1
|
Pezzotti G, Tsubota Y, Zhu W, Marin E, Masumura T, Kobayashi T, Nakazaki T. Raman Multi-Omic Snapshots of Koshihikari Rice Kernels Reveal Important Molecular Diversities with Potential Benefits in Healthcare. Foods 2023; 12:3771. [PMID: 37893662 PMCID: PMC10606906 DOI: 10.3390/foods12203771] [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: 09/11/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
This study exploits quantitative algorithms of Raman spectroscopy to assess, at the molecular scale, the nutritional quality of individual kernels of the Japanese short-grain rice cultivar Koshihikari in terms of amylose-to-amylopectin ratio, fractions of phenylalanine and tryptophan aromatic amino acid residues, protein-to-carbohydrate ratio, and fractions of protein secondary structures. Statistical assessments on a large number of rice kernels reveal wide distributions of the above nutritional parameters over nominally homogeneous kernel batches. This demonstrates that genetic classifications cannot catch omic fluctuations, which are strongly influenced by a number of extrinsic factors, including the location of individual grass plants within the same rice field and the level of kernel maturation. The possibility of collecting nearly real-time Raman "multi-omic snapshots" of individual rice kernels allows for the automatic (low-cost) differentiation of groups of kernels with restricted nutritional characteristics that could be used in the formulation of functional foods for specific diseases and in positively modulating the intestinal microbiota for protection against bacterial infection and cancer prevention.
Collapse
Affiliation(s)
- Giuseppe Pezzotti
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan; (Y.T.); (W.Z.)
- Department of Molecular Genetics, Institute of Biomedical Science, Kansai Medical University, 2-5-1 Shinmachi, Hirakata, Osaka 573-1010, Japan
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, 465 Kajii-cho, Kyoto 602-8566, Japan
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
- Department of Orthopedic Surgery, Tokyo Medical University, 6-7-1 Nishi-Shinjuku, Shinjuku-ku, Tokyo 160-0023, Japan
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
- Department of Molecular Science and Nanosystems, Ca’ Foscari University of Venice, Via Torino 155, 30172 Venice, Italy
| | - Yusuke Tsubota
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan; (Y.T.); (W.Z.)
| | - Wenliang Zhu
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan; (Y.T.); (W.Z.)
| | - Elia Marin
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan; (Y.T.); (W.Z.)
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Takehiro Masumura
- Laboratory of Genetic Engineering, Kyoto Prefectural University, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-8522, Japan;
| | - Takuya Kobayashi
- Department of Medical Chemistry, Kansai Medical University, 2-5-1 Shinmachi, Osaka Prefecture, Hirakata 573-1010, Japan;
| | - Tetsuya Nakazaki
- Experimental Farm, Graduate School of Agriculture, Kyoto University, Kizugawa 619-0218, Japan;
| |
Collapse
|
2
|
Advances in Metabolomics-Driven Diagnostic Breeding and Crop Improvement. Metabolites 2022; 12:metabo12060511. [PMID: 35736444 PMCID: PMC9228725 DOI: 10.3390/metabo12060511] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 05/25/2022] [Accepted: 05/26/2022] [Indexed: 02/04/2023] Open
Abstract
Climate change continues to threaten global crop output by reducing annual productivity. As a result, global food security is now considered as one of the most important challenges facing humanity. To address this challenge, modern crop breeding approaches are required to create plants that can cope with increased abiotic/biotic stress. Metabolomics is rapidly gaining traction in plant breeding by predicting the metabolic marker for plant performance under a stressful environment and has emerged as a powerful tool for guiding crop improvement. The advent of more sensitive, automated, and high-throughput analytical tools combined with advanced bioinformatics and other omics techniques has laid the foundation to broadly characterize the genetic traits for crop improvement. Progress in metabolomics allows scientists to rapidly map specific metabolites to the genes that encode their metabolic pathways and offer plant scientists an excellent opportunity to fully explore and rationally harness the wealth of metabolites that plants biosynthesize. Here, we outline the current application of advanced metabolomics tools integrated with other OMICS techniques that can be used to: dissect the details of plant genotype–metabolite–phenotype interactions facilitating metabolomics-assisted plant breeding for probing the stress-responsive metabolic markers, explore the hidden metabolic networks associated with abiotic/biotic stress resistance, facilitate screening and selection of climate-smart crops at the metabolite level, and enable accurate risk-assessment and characterization of gene edited/transgenic plants to assist the regulatory process. The basic concept behind metabolic editing is to identify specific genes that govern the crucial metabolic pathways followed by the editing of one or more genes associated with those pathways. Thus, metabolomics provides a superb platform for not only rapid assessment and commercialization of future genome-edited crops, but also for accelerated metabolomics-assisted plant breeding. Furthermore, metabolomics can be a useful tool to expedite the crop research if integrated with speed breeding in future.
