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Patan SSVK, Vallepu S, Shaik KB, Shaik N, Adi Reddy NRY, Terry RG, Sergeant K, Hausman JF. Drought resistance strategies in minor millets: a review. PLANTA 2024; 260:29. [PMID: 38879859 DOI: 10.1007/s00425-024-04427-w] [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: 12/22/2023] [Accepted: 04/26/2024] [Indexed: 07/03/2024]
Abstract
MAIN CONCLUSION The review discusses growth and drought-response mechanisms in minor millets under three themes: drought escape, drought avoidance and drought tolerance. Drought is one of the most prominent abiotic stresses impacting plant growth, performance, and productivity. In the context of climate change, the prevalence and severity of drought is expected to increase in many agricultural regions worldwide. Millets (coarse grains) are a group of small-seeded grasses cultivated in arid and semi-arid regions throughout the world and are an important source of food and feed for humans and livestock. Although minor millets, i.e., foxtail millet, finger millet, proso millet, barnyard millet, kodo millet and little millet are generally hardier and more drought-resistant than cereals and major millets (sorghum and pearl millet), understanding their responses, processes and strategies in response to drought is more limited. Here, we review drought resistance strategies in minor millets under three themes: drought escape (e.g., short crop cycle, short vegetative period, developmental plasticity and remobilization of assimilates), drought avoidance (e.g., root traits for better water absorption and leaf traits to control water loss), and drought tolerance (e.g., osmotic adjustment, maintenance of photosynthetic ability and antioxidant potential). Data from 'omics' studies are summarized to provide an overview of the molecular mechanisms important in drought tolerance. In addition, the final section highlights knowledge gaps and challenges to improving minor millets. This review is intended to enhance major cereals and millet per se in light of climate-related increases in aridity.
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Affiliation(s)
| | - Suneetha Vallepu
- Department of Botany, Yogi Vemana University, Kadapa, Andhra Pradesh, 516005, India
| | - Khader Basha Shaik
- Department of Botany, Yogi Vemana University, Kadapa, Andhra Pradesh, 516005, India
| | - Naseem Shaik
- Department of Botany, Yogi Vemana University, Kadapa, Andhra Pradesh, 516005, India
| | | | | | - Kjell Sergeant
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, (LIST), Avenue Des Hauts Fourneaux 5, Esch-Sur-Alzette, Luxembourg
| | - Jean François Hausman
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, (LIST), Avenue Des Hauts Fourneaux 5, Esch-Sur-Alzette, Luxembourg
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2
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Ludwig M, Hartwell J, Raines CA, Simkin AJ. The Calvin-Benson-Bassham cycle in C 4 and Crassulacean acid metabolism species. Semin Cell Dev Biol 2024; 155:10-22. [PMID: 37544777 DOI: 10.1016/j.semcdb.2023.07.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 07/03/2023] [Accepted: 07/25/2023] [Indexed: 08/08/2023]
Abstract
The Calvin-Benson-Bassham (CBB) cycle is the ancestral CO2 assimilation pathway and is found in all photosynthetic organisms. Biochemical extensions to the CBB cycle have evolved that allow the resulting pathways to act as CO2 concentrating mechanisms, either spatially in the case of C4 photosynthesis or temporally in the case of Crassulacean acid metabolism (CAM). While the biochemical steps in the C4 and CAM pathways are known, questions remain on their integration and regulation with CBB cycle activity. The application of omic and transgenic technologies is providing a more complete understanding of the biochemistry of C4 and CAM species and will also provide insight into the CBB cycle in these plants. As the global population increases, new solutions are required to increase crop yields and meet demands for food and other bioproducts. Previous work in C3 species has shown that increasing carbon assimilation through genetic manipulation of the CBB cycle can increase biomass and yield. There may also be options to improve photosynthesis in species using C4 photosynthesis and CAM through manipulation of the CBB cycle in these plants. This is an underexplored strategy and requires more basic knowledge of CBB cycle operation in these species to enable approaches for increased productivity.
