yang
- Zhengzhou Tobacco Research Institute, Zhengzhou 450001, People's Republic of China
| | - Hao-Ru Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, People's Republic of China
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Kim YJ, Joo SC, Shi J, Hu C, Quan S, Hu J, Sukweenadhi J, Mohanan P, Yang DC, Zhang D. Metabolic dynamics and physiological adaptation of Panax ginseng during development. PLANT CELL REPORTS 2018; 37:393-410. [PMID: 29150823 DOI: 10.1007/s00299-017-2236-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Accepted: 11/09/2017] [Indexed: 05/27/2023]
Abstract
The dynamics of metabolites from leaves to roots of Panax ginseng during development has revealed the tissue-specific and year-specific metabolic networks. Being an essential Oriental medicinal plant, ginseng (Panax ginseng Meyer) is a slow-growing perennial herb-accumulating pharmaceutically active metabolites such as ginsenosides in roots during growth. However, little is known about how ginseng plants survive in the harsh environments such as winter cold and summer heat for a longer period and accumulates those active metabolites as the plant grows. To understand the metabolic kinetics in both source and sink organs such as leaves and roots of ginseng plant, respectively, and to assess the changes in ginsenosides biosynthesis during ginseng growth, we investigated the metabolic profiles from leaves and roots of 1-, 4-, and 6-year-old field-grown ginseng plants. Using an integrated non-targeted metabolomic approach, we identified in total 348 primary and secondary metabolites, which provided us for the first time a global metabolomic assessment of ginseng during growth, and morphogenesis. Strikingly, the osmoprotectants and oxidized chemicals were highly accumulated in 4- and 6-year-old ginseng leaves suggested that ginseng develop a wide range of metabolic strategies to adapt unfavorable conditions as they mature. In 6-year-old plants, ginsenosides were decreased in leaves but increased in roots up to 1.2- to sixfold, supporting the view that there is a long-distance transport of ginsenosides from leaves to roots as ginseng plants mature. Our findings provide insights into the metabolic kinetics during the development of ginseng plant and this could complement the pharmacological importance of ginseng and its compounds according to their age.
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Affiliation(s)
- Yu-Jin Kim
- Department of Oriental Medicinal Biotechnology, College of Life Science, Kyung Hee University, Giheung-gu, Yongin-si, Gyeonggi-do, 17104, Republic of Korea.
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 20040, People's Republic of China.
| | - Sung Chul Joo
- Department of Oriental Medicinal Biotechnology, College of Life Science, Kyung Hee University, Giheung-gu, Yongin-si, Gyeonggi-do, 17104, Republic of Korea
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 20040, People's Republic of China
| | - Chaoyang Hu
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 20040, People's Republic of China
| | - Sheng Quan
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 20040, People's Republic of China
| | - Jianping Hu
- Department of Energy Plant Research Laboratory and Plant Biology Department, Michigan State University, East Lansing, MI, 48824, USA
| | - Johan Sukweenadhi
- Department of Oriental Medicinal Biotechnology, College of Life Science, Kyung Hee University, Giheung-gu, Yongin-si, Gyeonggi-do, 17104, Republic of Korea
| | - Padmanaban Mohanan
- Graduate School of Biotechnology and Ginseng Bank, College of Life Sciences, Kyung Hee University, Giheung-gu, Yongin-si, Gyeonggi-do, 17104, Republic of Korea
| | - Deok-Chun Yang
- Department of Oriental Medicinal Biotechnology, College of Life Science, Kyung Hee University, Giheung-gu, Yongin-si, Gyeonggi-do, 17104, Republic of Korea.
- Graduate School of Biotechnology and Ginseng Bank, College of Life Sciences, Kyung Hee University, Giheung-gu, Yongin-si, Gyeonggi-do, 17104, Republic of Korea.
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 20040, People's Republic of China.
- Crop Biotech Institute and Department of Plant Molecular Systems Biotechnology, Kyung Hee University, Yongin, 446-701, Republic of Korea.
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Metabolic variation and cooking qualities of millet cultivars grown both organically and conventionally. Food Res Int 2018; 106:825-833. [PMID: 29579993 DOI: 10.1016/j.foodres.2018.01.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 12/27/2017] [Accepted: 01/12/2018] [Indexed: 12/30/2022]
Abstract
Millet plays a major role in food security in Africa and Asia. In addition to being a rich source of nutrients, millet contains many phytochemicals that are potentially beneficial for human health, and several of these compounds are related to its cooking properties. In this study, 172 metabolites and 3 cooking quality traits of millet from the same two cultivars grown both organically and conventionally were analyzed. The results indicated that the differences in the metabolities and cooking quality of the millets could be attributed mostly to the cultivar and whether the millet was grown conventionally or organically. Organic growing conditions only enhanced the accumulation of some carbohydrates such as fructose and glucose. Therefore, cultivar selection was important in organic millet cultivation. The relationships between metabolites and cooking quality traits showed that, overall, 57.43% of the variation in the cooking quality matrix was explained by metabolome matrix, which indicated that some chemical compounds could also be used to evaluate the cooking qualities of millet. These results could contribute to breeding millet to improve its the nutritional properties and cooking qualities.
