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Kumari M, Yagnik KN, Gupta V, Singh IK, Gupta R, Verma PK, Singh A. Metabolomics-driven investigation of plant defense response against pest and pathogen attack. PHYSIOLOGIA PLANTARUM 2024; 176:e14270. [PMID: 38566280 DOI: 10.1111/ppl.14270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 02/27/2024] [Accepted: 02/29/2024] [Indexed: 04/04/2024]
Abstract
The advancement of metabolomics has assisted in the identification of various bewildering characteristics of the biological system. Metabolomics is a standard approach, facilitating crucial aspects of system biology with absolute quantification of metabolites using minimum samples, based on liquid/gas chromatography, mass spectrometry and nuclear magnetic resonance. The metabolome profiling has narrowed the wide gaps of missing information and has enhanced the understanding of a wide spectrum of plant-environment interactions by highlighting the complex pathways regulating biochemical reactions and cellular physiology under a particular set of conditions. This high throughput technique also plays a prominent role in combined analyses of plant metabolomics and other omics datasets. Plant metabolomics has opened a wide paradigm of opportunities for developing stress-tolerant plants, ensuring better food quality and quantity. However, despite advantageous methods and databases, the technique has a few limitations, such as ineffective 3D capturing of metabolites, low comprehensiveness, and lack of cell-based sampling. In the future, an expansion of plant-pathogen and plant-pest response towards the metabolite architecture is necessary to understand the intricacies of plant defence against invaders, elucidation of metabolic pathway operational during defence and developing a direct correlation between metabolites and biotic stresses. Our aim is to provide an overview of metabolomics and its utilities for the identification of biomarkers or key metabolites associated with biotic stress, devising improved diagnostic methods to efficiently assess pest and pathogen attack and generating improved crop varieties with the help of combined application of analytical and molecular tools.
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Affiliation(s)
- Megha Kumari
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
| | - Kalpesh Nath Yagnik
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
| | - Vaishali Gupta
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Indrakant K Singh
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, New Delhi, India
| | - Ravi Gupta
- College of General Education, Kookmin University, Seoul, Republic of Korea
| | - Praveen K Verma
- Plant-Immunity Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Archana Singh
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
- Delhi School of Climate Change and Sustainability, Institution of Eminence, Maharishi Karnad Bhawan, University of Delhi, India
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Makhumbila P, Rauwane M, Muedi H, Figlan S. Metabolome Profiling: A Breeding Prediction Tool for Legume Performance under Biotic Stress Conditions. PLANTS 2022; 11:plants11131756. [PMID: 35807708 PMCID: PMC9268993 DOI: 10.3390/plants11131756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/17/2022] [Accepted: 06/22/2022] [Indexed: 11/16/2022]
Abstract
Legume crops such as common bean, pea, alfalfa, cowpea, peanut, soybean and others contribute significantly to the diet of both humans and animals. They are also important in the improvement of cropping systems that employ rotation and fix atmospheric nitrogen. Biotic stresses hinder the production of leguminous crops, significantly limiting their yield potential. There is a need to understand the molecular and biochemical mechanisms involved in the response of these crops to biotic stressors. Simultaneous expressions of a number of genes responsible for specific traits of interest in legumes under biotic stress conditions have been reported, often with the functions of the identified genes unknown. Metabolomics can, therefore, be a complementary tool to understand the pathways involved in biotic stress response in legumes. Reports on legume metabolomic studies in response to biotic stress have paved the way in understanding stress-signalling pathways. This review provides a progress update on metabolomic studies of legumes in response to different biotic stresses. Metabolome annotation and data analysis platforms are discussed together with future prospects. The integration of metabolomics with other “omics” tools in breeding programmes can aid greatly in ensuring food security through the production of stress tolerant cultivars.
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Affiliation(s)
- Penny Makhumbila
- Department of Agriculture and Animal Health, School of Agriculture and Life Sciences, College of Agriculture and Environmental Sciences, University of South Africa, 28 Pioneer Ave, Florida Park, Roodeport 1709, South Africa; (M.R.); (S.F.)
- Correspondence:
| | - Molemi Rauwane
- Department of Agriculture and Animal Health, School of Agriculture and Life Sciences, College of Agriculture and Environmental Sciences, University of South Africa, 28 Pioneer Ave, Florida Park, Roodeport 1709, South Africa; (M.R.); (S.F.)
| | - Hangwani Muedi
- Research Support Services, North West Provincial Department of Agriculture and Rural Development, 114 Chris Hani Street, Potchefstroom 2531, South Africa;
| | - Sandiswa Figlan
- Department of Agriculture and Animal Health, School of Agriculture and Life Sciences, College of Agriculture and Environmental Sciences, University of South Africa, 28 Pioneer Ave, Florida Park, Roodeport 1709, South Africa; (M.R.); (S.F.)
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Zargar SM, Mir RA, Ebinezer LB, Masi A, Hami A, Manzoor M, Salgotra RK, Sofi NR, Mushtaq R, Rohila JS, Rakwal R. Physiological and Multi-Omics Approaches for Explaining Drought Stress Tolerance and Supporting Sustainable Production of Rice. FRONTIERS IN PLANT SCIENCE 2022; 12:803603. [PMID: 35154193 PMCID: PMC8829427 DOI: 10.3389/fpls.2021.803603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 12/14/2021] [Indexed: 05/12/2023]
Abstract
Drought differs from other natural disasters in several respects, largely because of the complexity of a crop's response to it and also because we have the least understanding of a crop's inductive mechanism for addressing drought tolerance among all abiotic stressors. Overall, the growth and productivity of crops at a global level is now thought to be an issue that is more severe and arises more frequently due to climatic change-induced drought stress. Among the major crops, rice is a frontline staple cereal crop of the developing world and is critical to sustaining populations on a daily basis. Worldwide, studies have reported a reduction in rice productivity over the years as a consequence of drought. Plants are evolutionarily primed to withstand a substantial number of environmental cues by undergoing a wide range of changes at the molecular level, involving gene, protein and metabolite interactions to protect the growing plant. Currently, an in-depth, precise and systemic understanding of fundamental biological and cellular mechanisms activated by crop plants during stress is accomplished by an umbrella of -omics technologies, such as transcriptomics, metabolomics and proteomics. This combination of multi-omics approaches provides a comprehensive understanding of cellular dynamics during drought or other stress conditions in comparison to a single -omics approach. Thus a greater need to utilize information (big-omics data) from various molecular pathways to develop drought-resilient crop varieties for cultivation in ever-changing climatic conditions. This review article is focused on assembling current peer-reviewed published knowledge on the use of multi-omics approaches toward expediting the development of drought-tolerant rice plants for sustainable rice production and realizing global food security.
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Affiliation(s)
- Sajad Majeed Zargar
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Rakeeb Ahmad Mir
- Department of Biotechnology, School of Biosciences and Biotechnology, BGSB University, Rajouri, India
| | - Leonard Barnabas Ebinezer
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padova, Padua, Italy
| | - Antonio Masi
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padova, Padua, Italy
| | - Ammarah Hami
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Madhiya Manzoor
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Romesh K. Salgotra
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu, India
| | - Najeebul Rehman Sofi
- Division of Plant Breeding and Genetics, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Roohi Mushtaq
- Department of Biotechnology and Bioinformatics, SP College, Cluster University Srinagar, Srinagar, India
| | - Jai Singh Rohila
- Dale Bumpers National Rice Research Center, United States Department of Agriculture (USDA)-Agricultural Research Service (ARS), Stuttgart, AR, United States
| | - Randeep Rakwal
- Faculty of Health and Sport Sciences, University of Tsukuba, Ibaraki, Japan
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Vogel JT, Liu W, Olhoft P, Crafts-Brandner SJ, Pennycooke JC, Christiansen N. Soybean Yield Formation Physiology - A Foundation for Precision Breeding Based Improvement. FRONTIERS IN PLANT SCIENCE 2021; 12:719706. [PMID: 34868106 PMCID: PMC8634342 DOI: 10.3389/fpls.2021.719706] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 10/11/2021] [Indexed: 05/25/2023]
Abstract
The continued improvement of crop yield is a fundamental driver in agriculture and is the goal of both plant breeders and researchers. Plant breeders have been remarkably successful in improving crop yield, as demonstrated by the continued release of varieties with improved yield potential. This has largely been accomplished through performance-based selection, without specific knowledge of the molecular mechanisms underpinning these improvements. Insight into molecular mechanisms has been provided by plant molecular, genetic, and biochemical research through elucidation of the function of genes and pathways that underlie many of the physiological processes that contribute to yield potential. Despite this knowledge, the impact of most genes and pathways on yield components have not been tested in key crops or in a field environment for yield assessment. This gap is difficult to bridge, but field-based physiological knowledge offers a starting point for leveraging molecular targets to successfully apply precision breeding technologies such as genome editing. A better understanding of both the molecular mechanisms underlying crop yield physiology and yield limiting processes under field conditions is essential for elucidating which combinations of favorable alleles are required for yield improvement. Consequently, one goal in plant biology should be to more fully integrate crop physiology, breeding, genetics, and molecular knowledge to identify impactful precision breeding targets for relevant yield traits. The foundation for this is an understanding of yield formation physiology. Here, using soybean as an example, we provide a top-down review of yield physiology, starting with the fact that yield is derived from a population of plants growing together in a community. We review yield and yield-related components to provide a basic overview of yield physiology, synthesizing these concepts to highlight how such knowledge can be leveraged for soybean improvement. Using genome editing as an example, we discuss why multiple disciplines must be brought together to fully realize the promise of precision breeding-based crop improvement.