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Affiliation(s)
- Martha Ludwig
- School of Molecular Sciences, University of Western Australia, Perth, Western Australia, Australia.
| | - James Hartwell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | | | - Andrew J Simkin
- University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK; School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
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3
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Pandey S, Singh A, Jaiswal P, Singh MK, Meena KR, Singh SK. The potentialities of omics resources for millet improvement. Funct Integr Genomics 2023; 23:210. [PMID: 37355501 DOI: 10.1007/s10142-023-01149-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/16/2023] [Accepted: 06/21/2023] [Indexed: 06/26/2023]
Abstract
Millets are nutrient-rich (nutri-rich) cereals with climate resilience attributes. However, its full productive potential is not realized due to the lack of a focused yield improvement approach, as evidenced by the available literature. Also, the lack of well-characterized genomic resources significantly limits millet improvement. But the recent availability of genomic data and advancement in omics tools has shown its enormous potential to enhance the efficiency and precision faced by conventional breeding in millet improvement. The development of high throughput genotyping platforms based on next-generation sequencing (NGS) has provided a low-cost method for genomic information, specifically for neglected nutri-rich cereals with the availability of a limited number of reference genome sequences. NGS has created new avenues for millet biotechnological interventions such as mutation-based study, GWAS, GS, and other omics technologies. The simultaneous discovery of high-throughput markers and multiplexed genotyping platform has aggressively aided marker-assisted breeding for millet improvement. Therefore, omics technology offers excellent opportunities to explore and combine useful variations for targeted traits that could impart high nutritional value to high-yielding cultivars under changing climatic conditions. In millet improvement, an in-depth account of NGS, integrating genomics data with different biotechnology tools, is reviewed in this context.
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Affiliation(s)
- Saurabh Pandey
- Department of Agricultural, Guru Nanak Dev University, Amritsar, Punjab, 143005, India
| | - Ashutosh Singh
- Centre for Advanced Studies on Climate Change, RPCAU, Pusa, Samastipur, Bihar, 848125, India.
| | - Priyanka Jaiswal
- Lovely Professional University, Jalandhar - Delhi G.T. Road, Phagwara, Punjab, 144411, India
| | - Mithilesh Kumar Singh
- Department of Genetics and Plant Breeding, RPCAU, Pusa, Samastipur, Bihar, 848125, India
| | - Khem Raj Meena
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, Kishangarh, Rajasthan, 305817, India
| | - Satish Kumar Singh
- Department of Genetics and Plant Breeding, RPCAU, Pusa, Samastipur, Bihar, 848125, India
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Choudhary P, Shukla P, Muthamilarasan M. Genetic enhancement of climate-resilient traits in small millets: A review. Heliyon 2023; 9:e14502. [PMID: 37064482 PMCID: PMC10102230 DOI: 10.1016/j.heliyon.2023.e14502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 02/10/2023] [Accepted: 03/09/2023] [Indexed: 03/28/2023] Open
Abstract
Agriculture is facing the challenge of feeding the ever-growing population that is projected to reach ten billion by 2050. While improving crop yield and productivity can address this challenge, the increasing effects of global warming and climate change seriously threaten agricultural productivity. Thus, genomics and genome modification technologies are crucial to improving climate-resilient traits to enable sustained yield and productivity; however, significant research focuses on staple crops such as rice, wheat, and maize. Crops that are naturally climate-resilient and nutritionally superior to staple cereals, such as small millets, remain neglected and underutilized by mainstream research. The ability of small millets to grow in marginal regions having limited irrigation and poor soil fertility makes these crops a better choice for cultivation in arid and semi-arid areas. Hence, mainstreaming small millets for cultivation and using omics technologies to dissect the climate-resilient traits to identify the molecular determinants underlying these traits are imperative for addressing food and nutritional security. In this context, the review discusses the genomics and genome modification approaches for dissecting key traits in small millets and their application for improving these traits in cultivated germplasm. The review also discusses biofortification for nutritional security and machine-learning approaches for trait improvement in small millets. Altogether, the review provides a roadmap for the effective use of next-generation approaches for trait improvement in small millets. This will lead to the development of improved varieties for addressing multiple insecurities prevailing in the present climate change scenario.