Collapse
|
3
|
Melandri G, Monteverde E, Riewe D, AbdElgawad H, McCouch SR, Bouwmeester H. Can biochemical traits bridge the gap between genomics and plant performance? A study in rice under drought. PLANT PHYSIOLOGY 2022; 189:1139-1152. [PMID: 35166848 PMCID: PMC9157150 DOI: 10.1093/plphys/kiac053] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 01/17/2022] [Indexed: 05/13/2023]
Abstract
The possibility of introducing metabolic/biochemical phenotyping to complement genomics-based predictions in breeding pipelines has been considered for years. Here we examine to what extent and under what environmental conditions metabolic/biochemical traits can effectively contribute to understanding and predicting plant performance. In this study, multivariable statistical models based on flag leaf central metabolism and oxidative stress status were used to predict grain yield (GY) performance for 271 indica rice (Oryza sativa) accessions grown in the field under well-watered and reproductive stage drought conditions. The resulting models displayed significantly higher predictability than multivariable models based on genomic data for the prediction of GY under drought (Q2 = 0.54-0.56 versus 0.35) and for stress-induced GY loss (Q2 = 0.59-0.64 versus 0.03-0.06). Models based on the combined datasets showed predictabilities similar to metabolic/biochemical-based models alone. In contrast to genetic markers, models with enzyme activities and metabolite values also quantitatively integrated the effect of physiological differences such as plant height on GY. The models highlighted antioxidant enzymes of the ascorbate-glutathione cycle and a lipid oxidation stress marker as important predictors of rice GY stability under drought at the reproductive stage, and these stress-related variables were more predictive than leaf central metabolites. These findings provide evidence that metabolic/biochemical traits can integrate dynamic cellular and physiological responses to the environment and can help bridge the gap between the genome and the phenome of crops as predictors of GY performance under drought.
Collapse
Affiliation(s)
- Giovanni Melandri
- Laboratory of Plant Physiology, Wageningen University and Research, Wageningen, the Netherlands
- School of Integrative Plant Sciences, Plant Breeding and Genetics Section, Cornell University, Ithaca, New York, USA
| | - Eliana Monteverde
- School of Integrative Plant Sciences, Plant Breeding and Genetics Section, Cornell University, Ithaca, New York, USA
- Departamento de Biología Vegetal, Facultad de Agronomía, Laboratorio de Evolución y Domesticación de las Plantas, Universidad de La República, Montevideo, Uruguay
| | - David Riewe
- Julius Kühn-Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Ecological Chemistry, Plant Analysis and Stored Product Protection, Berlin, Germany
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Hamada AbdElgawad
- Laboratory for Integrated Molecular Plant Physiology Research, University of Antwerp, Antwerp, Belgium
- Department of Botany, Faculty of Science, Beni-Suef University, Beni Suef, Egypt
| | - Susan R McCouch
- School of Integrative Plant Sciences, Plant Breeding and Genetics Section, Cornell University, Ithaca, New York, USA
| | - Harro Bouwmeester
- Laboratory of Plant Physiology, Wageningen University and Research, Wageningen, the Netherlands
- Plant Hormone Biology group, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| |
Collapse
|
4
|
Johnson R, Vishwakarma K, Hossen MS, Kumar V, Shackira AM, Puthur JT, Abdi G, Sarraf M, Hasanuzzaman M. Potassium in plants: Growth regulation, signaling, and environmental stress tolerance. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 172:56-69. [PMID: 35032888 DOI: 10.1016/j.plaphy.2022.01.001] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 12/02/2021] [Accepted: 01/02/2022] [Indexed: 05/14/2023]
Abstract
Potassium (K) is an essential element for the growth and development of plants; however, its scarcity or excessive level leads to distortion of numerous functions in plants. It takes part in the control of various significant functions in plant advancement. Because of the importance index, K is regarded second after nitrogen for whole plant growth. Approximately, higher than 60 enzymes are reliant on K for activation within the plant system, in which K plays a vital function as a regulator. Potassium provides assistance in plants against abiotic stress conditions in the environment. With this background, the present paper reviews the physiological functions of K in plants like stomatal regulation, photosynthesis and water uptake. The article also focuses upon the uptake and transport mechanisms of K along with its role in detoxification of reactive oxygen species and in conferring tolerance to plants against abiotic stresses. It also highlights the research progress made in the direction of K mediated signaling cascades.