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Mahatma MK, Thawait LK, Jadon KS, Thirumalaisamy PP, Bishi SK, Rathod KJ, Verma A, Kumar N, Golakiya BA. Metabolic profiling for dissection of late leaf spot disease resistance mechanism in groundnut. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:1027-1041. [PMID: 34108825 PMCID: PMC8140181 DOI: 10.1007/s12298-021-00985-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 01/18/2021] [Accepted: 03/30/2021] [Indexed: 06/08/2023]
Abstract
UNLABELLED Late leaf spot (LLS) caused by fungi Passalora personata is generally more destructive and difficult to control than early leaf spot. The aim of this study was to decipher biochemical defense mechanism in groundnut genotypes against P. personata by identifying resistance specific biomarkers and metabolic pathways induced during host-pathogen interaction. Metabolomics of non-infected and infected leaves of moderately resistant (GPBD4 and ICGV86590), resistant (KDG128 and RHRG06083) and susceptible (GG20, JL24 and TMV2) genotypes was carried out at 5 days after infection (65 days after sowing). Non-targeted metabolite analysis using GC-MS revealed total 77 metabolites including carbohydrates, sugar alcohols, amino acids, fatty acids, polyamines, phenolics, terpenes and sterols. Variable importance in projection (VIP) measure of partial least squares-discriminant analysis (PLS-DA) showed that resistant and moderately resistant genotypes possessed higher intensities of ribonic acid, cinnamic acid, malic acid, squalene, xylulose, galactose, fructose, glucose, β-amyrin and hydroquinone while susceptible genotypes had higher amount of gluconic acid 2-methoxime, ribo-hexose-3-ulose and gluconic acid. Heat map analysis showed that resistant genotypes had higher intensities of β-amyrin, hydroquinone in non-infected and malic acid, squalene, putrescine and 2,3,4-trihydroxybutyric acid in infected leaves. Dendrogram analysis further separated resistant genotypes in the same cluster along with infected moderately resistant genotypes. The most significant pathways identified are: linoleic acid metabolism, flavone and flavonol biosynthesis, cutin, suberin and wax biosynthesis, pentose and glucuronate interconversions, starch and sucrose metabolism, stilbenoid biosynthesis and ascorbate and aldarate metabolism. Targeted metabolite analysis further confirmed that resistant genotypes possessed higher content of primary metabolites sucrose, glucose, fructose, malic acid and citric acid. Moreover, resistant genotypes possessed higher content of salicylic, coumaric, ferulic, cinnamic, gallic acid (phenolic acids) and kaempferol, quercetin and catechin (flavonols). Thus metabolites having higher accumulation in resistant genotypes can be used as biomarkers for screening of LSS resistant germplasm. These results unravel that higher amount of primary metabolites leads to stimulate the accumulation of more amounts of secondary metabolites such as phenolic acid, flavanols, stilbenes and terpenoids (squalene and β-amyrin) biosynthesis which are ultimately involved in defense mechanism against LLS pathogen. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-00985-5.
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Affiliation(s)
- M. K. Mahatma
- ICAR-Directorate of Groundnut Research, Post Box No.5, Junagadh, 362001 Gujarat India
| | - Lokesh Kumar Thawait
- ICAR-Directorate of Groundnut Research, Post Box No.5, Junagadh, 362001 Gujarat India
| | - K. S. Jadon
- ICAR-Directorate of Groundnut Research, Post Box No.5, Junagadh, 362001 Gujarat India
- ICAR-Central Arid Zone Research Institute, Jodhpur, India
| | - P. P. Thirumalaisamy
- ICAR-Directorate of Groundnut Research, Post Box No.5, Junagadh, 362001 Gujarat India
| | - S. K. Bishi
- ICAR-Directorate of Groundnut Research, Post Box No.5, Junagadh, 362001 Gujarat India
- ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, India
| | - Khyati J. Rathod
- Food Testing Laboratory, Department of Biotechnology, Junagadh Agricultural University, Junagadh, 362 001 India
| | - Aman Verma
- ICAR-Directorate of Groundnut Research, Post Box No.5, Junagadh, 362001 Gujarat India
| | - Narendra Kumar
- ICAR-Directorate of Groundnut Research, Post Box No.5, Junagadh, 362001 Gujarat India
| | - B. A. Golakiya
- Food Testing Laboratory, Department of Biotechnology, Junagadh Agricultural University, Junagadh, 362 001 India
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Geange SR, Arnold PA, Catling AA, Coast O, Cook AM, Gowland KM, Leigh A, Notarnicola RF, Posch BC, Venn SE, Zhu L, Nicotra AB. The thermal tolerance of photosynthetic tissues: a global systematic review and agenda for future research. THE NEW PHYTOLOGIST 2021; 229:2497-2513. [PMID: 33124040 DOI: 10.1111/nph.17052] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/25/2020] [Indexed: 05/09/2023]
Abstract
Understanding plant thermal tolerance is fundamental to predicting impacts of extreme temperature events that are increasing in frequency and intensity across the globe. Extremes, not averages, drive species evolution, determine survival and increase crop performance. To better prioritize agricultural and natural systems research, it is crucial to evaluate how researchers are assessing the capacity of plants to tolerate extreme events. We conducted a systematic review to determine how plant thermal tolerance research is distributed across wild and domesticated plants, growth forms and biomes, and to identify crucial knowledge gaps. Our review shows that most thermal tolerance research examines cold tolerance of cultivated species; c. 5% of articles consider both heat and cold tolerance. Plants of extreme environments are understudied, and techniques widely applied in cultivated systems are largely unused in natural systems. Lastly, we find that lack of standardized methods and metrics compromises the potential for mechanistic insight. Our review provides an entry point for those new to the methods used in plant thermal tolerance research and bridges often disparate ecological and agricultural perspectives for the more experienced. We present a considered agenda of thermal tolerance research priorities to stimulate efficient, reliable and repeatable research across the spectrum of plant thermal tolerance.
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Affiliation(s)
- Sonya R Geange
- Research School of Biology, The Australian National University, Canberra, ACT, 2600, Australia
- Department of Biological Sciences, University of Bergen, Bergen, 5008, Norway
- Bjerknes Centre for Climate Research, University of Bergen, Bergen, 5008, Norway
| | - Pieter A Arnold
- Research School of Biology, The Australian National University, Canberra, ACT, 2600, Australia
| | - Alexandra A Catling
- Research School of Biology, The Australian National University, Canberra, ACT, 2600, Australia
- School of Biological Sciences, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Onoriode Coast
- Research School of Biology, The Australian National University, Canberra, ACT, 2600, Australia
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent,, ME4 4TB, UK
| | - Alicia M Cook
- School of Life Sciences, University of Technology Sydney, Broadway, NSW, 2007, Australia
| | - Kelli M Gowland
- Research School of Biology, The Australian National University, Canberra, ACT, 2600, Australia
| | - Andrea Leigh
- School of Life Sciences, University of Technology Sydney, Broadway, NSW, 2007, Australia
| | - Rocco F Notarnicola
- Research School of Biology, The Australian National University, Canberra, ACT, 2600, Australia
| | - Bradley C Posch
- Research School of Biology, The Australian National University, Canberra, ACT, 2600, Australia
| | - Susanna E Venn
- School of Life and Environmental Sciences, Deakin University, Melbourne, Vic., 3125, Australia
| | - Lingling Zhu
- Research School of Biology, The Australian National University, Canberra, ACT, 2600, Australia
| | - Adrienne B Nicotra
- Research School of Biology, The Australian National University, Canberra, ACT, 2600, Australia
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Villate A, San Nicolas M, Gallastegi M, Aulas PA, Olivares M, Usobiaga A, Etxebarria N, Aizpurua-Olaizola O. Review: Metabolomics as a prediction tool for plants performance under environmental stress. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 303:110789. [PMID: 33487364 DOI: 10.1016/j.plantsci.2020.110789] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/30/2020] [Accepted: 12/05/2020] [Indexed: 05/05/2023]
Abstract
Metabolomics as a diagnosis tool for plant performance has shown good features for breeding and crop improvement. Additionally, due to limitations in land area and the increasing climate changes, breeding projects focusing on abiotic stress tolerance are becoming essential. Nowadays no universal method is available to identify predictive metabolic markers. As a result, research aims must dictate the best method or combination of methods. To this end, we will introduce the key aspects to consider regarding growth scenarios and sampling strategies and discuss major analytical and data treatment approaches that are available to find metabolic markers of plant performance.