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Vidya Muthulakshmi M, Srinivasan A, Srivastava S. Antioxidant Green Factories: Toward Sustainable Production of Vitamin E in Plant In Vitro Cultures. ACS OMEGA 2023; 8:3586-3605. [PMID: 36743063 PMCID: PMC9893489 DOI: 10.1021/acsomega.2c05819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 12/14/2022] [Indexed: 06/18/2023]
Abstract
Vitamin E is a dietary supplement synthesized only by photosynthetic organisms and, hence, is an essential vitamin for human well-being. Because of the ever-increasing demand for natural vitamin E and limitations in existing synthesis modes, attempts to improve its yield using plant in vitro cultures have gained traction in recent years. With inflating industrial production costs, integrative approaches to conventional bioprocess optimization is the need of the hour for multifold vitamin E productivity enhancement. In this review, we briefly discuss the structure, isomers, and important metabolic routes of biosynthesis for vitamin E in plants. We then emphasize its vital role in human health and its industrial applications and highlight the market demand and supply. We illustrate the advantages of in vitro plant cell/tissue culture cultivation as an alternative to current commercial production platforms for natural vitamin E. We touch upon the conventional vitamin E metabolic pathway engineering strategies, such as single/multigene overexpression and chloroplast engineering. We highlight the recent progress in plant systems biology to rationally identify metabolic bottlenecks and knockout targets in the vitamin E biosynthetic pathway. We then discuss bioprocess optimization strategies for sustainable vitamin E production, including media/process optimization, precursor/elicitor addition, and scale-up to bioreactors. We culminate the review with a short discussion on kinetic modeling to predict vitamin E production in plant cell cultures and suggestions on sustainable green extraction methods of vitamin E for reduced environmental impact. This review will be of interest to a wider research fraternity, including those from industry and academia working in the field of plant cell biology, plant biotechnology, and bioprocess engineering for phytochemical enhancement.
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Affiliation(s)
- M. Vidya Muthulakshmi
- Department
of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras (IIT Madras), Chennai, 600 036 Tamil Nadu, India
| | - Aparajitha Srinivasan
- Department
of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras (IIT Madras), Chennai, 600 036 Tamil Nadu, India
| | - Smita Srivastava
- Department
of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras (IIT Madras), Chennai, 600 036 Tamil Nadu, India
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Aggarwal PR, Pramitha L, Choudhary P, Singh RK, Shukla P, Prasad M, Muthamilarasan M. Multi-omics intervention in Setaria to dissect climate-resilient traits: Progress and prospects. FRONTIERS IN PLANT SCIENCE 2022; 13:892736. [PMID: 36119586 PMCID: PMC9470963 DOI: 10.3389/fpls.2022.892736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
Millets constitute a significant proportion of underutilized grasses and are well known for their climate resilience as well as excellent nutritional profiles. Among millets, foxtail millet (Setaria italica) and its wild relative green foxtail (S. viridis) are collectively regarded as models for studying broad-spectrum traits, including abiotic stress tolerance, C4 photosynthesis, biofuel, and nutritional traits. Since the genome sequence release, the crop has seen an exponential increase in omics studies to dissect agronomic, nutritional, biofuel, and climate-resilience traits. These studies have provided first-hand information on the structure, organization, evolution, and expression of several genes; however, knowledge of the precise roles of such genes and their products remains elusive. Several open-access databases have also been instituted to enable advanced scientific research on these important crops. In this context, the current review enumerates the contemporary trend of research on understanding the climate resilience and other essential traits in Setaria, the knowledge gap, and how the information could be translated for the crop improvement of related millets, biofuel crops, and cereals. Also, the review provides a roadmap for studying other underutilized crop species using Setaria as a model.