Collapse
Affiliation(s)
- Riya Johnson
- Plant Physiology and Biochemistry Division, Department of Botany, University of Calicut, C.U. Campus P.O, Kerala, 673635, India
| | | | - Md Shahadat Hossen
- Independent Researcher, C/O: Prof. Mirza Hasanuzzaman, Department of Agronomy, Sher-e-Bangla Agricultural University, Dhaka-1207, Bangladesh
| | - Vinod Kumar
- Department of Botany, Government Degree College, Ramban, 182144, Jammu and Kashmir, India
| | - A M Shackira
- Department of Botany, Sir Syed College, Taliparamba, Kannur, Kerala, 670142, India
| | - Jos T Puthur
- Plant Physiology and Biochemistry Division, Department of Botany, University of Calicut, C.U. Campus P.O, Kerala, 673635, India
| | - Gholamreza Abdi
- Department of Biotechnology, Persian Gulf Research Institute, Persian Gulf University, Bushehr 75169, Iran
| | - Mohammad Sarraf
- Department of Horticulture Science, Shiraz Branch, Islamic Azad University, Shiraz, Iran.
| | - Mirza Hasanuzzaman
- Department of Agronomy, Faculty of Agriculture, Sher-e-Bangla Agricultural University, Dhaka, 1207, Bangladesh.
| |
Collapse
|
5
|
Abstract
Recent methodological advances in both gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS) have provided a deep understanding of metabolic regulation occurring in plant cells. The application of these techniques to agricultural systems is, however, subject to more complex interactions. Here we summarize a step-by-step modern metabolomics methodology that generates metabolome data toward the implementation of metabolomics in crop breeding. We describe a metabolic workflow, and provide guidelines for handling large sample numbers for the specific purpose of metabolic quantitative trait loci approaches.
Collapse
Affiliation(s)
- Saleh Alseekh
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany. .,Center of Plant System Biology and Biotechnology, Plovdiv, Bulgaria.
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.,Center of Plant System Biology and Biotechnology, Plovdiv, Bulgaria
| |
Collapse
|
6
|
Jacobs DM, van den Berg MA, Hall RD. Towards superior plant-based foods using metabolomics. Curr Opin Biotechnol 2020; 70:23-28. [PMID: 33086174 DOI: 10.1016/j.copbio.2020.08.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 08/29/2020] [Indexed: 12/16/2022]
Abstract
Metabolomics is proving a useful approach for many of the main future goals in agronomy and food production such as sustainability/crop resilience, food quality, safety, storage, and nutrition. Targeted and/or untargeted small-molecule analysis, coupled to chemometric analysis, has already unveiled a great deal of the complexity of plant-based foods, but there is still 'dark matter' to be discovered. Moreover, state-of-the-art food metabolomics offers insights into the molecular mechanisms underlying sensorial and nutritional characteristics of foods and thus enables higher precision and speed. This review describes recent applications of food metabolomics from fork to farm and focuses on the opportunities these bring to continue food innovation and support the shift to plant-based foods.
Collapse
Affiliation(s)
- Doris M Jacobs
- Unilever Foods Innovation Center, Bronland 14, 6708 WH Wageningen, Netherlands.
| | - Marco A van den Berg
- DSM Biotechnology Center, Biotech Campus Delft, Alexander Fleminglaan 1, Delft, 2613 AX, Netherlands
| | - Robert D Hall
- Business Unit Bioscience, Wageningen University & Research and Laboratory of Plant Physiology, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, 6708 PB, Netherlands
| |
Collapse
|
7
|
Pareek A, Dhankher OP, Foyer CH. Mitigating the impact of climate change on plant productivity and ecosystem sustainability. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:451-456. [PMID: 31909813 PMCID: PMC6945998 DOI: 10.1093/jxb/erz518] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Affiliation(s)
- Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Om Parkash Dhankher
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA, USA
| | - Christine H Foyer
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, UK
| |
Collapse
|