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Affiliation(s)
- Aitor Villate
- Department of Analytical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain
| | - Markel San Nicolas
- Dinafem Seeds (Pot Sistemak S.L.), 20018, San Sebastian, Basque Country, Spain; Department of Analytical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain; Sovereign Fields S.L., 20006, San Sebastian, Basque Country, Spain
| | - Mara Gallastegi
- Dinafem Seeds (Pot Sistemak S.L.), 20018, San Sebastian, Basque Country, Spain; Sovereign Fields S.L., 20006, San Sebastian, Basque Country, Spain
| | - Pierre-Antoine Aulas
- Dinafem Seeds (Pot Sistemak S.L.), 20018, San Sebastian, Basque Country, Spain; Sovereign Fields S.L., 20006, San Sebastian, Basque Country, Spain
| | - Maitane Olivares
- Department of Analytical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain; Research Centre for Experimental Marine Biology and Biotechnology (PIE), University of the Basque Country (UPV/EHU), Plentzia, Basque Country, Spain
| | - Aresatz Usobiaga
- Department of Analytical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain; Research Centre for Experimental Marine Biology and Biotechnology (PIE), University of the Basque Country (UPV/EHU), Plentzia, Basque Country, Spain
| | - Nestor Etxebarria
- Department of Analytical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain; Research Centre for Experimental Marine Biology and Biotechnology (PIE), University of the Basque Country (UPV/EHU), Plentzia, Basque Country, Spain
| | - Oier Aizpurua-Olaizola
- Dinafem Seeds (Pot Sistemak S.L.), 20018, San Sebastian, Basque Country, Spain; Sovereign Fields S.L., 20006, San Sebastian, Basque Country, Spain.
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Baslam M, Mitsui T, Sueyoshi K, Ohyama T. Recent Advances in Carbon and Nitrogen Metabolism in C3 Plants. Int J Mol Sci 2020; 22:E318. [PMID: 33396811 PMCID: PMC7795015 DOI: 10.3390/ijms22010318] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/23/2020] [Accepted: 12/23/2020] [Indexed: 12/19/2022] Open
Abstract
C and N are the most important essential elements constituting organic compounds in plants. The shoots and roots depend on each other by exchanging C and N through the xylem and phloem transport systems. Complex mechanisms regulate C and N metabolism to optimize plant growth, agricultural crop production, and maintenance of the agroecosystem. In this paper, we cover the recent advances in understanding C and N metabolism, regulation, and transport in plants, as well as their underlying molecular mechanisms. Special emphasis is given to the mechanisms of starch metabolism in plastids and the changes in responses to environmental stress that were previously overlooked, since these changes provide an essential store of C that fuels plant metabolism and growth. We present general insights into the system biology approaches that have expanded our understanding of core biological questions related to C and N metabolism. Finally, this review synthesizes recent advances in our understanding of the trade-off concept that links C and N status to the plant's response to microorganisms.
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Affiliation(s)
- Marouane Baslam
- Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan; (M.B.); (T.M.)
| | - Toshiaki Mitsui
- Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan; (M.B.); (T.M.)
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan;
| | - Kuni Sueyoshi
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan;
| | - Takuji Ohyama
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan;
- Faculty of Applied Biosciences, Tokyo University of Agriculture, Tokyo 156-8502, Japan
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9
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Djemiel C, Goulas E, Badalato N, Chabbert B, Hawkins S, Grec S. Targeted Metagenomics of Retting in Flax: The Beginning of the Quest to Harness the Secret Powers of the Microbiota. Front Genet 2020; 11:581664. [PMID: 33193706 PMCID: PMC7652851 DOI: 10.3389/fgene.2020.581664] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 09/21/2020] [Indexed: 12/13/2022] Open
Abstract
The mechanical and chemical properties of natural plant fibers are determined by many different factors, both intrinsic and extrinsic to the plant, during growth but also after harvest. A better understanding of how all these factors exert their effect and how they interact is necessary to be able to optimize fiber quality for use in different industries. One important factor is the post-harvest process known as retting, representing the first step in the extraction of bast fibers from the stem of species such as flax and hemp. During this process microorganisms colonize the stem and produce hydrolytic enzymes that target cell wall polymers thereby facilitating the progressive destruction of the stem and fiber bundles. Recent advances in sequencing technology have allowed researchers to implement targeted metagenomics leading to a much better characterization of the microbial communities involved in retting, as well as an improved understanding of microbial dynamics. In this paper we review how our current knowledge of the microbiology of retting has been improved by targeted metagenomics and discuss how related '-omics' approaches might be used to fully characterize the functional capability of the retting microbiome.
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Affiliation(s)
- Christophe Djemiel
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Estelle Goulas
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Nelly Badalato
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Brigitte Chabbert
- Université de Reims Champagne Ardenne, INRAE, UMR FARE A 614, Reims, France
| | - Simon Hawkins
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Sébastien Grec
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
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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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11
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Ranjbar Sistani N, Desalegn G, Kaul HP, Wienkoop S. Seed Metabolism and Pathogen Resistance Enhancement in Pisum sativum During Colonization of Arbuscular Mycorrhizal Fungi: An Integrative Metabolomics-Proteomics Approach. FRONTIERS IN PLANT SCIENCE 2020; 11:872. [PMID: 32612631 PMCID: PMC7309134 DOI: 10.3389/fpls.2020.00872] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 05/28/2020] [Indexed: 06/11/2023]
Abstract
Pulses are one of the most important categories of food plants, and Pea (Pisum sativum L.) as a member of pulses is considered a key crop for food and feed and sustainable agriculture. Integrative multi-omics and microsymbiont impact studies on the plant's immune system are important steps toward more productive and tolerant food plants and thus will help to find solutions against food poverty. Didymella pinodes is a main fungal pathogen of pea plants. Arbuscular mycorrhizal fungi (AMF) promote plant growth and alleviate various stresses. However, it remained unclear as to how the AMF effect on seed metabolism and how this influences resistance against the pathogen. This study assesses the AMF impacts on yield components and seed quality upon D. pinodes infection on two different P. sativum cultivars, susceptible versus tolerant, grown in pots through phenotypic and seed molecular analyses. We found that AMF symbiosis affects the majority of all tested yield components as well as a reduction of disease severity in both cultivars. Seeds of mycorrhizal pea plants showed strong responses of secondary metabolites with nutritional, medicinal, and pharmaceutical attributes, also involved in pathogen response. This is further supported by proteomic data, functionally determining those primary and secondary metabolic pathways, involved in pathogen response and induced upon AMF-colonization. The data also revealed cultivar specific effects of AMF symbiosis that increase understanding of genotype related differences. Additionally, a suite of proteins and secondary metabolites are presented, induced in seeds of P. sativum upon AMF-colonization and pathogen attack, and possibly involved in induced systemic resistance against D. pinodes, useful for modern breeding strategies implementing microsymbionts toward increased pathogen resistance.
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Affiliation(s)
- Nima Ranjbar Sistani
- Department of Ecogenomics and Systems Biology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Getinet Desalegn
- Department of Crop Sciences, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Hans-Peter Kaul
- Department of Crop Sciences, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Stefanie Wienkoop
- Department of Ecogenomics and Systems Biology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
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12
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Price EJ, Drapal M, Perez‐Fons L, Amah D, Bhattacharjee R, Heider B, Rouard M, Swennen R, Becerra Lopez‐Lavalle LA, Fraser PD. Metabolite database for root, tuber, and banana crops to facilitate modern breeding in understudied crops. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:1258-1268. [PMID: 31845400 PMCID: PMC7383867 DOI: 10.1111/tpj.14649] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 11/09/2019] [Accepted: 11/28/2019] [Indexed: 05/06/2023]
Abstract
Roots, tubers, and bananas (RTB) are vital staples for food security in the world's poorest nations. A major constraint to current RTB breeding programmes is limited knowledge on the available diversity due to lack of efficient germplasm characterization and structure. In recent years large-scale efforts have begun to elucidate the genetic and phenotypic diversity of germplasm collections and populations and, yet, biochemical measurements have often been overlooked despite metabolite composition being directly associated with agronomic and consumer traits. Here we present a compound database and concentration range for metabolites detected in the major RTB crops: banana (Musa spp.), cassava (Manihot esculenta), potato (Solanum tuberosum), sweet potato (Ipomoea batatas), and yam (Dioscorea spp.), following metabolomics-based diversity screening of global collections held within the CGIAR institutes. The dataset including 711 chemical features provides a valuable resource regarding the comparative biochemical composition of each RTB crop and highlights the potential diversity available for incorporation into crop improvement programmes. Particularly, the tropical crops cassava, sweet potato and banana displayed more complex compositional metabolite profiles with representations of up to 22 chemical classes (unknowns excluded) than that of potato, for which only metabolites from 10 chemical classes were detected. Additionally, over 20% of biochemical signatures remained unidentified for every crop analyzed. Integration of metabolomics with the on-going genomic and phenotypic studies will enhance 'omics-wide associations of molecular signatures with agronomic and consumer traits via easily quantifiable biochemical markers to aid gene discovery and functional characterization.