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Affiliation(s)
- Pooja Rani Aggarwal
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Lydia Pramitha
- School of Agriculture and Biosciences, Karunya Institute of Technology and Sciences, Coimbatore, Tamil Nadu, India
| | - Pooja Choudhary
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | | | - Pooja Shukla
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Manoj Prasad
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
- National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Mehanathan Muthamilarasan
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
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7
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Jamil IN, Remali J, Azizan KA, Nor Muhammad NA, Arita M, Goh HH, Aizat WM. Systematic Multi-Omics Integration (MOI) Approach in Plant Systems Biology. FRONTIERS IN PLANT SCIENCE 2020; 11:944. [PMID: 32754171 PMCID: PMC7371031 DOI: 10.3389/fpls.2020.00944] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 06/10/2020] [Indexed: 05/03/2023]
Abstract
Across all facets of biology, the rapid progress in high-throughput data generation has enabled us to perform multi-omics systems biology research. Transcriptomics, proteomics, and metabolomics data can answer targeted biological questions regarding the expression of transcripts, proteins, and metabolites, independently, but a systematic multi-omics integration (MOI) can comprehensively assimilate, annotate, and model these large data sets. Previous MOI studies and reviews have detailed its usage and practicality on various organisms including human, animals, microbes, and plants. Plants are especially challenging due to large poorly annotated genomes, multi-organelles, and diverse secondary metabolites. Hence, constructive and methodological guidelines on how to perform MOI for plants are needed, particularly for researchers newly embarking on this topic. In this review, we thoroughly classify multi-omics studies on plants and verify workflows to ensure successful omics integration with accurate data representation. We also propose three levels of MOI, namely element-based (level 1), pathway-based (level 2), and mathematical-based integration (level 3). These MOI levels are described in relation to recent publications and tools, to highlight their practicality and function. The drawbacks and limitations of these MOI are also discussed for future improvement toward more amenable strategies in plant systems biology.
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Affiliation(s)
- Ili Nadhirah Jamil
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi, Malaysia
| | - Juwairiah Remali
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi, Malaysia
| | - Kamalrul Azlan Azizan
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi, Malaysia
| | - Nor Azlan Nor Muhammad
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi, Malaysia
| | - Masanori Arita
- Bioinformation & DDBJ Center, National Institute of Genetics (NIG), Mishima, Japan
- Metabolome Informatics Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Hoe-Han Goh
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi, Malaysia
| | - Wan Mohd Aizat
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi, Malaysia
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8
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Shameer S, Ratcliffe RG, Sweetlove LJ. Leaf Energy Balance Requires Mitochondrial Respiration and Export of Chloroplast NADPH in the Light. PLANT PHYSIOLOGY 2019; 180:1947-1961. [PMID: 31213510 PMCID: PMC6670072 DOI: 10.1104/pp.19.00624] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 06/04/2019] [Indexed: 05/04/2023]
Abstract
Key aspects of leaf mitochondrial metabolism in the light remain unresolved. For example, there is debate about the relative importance of exporting reducing equivalents from mitochondria for the peroxisomal steps of photorespiration versus oxidation of NADH to generate ATP by oxidative phosphorylation. Here, we address this and explore energetic coupling between organelles in the light using a diel flux balance analysis model. The model included more than 600 reactions of central metabolism with full stoichiometric accounting of energy production and consumption. Different scenarios of energy availability (light intensity) and demand (source leaf versus a growing leaf) were considered, and the model was constrained by the nonlinear relationship between light and CO2 assimilation rate. The analysis demonstrated that the chloroplast can theoretically generate sufficient ATP to satisfy the energy requirements of the rest of the cell in addition to its own. However, this requires unrealistic high light use efficiency and, in practice, the availability of chloroplast-derived ATP is limited by chloroplast energy dissipation systems, such as nonphotochemical quenching, and the capacity of the chloroplast ATP export shuttles. Given these limitations, substantial mitochondrial ATP synthesis is required to fulfill cytosolic ATP requirements, with only minimal, or zero, export of mitochondrial reducing equivalents. The analysis also revealed the importance of exporting reducing equivalents from chloroplasts to sustain photorespiration. Hence, the chloroplast malate valve and triose phosphate-3-phosphoglycerate shuttle are predicted to have important metabolic roles, in addition to their more commonly discussed contribution to the avoidance of photooxidative stress.