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Yang X, Wei S, Liu B, Guo D, Zheng B, Feng L, Liu Y, Tomás-Barberán FA, Luo L, Huang D. A novel integrated non-targeted metabolomic analysis reveals significant metabolite variations between different lettuce ( Lactuca sativa. L) varieties. HORTICULTURE RESEARCH 2018; 5:33. [PMID: 29977569 PMCID: PMC6015802 DOI: 10.1038/s41438-018-0050-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 04/06/2018] [Accepted: 05/13/2018] [Indexed: 05/02/2023]
Abstract
Lettuce is an important leafy vegetable that represents a significant dietary source of antioxidants and bioactive compounds. However, the levels of metabolites in different lettuce cultivars are poorly characterized. In this study, we used combined GC × GC-TOF/MS and UPLC-IMS-QTOF/MS to detect and relatively quantify metabolites in 30 lettuce cultivars representing large genetic diversity. Comparison with online databases, the published literature, standards as well using collision cross-section values enabled putative identification of 171 metabolites. Sixteen of these 171 metabolites (including phenolic acid derivatives, glycosylated flavonoids, and one iridoid) were present at significantly different levels in leaf and head type lettuces, which suggested the significant metabolomic variations between the leaf and head types of lettuce are related to secondary metabolism. A combination of the results and metabolic network analysis techniques suggested that leaf and head type lettuces contain not only different levels of metabolites but also have significant variations in the corresponding associated metabolic networks. The novel lettuce metabolite library and novel non-targeted metabolomics strategy devised in this study could be used to further characterize metabolic variations between lettuce cultivars or other plants. Moreover, the findings of this study provide important insight into metabolic adaptations due to natural and human selection, which could stimulate further research to potentially improve lettuce quality, yield, and nutritional value.
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Affiliation(s)
- Xiao Yang
- 1School of Agriculture and Biology, Shanghai Jiao Tong University, Key Laboratory of Urban Agriculture, Ministry of Agriculture, Shanghai, 200240 China
- 2Shanghai Agrobiological Gene Center, Shanghai, 201106 China
- 3Research Group on Quality, Safety and Bioactivity of Plant Foods, Center for Applied Soil Science and Biology of the Segura, the Spanish National Research Council, (CEBAS-CSIC), Murcia, 30100 Spain
| | - Shiwei Wei
- 2Shanghai Agrobiological Gene Center, Shanghai, 201106 China
| | - Bin Liu
- 1School of Agriculture and Biology, Shanghai Jiao Tong University, Key Laboratory of Urban Agriculture, Ministry of Agriculture, Shanghai, 200240 China
| | - Doudou Guo
- 1School of Agriculture and Biology, Shanghai Jiao Tong University, Key Laboratory of Urban Agriculture, Ministry of Agriculture, Shanghai, 200240 China
| | - Bangxiao Zheng
- 4Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021 China
- 5University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Lei Feng
- 6Instrumental Analysis Center, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Yumin Liu
- 6Instrumental Analysis Center, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Francisco A Tomás-Barberán
- 3Research Group on Quality, Safety and Bioactivity of Plant Foods, Center for Applied Soil Science and Biology of the Segura, the Spanish National Research Council, (CEBAS-CSIC), Murcia, 30100 Spain
| | - Lijun Luo
- 2Shanghai Agrobiological Gene Center, Shanghai, 201106 China
| | - Danfeng Huang
- 1School of Agriculture and Biology, Shanghai Jiao Tong University, Key Laboratory of Urban Agriculture, Ministry of Agriculture, Shanghai, 200240 China
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Ning K, Ding C, Zhu W, Zhang W, Dong Y, Shen Y, Su X. Comparative Metabolomic Analysis of the Cambium Tissue of Non-transgenic and Multi-Gene Transgenic Poplar ( Populus × euramericana 'Guariento'). FRONTIERS IN PLANT SCIENCE 2018; 9:1201. [PMID: 30174679 PMCID: PMC6108131 DOI: 10.3389/fpls.2018.01201] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 07/26/2018] [Indexed: 05/09/2023]
Abstract
Poplar, a model for woody plant research, is the most widely distributed tree species in the world. Metabolites are the basis of phenotypes, allowing an intuitive and effective understanding of biological processes and their mechanisms. However, metabolites in non-transgenic and multi-gene transgenic poplar remains poorly characterized, especially in regards of the influences on quantity and in the analysis of the relative abundance of metabolites after the introduction of multi stress-related genes. In this study, we investigated the cambium metabolomes of one non-transgenic (D5-0) and two multi-gene (vgb, SacB, ERF36, BtCry3A, and OC-I) transgenic lines (D5-20 and D5-21) of hybrid poplar (Populus × euramericana 'Guariento') using both gas chromatography-mass spectrometry (GC-MS) and ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). We aimed to explore the effects of the exogenous genes on metabolite composition and to screen out metabolites with important biological functions. Finally, we identified 239 named metabolites and determined their relative abundance. Among these, 197 metabolites had a different abundance across the three lines. These methabolites spanned nine primary and 44 secondary metabolism pathways. Arginine and glutamate, as substrates and intermediates in nitrogen metabolism, and important in growth and stress-related processes, as well as sucrose, uridine diphosphate glucose, and their derivatives, precursors in cell wall pathways, and catechol, relevant to insect resistance, differed greatly between the genetically modified and non-transgenic poplar. These findings may provide a basis for further study of cambium metabolism, and fully understand metabolites associated with stress response.
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Affiliation(s)
- Kun Ning
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Beijing, China
| | - Changjun Ding
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Beijing, China
| | - Wenxu Zhu
- College of Forestry, Shenyang Agricultural University, Shenyang, China
| | - Weixi Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Beijing, China
| | - Yufeng Dong
- Shandong Provincial Key Laboratory of Forest Tree Genetic Improvement, Shandong Academy of Forestry, Jinan, China
| | - Yingbai Shen
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xiaohua Su
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Beijing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- *Correspondence: Xiaohua Su,
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Xu JL, Shin JS, Park SK, Kang S, Jeong SC, Moon JK, Choi Y. Differences in the metabolic profiles and antioxidant activities of wild and cultivated black soybeans evaluated by correlation analysis. Food Res Int 2017; 100:166-174. [PMID: 28888437 DOI: 10.1016/j.foodres.2017.08.026] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 08/10/2017] [Accepted: 08/12/2017] [Indexed: 12/31/2022]
Abstract
Wild soybeans are considered a potential resource for soybean domestication and an important source of genetic diversity for soybean crop improvement. Understanding metabolite-caused bioactivity differences between cultivated and wild soybeans is essential for designing a soybean with enhanced nutritional traits. In this study, the non-targeted metabolic profiling of 26 soybean varieties, 15 wild black soybeans (WBS) and 11 cultivated black soybeans (CBS), using liquid chromatography-mass spectrometry (LC-MS) in combination with multivariate analysis revealed significant differences in 25 differential metabolites. Among these, the soyasaponins Ab and Bb were found to be characteristic metabolites expressed more substantially in CBS than in WBS. Three different antioxidant assays and correlation analysis identified major and minor antioxidants that contributed to WBS having an antioxidant activity 4- to 8-fold stronger than that of CBS. Epicatechin, procyanidin B2, and cyanidin-3-O-glucoside were identified by both association analysis and the online LC-ABTS radical scavenging assay as being major antioxidants.