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Affiliation(s)
- Elliott J. Price
- Royal Holloway University of London, SurreyTW20 0EXEghamUnited Kingdom
- Present address:
Masaryk UniversityBrno‐Bohunice625 00Czech Republic
| | - Margit Drapal
- Royal Holloway University of London, SurreyTW20 0EXEghamUnited Kingdom
| | - Laura Perez‐Fons
- Royal Holloway University of London, SurreyTW20 0EXEghamUnited Kingdom
| | - Delphine Amah
- International Institute of Tropical AgriculturePMB 5320IbadanNigeria
| | | | | | - Mathieu Rouard
- Bioversity InternationalParc Scientifique Agropolis II34397MontpellierFrance
| | - Rony Swennen
- Laboratory of Tropical Crop ImprovementDivision of Crop BiotechnicsKU LeuvenB‐3001LeuvenBelgium
- Bioversity InternationalWillem De Croylaan 42B‐3001LeuvenBelgium
- International Institute of Tropical Agriculture. C/0 The Nelson Mandela African Institution of Science and TechnologyP.O. Box 44ArushaTanzania
| | | | - Paul D. Fraser
- Royal Holloway University of London, SurreyTW20 0EXEghamUnited Kingdom
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13
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Agtuca BJ, Stopka SA, Tuleski TR, do Amaral FP, Evans S, Liu Y, Xu D, Monteiro RA, Koppenaal DW, Paša-Tolić L, Anderton CR, Vertes A, Stacey G. In-Situ Metabolomic Analysis of Setaria viridis Roots Colonized by Beneficial Endophytic Bacteria. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:272-283. [PMID: 31544655 DOI: 10.1094/mpmi-06-19-0174-r] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Over the past decades, crop yields have risen in parallel with increasing use of fossil fuel-derived nitrogen (N) fertilizers but with concomitant negative impacts on climate and water resources. There is a need for more sustainable agricultural practices, and biological nitrogen fixation (BNF) could be part of the solution. A variety of nitrogen-fixing, epiphytic, and endophytic plant growth-promoting bacteria (PGPB) are known to stimulate plant growth. However, compared with the rhizobium-legume symbiosis, little mechanistic information is available as to how PGPB affect plant metabolism. Therefore, we investigated the metabolic changes in roots of the model grass species Setaria viridis upon endophytic colonization by Herbaspirillum seropedicae SmR1 (fix+) or a fix- mutant strain (SmR54) compared with uninoculated roots. Endophytic colonization of the root is highly localized and, hence, analysis of whole-root segments dilutes the metabolic signature of those few cells impacted by the bacteria. Therefore, we utilized in-situ laser ablation electrospray ionization mass spectrometry to sample only those root segments at or adjacent to the sites of bacterial colonization. Metabolites involved in purine, zeatin, and riboflavin pathways were significantly more abundant in inoculated plants, while metabolites indicative of nitrogen, starch, and sucrose metabolism were reduced in roots inoculated with the fix- strain or uninoculated, presumably due to N limitation. Interestingly, compounds, involved in indole-alkaloid biosynthesis were more abundant in the roots colonized by the fix- strain, perhaps reflecting a plant defense response.
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Affiliation(s)
- Beverly J Agtuca
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, U.S.A
| | - Sylwia A Stopka
- Department of Chemistry, The George Washington University, Washington, DC 20052, U.S.A
| | - Thalita R Tuleski
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, U.S.A
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, CP 19046, 81.531-990 Curitiba, PR, Brazil
| | - Fernanda P do Amaral
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, U.S.A
| | - Sterling Evans
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, U.S.A
| | - Yang Liu
- Department of Electrical Engineering and Computer Science, Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri Columbia
| | - Dong Xu
- Department of Electrical Engineering and Computer Science, Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri Columbia
| | - Rose Adele Monteiro
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, CP 19046, 81.531-990 Curitiba, PR, Brazil
| | - David W Koppenaal
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99354, U.S.A
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99354, U.S.A
| | - Christopher R Anderton
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99354, U.S.A
| | - Akos Vertes
- Department of Chemistry, The George Washington University, Washington, DC 20052, U.S.A
| | - Gary Stacey
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, U.S.A
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14
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Nongpiur RC, Singla-Pareek SL, Pareek A. The quest for osmosensors in plants. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:595-607. [PMID: 31145792 DOI: 10.1093/jxb/erz263] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 05/22/2019] [Indexed: 05/20/2023]
Abstract
Osmotic stress has severe effects on crop productivity. Since climate change is predicted to exacerbate this problem, the development of new crops that are tolerant to osmotic stresses, especially drought and salinity stress, is required. However, only limited success has been achieved to date, primarily because of the lack of a clear understanding of the mechanisms that facilitate osmosensing. Here, we discuss the potential mechanisms of osmosensing in plants. We highlight the roles of proteins such as receptor-like kinases, which sense stress-induced cell wall damage, mechanosensitive calcium channels, which initiate a calcium-induced stress response, and phospholipase C, a membrane-bound enzyme that is integral to osmotic stress perception. We also discuss the roles of aquaporins and membrane-bound histidine kinases, which could potentially detect changes in extracellular osmolarity in plants, as they do in prokaryotes and lower eukaryotes. These putative osmosensors have the potential to serve as master regulators of the osmotic stress response in plants and could prove to be useful targets for the selection of osmotic stress-tolerant crops.
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Affiliation(s)
- Ramsong Chantre Nongpiur
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sneh Lata Singla-Pareek
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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15
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Carpentier SC. The Use of Proteomics in Search of Allele-Specific Proteins in (Allo)polyploid Crops. Methods Mol Biol 2020; 2139:297-308. [PMID: 32462595 DOI: 10.1007/978-1-0716-0528-8_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Most organisms are diploid, meaning they only have two copies of each chromosome (one set inherited from each parent). Polyploid organisms have more than two paired (homologous) sets of chromosomes. Many plant species are polyploid. Polyploid species cope better with stresses thanks to the redundancy in the chromosome copy number and dispose in this way a greater flexibility in gene expression. Allopolyploid species are polyploids that contain an alternative set of chromosomes by the cross of two (or more) species. Gene variants unique for a preferential phenotype are most probable candidate markers controlling the observed phenotype. Organ or tissue-specific silencing or overexpression of one parental homeolog is quite common. It is very challenging to find those tissue-specific gene variants. High-throughput proteomics is a successful method to discover them. This chapter proposes two possible workflows depending on the available resources and the knowledge of the species. An example is given for an AAB hybrid and an ABB hybrid. Allele-specific gene responses are picked up in this workflow as gene loci displaying genotype-specific differential expression that often have single amino acid polymorphisms. If the resources are sufficient, a genotype-specific mRNAseq database is recommended where a link is made to the allele-specific transcription levels. If the resources are limited, allele-specific proteins can be detected by the detection of genotype-specific peptides and the identification against existing genomics libraries of the parents.
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Affiliation(s)
- Sebastien Christian Carpentier
- SYBIOMA: Facility for Systems Biology-Based Mass Spectrometry, KULeuven, Leuven, Belgium.
- Bioversity International, Genetic Resources, Leuven, Belgium.
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16
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Razzaq A, Sadia B, Raza A, Khalid Hameed M, Saleem F. Metabolomics: A Way Forward for Crop Improvement. Metabolites 2019; 9:E303. [PMID: 31847393 PMCID: PMC6969922 DOI: 10.3390/metabo9120303] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 12/02/2019] [Accepted: 12/11/2019] [Indexed: 12/15/2022] Open
Abstract
Metabolomics is an emerging branch of "omics" and it involves identification and quantification of metabolites and chemical footprints of cellular regulatory processes in different biological species. The metabolome is the total metabolite pool in an organism, which can be measured to characterize genetic or environmental variations. Metabolomics plays a significant role in exploring environment-gene interactions, mutant characterization, phenotyping, identification of biomarkers, and drug discovery. Metabolomics is a promising approach to decipher various metabolic networks that are linked with biotic and abiotic stress tolerance in plants. In this context, metabolomics-assisted breeding enables efficient screening for yield and stress tolerance of crops at the metabolic level. Advanced metabolomics analytical tools, like non-destructive nuclear magnetic resonance spectroscopy (NMR), liquid chromatography mass-spectroscopy (LC-MS), gas chromatography-mass spectrometry (GC-MS), high performance liquid chromatography (HPLC), and direct flow injection (DFI) mass spectrometry, have sped up metabolic profiling. Presently, integrating metabolomics with post-genomics tools has enabled efficient dissection of genetic and phenotypic association in crop plants. This review provides insight into the state-of-the-art plant metabolomics tools for crop improvement. Here, we describe the workflow of plant metabolomics research focusing on the elucidation of biotic and abiotic stress tolerance mechanisms in plants. Furthermore, the potential of metabolomics-assisted breeding for crop improvement and its future applications in speed breeding are also discussed. Mention has also been made of possible bottlenecks and future prospects of plant metabolomics.