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Affiliation(s)
- Sanu Shameer
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - R George Ratcliffe
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - Lee J Sweetlove
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom
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9
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A mass and charge balanced metabolic model of Setaria viridis revealed mechanisms of proton balancing in C4 plants. BMC Bioinformatics 2019; 20:357. [PMID: 31248364 PMCID: PMC6598292 DOI: 10.1186/s12859-019-2941-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 06/07/2019] [Indexed: 11/18/2022] Open
Abstract
Background C4 photosynthesis is a key domain of plant research with outcomes ranging from crop quality improvement, biofuel production and efficient use of water and nutrients. A metabolic network model of C4 “lab organism” Setaria viridis with extensive gene-reaction associations can accelerate target identification for desired metabolic manipulations and thereafter in vivo validation. Moreover, metabolic reconstructions have also been shown to be a significant tool to investigate fundamental metabolic traits. Results A mass and charge balance genome-scale metabolic model of Setaria viridis was constructed, which was tested to be able to produce all major biomass components in phototrophic and heterotrophic conditions. Our model predicted an important role of the utilization of NH\documentclass[12pt]{minimal}
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\begin{document}$_{3}^{-}$\end{document}3− ratio in balancing charges in plants. A multi-tissue extension of the model representing C4 photosynthesis was able to utilize NADP-ME subtype of C4 carbon fixation for the production of lignocellulosic biomass in stem, providing a tool for identifying gene associations for cellulose, hemi-cellulose and lignin biosynthesis that could be potential target for improved lignocellulosic biomass production. Besides metabolic engineering, our modeling results uncovered a previously unrecognized role of the 3-PGA/triosephosphate shuttle in proton balancing. Conclusions A mass and charge balance model of Setaria viridis, a model C4 plant, provides the possibility of system-level investigation to identify metabolic characteristics based on stoichiometric constraints. This study demonstrated the use of metabolic modeling in identifying genes associated with the synthesis of particular biomass components, and elucidating new role of previously known metabolic processes. Electronic supplementary material The online version of this article (10.1186/s12859-019-2941-z) contains supplementary material, which is available to authorized users.
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Skraly FA, Ambavaram MMR, Peoples O, Snell KD. Metabolic engineering to increase crop yield: From concept to execution. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 273:23-32. [PMID: 29907305 DOI: 10.1016/j.plantsci.2018.03.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 03/07/2018] [Accepted: 03/10/2018] [Indexed: 05/18/2023]
Abstract
Although the return on investment over the last 20 years for mass screening of individual plant genes to improve crop performance has been low, the investment in these activities was essential to establish the infrastructure and tools of modern plant genomics. Complex traits such as crop yield are likely multigenic, and the exhaustive screening of random gene combinations to achieve yield gains is not realistic. Clearly, smart approaches must be developed. In silico analyses of plant metabolism and gene networks can move a trait discovery program beyond trial-and-error approaches and towards rational design strategies. Metabolic models employing flux-balance analysis are useful to determine the contribution of individual genes to a trait, or to compare, optimize, or even design metabolic pathways. Regulatory association networks provide a transcriptome-based view of the plant and can lead to the identification of transcription factors that control expression of multiple genes affecting a trait. In this review, the use of these models from the perspective of an Ag innovation company's trait discovery and development program will be discussed. Important decisions that can have significant impacts on the cost and timeline to develop a commercial trait will also be presented.