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Affiliation(s)
- Jiu Liang Xu
- Systems Biotechnology Research Center, Korea Institute of Science and Technology (KIST), Gangneung 25451, Republic of Korea; Department of Food and Nutrition, Gangneung-Wonju National University, Gangneung, Gangwon 210-702, Republic of Korea
| | - Jeong-Sook Shin
- Systems Biotechnology Research Center, Korea Institute of Science and Technology (KIST), Gangneung 25451, Republic of Korea
| | - Soo-Kwon Park
- National Institute of Crop Science, Wanju-gun, Jeollabuk-do 565-851, Republic of Korea
| | - Sungtaeg Kang
- Department of Crop Science and Biotechnology, Dankook University, Cheonan 31116, Republic of Korea
| | - Soon-Chun Jeong
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungbuk 28116, Republic of Korea
| | - Jung-Kyung Moon
- National Institute of Agricultural Sciences, Rural Development Administration, Jeongju-si, JeongBook, Republic of Korea
| | - Yongsoo Choi
- Systems Biotechnology Research Center, Korea Institute of Science and Technology (KIST), Gangneung 25451, Republic of Korea; Department of Biological Chemistry, University of Science and Technology, Youseng-gu, Daejeon 305-350, Republic of Korea.
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36
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Gupta M, Bhaskar PB, Sriram S, Wang PH. Integration of omics approaches to understand oil/protein content during seed development in oilseed crops. PLANT CELL REPORTS 2017; 36:637-652. [PMID: 27796489 DOI: 10.1007/s00299-016-2064-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 10/11/2016] [Indexed: 05/23/2023]
Abstract
Oilseed crops, especially soybean (Glycine max) and canola/rapeseed (Brassica napus), produce seeds that are rich in both proteins and oils and that are major sources of energy and nutrition worldwide. Most of the nutritional content in the seed is accumulated in the embryo during the seed filling stages of seed development. Understanding the metabolic pathways that are active during seed filling and how they are regulated are essential prerequisites to crop improvement. In this review, we summarize various omics studies of soybean and canola/rapeseed during seed filling, with emphasis on oil and protein traits, to gain a systems-level understanding of seed development. Currently, most (80-85%) of the soybean and rapeseed reference genomes have been sequenced (950 and 850 megabases, respectively). Parallel to these efforts, extensive omics datasets from different seed filling stages have become available. Transcriptome and proteome studies have detected preponderance of starch metabolism and glycolysis enzymes to be the possible cause of higher oil in B. napus compared to other crops. Small RNAome studies performed during the seed filling stages have revealed miRNA-mediated regulation of transcription factors, with the suggestion that this interaction could be responsible for transitioning the seeds from embryogenesis to maturation. In addition, progress made in dissecting the regulation of de novo fatty acid synthesis and protein storage pathways is described. Advances in high-throughput omics and comprehensive tissue-specific analyses make this an exciting time to attempt knowledge-driven investigation of complex regulatory pathways.
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Affiliation(s)
- Manju Gupta
- Dow AgroSciences, 9330 Zionsville Road, Indianapolis, IN, 46268, USA.
| | - Pudota B Bhaskar
- Dow AgroSciences, 9330 Zionsville Road, Indianapolis, IN, 46268, USA
| | | | - Po-Hao Wang
- Dow AgroSciences, 9330 Zionsville Road, Indianapolis, IN, 46268, USA
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Knoch D, Riewe D, Meyer RC, Boudichevskaia A, Schmidt R, Altmann T. Genetic dissection of metabolite variation in Arabidopsis seeds: evidence for mQTL hotspots and a master regulatory locus of seed metabolism. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:1655-1667. [PMID: 28338798 PMCID: PMC5444479 DOI: 10.1093/jxb/erx049] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
To gain insight into genetic factors controlling seed metabolic composition and its relationship to major seed properties, an Arabidopsis recombinant inbred line (RIL) population, derived from accessions Col-0 and C24, was studied using an MS-based metabolic profiling approach. Relative intensities of 311 polar primary metabolites were used to identify associated genomic loci and to elucidate their interactions by quantitative trait locus (QTL) mapping. A total of 786 metabolic QTLs (mQTLs) were unequally distributed across the genome, forming several hotspots. For the branched-chain amino acid leucine, mQTLs and candidate genes were elucidated in detail. Correlation studies displayed links between metabolite levels, seed protein content, and seed weight. Principal component analysis revealed a clustering of samples, with PC1 mapping to a region on the short arm of chromosome IV. The overlap of this region with mQTL hotspots indicates the presence of a potential master regulatory locus of seed metabolism. As a result of database queries, a series of candidate regulatory genes, including bZIP10, were identified within this region. Depending on the search conditions, metabolic pathway-derived candidate genes for 40-61% of tested mQTLs could be determined, providing an extensive basis for further identification and characterization of hitherto unknown genes causal for natural variation of Arabidopsis seed metabolism.