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Affiliation(s)
- Ali Razzaq
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38040, Pakistan; (A.R.); (B.S.)
| | - Bushra Sadia
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38040, Pakistan; (A.R.); (B.S.)
| | - Ali Raza
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan 430062, China;
| | - Muhammad Khalid Hameed
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China;
| | - Fozia Saleem
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38040, Pakistan; (A.R.); (B.S.)
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17
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Costa JM, Marques da Silva J, Pinheiro C, Barón M, Mylona P, Centritto M, Haworth M, Loreto F, Uzilday B, Turkan I, Oliveira MM. Opportunities and Limitations of Crop Phenotyping in Southern European Countries. FRONTIERS IN PLANT SCIENCE 2019; 10:1125. [PMID: 31608085 PMCID: PMC6774291 DOI: 10.3389/fpls.2019.01125] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 08/15/2019] [Indexed: 05/31/2023]
Abstract
The Mediterranean climate is characterized by hot dry summers and frequent droughts. Mediterranean crops are frequently subjected to high evapotranspiration demands, soil water deficits, high temperatures, and photo-oxidative stress. These conditions will become more severe due to global warming which poses major challenges to the sustainability of the agricultural sector in Mediterranean countries. Selection of crop varieties adapted to future climatic conditions and more tolerant to extreme climatic events is urgently required. Plant phenotyping is a crucial approach to address these challenges. High-throughput plant phenotyping (HTPP) helps to monitor the performance of improved genotypes and is one of the most effective strategies to improve the sustainability of agricultural production. In spite of the remarkable progress in basic knowledge and technology of plant phenotyping, there are still several practical, financial, and political constraints to implement HTPP approaches in field and controlled conditions across the Mediterranean. The European panorama of phenotyping is heterogeneous and integration of phenotyping data across different scales and translation of "phytotron research" to the field, and from model species to crops, remain major challenges. Moreover, solutions specifically tailored to Mediterranean agriculture (e.g., crops and environmental stresses) are in high demand, as the region is vulnerable to climate change and to desertification processes. The specific phenotyping requirements of Mediterranean crops have not yet been fully identified. The high cost of HTPP infrastructures is a major limiting factor, though the limited availability of skilled personnel may also impair its implementation in Mediterranean countries. We propose that the lack of suitable phenotyping infrastructures is hindering the development of new Mediterranean agricultural varieties and will negatively affect future competitiveness of the agricultural sector. We provide an overview of the heterogeneous panorama of phenotyping within Mediterranean countries, describing the state of the art of agricultural production, breeding initiatives, and phenotyping capabilities in five countries: Italy, Greece, Portugal, Spain, and Turkey. We characterize some of the main impediments for development of plant phenotyping in those countries and identify strategies to overcome barriers and maximize the benefits of phenotyping and modeling approaches to Mediterranean agriculture and related sustainability.
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Affiliation(s)
| | - Jorge Marques da Silva
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, Universidade de Lisboa, Lisbon, Portugal
| | - Carla Pinheiro
- FCT NOVA, Universidade Nova de Lisboa, Monte da Caparica, Portugal
- ITQB NOVA, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Matilde Barón
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Photini Mylona
- HAO-DEMETER, Institute of Plant Breeding and Genetic Resources, Thermi, Greece
| | - Mauro Centritto
- Institute for Sustainable Plant Protection, Italian National Research Council (IPSP-CNR), Sesto Fiorentino, Italy
| | | | - Francesco Loreto
- Department of Biology, Agriculture and Food Sciences, CNR, Rome, Italy
| | - Baris Uzilday
- Department of Biology, Faculty of Science, Ege University, I˙zmir, Turkey
| | - Ismail Turkan
- Department of Biology, Faculty of Science, Ege University, I˙zmir, Turkey
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18
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Kumar J, Choudhary AK, Gupta DS, Kumar S. Towards Exploitation of Adaptive Traits for Climate-Resilient Smart Pulses. Int J Mol Sci 2019; 20:E2971. [PMID: 31216660 PMCID: PMC6627977 DOI: 10.3390/ijms20122971] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/18/2019] [Accepted: 05/28/2019] [Indexed: 12/20/2022] Open
Abstract
Pulses are the main source of protein and minerals in the vegetarian diet. These are primarily cultivated on marginal lands with few inputs in several resource-poor countries of the world, including several in South Asia. Their cultivation in resource-scarce conditions exposes them to various abiotic and biotic stresses, leading to significant yield losses. Furthermore, climate change due to global warming has increased their vulnerability to emerging new insect pests and abiotic stresses that can become even more serious in the coming years. The changing climate scenario has made it more challenging to breed and develop climate-resilient smart pulses. Although pulses are climate smart, as they simultaneously adapt to and mitigate the effects of climate change, their narrow genetic diversity has always been a major constraint to their improvement for adaptability. However, existing genetic diversity still provides opportunities to exploit novel attributes for developing climate-resilient cultivars. The mining and exploitation of adaptive traits imparting tolerance/resistance to climate-smart pulses can be accelerated further by using cutting-edge approaches of biotechnology such as transgenics, genome editing, and epigenetics. This review discusses various classical and molecular approaches and strategies to exploit adaptive traits for breeding climate-smart pulses.
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Affiliation(s)
- Jitendra Kumar
- Indian Institute of Pulses Research, Kalyanpur, Kanpur 208 024, Uttar Pradesh, India.
| | | | - Debjyoti Sen Gupta
- Indian Institute of Pulses Research, Kalyanpur, Kanpur 208 024, Uttar Pradesh, India.
| | - Shiv Kumar
- Biodiversity and Integrated Gene Management Program, International Centre for Agricultural Research in the Dry Areas (ICARDA), P.O. Box 6299, Rabat-Institute, Rabat, Morocco.
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19
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Ranilla LG, Huamán-Alvino C, Flores-Báez O, Aquino-Méndez EM, Chirinos R, Campos D, Sevilla R, Fuentealba C, Pedreschi R, Sarkar D, Shetty K. Evaluation of phenolic antioxidant-linked in vitro bioactivity of Peruvian corn ( Zea mays L.) diversity targeting for potential management of hyperglycemia and obesity. Journal of Food Science and Technology 2019; 56:2909-2924. [PMID: 31205346 DOI: 10.1007/s13197-019-03748-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 03/15/2019] [Accepted: 03/21/2019] [Indexed: 11/28/2022]
Abstract
Peruvian corn biodiversity is one of the highest in the world and may represent an important natural source of health relevant phenolic bioactive compounds whose potential needs to be investigated. This study investigated twenty-two Peruvian corn samples corresponding to five corn races (Arequipeño, Cabanita, Kculli, Granada and Coruca) in relation to their total phenolic contents (TPC), anthocyanin contents, Ultra-Performance Liquid Chromatography (UPLC) phenolic profiles and antioxidant capacity (ABTS and ORAC methods). Subsequently using both free and cell-wall bound phenolic fractions their health relevance targeting hyperglycemia (α-glucosidase and α-amylase inhibition) and obesity (lipase inhibition) potentials was evaluated using in vitro assay models. Antioxidant capacity and TPC were high in bound fractions from yellow-colored races in contrast to the purple-colored race (Kculli) which had high TPC (mainly anthocyanins) and antioxidant capacity in the free form. The major phenolic acids detected by UPLC were ferulic and p-coumaric acids. High α-glucosidase (32.5-76.1%, 25 mg sample dose) and moderate α-amylase inhibitory activities (13.6-29.0%, 250 mg sample dose) were found in all free fractions, but only samples from the Kculli race had lipase inhibitory activity (58.45-92.16%, 12.5 mg sample dose). Principal component analysis revealed that the variability of data was affected by the race and the α-glucosidase and lipase inhibitory activities positively correlated with anthocyanins and antioxidant capacity. Some accessions of Kculli, Granada and Cabanita races are promising for future breeding strategies focused on the development of improved corn varieties targeted for the design of functional foods relevant for hyperglycemia and obesity prevention.