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Affiliation(s)
- Frank A Skraly
- Yield10 Bioscience, Inc., 19 Presidential Way, Woburn, MA 01801, United States
| | | | - Oliver Peoples
- Yield10 Bioscience, Inc., 19 Presidential Way, Woburn, MA 01801, United States
| | - Kristi D Snell
- Yield10 Bioscience, Inc., 19 Presidential Way, Woburn, MA 01801, United States.
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11
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Li S, Dong X, Fan G, Yang Q, Shi J, Wei W, Zhao F, Li N, Wang X, Wang F, Feng X, Zhang X, Song G, Shi G, Zhang W, Qiu F, Wang D, Li X, Zhang Y, Zhao Z. Comprehensive Profiling and Inheritance Patterns of Metabolites in Foxtail Millet. FRONTIERS IN PLANT SCIENCE 2018; 9:1716. [PMID: 30542359 PMCID: PMC6277888 DOI: 10.3389/fpls.2018.01716] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 11/05/2018] [Indexed: 05/03/2023]
Abstract
Metabolomics aims at determining a sample's metabolites profile and hence provides a straight functional statement of an organism's physiological condition. Here, we investigated comprehensive profiling, natural variation and species-specific accumulation of both primary and secondary metabolites in foxtail millet using LC-MS, and inheritance patterns of metabolome in millet hybrids. The application of a broad target metabolomics method facilitated the simultaneous identification and quantification of more than 300 metabolites. The metabolic analysis of these compounds, such as flavonoids, phenolamides, hydrocinnamoyl derivatives, vitamins and LPCs, revealed their developmentally controlled accumulation, and natural variation in different tissues/varieties. Species-specific accumulation of secondary metabolites was observed based on a comparative metabolic analysis between millet and rice, such as flavonoid O-rutinosides/neohesperidosides and malonylated flavonoid O-glycosides. In analyzing the metabolic variations between hybrid progenies and their parental lines, including a photothermo-sensitive genic male sterility line and five Zhangzagu varieties, metabolic overdominant, and dominant patterns of inheritance could be observed. For example, hydrocinnamoyl derivatives and feruloylated flavonoids were identified as over-parent heterosis (overdominant) metabolites in milet hybrids. Our work paves the way for developing predictors of hybrid performance and the future analysis of the biosynthesis and regulation of relevant metabolic pathways in millet.
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Affiliation(s)
- Shuangdong Li
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Xuekui Dong
- Wuhan Metware Biotechnology Co., Ltd., Wuhan, China
| | - Guangyu Fan
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | | | - Jian Shi
- Wuhan Metware Biotechnology Co., Ltd., Wuhan, China
| | - Wei Wei
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Fang Zhao
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Ning Li
- Wuhan Metware Biotechnology Co., Ltd., Wuhan, China
| | - Xiaoming Wang
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Feng Wang
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Xiaolei Feng
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Xiaolei Zhang
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Guoliang Song
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Gaolei Shi
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Wenying Zhang
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Fengcang Qiu
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Dequan Wang
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Xinru Li
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Yali Zhang
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Zhihai Zhao
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
- *Correspondence: Zhihai Zhao
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12
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Khoomrung S, Wanichthanarak K, Nookaew I, Thamsermsang O, Seubnooch P, Laohapand T, Akarasereenont P. Metabolomics and Integrative Omics for the Development of Thai Traditional Medicine. Front Pharmacol 2017; 8:474. [PMID: 28769804 PMCID: PMC5513896 DOI: 10.3389/fphar.2017.00474] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Accepted: 07/03/2017] [Indexed: 12/28/2022] Open
Abstract
In recent years, interest in studies of traditional medicine in Asian and African countries has gradually increased due to its potential to complement modern medicine. In this review, we provide an overview of Thai traditional medicine (TTM) current development, and ongoing research activities of TTM related to metabolomics. This review will also focus on three important elements of systems biology analysis of TTM including analytical techniques, statistical approaches and bioinformatics tools for handling and analyzing untargeted metabolomics data. The main objective of this data analysis is to gain a comprehensive understanding of the system wide effects that TTM has on individuals. Furthermore, potential applications of metabolomics and systems medicine in TTM will also be discussed.