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Affiliation(s)
- Dominic Knoch
- Department of Molecular Genetics/Heterosis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466 Seeland/OT Gatersleben, Germany
| | - David Riewe
- Department of Molecular Genetics/Heterosis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466 Seeland/OT Gatersleben, Germany
| | - Rhonda Christiane Meyer
- Department of Molecular Genetics/Heterosis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466 Seeland/OT Gatersleben, Germany
| | - Anastassia Boudichevskaia
- Department of Breeding Research/Genome Plasticity, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466 Seeland/OT Gatersleben, Germany
| | - Renate Schmidt
- Department of Breeding Research/Genome Plasticity, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466 Seeland/OT Gatersleben, Germany
| | - Thomas Altmann
- Department of Molecular Genetics/Heterosis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466 Seeland/OT Gatersleben, Germany
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38
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Zhang Y, Wang Y, Ding Z, Wang H, Song L, Jia S, Ma D. Zinc stress affects ionome and metabolome in tea plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2017; 111:318-328. [PMID: 27992770 DOI: 10.1016/j.plaphy.2016.12.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 12/10/2016] [Accepted: 12/11/2016] [Indexed: 05/28/2023]
Abstract
The research of physiological responses to Zn stress in plants has been extensively studied. However, the ionomics and metabolomics responses of plants to Zn stress remain largely unknown. In present study, the nutrient elements were identified involved in ion homeostasis and metabolomics changes related to Zn deficiency or excess in tea plants. Nutrient element analysis demonstrated that the concentrations of Zn affected the ion-uptake in roots and the nutrient element transportation to leaves, leading to the different distribution of P, S, Al, Ca, Fe and Cu in the tea leaves or roots. Metabolomics analysis revealed that Zn deficiency or excess differentially influenced the metabolic pathways in the tea leaves. More specifically, Zn deficiency affected the metabolism of carbohydrates, and Zn excess affected flavonoids metabolism. Additionally, the results showed that both Zn deficiency and Zn excess led to reduced nicotinamide levels, which speeded up NAD+ degradation and thus reduced energy metabolism. Furthermore, element-metabolite correlation analysis illustrated that Zn contents in the tea leaves were positively correlated with organic acids, nitrogenous metabolites and some carbohydrate metabolites, and negatively correlated with the metabolites involved in secondary metabolism and some other carbohydrate metabolites. Meanwhile, metabolite-metabolite correlation analysis demonstrated that organic acids, sugars, amino acids and flavonoids played dominant roles in the regulation of the tea leaf metabolism under Zn stress. Therefore, the conclusion should be drawn that the tea plants responded to Zn stress by coordinating ion-uptake and regulation of metabolism of carbohydrates, nitrogenous metabolites, and flavonoids.
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Affiliation(s)
- Yinfei Zhang
- Tea Research Institute, Qingdao Agricultural University, Qingdao 266109, China
| | - Yu Wang
- Tea Research Institute, Qingdao Agricultural University, Qingdao 266109, China
| | - Zhaotang Ding
- Tea Research Institute, Qingdao Agricultural University, Qingdao 266109, China.
| | - Hui Wang
- Rizhao Tea Research Institute of Shandong, Rizhao 276800, China
| | - Lubin Song
- Institue of Pomology, Shandong Academy of Agricultural Sciences, Taian 271000, China
| | - Sisi Jia
- Tea Research Institute, Qingdao Agricultural University, Qingdao 266109, China
| | - Dexin Ma
- Tea Research Institute, Qingdao Agricultural University, Qingdao 266109, China
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39
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Tripathi N, Khare D. Molecular approaches for genetic improvement of seed quality and characterization of genetic diversity in soybean: a critical review. Biotechnol Lett 2016; 38:1645-54. [PMID: 27334709 DOI: 10.1007/s10529-016-2154-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 06/15/2016] [Indexed: 10/21/2022]
Abstract
Soybean is an economically important leguminous crop. Genetic improvements of soybeans have focused on enhancement of seed and oil yield, development of varieties suited to different cropping systems, and breeding resistant/tolerant varieties for various biotic and abiotic stresses. Plant breeders have used conventional breeding techniques for the improvement of these traits in soybean. The conventional breeding process can be greatly accelerated through the application of molecular and genomic approaches. Molecular markers have proved to be a new tool in soybean breeding by enhancing selection efficiency in a rapid and time-bound manner. An overview of molecular approaches for the genetic improvement of soybean seed quality parameters, considering recent applications of marker-assisted selection and 'omics' research, is provided in this article.
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Affiliation(s)
- Niraj Tripathi
- Biotechnology Centre, Jawaharlal Nehru Agricultural University, Jabalpur, 482004, India.
| | - Dhirendra Khare
- Department of Plant Breeding and Genetics, Jawaharlal Nehru Agricultural University, Jabalpur, 482004, India
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40
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Albrecht U, Fiehn O, Bowman KD. Metabolic variations in different citrus rootstock cultivars associated with different responses to Huanglongbing. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 107:33-44. [PMID: 27236226 DOI: 10.1016/j.plaphy.2016.05.030] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 05/17/2016] [Accepted: 05/18/2016] [Indexed: 05/03/2023]
Abstract
Huanglongbing (HLB) is one of the most destructive bacterial diseases of citrus. No resistant cultivars have been identified, although tolerance has been observed in the genus Poncirus and some of its hybrids with Citrus that are commonly used as rootstocks. In this study we exploited this tolerance by comparing five different tolerant hybrids with a cultivar that shows pronounced HLB sensitivity to discern potential contributing metabolic factors. Whole leaves of infected and non-infected greenhouse-grown seedlings were extracted and subjected to untargeted GC-TOF MS based metabolomics. After BinBase data filtering, 342 (experiment 1) and 650 (experiment 2) unique metabolites were quantified, of which 122 and 195, respectively, were assigned by chemical structures. The number of metabolites found to be differently regulated in the infected state compared with the non-infected state varied between the cultivars and was largest (166) in the susceptible cultivar Cleopatra mandarin (Citrus reticulata) and lowest (3) in the tolerant cultivars US-897 (C. reticulata 'Cleopatra' × Poncirus trifoliata) and US-942 (C. reticulata 'Sunki' × P. trifoliata) from experiment 2. Tolerance to HLB did not appear to be associated with accumulation of higher amounts of protective metabolites in response to infection. Many metabolites were found in higher concentrations in the tolerant cultivars compared with susceptible Cleopatra mandarin and may play important roles in conferring tolerance to HLB. Lower availability of specific sugars necessary for survival of the pathogen may also be a contributing factor in the decreased disease severity observed for these cultivars.