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Affiliation(s)
- Lena Gálvez Ranilla
- 1Laboratory of Research in Food Science, Universidad Catolica de Santa Maria, Urb. San José s/n Umacollo, Arequipa, Peru
| | - Cinthya Huamán-Alvino
- 2Instituto de Biotecnología, Universidad Nacional Agraria La Molina, Av. La Molina s/n, Lima, Peru
| | - Orlando Flores-Báez
- 2Instituto de Biotecnología, Universidad Nacional Agraria La Molina, Av. La Molina s/n, Lima, Peru
| | | | - Rosana Chirinos
- 2Instituto de Biotecnología, Universidad Nacional Agraria La Molina, Av. La Molina s/n, Lima, Peru
| | - David Campos
- 2Instituto de Biotecnología, Universidad Nacional Agraria La Molina, Av. La Molina s/n, Lima, Peru
| | - Ricardo Sevilla
- 3Maize Research Program, Universidad Nacional Agraria La Molina, Av. La Molina s/n, Lima, Peru
| | - Claudia Fuentealba
- 4School of Agronomy, Pontificia Universidad Católica de Valparaíso, Calle San Francisco s/n La Palma, Quillota, Chile
| | - Romina Pedreschi
- 4School of Agronomy, Pontificia Universidad Católica de Valparaíso, Calle San Francisco s/n La Palma, Quillota, Chile
| | - Dipayan Sarkar
- 5Department of Plant Sciences, North Dakota State University, Fargo, ND 58108 USA
| | - Kalidas Shetty
- 5Department of Plant Sciences, North Dakota State University, Fargo, ND 58108 USA
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20
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Shah T, Xu J, Zou X, Cheng Y, Nasir M, Zhang X. Omics Approaches for Engineering Wheat Production under Abiotic Stresses. Int J Mol Sci 2018; 19:E2390. [PMID: 30110906 PMCID: PMC6121627 DOI: 10.3390/ijms19082390] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 07/14/2018] [Accepted: 07/24/2018] [Indexed: 02/05/2023] Open
Abstract
Abiotic stresses greatly influenced wheat productivity executed by environmental factors such as drought, salt, water submergence and heavy metals. The effective management at the molecular level is mandatory for a thorough understanding of plant response to abiotic stress. Understanding the molecular mechanism of stress tolerance is complex and requires information at the omic level. In the areas of genomics, transcriptomics and proteomics enormous progress has been made in the omics field. The rising field of ionomics is also being utilized for examining abiotic stress resilience in wheat. Omic approaches produce a huge amount of data and sufficient developments in computational tools have been accomplished for efficient analysis. However, the integration of omic-scale information to address complex genetics and physiological questions is still a challenge. Though, the incorporation of omic-scale data to address complex genetic qualities and physiological inquiries is as yet a challenge. In this review, we have reported advances in omic tools in the perspective of conventional and present day approaches being utilized to dismember abiotic stress tolerance in wheat. Attention was given to methodologies, for example, quantitative trait loci (QTL), genome-wide association studies (GWAS) and genomic selection (GS). Comparative genomics and candidate genes methodologies are additionally talked about considering the identification of potential genomic loci, genes and biochemical pathways engaged with stress resilience in wheat. This review additionally gives an extensive list of accessible online omic assets for wheat and its effective use. We have additionally addressed the significance of genomics in the integrated approach and perceived high-throughput multi-dimensional phenotyping as a significant restricting component for the enhancement of abiotic stress resistance in wheat.
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Affiliation(s)
- Tariq Shah
- Key Lab of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan 430062, China.
| | - Jinsong Xu
- Key Lab of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan 430062, China.
| | - Xiling Zou
- Key Lab of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan 430062, China.
| | - Yong Cheng
- Key Lab of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan 430062, China.
| | - Mubasher Nasir
- College of Natural Resources and Environment, Northwest Agriculture and Forestry University, Yangling 712100, China.
| | - Xuekun Zhang
- Key Lab of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan 430062, China.
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Arora N, Pienkos PT, Pruthi V, Poluri KM, Guarnieri MT. Leveraging algal omics to reveal potential targets for augmenting TAG accumulation. Biotechnol Adv 2018; 36:1274-1292. [PMID: 29678388 DOI: 10.1016/j.biotechadv.2018.04.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 04/11/2018] [Accepted: 04/15/2018] [Indexed: 02/08/2023]
Abstract
Ongoing global efforts to commercialize microalgal biofuels have expedited the use of multi-omics techniques to gain insights into lipid biosynthetic pathways. Functional genomics analyses have recently been employed to complement existing sequence-level omics studies, shedding light on the dynamics of lipid synthesis and its interplay with other cellular metabolic pathways, thus revealing possible targets for metabolic engineering. Here, we review the current status of algal omics studies to reveal potential targets to augment TAG accumulation in various microalgae. This review specifically aims to examine and catalog systems level data related to stress-induced TAG accumulation in oleaginous microalgae and inform future metabolic engineering strategies to develop strains with enhanced bioproductivity, which could pave a path for sustainable green energy.
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Affiliation(s)
- Neha Arora
- Department of Biotechnology, Indian Institute of Technology Roorkee, Uttarakhand 247667, India
| | - Philip T Pienkos
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Vikas Pruthi
- Department of Biotechnology, Indian Institute of Technology Roorkee, Uttarakhand 247667, India
| | - Krishna Mohan Poluri
- Department of Biotechnology, Indian Institute of Technology Roorkee, Uttarakhand 247667, India
| | - Michael T Guarnieri
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401, USA.
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22
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Campos NA, Swennen R, Carpentier SC. The Plantain Proteome, a Focus on Allele Specific Proteins Obtained from Plantain Fruits. Proteomics 2018; 18:1700227. [PMID: 29333696 PMCID: PMC6084372 DOI: 10.1002/pmic.201700227] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 12/31/2017] [Indexed: 01/07/2023]
Abstract
Proteomics has been applied with great potential to elucidate molecular mechanisms in plants. This is especially valid in the case of non-model crops of which their genome has not been sequenced yet, or is not well annotated. Plantains are a kind of cooking bananas that are economically very important in Africa, India, and Latin America. The aim of this work was to characterize the fruit proteome of common dessert bananas and plantains and to identify proteins that are only encoded by the plantain genome. We present the first plantain fruit proteome. All data are available via ProteomeXchange with identifier PXD005589. Using our in-house workflow, we found 37 alleles to be unique for plantain covered by 59 peptides. Although we do not have access (yet) to whole-genome sequencing data from triploid banana cultivars, we show that proteomics is an easily accessible complementary alternative to detect different allele specific SNPs/SAAPs. These unique alleles might contribute toward the differences in the metabolism between dessert bananas and plantains. This dataset will stimulate further analysis by the scientific community, boost plantain research, and facilitate plantain breeding.
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Affiliation(s)
| | - Rony Swennen
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Department of BiosystemsKU LeuvenLeuvenBelgium
- International Institute of Tropical AgricultureArushaTanzania
- Bioversity InternationalLeuvenBelgium
| | - Sebastien C. Carpentier
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Department of BiosystemsKU LeuvenLeuvenBelgium
- Bioversity InternationalLeuvenBelgium
- SYBIOMA: Facility for SYstems BIOlogy based MAss spectrometryKU LeuvenLeuvenBelgium
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van Wesemael J, Hueber Y, Kissel E, Campos N, Swennen R, Carpentier S. Homeolog expression analysis in an allotriploid non-model crop via integration of transcriptomics and proteomics. Sci Rep 2018; 8:1353. [PMID: 29358676 PMCID: PMC5777989 DOI: 10.1038/s41598-018-19684-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 01/08/2018] [Indexed: 01/14/2023] Open
Abstract
The fate of doubled genes, from allopolyploid or autopolyploid origin, is controlled at multiple levels, resulting in the modern day cultivars. We studied the root growth of 3 different triploid banana cultivars under control and osmotic stress conditions. The root growth of the allopolyploid ABB cultivar was 42% higher under control and 61% higher under osmotic stress. By integrating transcriptomics and proteomics, we studied the gene expression of all 3 cultivars, resulting in 2,749 identified root proteins. 383 gene loci displayed genotype specific differential expression whereof 252 showed at least one Single Amino Acid Polymorphism (SAAP). In the ABB cultivar, allele expressions supposedly follow a 1/3 and 2/3 pattern for respectively the A and the B allele. Using transcriptome read alignment to assess the homeoallelic contribution we found that 63% of the allele specific genes deviated from this expectation. 32 gene loci even did not express the A allele. The identified ABB allele- specific proteins correlate well with the observed growth phenotype as they are enriched in energy related functions such as ATP metabolic processes, nicotinamide nucleotide metabolic processes, and glycolysis.
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Affiliation(s)
- Jelle van Wesemael
- Laboratory of Tropical Crop Improvement, KU Leuven, Willem Decroylaan 42, Leuven, Belgium
| | - Yann Hueber
- Bioversity International, Parc Scientifique Argropolis II, Montpellier, France
| | - Ewaut Kissel
- Laboratory of Tropical Crop Improvement, KU Leuven, Willem Decroylaan 42, Leuven, Belgium
| | - Nádia Campos
- Laboratory of Tropical Crop Improvement, KU Leuven, Willem Decroylaan 42, Leuven, Belgium
| | - Rony Swennen
- Laboratory of Tropical Crop Improvement, KU Leuven, Willem Decroylaan 42, Leuven, Belgium
- Bioversity International, Willem Decroylaan 42, Leuven, Belgium
- International Institute for Tropical Agriculture, C/O Nelson Mandela Institute of Science and technology, P.O. Box 44, Arusha, Tanzania
| | - Sebastien Carpentier
- Laboratory of Tropical Crop Improvement, KU Leuven, Willem Decroylaan 42, Leuven, Belgium.