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Affiliation(s)
- Sakda Khoomrung
- Center of Applied Thai Traditional Medicine, Faculty of Medicine Siriraj Hospital, Mahidol UniversityBangkok, Thailand.,Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol UniversityBangkok, Thailand.,Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of TechnologyGothenburg, Sweden
| | - Kwanjeera Wanichthanarak
- Center of Applied Thai Traditional Medicine, Faculty of Medicine Siriraj Hospital, Mahidol UniversityBangkok, Thailand.,Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol UniversityBangkok, Thailand
| | - Intawat Nookaew
- Center of Applied Thai Traditional Medicine, Faculty of Medicine Siriraj Hospital, Mahidol UniversityBangkok, Thailand.,Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of TechnologyGothenburg, Sweden.,Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical SciencesLittle Rock, AR, United States
| | - Onusa Thamsermsang
- Center of Applied Thai Traditional Medicine, Faculty of Medicine Siriraj Hospital, Mahidol UniversityBangkok, Thailand
| | - Patcharamon Seubnooch
- Department of Pharmacology, Faculty of Medicine Siriraj Hospital, Mahidol UniversityBangkok, Thailand
| | - Tawee Laohapand
- Center of Applied Thai Traditional Medicine, Faculty of Medicine Siriraj Hospital, Mahidol UniversityBangkok, Thailand
| | - Pravit Akarasereenont
- Center of Applied Thai Traditional Medicine, Faculty of Medicine Siriraj Hospital, Mahidol UniversityBangkok, Thailand.,Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol UniversityBangkok, Thailand.,Department of Pharmacology, Faculty of Medicine Siriraj Hospital, Mahidol UniversityBangkok, Thailand
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Peyraud R, Dubiella U, Barbacci A, Genin S, Raffaele S, Roby D. Advances on plant-pathogen interactions from molecular toward systems biology perspectives. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:720-737. [PMID: 27870294 PMCID: PMC5516170 DOI: 10.1111/tpj.13429] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 11/14/2016] [Accepted: 11/14/2016] [Indexed: 05/21/2023]
Abstract
In the past 2 decades, progress in molecular analyses of the plant immune system has revealed key elements of a complex response network. Current paradigms depict the interaction of pathogen-secreted molecules with host target molecules leading to the activation of multiple plant response pathways. Further research will be required to fully understand how these responses are integrated in space and time, and exploit this knowledge in agriculture. In this review, we highlight systems biology as a promising approach to reveal properties of molecular plant-pathogen interactions and predict the outcome of such interactions. We first illustrate a few key concepts in plant immunity with a network and systems biology perspective. Next, we present some basic principles of systems biology and show how they allow integrating multiomics data and predict cell phenotypes. We identify challenges for systems biology of plant-pathogen interactions, including the reconstruction of multiscale mechanistic models and the connection of host and pathogen models. Finally, we outline studies on resistance durability through the robustness of immune system networks, the identification of trade-offs between immunity and growth and in silico plant-pathogen co-evolution as exciting perspectives in the field. We conclude that the development of sophisticated models of plant diseases incorporating plant, pathogen and climate properties represent a major challenge for agriculture in the future.
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Affiliation(s)
- Rémi Peyraud
- LIPMUniversité de ToulouseINRACNRSCastanet‐TolosanFrance
| | | | | | - Stéphane Genin
- LIPMUniversité de ToulouseINRACNRSCastanet‐TolosanFrance
| | | | - Dominique Roby
- LIPMUniversité de ToulouseINRACNRSCastanet‐TolosanFrance
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