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Affiliation(s)
- Ute Albrecht
- Southwest Florida Research and Education Center, University of Florida, Institute of Food and Agricultural Sciences, 2685 SR 29 North, Immokalee, FL 34142, USA; US Horticultural Research Laboratory, United States Department of Agriculture, Agricultural Research Service, 2001 South Rock Rd., Fort Pierce, FL 34945, USA.
| | - Oliver Fiehn
- UC Davis Genome Center - Metabolomics, University of California, 451 Health Drive, Davis, CA 95616, USA; King Abdulaziz University, Biochemistry Department, Jeddah, Saudi Arabia
| | - Kim D Bowman
- US Horticultural Research Laboratory, United States Department of Agriculture, Agricultural Research Service, 2001 South Rock Rd., Fort Pierce, FL 34945, USA
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41
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Zhen S, Dong K, Deng X, Zhou J, Xu X, Han C, Zhang W, Xu Y, Wang Z, Yan Y. Dynamic metabolome profiling reveals significant metabolic changes during grain development of bread wheat (Triticum aestivum L.). JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2016; 96:3731-3740. [PMID: 26676564 DOI: 10.1002/jsfa.7561] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 11/27/2015] [Accepted: 12/03/2015] [Indexed: 05/29/2023]
Abstract
BACKGROUND Metabolites in wheat grains greatly influence nutritional values. Wheat provides proteins, minerals, B-group vitamins and dietary fiber to humans. These metabolites are important to human health. However, the metabolome of the grain during the development of bread wheat has not been studied so far. In this work the first dynamic metabolome of the developing grain of the elite Chinese bread wheat cultivar Zhongmai 175 was analyzed, using non-targeted gas chromatography/mass spectrometry (GC/MS) for metabolite profiling. RESULTS In total, 74 metabolites were identified over the grain developmental stages. Metabolite-metabolite correlation analysis revealed that the metabolism of amino acids, carbohydrates, organic acids, amines and lipids was interrelated. An integrated metabolic map revealed a distinct regulatory profile. The results provide information that can be used by metabolic engineers and molecular breeders to improve wheat grain quality. CONCLUSION The present metabolome approach identified dynamic changes in metabolite levels, and correlations among such levels, in developing seeds. The comprehensive metabolic map may be useful when breeding programs seek to improve grain quality. The work highlights the utility of GC/MS-based metabolomics, in conjunction with univariate and multivariate data analysis, when it is sought to understand metabolic changes in developing seeds. © 2015 Society of Chemical Industry.
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Affiliation(s)
- Shoumin Zhen
- College of Life Science, Capital Normal University, 100048, Beijing, China
| | - Kun Dong
- College of Life Science, Capital Normal University, 100048, Beijing, China
| | - Xiong Deng
- College of Life Science, Capital Normal University, 100048, Beijing, China
| | - Jiaxing Zhou
- College of Life Science, Capital Normal University, 100048, Beijing, China
| | - Xuexin Xu
- College of Agricultural and Biotechnology, China Agricultural University, 100091, Beijing, China
| | - Caixia Han
- College of Life Science, Capital Normal University, 100048, Beijing, China
| | - Wenying Zhang
- Hubei Collaborative Innovation Center for Grain Industry (HCICGI), Yangtze University, 434025, Jingzhou, China
| | - Yanhao Xu
- Hubei Collaborative Innovation Center for Grain Industry (HCICGI), Yangtze University, 434025, Jingzhou, China
| | - Zhimin Wang
- College of Agricultural and Biotechnology, China Agricultural University, 100091, Beijing, China
| | - Yueming Yan
- College of Life Science, Capital Normal University, 100048, Beijing, China
- Hubei Collaborative Innovation Center for Grain Industry (HCICGI), Yangtze University, 434025, Jingzhou, China
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42
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Hong J, Yang L, Zhang D, Shi J. Plant Metabolomics: An Indispensable System Biology Tool for Plant Science. Int J Mol Sci 2016; 17:ijms17060767. [PMID: 27258266 PMCID: PMC4926328 DOI: 10.3390/ijms17060767] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 05/04/2016] [Accepted: 05/06/2016] [Indexed: 11/16/2022] Open
Abstract
As genomes of many plant species have been sequenced, demand for functional genomics has dramatically accelerated the improvement of other omics including metabolomics. Despite a large amount of metabolites still remaining to be identified, metabolomics has contributed significantly not only to the understanding of plant physiology and biology from the view of small chemical molecules that reflect the end point of biological activities, but also in past decades to the attempts to improve plant behavior under both normal and stressed conditions. Hereby, we summarize the current knowledge on the genetic and biochemical mechanisms underlying plant growth, development, and stress responses, focusing further on the contributions of metabolomics to practical applications in crop quality improvement and food safety assessment, as well as plant metabolic engineering. We also highlight the current challenges and future perspectives in this inspiring area, with the aim to stimulate further studies leading to better crop improvement of yield and quality.