- Bioversity International, Willem Decroylaan 42, Leuven, Belgium.
- Facility for SYstems BIOlogy based MAss spectrometry, Herestraat 49, Leuven, Belgium.
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24
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Soares ALC, Geilfus CM, Carpentier SC. Genotype-Specific Growth and Proteomic Responses of Maize Toward Salt Stress. FRONTIERS IN PLANT SCIENCE 2018; 9:661. [PMID: 29899749 PMCID: PMC5989331 DOI: 10.3389/fpls.2018.00661] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 04/30/2018] [Indexed: 05/20/2023]
Abstract
Salt stress in plants triggers complex physiological responses that are genotype specific. Many of these responses are either not yet described or not fully understood or both. In this work, we phenotyped three maize genotypes of the CIMMYT gene bank alongside the reference B73 genotype (NCRPIS - United States) under both control and salt-stressed conditions. We have ranked their growth potential and we observed significant differences in Na+ and Cl- ion accumulation. Genotype CML421 showed the slowest growth, while CML451 had the lowest accumulation of ions in its leaves. The phenotyping defined the right timing for the proteomics analysis, allowing us to compare the contrasting genotypes. In general 1,747 proteins were identified, of which 209 were significantly more abundant in response to salt stress. The five most significantly enriched annotations that positively correlated with stress were oxidation reduction, catabolic process, response to chemical stimulus, translational elongation and response to water. We observed a higher abundance of proteins involved in reactions to oxidative stress, dehydration, respiration, and translation. The five most significantly enriched annotations negatively correlated with stress were nucleosome organization, chromatin assembly, protein-DNA complex assembly, DNA packaging and nucleosome assembly. The genotypic analysis revealed 52 proteins that were correlated to the slow-growing genotype CML421. Their annotations point toward cellular dehydration and oxidative stress. Three root proteins correlated to the CML451 genotype were annotated to protein synthesis and ion compartmentalization. In conclusion, our results highlight the importance of the anti-oxidative system for acclimatization to salt stress and identify potential genotypic marker proteins involved in salt-stress responses.
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Affiliation(s)
- Ana L. C. Soares
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, KU Leuven, Leuven, Belgium
| | - Christoph-Martin Geilfus
- Controlled Environment Horticulture, Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt University of Berlin, Berlin, Germany
| | - Sebastien C. Carpentier
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, KU Leuven, Leuven, Belgium
- Genetic Resources, Bioversity International, Leuven, Belgium
- SYBIOMA, KU Leuven, Leuven, Belgium
- *Correspondence: Sebastien C. Carpentier,
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Veley KM, Berry JC, Fentress SJ, Schachtman DP, Baxter I, Bart R. High-throughput profiling and analysis of plant responses over time to abiotic stress. PLANT DIRECT 2017; 1:e00023. [PMID: 31245669 PMCID: PMC6508565 DOI: 10.1002/pld3.23] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 09/28/2017] [Indexed: 05/21/2023]
Abstract
Sorghum (Sorghum bicolor (L.) Moench) is a rapidly growing, high-biomass crop prized for abiotic stress tolerance. However, measuring genotype-by-environment (G x E) interactions remains a progress bottleneck. We subjected a panel of 30 genetically diverse sorghum genotypes to a spectrum of nitrogen deprivation and measured responses using high-throughput phenotyping technology followed by ionomic profiling. Responses were quantified using shape (16 measurable outputs), color (hue and intensity), and ionome (18 elements). We measured the speed at which specific genotypes respond to environmental conditions, in terms of both biomass and color changes, and identified individual genotypes that perform most favorably. With this analysis, we present a novel approach to quantifying color-based stress indicators over time. Additionally, ionomic profiling was conducted as an independent, low-cost, and high-throughput option for characterizing G x E, identifying the elements most affected by either genotype or treatment and suggesting signaling that occurs in response to the environment. This entire dataset and associated scripts are made available through an open-access, user-friendly, web-based interface. In summary, this work provides analysis tools for visualizing and quantifying plant abiotic stress responses over time. These methods can be deployed as a time-efficient method of dissecting the genetic mechanisms used by sorghum to respond to the environment to accelerate crop improvement.
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Affiliation(s)
- Kira M. Veley
- Donald Danforth Plant Science CenterSaint LouisMOUSA
| | | | | | - Daniel P. Schachtman
- Department of Agronomy and Horticulture and Center for Plant Science InnovationUniversity of Nebraska–LincolnLincolnNEUSA
| | - Ivan Baxter
- Donald Danforth Plant Science CenterSaint LouisMOUSA
- USDA‐ARSSaint LouisMOUSA
| | - Rebecca Bart
- Donald Danforth Plant Science CenterSaint LouisMOUSA
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26
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Campos NA, Panis B, Carpentier SC. Somatic Embryogenesis in Coffee: The Evolution of Biotechnology and the Integration of Omics Technologies Offer Great Opportunities. FRONTIERS IN PLANT SCIENCE 2017; 8:1460. [PMID: 28871271 PMCID: PMC5566963 DOI: 10.3389/fpls.2017.01460] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 08/07/2017] [Indexed: 05/22/2023]
Abstract
One of the most important crops cultivated around the world is coffee. There are two main cultivated species, Coffea arabica and C. canephora. Both species are difficult to improve through conventional breeding, taking at least 20 years to produce a new cultivar. Biotechnological tools such as genetic transformation, micropropagation and somatic embryogenesis (SE) have been extensively studied in order to provide practical results for coffee improvement. While genetic transformation got many attention in the past and is booming with the CRISPR technology, micropropagation and SE are still the major bottle neck and urgently need more attention. The methodologies to induce SE and the further development of the embryos are genotype-dependent, what leads to an almost empirical development of specific protocols for each cultivar or clone. This is a serious limitation and excludes a general comprehensive understanding of the process as a whole. The aim of this review is to provide an overview of which achievements and molecular insights have been gained in (coffee) somatic embryogenesis and encourage researchers to invest further in the in vitro technology and combine it with the latest omics techniques (genomics, transcriptomics, proteomics, metabolomics, and phenomics). We conclude that the evolution of biotechnology and the integration of omics technologies offer great opportunities to (i) optimize the production process of SE and the subsequent conversion into rooted plantlets and (ii) to screen for possible somaclonal variation. However, currently the usage of the latest biotechnology did not pass the stage beyond proof of potential and needs to further improve.
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Affiliation(s)
| | | | - Sebastien C. Carpentier
- Department of Biosystems, KU LeuvenLeuven, Belgium
- Facility for Systems Biology Based Mass Spectrometry, KU LeuvenLeuven, Belgium
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27
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Kumar R, Bohra A, Pandey AK, Pandey MK, Kumar A. Metabolomics for Plant Improvement: Status and Prospects. FRONTIERS IN PLANT SCIENCE 2017; 8:1302. [PMID: 28824660 PMCID: PMC5545584 DOI: 10.3389/fpls.2017.01302] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 07/11/2017] [Indexed: 05/12/2023]
Abstract
Post-genomics era has witnessed the development of cutting-edge technologies that have offered cost-efficient and high-throughput ways for molecular characterization of the function of a cell or organism. Large-scale metabolite profiling assays have allowed researchers to access the global data sets of metabolites and the corresponding metabolic pathways in an unprecedented way. Recent efforts in metabolomics have been directed to improve the quality along with a major focus on yield related traits. Importantly, an integration of metabolomics with other approaches such as quantitative genetics, transcriptomics and genetic modification has established its immense relevance to plant improvement. An effective combination of these modern approaches guides researchers to pinpoint the functional gene(s) and the characterization of massive metabolites, in order to prioritize the candidate genes for downstream analyses and ultimately, offering trait specific markers to improve commercially important traits. This in turn will improve the ability of a plant breeder by allowing him to make more informed decisions. Given this, the present review captures the significant leads gained in the past decade in the field of plant metabolomics accompanied by a brief discussion on the current contribution and the future scope of metabolomics to accelerate plant improvement.