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Affiliation(s)
- Jun Hong
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Litao Yang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
- Plant Genomics Center, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, South Australia 5064, Australia.
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
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Zhen S, Zhou J, Deng X, Zhu G, Cao H, Wang Z, Yan Y. Metabolite profiling of the response to high-nitrogen fertilizer during grain development of bread wheat ( Triticum aestivum L.). J Cereal Sci 2016. [DOI: 10.1016/j.jcs.2016.02.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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44
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Kim YJ, Silva J, Zhang D, Shi J, Joo SC, Jang MG, Kwon WS, Yang DC. Development of interspecies hybrids to increase ginseng biomass and ginsenoside yield. PLANT CELL REPORTS 2016; 35:779-90. [PMID: 26800977 DOI: 10.1007/s00299-015-1920-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 11/27/2015] [Accepted: 12/09/2015] [Indexed: 05/27/2023]
Abstract
Interspecific hybrids between Panax ginseng and P. quinquefolius results in hybrid vigor and higher ginsenoside contents. Ginseng is one of the most important herbs with valued pharmaceutical effects contributing mainly by the presence of bioactive ginsenosides in the roots. However, ginseng industry is impeded largely by its biological properties, because ginseng plants are slow-growing perennial herbs with lower yield. To increase the ginseng yield and amounts of ginsenosides, we developed an effective ginseng production system using the F(1) progenies obtained from the interspecific reciprocal cross between two Panax species: P. ginseng and P. quinquefolius. Although hybrid plants show reduced male fertility, F(1) hybrids with the maternal origin either from P. ginseng or P. quinquefolius displayed heterosis; they had larger roots and higher contents of ginsenosides as compared with non-hybrid parental lines. Remarkably, the F(1) hybrids with the maternal origin of P. quinquefolius had much higher ginsenoside contents, especially ginsenoside Re and Rb1, than those with the maternal origin of P. ginseng. Additionally, non-targeted metabolomic profiling revealed a clear increase of a large number of primary and secondary metabolites including fatty acids, amino acids and ginsenosides in hybrid plants. To effectively identify the F(1) hybrids for the large-scale cultivation, we successfully developed a molecular marker detection system for discriminating F(1) reciprocal hybrids. In summary, this work provided a practical system for reciprocal hybrid ginseng production, which would facilitate the ginseng production in the future.
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Affiliation(s)
- Yu-Jin Kim
- Department of Oriental Medicinal Biotechnology, College of Life Science, Kyung Hee University, Yongin, 446-701, Korea.
| | - Jeniffer Silva
- Graduate School of Biotechnology and Ginseng Bank, College of Life Science, Kyung Hee University, Yongin, 446-701, Korea
| | - Dabing Zhang
- Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 20040, China
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia
| | - Jianxin Shi
- Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 20040, China
| | - Sung Chul Joo
- Department of Oriental Medicinal Biotechnology, College of Life Science, Kyung Hee University, Yongin, 446-701, Korea
| | - Moon-Gi Jang
- Department of Oriental Medicinal Biotechnology, College of Life Science, Kyung Hee University, Yongin, 446-701, Korea
| | - Woo-Saeng Kwon
- Department of Oriental Medicinal Biotechnology, College of Life Science, Kyung Hee University, Yongin, 446-701, Korea
| | - Deok-Chun Yang
- Department of Oriental Medicinal Biotechnology, College of Life Science, Kyung Hee University, Yongin, 446-701, Korea.
- Graduate School of Biotechnology and Ginseng Bank, College of Life Science, Kyung Hee University, Yongin, 446-701, Korea.
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45
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Hu C, Tohge T, Chan SA, Song Y, Rao J, Cui B, Lin H, Wang L, Fernie AR, Zhang D, Shi J. Identification of Conserved and Diverse Metabolic Shifts during Rice Grain Development. Sci Rep 2016; 6:20942. [PMID: 26860358 PMCID: PMC4748235 DOI: 10.1038/srep20942] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 01/14/2016] [Indexed: 11/26/2022] Open
Abstract
Seed development dedicates to reserve synthesis and accumulation and uncovering its genetic and biochemical mechanisms has been a major research focus. Although proteomic and transcriptomic analyses revealed dynamic changes of genes and enzymes involved, the information regarding concomitant metabolic changes is missing. Here we investigated the dynamic metabolic changes along the rice grain development of two japonica and two indica cultivars using non-targeted metabolomics approach, in which we successfully identified 214 metabolites. Statistical analyses revealed both cultivar and developmental stage dependent metabolic changes in rice grains. Generally, the stage specific metabolic kinetics corresponded well to the physiological status of the developing grains, and metabolic changes in developing rice grain are similar to those of dicot Arabidopsis and tomato at reserve accumulation stage but are different from those of dicots at seed desiccation stage. The remarkable difference in metabolite abundances between japonica and indica rice grain was observed at the reserve accumulation stage. Metabolite-metabolite correlation analysis uncovered potential new pathways for several metabolites. Taken together, this study uncovered both conserved and diverse development associated metabolic kinetics of rice grains, which facilitates further study to explore fundamental questions regarding the evolution of seed metabolic capabilities as well as their potential applications in crop improvement.
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Affiliation(s)
- Chaoyang Hu
- Joint International Research Laboratory of Metabolic & Developmental Sciences, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minghan District, Shanghai 200240, China
| | - Takayuki Tohge
- Central Metabolism Group, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | | | - Yue Song
- Agilent Technology, Inc. Shanghai, China
| | - Jun Rao
- Joint International Research Laboratory of Metabolic & Developmental Sciences, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minghan District, Shanghai 200240, China
- Jiangxi Cancer Hospital, No. 519 East Beijing Road, Nanchang 330029, China
| | - Bo Cui
- Joint International Research Laboratory of Metabolic & Developmental Sciences, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minghan District, Shanghai 200240, China
| | - Hong Lin
- Joint International Research Laboratory of Metabolic & Developmental Sciences, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minghan District, Shanghai 200240, China
| | - Lei Wang
- Agilent Technology, Inc. Beijing 100000, China
| | - Alisdair R. Fernie
- Central Metabolism Group, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minghan District, Shanghai 200240, China
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic & Developmental Sciences, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minghan District, Shanghai 200240, China
- Shanghai Ruifeng Agro-biotechnology Co., Ltd, Room 108, No 233 Rushan Rd., Shanghai 200120, China
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Jervis J, Kastl C, Hildreth SB, Biyashev R, Grabau EA, Saghai-Maroof MA, Helm RF. Metabolite Profiling of Soybean Seed Extracts from Near-Isogenic Low and Normal Phytate Lines Using Orthogonal Separation Strategies. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:9879-87. [PMID: 26487475 DOI: 10.1021/acs.jafc.5b04002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Untargeted metabolomic profiling using liquid chromatography-mass spectrometry (LC-MS) was applied to lipid-depleted methanolic extracts of soybean seeds utilizing orthogonal chromatographic separations (reversed-phase and hydrophilic interaction) in both positive and negative ionization modes. Four near-isogenic lines (NILs) differing in mutations for two genes encoding highly homologous multidrug resistant proteins (MRPs) were evaluated. The double mutant exhibited a low phytate phenotype, whereas the other three NILs, the two single mutants and the wild type, did not. Principal component analysis (PCA) of the four LC-MS data sets fully separated the low phytate line from the other three. While the levels of neutral oligosaccharides were the same for all lines, there were significant metabolite differences residing in the levels of malonyl isoflavones, soyasaponins, and arginine. Two methanol-soluble polypeptides were also found as differing in abundance levels, one of which was identified as the allergen Gly m 1.
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Affiliation(s)
- Judith Jervis
- Departments of Biochemistry, ‡Crop and Soil Environmental Sciences, §Biological Sciences, and Plant Pathology, and ∥Physiology and Weed Science, Virginia Tech , Blacksburg, Virginia 24061, United States
| | - Christin Kastl
- Departments of Biochemistry, ‡Crop and Soil Environmental Sciences, §Biological Sciences, and Plant Pathology, and ∥Physiology and Weed Science, Virginia Tech , Blacksburg, Virginia 24061, United States
| | - Sherry B Hildreth
- Departments of Biochemistry, ‡Crop and Soil Environmental Sciences, §Biological Sciences, and Plant Pathology, and ∥Physiology and Weed Science, Virginia Tech , Blacksburg, Virginia 24061, United States
| | - Ruslan Biyashev
- Departments of Biochemistry, ‡Crop and Soil Environmental Sciences, §Biological Sciences, and Plant Pathology, and ∥Physiology and Weed Science, Virginia Tech , Blacksburg, Virginia 24061, United States
| | - Elizabeth A Grabau
- Departments of Biochemistry, ‡Crop and Soil Environmental Sciences, §Biological Sciences, and Plant Pathology, and ∥Physiology and Weed Science, Virginia Tech , Blacksburg, Virginia 24061, United States
| | - Mohammad A Saghai-Maroof
- Departments of Biochemistry, ‡Crop and Soil Environmental Sciences, §Biological Sciences, and Plant Pathology, and ∥Physiology and Weed Science, Virginia Tech , Blacksburg, Virginia 24061, United States
| | - Richard F Helm
- Departments of Biochemistry, ‡Crop and Soil Environmental Sciences, §Biological Sciences, and Plant Pathology, and ∥Physiology and Weed Science, Virginia Tech , Blacksburg, Virginia 24061, United States
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47
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Lesiak AD, Cody RB, Dane AJ, Musah RA. Plant Seed Species Identification from Chemical Fingerprints: A High-Throughput Application of Direct Analysis in Real Time Mass Spectrometry. Anal Chem 2015; 87:8748-57. [DOI: 10.1021/acs.analchem.5b01611] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Ashton D. Lesiak
- Department
of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Robert B. Cody
- JEOL USA Inc., 11 Dearborn
Road, Peabody, Massachusetts 01960, United States
| | - A. John Dane
- JEOL USA Inc., 11 Dearborn
Road, Peabody, Massachusetts 01960, United States
| | - Rabi A. Musah
- Department
of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
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48
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Harrigan GG, Skogerson K, MacIsaac S, Bickel A, Perez T, Li X. Application of (1)h NMR profiling to assess seed metabolomic diversity. A case study on a soybean era population. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:4690-7. [PMID: 25940152 DOI: 10.1021/acs.jafc.5b01069] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
(1)H NMR spectroscopy offers advantages in metabolite quantitation and platform robustness when applied in food metabolomics studies. This paper provides a (1)H NMR-based assessment of seed metabolomic diversity in conventional and glyphosate-resistant genetically modified (GM) soybean from a genetic lineage representing ∼35 years of breeding and differing yield potential. (1)H NMR profiling of harvested seed allowed quantitation of 27 metabolites, including free amino acids, sugars, and organic acids, as well as choline, O-acetylcholine, dimethylamine, trigonelline, and p-cresol. Data were analyzed by canonical discriminant analysis (CDA) and principal variance component analysis (PVCA). Results demonstrated that (1)H NMR spectroscopy was effective in highlighting variation in metabolite levels in the genetically diverse sample set presented. The results also confirmed that metabolite variability is influenced by selective breeding and environment, but not genetic modification. Therefore, metabolite variability is an integral part of crop improvement that has occurred for decades and is associated with a history of safe use.