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Affiliation(s)
- Rakesh Kumar
- Department of Plant Sciences, University of Hyderabad (UoH)Hyderabad, India
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Hyderabad, India
| | - Abhishek Bohra
- Crop Improvement Division, Indian Institute of Pulses Research (IIPR)Kanpur, India
| | - Arun K. Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Hyderabad, India
| | - Manish K. Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Hyderabad, India
| | - Anirudh Kumar
- Department of Botany, Indira Gandhi National Tribal University (IGNTU)Amarkantak, India
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Salon C, Avice JC, Colombié S, Dieuaide-Noubhani M, Gallardo K, Jeudy C, Ourry A, Prudent M, Voisin AS, Rolin D. Fluxomics links cellular functional analyses to whole-plant phenotyping. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:2083-2098. [PMID: 28444347 DOI: 10.1093/jxb/erx126] [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: 05/19/2023]
Abstract
Fluxes through metabolic pathways reflect the integration of genetic and metabolic regulations. While it is attractive to measure all the mRNAs (transcriptome), all the proteins (proteome), and a large number of the metabolites (metabolome) in a given cellular system, linking and integrating this information remains difficult. Measurement of metabolome-wide fluxes (termed the fluxome) provides an integrated functional output of the cell machinery and a better tool to link functional analyses to plant phenotyping. This review presents and discusses sets of methodologies that have been developed to measure the fluxome. First, the principles of metabolic flux analysis (MFA), its 'short time interval' version Inst-MFA, and of constraints-based methods, such as flux balance analysis and kinetic analysis, are briefly described. The use of these powerful methods for flux characterization at the cellular scale up to the organ (fruits, seeds) and whole-plant level is illustrated. The added value given by fluxomics methods for unravelling how the abiotic environment affects flux, the process, and key metabolic steps are also described. Challenges associated with the development of fluxomics and its integration with 'omics' for thorough plant and organ functional phenotyping are discussed. Taken together, these will ultimately provide crucial clues for identifying appropriate target plant phenotypes for breeding.
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Affiliation(s)
- Christophe Salon
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, 17 Rue Sully, BP 86510, 21065 Dijon Cedex, France
| | - Jean-Christophe Avice
- UNICAEN, UMR INRA 950 Ecophysiologie Végétale, Agronomie et nutritions N, C, S, Esplanade de la Paix, Université Caen Normandie, 14032 Caen Cedex 5, France
| | - Sophie Colombié
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, 33882 Villenave d'Ornon, France
| | - Martine Dieuaide-Noubhani
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, 33882 Villenave d'Ornon, France
| | - Karine Gallardo
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, 17 Rue Sully, BP 86510, 21065 Dijon Cedex, France
| | - Christian Jeudy
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, 17 Rue Sully, BP 86510, 21065 Dijon Cedex, France
| | - Alain Ourry
- UNICAEN, UMR INRA 950 Ecophysiologie Végétale, Agronomie et nutritions N, C, S, Esplanade de la Paix, Université Caen Normandie, 14032 Caen Cedex 5, France
| | - Marion Prudent
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, 17 Rue Sully, BP 86510, 21065 Dijon Cedex, France
| | - Anne-Sophie Voisin
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, 17 Rue Sully, BP 86510, 21065 Dijon Cedex, France
| | - Dominique Rolin
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, 33882 Villenave d'Ornon, France
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30
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Littlefair JE, Clare EL. Barcoding the food chain: from Sanger to high-throughput sequencing. Genome 2016; 59:946-958. [DOI: 10.1139/gen-2016-0028] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Society faces the complex challenge of supporting biodiversity and ecosystem functioning, while ensuring food security by providing safe traceable food through an ever-more-complex global food chain. The increase in human mobility brings the added threat of pests, parasites, and invaders that further complicate our agro-industrial efforts. DNA barcoding technologies allow researchers to identify both individual species, and, when combined with universal primers and high-throughput sequencing techniques, the diversity within mixed samples (metabarcoding). These tools are already being employed to detect market substitutions, trace pests through the forensic evaluation of trace “environmental DNA”, and to track parasitic infections in livestock. The potential of DNA barcoding to contribute to increased security of the food chain is clear, but challenges remain in regulation and the need for validation of experimental analysis. Here, we present an overview of the current uses and challenges of applied DNA barcoding in agriculture, from agro-ecosystems within farmland to the kitchen table.
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Affiliation(s)
- Joanne E. Littlefair
- School of Biological and Chemical Sciences, Queen Mary University of London. Mile End Rd., London, E1 4NS, UK
- School of Biological and Chemical Sciences, Queen Mary University of London. Mile End Rd., London, E1 4NS, UK
| | - Elizabeth L. Clare
- School of Biological and Chemical Sciences, Queen Mary University of London. Mile End Rd., London, E1 4NS, UK
- School of Biological and Chemical Sciences, Queen Mary University of London. Mile End Rd., London, E1 4NS, UK
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31
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Barkla BJ. Identification of Abiotic Stress Protein Biomarkers by Proteomic Screening of Crop Cultivar Diversity. Proteomes 2016; 4:proteomes4030026. [PMID: 28248236 PMCID: PMC5217352 DOI: 10.3390/proteomes4030026] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 09/01/2016] [Accepted: 09/03/2016] [Indexed: 12/11/2022] Open
Abstract
Modern day agriculture practice is narrowing the genetic diversity in our food supply. This may compromise the ability to obtain high yield under extreme climactic conditions, threatening food security for a rapidly growing world population. To identify genetic diversity, tolerance mechanisms of cultivars, landraces and wild relatives of major crops can be identified and ultimately exploited for yield improvement. Quantitative proteomics allows for the identification of proteins that may contribute to tolerance mechanisms by directly comparing protein abundance under stress conditions between genotypes differing in their stress responses. In this review, a summary is provided of the data accumulated from quantitative proteomic comparisons of crop genotypes/cultivars which present different stress tolerance responses when exposed to various abiotic stress conditions, including drought, salinity, high/low temperature, nutrient deficiency and UV-B irradiation. This field of research aims to identify molecular features that can be developed as biomarkers for crop improvement, however without accurate phenotyping, careful experimental design, statistical robustness and appropriate biomarker validation and verification it will be challenging to deliver what is promised.
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Affiliation(s)
- Bronwyn J Barkla
- Southern Cross Plant Sciences, Southern Cross University, Lismore 2481, NSW, Australia.
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32
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Divya Bhanu B, Ulaganathan K, Shanker AK, Desai S. RNA-seq Analysis of Irrigated vs. Water Stressed Transcriptomes of Zea mays Cultivar Z59. FRONTIERS IN PLANT SCIENCE 2016; 7:239. [PMID: 26973681 PMCID: PMC4771728 DOI: 10.3389/fpls.2016.00239] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 02/12/2016] [Indexed: 06/05/2023]
Affiliation(s)
- B. Divya Bhanu
- Centre for Plant Molecular Biology, Osmania UniversityHyderabad, India
| | | | - Arun K. Shanker
- Central Research Institute for Dryland AgricultureHyderabad, India
| | - S. Desai
- Central Research Institute for Dryland AgricultureHyderabad, India
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33
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Sanchez-Lucas R, Mehta A, Valledor L, Cabello-Hurtado F, Romero-Rodrıguez MC, Simova-Stoilova L, Demir S, Rodriguez-de-Francisco LE, Maldonado-Alconada AM, Jorrin-Prieto AL, Jorrín-Novo JV. A year (2014-2015) of plants in Proteomics journal. Progress in wet and dry methodologies, moving from protein catalogs, and the view of classic plant biochemists. Proteomics 2016; 16:866-76. [PMID: 26621614 DOI: 10.1002/pmic.201500351] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 10/26/2015] [Accepted: 11/04/2015] [Indexed: 12/23/2022]
Abstract
The present review is an update of the previous one published in Proteomics 2015 Reviews special issue [Jorrin-Novo, J. V. et al., Proteomics 2015, 15, 1089-1112] covering the July 2014-2015 period. It has been written on the bases of the publications that appeared in Proteomics journal during that period and the most relevant ones that have been published in other high-impact journals. Methodological advances and the contribution of the field to the knowledge of plant biology processes and its translation to agroforestry and environmental sectors will be discussed. This review has been organized in four blocks, with a starting general introduction (literature survey) followed by sections focusing on the methodology (in vitro, in vivo, wet, and dry), proteomics integration with other approaches (systems biology and proteogenomics), biological information, and knowledge (cell communication, receptors, and signaling), ending with a brief mention of some other biological and translational topics to which proteomics has made some contribution.
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Affiliation(s)
- Rosa Sanchez-Lucas
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain
| | - Angela Mehta
- Embrapa Recursos Genéticos e Biotecnologia (CENARGEN), Brasília, DF, Brazil
| | - Luis Valledor
- Department of Biology of Organisms and Systems (BOS), University of Oviedo, Oviedo, Spain
| | | | - M Cristina Romero-Rodrıguez
- Centro Multidisciplinario de Investigaciones Tecnológicas, and Departamento de Fitoquímica, Facultad de Ciencias Químicas, Universidad Nacional de Asunción, San Lorenzo, Paraguay
| | - Lyudmila Simova-Stoilova
- Plant Molecular Biology Department, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Sekvan Demir
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain
| | - Luis E Rodriguez-de-Francisco
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain.,INTEC-Sto. Domingo, Santo Domingo, República Dominicana
| | - Ana M Maldonado-Alconada
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain
| | - Ana L Jorrin-Prieto
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain
| | - Jesus V Jorrín-Novo
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain
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