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Affiliation(s)
- George G Harrigan
- †Monsanto Company, 800 North Lindbergh Boulevard, St. Louis, Missouri 63167, United States
| | - Kirsten Skogerson
- †Monsanto Company, 800 North Lindbergh Boulevard, St. Louis, Missouri 63167, United States
| | - Susan MacIsaac
- §150 North Research Campus Drive, Kannapolis, North Carolina 28081, United States
| | - Anna Bickel
- †Monsanto Company, 800 North Lindbergh Boulevard, St. Louis, Missouri 63167, United States
| | - Tim Perez
- †Monsanto Company, 800 North Lindbergh Boulevard, St. Louis, Missouri 63167, United States
| | - Xin Li
- †Monsanto Company, 800 North Lindbergh Boulevard, St. Louis, Missouri 63167, United States
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Dastmalchi M, Dhaubhadel S. Proteomic insights into synthesis of isoflavonoids in soybean seeds. Proteomics 2015; 15:1646-57. [PMID: 25757747 DOI: 10.1002/pmic.201400444] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 11/25/2014] [Accepted: 12/30/2014] [Indexed: 12/13/2022]
Abstract
Soybean seeds are the major human dietary source of isoflavonoids, a class of plant natural products almost entirely exclusive to legumes. Isoflavonoids reduce the risk of a number of chronic human illnesses. Biosynthesis and accumulation of this class of compounds is a multigenic and complex trait, with a great deal of variability among soybean cultivars and with respect to the environment. There is a wealth of genomic, transcriptomic, and metabolomics data regarding isoflavonoid biosynthesis, but the connection between multigene families and their cognate proteins is a missing link that could provide us with a great deal of functional information. The changing proteome of the developing seed can shed light on the correlative increase in isoflavonoids, while the maternal seed coat proteome can provide the link with inherited metabolic and signaling machinery. In this effort, 'seed-filling' proteomics has revealed key secondary metabolite enzymes that quantitatively vary throughout seed development. Seed coat proteomics has revealed the existence of metabolic apparatus specific to isoflavonoid biosynthesis (isoflavonoid reductase) that could potentially influence the chemical content of this organ. The future of proteomic analysis of isoflavonoid biosynthesis should be centered on the development of quantitative, tissue-specific proteomes that emphasize low-abundance metabolic proteins to extract the whole suite of factors involved.
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Affiliation(s)
- Mehran Dastmalchi
- Department of Biology, University of Western Ontario, London, Canada
- Southern Crop Protection and Food Research Center, Agriculture and Agri-Food Canada, London, Canada
| | - Sangeeta Dhaubhadel
- Department of Biology, University of Western Ontario, London, Canada
- Southern Crop Protection and Food Research Center, Agriculture and Agri-Food Canada, London, Canada
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Li L, Hur M, Lee JY, Zhou W, Song Z, Ransom N, Demirkale CY, Nettleton D, Westgate M, Arendsee Z, Iyer V, Shanks J, Nikolau B, Wurtele ES. A systems biology approach toward understanding seed composition in soybean. BMC Genomics 2015; 16 Suppl 3:S9. [PMID: 25708381 PMCID: PMC4331812 DOI: 10.1186/1471-2164-16-s3-s9] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The molecular, biochemical, and genetic mechanisms that regulate the complex metabolic network of soybean seed development determine the ultimate balance of protein, lipid, and carbohydrate stored in the mature seed. Many of the genes and metabolites that participate in seed metabolism are unknown or poorly defined; even more remains to be understood about the regulation of their metabolic networks. A global omics analysis can provide insights into the regulation of seed metabolism, even without a priori assumptions about the structure of these networks. RESULTS With the future goal of predictive biology in mind, we have combined metabolomics, transcriptomics, and metabolic flux technologies to reveal the global developmental and metabolic networks that determine the structure and composition of the mature soybean seed. We have coupled this global approach with interactive bioinformatics and statistical analyses to gain insights into the biochemical programs that determine soybean seed composition. For this purpose, we used Plant/Eukaryotic and Microbial Metabolomics Systems Resource (PMR, http://www.metnetdb.org/pmr, a platform that incorporates metabolomics data to develop hypotheses concerning the organization and regulation of metabolic networks, and MetNet systems biology tools http://www.metnetdb.org for plant omics data, a framework to enable interactive visualization of metabolic and regulatory networks. CONCLUSIONS This combination of high-throughput experimental data and bioinformatics analyses has revealed sets of specific genes, genetic perturbations and mechanisms, and metabolic changes that are associated with the developmental variation in soybean seed composition. Researchers can explore these metabolomics and transcriptomics data interactively at PMR.
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Affiliation(s)
- Ling Li
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
- Center for Metabolic Biology, Iowa State University, Ames, Iowa 50011, USA
- Center for Biorenewable Chemicals, Iowa State University, Ames, Iowa 50011, USA
| | - Manhoi Hur
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
- Center for Metabolic Biology, Iowa State University, Ames, Iowa 50011, USA
- Center for Biorenewable Chemicals, Iowa State University, Ames, Iowa 50011, USA
| | - Joon-Yong Lee
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Wenxu Zhou
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Zhihong Song
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Nick Ransom
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
| | | | - Dan Nettleton
- Department of Statistics, Iowa State University, Ames, Iowa 50011, USA
| | - Mark Westgate
- Department of Agronomy, Iowa State University, Ames, Iowa 50011, USA
| | - Zebulun Arendsee
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Vidya Iyer
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, USA
| | - Jackie Shanks
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, USA
- Center for Biorenewable Chemicals, Iowa State University, Ames, Iowa 50011, USA
| | - Basil Nikolau
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA
- Center for Metabolic Biology, Iowa State University, Ames, Iowa 50011, USA
- Center for Biorenewable Chemicals, Iowa State University, Ames, Iowa 50011, USA
| | - Eve Syrkin Wurtele
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
- Center for Metabolic Biology, Iowa State University, Ames, Iowa 50011, USA
- Center for Biorenewable Chemicals, Iowa State University, Ames, Iowa 50011, USA
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